From 2ede57d571e382f5aae167bd2a059a12fa1108ea Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Mon, 26 Feb 2024 12:09:08 -0700 Subject: add new post --- ...ntrol-element-under-another-element-html-css.md | 35 ++++++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 Content/posts/2024-02-26-control-element-under-another-element-html-css.md (limited to 'Content/posts') diff --git a/Content/posts/2024-02-26-control-element-under-another-element-html-css.md b/Content/posts/2024-02-26-control-element-under-another-element-html-css.md new file mode 100644 index 0000000..1c253fe --- /dev/null +++ b/Content/posts/2024-02-26-control-element-under-another-element-html-css.md @@ -0,0 +1,35 @@ +--- +date: 2024-02-26 11:57 +description: With CSS you can disable any interactions with an element and directly control the underlying element +tags: HTML, CSS +draft: false +--- + +# Interacting with underlying element in HTML + +I know that the title is a bit weird. I was trying to interact with a video under an iPhone Bezel Screen frame. + +```html +
+
+ + + +
+
+``` + +![Video Under a Transparent Image](/assets/underlying/video-under-element.jpg) + +Turns out, you can disable pointer events! + +In Tailwind, it is as simple as adding `pointer-events-none` to the bezel screen. + +In CSS, this can be done by: + +```css +.className { + pointer-events: none +} +``` + -- cgit v1.2.3 From 507d51b356de707b5b8d3e1832fbf3684415f07c Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Wed, 28 Feb 2024 11:51:41 -0700 Subject: add example to post --- ...ntrol-element-under-another-element-html-css.md | 42 +++++++++++++++++++ docs/feed.rss | 47 +++++++++++++++++++++- ...rol-element-under-another-element-html-css.html | 43 ++++++++++++++++++++ 3 files changed, 130 insertions(+), 2 deletions(-) (limited to 'Content/posts') diff --git a/Content/posts/2024-02-26-control-element-under-another-element-html-css.md b/Content/posts/2024-02-26-control-element-under-another-element-html-css.md index 1c253fe..cbdfe6a 100644 --- a/Content/posts/2024-02-26-control-element-under-another-element-html-css.md +++ b/Content/posts/2024-02-26-control-element-under-another-element-html-css.md @@ -33,3 +33,45 @@ In CSS, this can be done by: } ``` +Let us try this in a simple example. + +## Example + +Here, we create a button and overlay a transparent box + +```html +
+A box with 200px height and 200px width +
+ +``` + +
+ +
+A box with 200px height and 300px width +
+ +
+ +As you can see, you cannot click the button because the red box comes in the way. We can fix this by adding `pointer-events: none` to the box. + +```html +
+A box with 200px height and 300px width +
+ + +``` + +
+ +
+A box with 200px height and 300px width +
+ + + + + + diff --git a/docs/feed.rss b/docs/feed.rss index 244ab87..4f92bc6 100644 --- a/docs/feed.rss +++ b/docs/feed.rss @@ -4,8 +4,8 @@ Navan's Archive Rare Tips, Tricks and Posts https://web.navan.dev/en - Mon, 26 Feb 2024 12:07:42 -0000 - Mon, 26 Feb 2024 12:07:42 -0000 + Wed, 28 Feb 2024 11:50:15 -0000 + Wed, 28 Feb 2024 11:50:15 -0000 250 @@ -3588,6 +3588,49 @@ Otherwise, it calls the custom action.

} + +

Let us try this in a simple example.

+ +

Example

+ +

Here, we create a button and overlay a transparent box

+ +
+
<div style="height: 200px; width: 300px; background-color: rgba(255, 0, 0, 0.4); z-index: 2; position: absolute;">
+A box with 200px height and 200px width
+</div>
+<button style="z-index: 1; margin-top: 20px; margin-bottom: 200px;" onclick="alert('You were able to click this button')">Try clicking me</button>
+
+
+ +
+ +
+A box with 200px height and 300px width +
+ +

+

+ +

As you can see, you cannot click the button because the red box comes in the way. We can fix this by adding pointer-events: none to the box.

+ +
+
<div style="height: 200px; width: 300px; background-color: rgba(0, 255, 0, 0.4); z-index: 2; position: absolute; pointer-events: none;">
+A box with 200px height and 300px width
+</div>
+<button style="z-index: 1; margin-top: 20px; margin-bottom: 200px" onclick="alert('You were able to click this button')">Try clicking me</button>
+</div>
+
+
+ +
+ +
+A box with 200px height and 300px width +
+ +

+

]]> diff --git a/docs/posts/2024-02-26-control-element-under-another-element-html-css.html b/docs/posts/2024-02-26-control-element-under-another-element-html-css.html index 8b72ac5..b9c9ebc 100644 --- a/docs/posts/2024-02-26-control-element-under-another-element-html-css.html +++ b/docs/posts/2024-02-26-control-element-under-another-element-html-css.html @@ -74,6 +74,49 @@ +

Let us try this in a simple example.

+ +

Example

+ +

Here, we create a button and overlay a transparent box

+ +
+
<div style="height: 200px; width: 300px; background-color: rgba(255, 0, 0, 0.4); z-index: 2; position: absolute;">
+A box with 200px height and 200px width
+</div>
+<button style="z-index: 1; margin-top: 20px; margin-bottom: 200px;" onclick="alert('You were able to click this button')">Try clicking me</button>
+
+
+ +
+ +
+A box with 200px height and 300px width +
+ +

+

+ +

As you can see, you cannot click the button because the red box comes in the way. We can fix this by adding pointer-events: none to the box.

+ +
+
<div style="height: 200px; width: 300px; background-color: rgba(0, 255, 0, 0.4); z-index: 2; position: absolute; pointer-events: none;">
+A box with 200px height and 300px width
+</div>
+<button style="z-index: 1; margin-top: 20px; margin-bottom: 200px" onclick="alert('You were able to click this button')">Try clicking me</button>
+</div>
+
+
+ +
+ +
+A box with 200px height and 300px width +
+ +

+

+
If you have scrolled this far, consider subscribing to my mailing list here. You can subscribe to either a specific type of post you are interested in, or subscribe to everything with the "Everything" list.
-- cgit v1.2.3 From ea7a6ce794dbda1a7eded1d5e663897d46d21fa2 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Fri, 15 Mar 2024 15:00:41 -0600 Subject: add post about compiling for dos --- .../posts/2024-03-04-opencvjs-video-processing.md | 12 + ...2024-03-15-setting-up-macos-for-8088-dos-dev.md | 267 +++++++++++++++++ Resources/assets/posts/dosbox/hello-world.png | Bin 0 -> 233460 bytes .../posts/2024-03-04-opencvjs-video-processing.png | Bin 0 -> 27820 bytes ...024-03-15-setting-up-macos-for-8088-dos-dev.png | Bin 0 -> 32566 bytes docs/assets/posts/dosbox/hello-world.png | Bin 0 -> 233460 bytes docs/feed.rss | 290 +++++++++++++++++- .../posts/2024-03-04-opencvjs-video-processing.png | Bin 0 -> 27820 bytes ...024-03-15-setting-up-macos-for-8088-dos-dev.png | Bin 0 -> 32566 bytes docs/index.html | 34 +-- ...24-03-15-setting-up-macos-for-8088-dos-dev.html | 330 +++++++++++++++++++++ docs/posts/index.html | 15 + docs/tags/DOS.html | 73 +++++ docs/tags/JS.html | 73 +++++ docs/tags/OpenCV.html | 73 +++++ docs/tags/macOS.html | 15 + docs/tags/x86.html | 73 +++++ 17 files changed, 1234 insertions(+), 21 deletions(-) create mode 100644 Content/posts/2024-03-04-opencvjs-video-processing.md create mode 100644 Content/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.md create mode 100644 Resources/assets/posts/dosbox/hello-world.png create mode 100644 Resources/images/opengraph/posts/2024-03-04-opencvjs-video-processing.png create mode 100644 Resources/images/opengraph/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.png create mode 100644 docs/assets/posts/dosbox/hello-world.png create mode 100644 docs/images/opengraph/posts/2024-03-04-opencvjs-video-processing.png create mode 100644 docs/images/opengraph/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.png create mode 100644 docs/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.html create mode 100644 docs/tags/DOS.html create mode 100644 docs/tags/JS.html create mode 100644 docs/tags/OpenCV.html create mode 100644 docs/tags/x86.html (limited to 'Content/posts') diff --git a/Content/posts/2024-03-04-opencvjs-video-processing.md b/Content/posts/2024-03-04-opencvjs-video-processing.md new file mode 100644 index 0000000..cf87fb1 --- /dev/null +++ b/Content/posts/2024-03-04-opencvjs-video-processing.md @@ -0,0 +1,12 @@ +--- +date: 2024-03-04 12:01 +description: Real time video processing with OpenCV.js in the browser +tags: HTML, JS, OpenCV +draft: true +--- + +# Video Processing W/ OpenCV.js + +Note: A really weird bug you might run into when you are trying to mess around +and reloading the page on iOS is that OpenCV just stops loading. This is a bug in +WebKit.: diff --git a/Content/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.md b/Content/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.md new file mode 100644 index 0000000..15161f5 --- /dev/null +++ b/Content/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.md @@ -0,0 +1,267 @@ +--- +date: 2024-03-15 13:16 +description: This goes through compiling Open Watcom 2 and creating simple hello-world exampls +tags: DOS, x86, macOS +draft: false +--- + +# Cross-Compiling Hello World for DOS on macOS + +Technically this should work for any platform that OpenWatcom 2 supports compiling binaries for. Some instructions are based on [a post at retrocoding.net](https://retrocoding.net/openwatcom-gateway-to-ancient-world-of-x86), + and [John Tsiombikas's post](http://nuclear.mutantstargoat.com/articles/retrocoding/dos01-setup/#hello-world-program) + +## Prerequisites + +You should already have XCode / Command Line Tools, and Homebrew installed. To compile Open Watcom for DOS you will need DOSBox (I use DOSBox-X). + +```bash +brew install --cask dosbox-x +``` + +## Compiling Open Watcom v2 + +*If this process is super annoying, I might make a custom homebrew tap to build and install Open Watcom* + +```bash +git clone https://github.com/open-watcom/open-watcom-v2 +cp open-watcom-v2/setvars.sh custom_setvars.sh +``` + +Now, edit this `setvars.sh` file. My file looks like this: + +```bash +#!/bin/zsh +export OWROOT="/Users/navanchauhan/Developer/8088Stuff/open-watcom-v2" +export OWTOOLS=CLANG +export OWDOCBUILD=0 +export OWGUINOBUILD=0 +export OWDISTRBUILD=0 +export OWDOSBOX="/Applications/dosbox-x.app/Contents/MacOS/dosbox-x" +export OWOBJDIR=binbuildV01 +. "$OWROOT/cmnvars.sh" +echo "OWROOT=$OWROOT" +cd "$OWROOT" +``` + +Note, your `OWRTOOT` is definitely going to be in a different location. + +```bash +source ./custom_setvars.sh +./build.sh +./build.sh rel +``` + +This will build, and then copy everything to the `rel` directory inside `open-watcom-v2` directory. Since I ran this on an Apple Silicon Mac, + all the binaries for me are in the `armo64` directory. You can now move everything inside the rel folder to another location, or create a simple + script to init all variables whenever you want. + +I like having a script called `exportVarsForDOS.sh` + +```bash +#!/bin/zsh + +export WATCOM=/Users/navanchauhan/Developer/8088Stuff/open-watcom-v2/rel +export PATH=$PATH:$WATCOM/armo64 +export EDDAT=$WATCOM/eddat + +# For DOS 8088/8086 development +export INCLUDE=$WATCOM/h +export LIB=$WATCOM/lib286 # You don't really need this +``` + +Then, when you need to load up these variables, you can simply run `source exportVarsForDOS.sh` or `. exportVarsForDOS.sh` + +## Hello World + +### Buliding without any Makefiles + +Create a new file called `example1.c` + +```c +#include + +int main() { + printf("Hello World!"); + return 0; +} +``` + +First we compile the code: + +```bash +$ wcc example1.c +Open Watcom C x86 16-bit Optimizing Compiler +Version 2.0 beta Mar 15 2024 13:11:55 +Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved. +Portions Copyright (c) 1984-2002 Sybase, Inc. All Rights Reserved. +Source code is available under the Sybase Open Watcom Public License. +See https://github.com/open-watcom/open-watcom-v2#readme for details. +example1.c: 7 lines, included 818, 0 warnings, 0 errors +Code size: 19 +``` + +Then, link to make an executable: + +```bash +$ wlink name example1.exe system dos file example1.o +Open Watcom Linker Version 2.0 beta Mar 15 2024 13:10:09 +Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved. +Portions Copyright (c) 1985-2002 Sybase, Inc. All Rights Reserved. +Source code is available under the Sybase Open Watcom Public License. +See https://github.com/open-watcom/open-watcom-v2#readme for details. +loading object files +searching libraries +creating a DOS executable +``` + +If you want to test this executable, jump to the section titled `Testing with DOSBox-X` below. + +### Simple Makefile + +```makefile +obj = main.o hello.o +bin = tizts.com + +CC = wcc +CFLAGS = -0 +LD = wlink + +$(bin): $(obj) + $(LD) name $@ system dos file main.o file hello.o + +.c.o: + $(CC) $(CFLAGS) $< + +clean: + rm $(obj) $(bin) +``` + +Where, `main.c` +```c +void hello(void); + +int main(void) +{ + hello(); + return 0; +} +``` + +and `hello.c` + +```c +/* hello.c */ +#include + +void hello(void) +{ + printf("Hello!"); +} +``` + +To compile into `tizts.com` simply run `wmake` + +```bash +$ wmake +➜ simple-cpp wmake +Open Watcom Make Version 2.0 beta Mar 15 2024 13:10:16 +Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved. +Portions Copyright (c) 1988-2002 Sybase, Inc. All Rights Reserved. +Source code is available under the Sybase Open Watcom Public License. +See https://github.com/open-watcom/open-watcom-v2#readme for details. + wcc -0 main.c +Open Watcom C x86 16-bit Optimizing Compiler +Version 2.0 beta Mar 15 2024 13:11:55 +Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved. +Portions Copyright (c) 1984-2002 Sybase, Inc. All Rights Reserved. +Source code is available under the Sybase Open Watcom Public License. +See https://github.com/open-watcom/open-watcom-v2#readme for details. +main.c(8): Warning! W138: No newline at end of file +main.c: 8 lines, included 53, 1 warnings, 0 errors +Code size: 12 + wcc -0 hello.c +Open Watcom C x86 16-bit Optimizing Compiler +Version 2.0 beta Mar 15 2024 13:11:55 +Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved. +Portions Copyright (c) 1984-2002 Sybase, Inc. All Rights Reserved. +Source code is available under the Sybase Open Watcom Public License. +See https://github.com/open-watcom/open-watcom-v2#readme for details. +hello.c: 8 lines, included 818, 0 warnings, 0 errors +Code size: 17 + wlink name tizts.com system dos file main.o file hello.o +Open Watcom Linker Version 2.0 beta Mar 15 2024 13:10:09 +Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved. +Portions Copyright (c) 1985-2002 Sybase, Inc. All Rights Reserved. +Source code is available under the Sybase Open Watcom Public License. +See https://github.com/open-watcom/open-watcom-v2#readme for details. +loading object files +searching libraries +creating a DOS executable +``` + +### Using CMake + +Create a file called `CMakeLists.txt` + +```CMake +project(hello) + +set(SOURCES abc.c) + +add_executable(hello ${SOURCES}) +``` + +Where, `abc.c` is: + +```c +#include + +int main() { + printf("Does this work?"); + return 0; +} +``` + +```bash +mkdir build +cd build +``` + +And build using CMake + +``` +cmake -DCMAKE_SYSTEM_NAME=DOS -DCMAKE_SYSTEM_PROCESSOR=I86 -DCMAKE_C_FLAGS="-0 -bt=dos -d0 -oaxt" -G "Watcom WMake" ../.. +``` + +There you have it. Three different ways to compile a C program on a macOS device in 2024 that can run on an IBM PC 5150 (which was released in 1981!) + +## Testing with DOSBox-X + +```bash +cp example1.exe ~/Downloads +/Applications/dosbox-x.app/Contents/MacOS/dosbox-x +``` + +In DOSBox-X we now mount the `~/Downloads` folder as our `C:` drive + +``` +mount C ~/Downloads +``` + +Switch to the C drive + +``` +C: +``` + +Run the program: + +``` +example1 +``` + +![Running our program in DOSBox-X](/assets/posts/dosbox/hello-world.png) + +*My DOSBox setup might look slightly different than yours...* + + diff --git a/Resources/assets/posts/dosbox/hello-world.png b/Resources/assets/posts/dosbox/hello-world.png new file mode 100644 index 0000000..4e2482e Binary files /dev/null and b/Resources/assets/posts/dosbox/hello-world.png differ diff --git a/Resources/images/opengraph/posts/2024-03-04-opencvjs-video-processing.png b/Resources/images/opengraph/posts/2024-03-04-opencvjs-video-processing.png new file mode 100644 index 0000000..e77d3d7 Binary files /dev/null and b/Resources/images/opengraph/posts/2024-03-04-opencvjs-video-processing.png differ diff --git a/Resources/images/opengraph/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.png b/Resources/images/opengraph/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.png new file mode 100644 index 0000000..8cba6d8 Binary files /dev/null and b/Resources/images/opengraph/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.png differ diff --git a/docs/assets/posts/dosbox/hello-world.png b/docs/assets/posts/dosbox/hello-world.png new file mode 100644 index 0000000..4e2482e Binary files /dev/null and b/docs/assets/posts/dosbox/hello-world.png differ diff --git a/docs/feed.rss b/docs/feed.rss index 4f92bc6..d242684 100644 --- a/docs/feed.rss +++ b/docs/feed.rss @@ -4,8 +4,8 @@ Navan's Archive Rare Tips, Tricks and Posts https://web.navan.dev/en - Wed, 28 Feb 2024 11:50:15 -0000 - Wed, 28 Feb 2024 11:50:15 -0000 + Fri, 15 Mar 2024 15:00:25 -0000 + Fri, 15 Mar 2024 15:00:25 -0000 250 @@ -196,6 +196,292 @@ I actually added the code to this post after running the program.

]]> + + + https://web.navan.dev/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.html + + + Cross-Compiling Hello World for DOS on macOS + + + This goes through compiling Open Watcom 2 and creating simple hello-world exampls + + https://web.navan.dev/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.html + Fri, 15 Mar 2024 13:16:00 -0000 + Cross-Compiling Hello World for DOS on macOS + +

Technically this should work for any platform that OpenWatcom 2 supports compiling binaries for. Some instructions are based on a post at retrocoding.net, + and John Tsiombikas's post

+ +

Prerequisites

+ +

You should already have XCode / Command Line Tools, and Homebrew installed. To compile Open Watcom for DOS you will need DOSBox (I use DOSBox-X).

+ +
+
brew install --cask dosbox-x
+
+
+ +

Compiling Open Watcom v2

+ +

If this process is super annoying, I might make a custom homebrew tap to build and install Open Watcom

+ +
+
git clone https://github.com/open-watcom/open-watcom-v2
+cp open-watcom-v2/setvars.sh custom_setvars.sh
+
+
+ +

Now, edit this setvars.sh file. My file looks like this:

+ +
+
#!/bin/zsh
+export OWROOT="/Users/navanchauhan/Developer/8088Stuff/open-watcom-v2"
+export OWTOOLS=CLANG
+export OWDOCBUILD=0
+export OWGUINOBUILD=0
+export OWDISTRBUILD=0
+export OWDOSBOX="/Applications/dosbox-x.app/Contents/MacOS/dosbox-x"
+export OWOBJDIR=binbuildV01
+. "$OWROOT/cmnvars.sh"
+echo "OWROOT=$OWROOT"
+cd "$OWROOT"
+
+
+ +

Note, your OWRTOOT is definitely going to be in a different location.

+ +
+
source ./custom_setvars.sh
+./build.sh
+./build.sh rel
+
+
+ +

This will build, and then copy everything to the rel directory inside open-watcom-v2 directory. Since I ran this on an Apple Silicon Mac, + all the binaries for me are in the armo64 directory. You can now move everything inside the rel folder to another location, or create a simple + script to init all variables whenever you want.

+ +

I like having a script called exportVarsForDOS.sh

+ +
+
#!/bin/zsh
+
+export WATCOM=/Users/navanchauhan/Developer/8088Stuff/open-watcom-v2/rel
+export PATH=$PATH:$WATCOM/armo64
+export EDDAT=$WATCOM/eddat
+
+# For DOS 8088/8086 development
+export INCLUDE=$WATCOM/h
+export LIB=$WATCOM/lib286 # You don't really need this
+
+
+ +

Then, when you need to load up these variables, you can simply run source exportVarsForDOS.sh or . exportVarsForDOS.sh

+ +

Hello World

+ +

Buliding without any Makefiles

+ +

Create a new file called example1.c

+ +
+
#include<stdio.h>
+
+int main() {
+    printf("Hello World!");
+    return 0;
+}
+
+
+ +

First we compile the code:

+ +
+
$ wcc example1.c
+Open Watcom C x86 16-bit Optimizing Compiler
+Version 2.0 beta Mar 15 2024 13:11:55
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1984-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+example1.c: 7 lines, included 818, 0 warnings, 0 errors
+Code size: 19
+
+
+ +

Then, link to make an executable:

+ +
+
$ wlink name example1.exe system dos file example1.o
+Open Watcom Linker Version 2.0 beta Mar 15 2024 13:10:09
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1985-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+loading object files
+searching libraries
+creating a DOS executable 
+
+
+ +

If you want to test this executable, jump to the section titled Testing with DOSBox-X below.

+ +

Simple Makefile

+ +
+
obj = main.o hello.o
+bin = tizts.com
+
+CC = wcc
+CFLAGS = -0
+LD = wlink
+
+$(bin): $(obj)
+    $(LD) name $@ system dos file main.o file hello.o 
+
+.c.o:
+    $(CC) $(CFLAGS) $<
+
+clean:
+    rm $(obj) $(bin)
+
+
+ +

Where, main.c

+ +
+
void hello(void);
+
+int main(void)
+{
+    hello();
+    return 0;
+}
+
+
+ +

and hello.c

+ +
+
/* hello.c */
+#include <stdio.h>
+
+void hello(void)
+{
+    printf("Hello!");
+}
+
+
+ +

To compile into tizts.com simply run wmake

+ +
+
$ wmake
+➜  simple-cpp wmake
+Open Watcom Make Version 2.0 beta Mar 15 2024 13:10:16
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1988-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+    wcc -0 main.c
+Open Watcom C x86 16-bit Optimizing Compiler
+Version 2.0 beta Mar 15 2024 13:11:55
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1984-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+main.c(8): Warning! W138: No newline at end of file
+main.c: 8 lines, included 53, 1 warnings, 0 errors
+Code size: 12
+    wcc -0 hello.c
+Open Watcom C x86 16-bit Optimizing Compiler
+Version 2.0 beta Mar 15 2024 13:11:55
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1984-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+hello.c: 8 lines, included 818, 0 warnings, 0 errors
+Code size: 17
+    wlink name tizts.com system dos file main.o file hello.o
+Open Watcom Linker Version 2.0 beta Mar 15 2024 13:10:09
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1985-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+loading object files
+searching libraries
+creating a DOS executable
+
+
+ +

Using CMake

+ +

Create a file called CMakeLists.txt

+ +
+
project(hello)
+
+set(SOURCES abc.c)
+
+add_executable(hello ${SOURCES})
+
+
+ +

Where, abc.c is:

+ +
+
#include <stdio.h>
+
+int main() {
+    printf("Does this work?");
+    return 0;
+}
+
+
+ +
+
mkdir build
+cd build
+
+
+ +

And build using CMake

+ +
cmake -DCMAKE_SYSTEM_NAME=DOS -DCMAKE_SYSTEM_PROCESSOR=I86 -DCMAKE_C_FLAGS="-0 -bt=dos -d0 -oaxt" -G "Watcom WMake" ../..
+
+ +

There you have it. Three different ways to compile a C program on a macOS device in 2024 that can run on an IBM PC 5150 (which was released in 1981!)

+ +

Testing with DOSBox-X

+ +
+
cp example1.exe ~/Downloads
+/Applications/dosbox-x.app/Contents/MacOS/dosbox-x
+
+
+ +

In DOSBox-X we now mount the ~/Downloads folder as our C: drive

+ +
mount C ~/Downloads
+
+ +

Switch to the C drive

+ +
C:
+
+ +

Run the program:

+ +
example1
+
+ +

Running our program in DOSBox-X

+ +

My DOSBox setup might look slightly different than yours...

+]]> + + https://web.navan.dev/posts/hello-world.html diff --git a/docs/images/opengraph/posts/2024-03-04-opencvjs-video-processing.png b/docs/images/opengraph/posts/2024-03-04-opencvjs-video-processing.png new file mode 100644 index 0000000..e77d3d7 Binary files /dev/null and b/docs/images/opengraph/posts/2024-03-04-opencvjs-video-processing.png differ diff --git a/docs/images/opengraph/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.png b/docs/images/opengraph/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.png new file mode 100644 index 0000000..8cba6d8 Binary files /dev/null and b/docs/images/opengraph/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.png differ diff --git a/docs/index.html b/docs/index.html index 3bee970..f6a4942 100644 --- a/docs/index.html +++ b/docs/index.html @@ -50,6 +50,21 @@

Recent Posts

For all posts go to Posts diff --git a/docs/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.html b/docs/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.html new file mode 100644 index 0000000..bb37d00 --- /dev/null +++ b/docs/posts/2024-03-15-setting-up-macos-for-8088-dos-dev.html @@ -0,0 +1,330 @@ + + + + + + + + + Cross-Compiling Hello World for DOS on macOS + + + + + + + + + + + + + + + + + + + + + +
+
+ +
+ +

Cross-Compiling Hello World for DOS on macOS

+ +

Technically this should work for any platform that OpenWatcom 2 supports compiling binaries for. Some instructions are based on a post at retrocoding.net, + and John Tsiombikas's post

+ +

Prerequisites

+ +

You should already have XCode / Command Line Tools, and Homebrew installed. To compile Open Watcom for DOS you will need DOSBox (I use DOSBox-X).

+ +
+
brew install --cask dosbox-x
+
+
+ +

Compiling Open Watcom v2

+ +

If this process is super annoying, I might make a custom homebrew tap to build and install Open Watcom

+ +
+
git clone https://github.com/open-watcom/open-watcom-v2
+cp open-watcom-v2/setvars.sh custom_setvars.sh
+
+
+ +

Now, edit this setvars.sh file. My file looks like this:

+ +
+
#!/bin/zsh
+export OWROOT="/Users/navanchauhan/Developer/8088Stuff/open-watcom-v2"
+export OWTOOLS=CLANG
+export OWDOCBUILD=0
+export OWGUINOBUILD=0
+export OWDISTRBUILD=0
+export OWDOSBOX="/Applications/dosbox-x.app/Contents/MacOS/dosbox-x"
+export OWOBJDIR=binbuildV01
+. "$OWROOT/cmnvars.sh"
+echo "OWROOT=$OWROOT"
+cd "$OWROOT"
+
+
+ +

Note, your OWRTOOT is definitely going to be in a different location.

+ +
+
source ./custom_setvars.sh
+./build.sh
+./build.sh rel
+
+
+ +

This will build, and then copy everything to the rel directory inside open-watcom-v2 directory. Since I ran this on an Apple Silicon Mac, + all the binaries for me are in the armo64 directory. You can now move everything inside the rel folder to another location, or create a simple + script to init all variables whenever you want.

+ +

I like having a script called exportVarsForDOS.sh

+ +
+
#!/bin/zsh
+
+export WATCOM=/Users/navanchauhan/Developer/8088Stuff/open-watcom-v2/rel
+export PATH=$PATH:$WATCOM/armo64
+export EDDAT=$WATCOM/eddat
+
+# For DOS 8088/8086 development
+export INCLUDE=$WATCOM/h
+export LIB=$WATCOM/lib286 # You don't really need this
+
+
+ +

Then, when you need to load up these variables, you can simply run source exportVarsForDOS.sh or . exportVarsForDOS.sh

+ +

Hello World

+ +

Buliding without any Makefiles

+ +

Create a new file called example1.c

+ +
+
#include<stdio.h>
+
+int main() {
+    printf("Hello World!");
+    return 0;
+}
+
+
+ +

First we compile the code:

+ +
+
$ wcc example1.c
+Open Watcom C x86 16-bit Optimizing Compiler
+Version 2.0 beta Mar 15 2024 13:11:55
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1984-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+example1.c: 7 lines, included 818, 0 warnings, 0 errors
+Code size: 19
+
+
+ +

Then, link to make an executable:

+ +
+
$ wlink name example1.exe system dos file example1.o
+Open Watcom Linker Version 2.0 beta Mar 15 2024 13:10:09
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1985-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+loading object files
+searching libraries
+creating a DOS executable 
+
+
+ +

If you want to test this executable, jump to the section titled Testing with DOSBox-X below.

+ +

Simple Makefile

+ +
+
obj = main.o hello.o
+bin = tizts.com
+
+CC = wcc
+CFLAGS = -0
+LD = wlink
+
+$(bin): $(obj)
+    $(LD) name $@ system dos file main.o file hello.o 
+
+.c.o:
+    $(CC) $(CFLAGS) $<
+
+clean:
+    rm $(obj) $(bin)
+
+
+ +

Where, main.c

+ +
+
void hello(void);
+
+int main(void)
+{
+    hello();
+    return 0;
+}
+
+
+ +

and hello.c

+ +
+
/* hello.c */
+#include <stdio.h>
+
+void hello(void)
+{
+    printf("Hello!");
+}
+
+
+ +

To compile into tizts.com simply run wmake

+ +
+
$ wmake
+➜  simple-cpp wmake
+Open Watcom Make Version 2.0 beta Mar 15 2024 13:10:16
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1988-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+    wcc -0 main.c
+Open Watcom C x86 16-bit Optimizing Compiler
+Version 2.0 beta Mar 15 2024 13:11:55
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1984-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+main.c(8): Warning! W138: No newline at end of file
+main.c: 8 lines, included 53, 1 warnings, 0 errors
+Code size: 12
+    wcc -0 hello.c
+Open Watcom C x86 16-bit Optimizing Compiler
+Version 2.0 beta Mar 15 2024 13:11:55
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1984-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+hello.c: 8 lines, included 818, 0 warnings, 0 errors
+Code size: 17
+    wlink name tizts.com system dos file main.o file hello.o
+Open Watcom Linker Version 2.0 beta Mar 15 2024 13:10:09
+Copyright (c) 2002-2024 The Open Watcom Contributors. All Rights Reserved.
+Portions Copyright (c) 1985-2002 Sybase, Inc. All Rights Reserved.
+Source code is available under the Sybase Open Watcom Public License.
+See https://github.com/open-watcom/open-watcom-v2#readme for details.
+loading object files
+searching libraries
+creating a DOS executable
+
+
+ +

Using CMake

+ +

Create a file called CMakeLists.txt

+ +
+
project(hello)
+
+set(SOURCES abc.c)
+
+add_executable(hello ${SOURCES})
+
+
+ +

Where, abc.c is:

+ +
+
#include <stdio.h>
+
+int main() {
+    printf("Does this work?");
+    return 0;
+}
+
+
+ +
+
mkdir build
+cd build
+
+
+ +

And build using CMake

+ +
cmake -DCMAKE_SYSTEM_NAME=DOS -DCMAKE_SYSTEM_PROCESSOR=I86 -DCMAKE_C_FLAGS="-0 -bt=dos -d0 -oaxt" -G "Watcom WMake" ../..
+
+ +

There you have it. Three different ways to compile a C program on a macOS device in 2024 that can run on an IBM PC 5150 (which was released in 1981!)

+ +

Testing with DOSBox-X

+ +
+
cp example1.exe ~/Downloads
+/Applications/dosbox-x.app/Contents/MacOS/dosbox-x
+
+
+ +

In DOSBox-X we now mount the ~/Downloads folder as our C: drive

+ +
mount C ~/Downloads
+
+ +

Switch to the C drive

+ +
C:
+
+ +

Run the program:

+ +
example1
+
+ +

Running our program in DOSBox-X

+ +

My DOSBox setup might look slightly different than yours...

+ +
If you have scrolled this far, consider subscribing to my mailing list here. You can subscribe to either a specific type of post you are interested in, or subscribe to everything with the "Everything" list.
+ +
+ +
+
+ + + + + \ No newline at end of file diff --git a/docs/posts/index.html b/docs/posts/index.html index 4194100..2d9d613 100644 --- a/docs/posts/index.html +++ b/docs/posts/index.html @@ -52,6 +52,21 @@
    +
  • Cross-Compiling Hello World for DOS on macOS
    • +
      +
    • This goes through compiling Open Watcom 2 and creating simple hello-world exampls
      • +
    • Published On: 2024-03-15 13:16
      • +
    • Tags: + + DOS, + + x86, + + macOS + +
    + +
  • Interacting with underlying element in HTML
    • With CSS you can disable any interactions with an element and directly control the underlying element
      • diff --git a/docs/tags/DOS.html b/docs/tags/DOS.html new file mode 100644 index 0000000..3a75f5b --- /dev/null +++ b/docs/tags/DOS.html @@ -0,0 +1,73 @@ + + + + + + + + + "DOS" + + + + + + + + + + + + + + + + + + + + + +
      +
      + + +
      +

      DOS

      Posts tagged 'DOS'

      +
      + + + + + + + + \ No newline at end of file diff --git a/docs/tags/JS.html b/docs/tags/JS.html new file mode 100644 index 0000000..b01594b --- /dev/null +++ b/docs/tags/JS.html @@ -0,0 +1,73 @@ + + + + + + + + + "JS" + + + + + + + + + + + + + + + + + + + + + +
      +
      + + +
      +

      JS

      Posts tagged 'JS'

      +
      + + + + + + + + \ No newline at end of file diff --git a/docs/tags/OpenCV.html b/docs/tags/OpenCV.html new file mode 100644 index 0000000..ddaa485 --- /dev/null +++ b/docs/tags/OpenCV.html @@ -0,0 +1,73 @@ + + + + + + + + + "OpenCV" + + + + + + + + + + + + + + + + + + + + + +
      +
      + + +
      +

      OpenCV

      Posts tagged 'OpenCV'

      +
      + + + + + + + + \ No newline at end of file diff --git a/docs/tags/macOS.html b/docs/tags/macOS.html index 8b70731..028aef3 100644 --- a/docs/tags/macOS.html +++ b/docs/tags/macOS.html @@ -49,6 +49,21 @@
        +
      • Cross-Compiling Hello World for DOS on macOS
        • +
          +
        • This goes through compiling Open Watcom 2 and creating simple hello-world exampls
          • +
        • Published On: 2024-03-15 13:16
          • +
        • Tags: + + DOS, + + x86, + + macOS + +
        + +
      • Interacting with Siri using the command line
        • Code snippet to interact with Siri by issuing commands from the command-line.
          • diff --git a/docs/tags/x86.html b/docs/tags/x86.html new file mode 100644 index 0000000..dab538b --- /dev/null +++ b/docs/tags/x86.html @@ -0,0 +1,73 @@ + + + + + + + + + "x86" + + + + + + + + + + + + + + + + + + + + + +
          +
          + + +
          +

          x86

          Posts tagged 'x86'

          +
          + + + + + + + + \ No newline at end of file -- cgit v1.2.3 From b484b8a672a907af87e73fe7006497a6ca86c259 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Thu, 21 Mar 2024 13:54:53 -0600 Subject: add polynomial regression for tf 2.0 --- ...-03-21-Polynomial-Regression-in-TensorFlow-2.md | 241 ++++++++++++++++ ...03-21-Polynomial-Regression-in-TensorFlow-2.png | Bin 0 -> 27498 bytes docs/feed.rss | 271 +++++++++++++++++- ...03-21-Polynomial-Regression-in-TensorFlow-2.png | Bin 0 -> 27498 bytes docs/index.html | 28 +- ...3-21-Polynomial-Regression-in-TensorFlow-2.html | 311 +++++++++++++++++++++ docs/posts/index.html | 15 + docs/tags/Colab.html | 15 + docs/tags/Tensorflow.html | 15 + 9 files changed, 881 insertions(+), 15 deletions(-) create mode 100644 Content/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.md create mode 100644 Resources/images/opengraph/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.png create mode 100644 docs/images/opengraph/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.png create mode 100644 docs/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.html (limited to 'Content/posts') diff --git a/Content/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.md b/Content/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.md new file mode 100644 index 0000000..4341f09 --- /dev/null +++ b/Content/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.md @@ -0,0 +1,241 @@ +--- +date: 2024-03-21 12:46 +description: Predicting n-th degree polynomials using TensorFlow 2.x +tags: Tutorial, Tensorflow, Colab +--- + +# Polynomial Regression Using TensorFlow 2.x + +I have a similar post titled [Polynomial Regression Using Tensorflow](/posts/2019-12-16-TensorFlow-Polynomial-Regression.html) that used `tensorflow.compat.v1` (Which still works as of TF 2.16). But, I thought it would be nicer to redo it with newer TF versions. + +I will be skipping all the introductions about polynomial regression and jumping straight to the code. Personally, I prefer using `scikit-learn` for this task. + +## Position vs Salary Dataset + +Again, we will be using https://drive.google.com/file/d/1tNL4jxZEfpaP4oflfSn6pIHJX7Pachm9/view (Salary vs Position Dataset) + +If you are in a Python Notebook environment like Kaggle or Google Colaboratory, you can simply run: +```Termcap +!wget --no-check-certificate 'https://docs.google.com/uc?export=download&id=1tNL4jxZEfpaP4oflfSn6pIHJX7Pachm9' -O data.csv +``` + +## Code + +If you just want to copy-paste the code, scroll to the bottom for the entire snippet. Here I will try and walk through setting up code for a 3rd-degree (cubic) polynomial + +### Imports + +```python +import pandas as pd +import tensorflow as tf +import matplotlib.pyplot as plt +import numpy as np +``` + +### Reading the Dataset + +```python +df = pd.read_csv("data.csv") +``` + +### Variables and Constants + +Here, we initialize the X and Y values as constants, since they are not going to change. The coefficients are defined as variables. + +```python +X = tf.constant(df["Level"], dtype=tf.float32) +Y = tf.constant(df["Salary"], dtype=tf.float32) + +coefficients = [tf.Variable(np.random.randn() * 0.01, dtype=tf.float32) for _ in range(4)] +``` + +Here, `X` and `Y` are the values from our dataset. We initialize the coefficients for the equations as small random values. + +These coefficients are evaluated by Tensorflow's `tf.math.poyval` function which returns the n-th order polynomial based on how many coefficients are passed. Since our list of coefficients contains 4 different variables, it will be evaluated as: + +``` +y = (x**3)*coefficients[3] + (x**2)*coefficients[2] + (x**1)*coefficients[1] (x**0)*coefficients[0] +``` + +Which is equivalent to the general cubic equation: + + + +$$ +y = ax^3 + bx^2 + cx + d +$$ + +### Optimizer Selection & Training + +```python +optimizer = tf.keras.optimizers.Adam(learning_rate=0.3) +num_epochs = 10_000 + +for epoch in range(num_epochs): + with tf.GradientTape() as tape: + y_pred = tf.math.polyval(coefficients, X) + loss = tf.reduce_mean(tf.square(y - y_pred)) + grads = tape.gradient(loss, coefficients) + optimizer.apply_gradients(zip(grads, coefficients)) + if (epoch+1) % 1000 == 0: + print(f"Epoch: {epoch+1}, Loss: {loss.numpy()}" +``` + +In TensorFlow 1, we would have been using `tf.Session` instead. + +Here we are using `GradientTape()` instead, to keep track of the loss evaluation and coefficients. This is crucial, as our optimizer needs these gradients to be able to optimize our coefficients. + +Our loss function is Mean Squared Error (MSE) + +$$ += \frac{1}{n}\sum_{i=1}^{n} (Y_i - \^{Y_i}) +$$ + +Where $\^{Y_i}$ is the predicted value and $Y_i$ is the actual value + +### Plotting Final Coefficients + +```python +final_coefficients = [c.numpy() for c in coefficients] +print("Final Coefficients:", final_coefficients) + +plt.plot(df["Level"], df["Salary"], label="Original Data") +plt.plot(df["Level"],[tf.math.polyval(final_coefficients, tf.constant(x, dtype=tf.float32)).numpy() for x in df["Level"]]) +plt.ylabel('Salary') +plt.xlabel('Position') +plt.title("Salary vs Position") +plt.show() +``` + + +## Code Snippet for a Polynomial of Degree N + +### Using Gradient Tape + +This should work regardless of the Keras backend version (2 or 3) + +```python +import tensorflow as tf +import numpy as np +import pandas as pd +import matplotlib.pyplot as plt + +df = pd.read_csv("data.csv") + +############################ +## Change Parameters Here ## +############################ +x_column = "Level" # +y_column = "Salary" # +degree = 2 # +learning_rate = 0.3 # +num_epochs = 25_000 # +############################ + +X = tf.constant(df[x_column], dtype=tf.float32) +Y = tf.constant(df[y_column], dtype=tf.float32) + +coefficients = [tf.Variable(np.random.randn() * 0.01, dtype=tf.float32) for _ in range(degree + 1)] + +optimizer = tf.keras.optimizers.Adam(learning_rate=learning_rate) + +for epoch in range(num_epochs): + with tf.GradientTape() as tape: + y_pred = tf.math.polyval(coefficients, X) + loss = tf.reduce_mean(tf.square(Y - y_pred)) + grads = tape.gradient(loss, coefficients) + optimizer.apply_gradients(zip(grads, coefficients)) + if (epoch+1) % 1000 == 0: + print(f"Epoch: {epoch+1}, Loss: {loss.numpy()}") + +final_coefficients = [c.numpy() for c in coefficients] +print("Final Coefficients:", final_coefficients) + +print("Final Equation:", end=" ") +for i in range(degree+1): + print(f"{final_coefficients[i]} * x^{degree-i}", end=" + " if i < degree else "\n") + +plt.plot(X, Y, label="Original Data") +plt.plot(X,[tf.math.polyval(final_coefficients, tf.constant(x, dtype=tf.float32)).numpy() for x in df[x_column]]), label="Our Poynomial" +plt.ylabel(y_column) +plt.xlabel(x_column) +plt.title(f"{x_column} vs {y_column}") +plt.legend() +plt.show() +``` + +### Without Gradient Tape + +This relies on the Optimizer's `minimize` function and uses the `var_list` parameter to update the variables. + +This will not work with Keras 3 backend in TF 2.16.0 and above unless you switch to the legacy backend. + +```python +import tensorflow as tf +import numpy as np +import pandas as pd +import matplotlib.pyplot as plt + +df = pd.read_csv("data.csv") + +############################ +## Change Parameters Here ## +############################ +x_column = "Level" # +y_column = "Salary" # +degree = 2 # +learning_rate = 0.3 # +num_epochs = 25_000 # +############################ + +X = tf.constant(df[x_column], dtype=tf.float32) +Y = tf.constant(df[y_column], dtype=tf.float32) + +coefficients = [tf.Variable(np.random.randn() * 0.01, dtype=tf.float32) for _ in range(degree + 1)] + +optimizer = tf.keras.optimizers.Adam(learning_rate=learning_rate) + +def loss_function(): + pred_y = tf.math.polyval(coefficients, X) + return tf.reduce_mean(tf.square(pred_y - Y)) + +for epoch in range(num_epochs): + optimizer.minimize(loss_function, var_list=coefficients) + if (epoch+1) % 1000 == 0: + current_loss = loss_function().numpy() + print(f"Epoch {epoch+1}: Training Loss: {current_loss}") + +final_coefficients = coefficients.numpy() +print("Final Coefficients:", final_coefficients) + +print("Final Equation:", end=" ") +for i in range(degree+1): + print(f"{final_coefficients[i]} * x^{degree-i}", end=" + " if i < degree else "\n") + +plt.plot(X, Y, label="Original Data") +plt.plot(X,[tf.math.polyval(final_coefficients, tf.constant(x, dtype=tf.float32)).numpy() for x in df[x_column]], label="Our Polynomial") +plt.ylabel(y_column) +plt.xlabel(x_column) +plt.legend() +plt.title(f"{x_column} vs {y_column}") +plt.show() +``` + + +As always, remember to tweak the parameters and choose the correct model for the job. A polynomial regression model might not even be the best model for this particular dataset. + +## Further Programming + +How would you modify this code to use another type of nonlinear regression? Say, $ y = ab^x $ + +Hint: Your loss calculation would be similar to: + +```python +bx = tf.pow(coefficients[1], X) +pred_y = tf.math.multiply(coefficients[0], bx) +loss = tf.reduce_mean(tf.square(pred_y - Y)) +``` + + diff --git a/Resources/images/opengraph/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.png b/Resources/images/opengraph/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.png new file mode 100644 index 0000000..0dbdd08 Binary files /dev/null and b/Resources/images/opengraph/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.png differ diff --git a/docs/feed.rss b/docs/feed.rss index d242684..df334a3 100644 --- a/docs/feed.rss +++ b/docs/feed.rss @@ -4,8 +4,8 @@ Navan's Archive Rare Tips, Tricks and Posts https://web.navan.dev/en - Fri, 15 Mar 2024 15:00:25 -0000 - Fri, 15 Mar 2024 15:00:25 -0000 + Thu, 21 Mar 2024 13:54:34 -0000 + Thu, 21 Mar 2024 13:54:34 -0000 250 @@ -482,6 +482,273 @@ creating a DOS + + + https://web.navan.dev/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.html + + + Polynomial Regression Using TensorFlow 2.x + + + Predicting n-th degree polynomials using TensorFlow 2.x + + https://web.navan.dev/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.html + Thu, 21 Mar 2024 12:46:00 -0000 + Polynomial Regression Using TensorFlow 2.x + +

          I have a similar post titled Polynomial Regression Using Tensorflow that used tensorflow.compat.v1 (Which still works as of TF 2.16). But, I thought it would be nicer to redo it with newer TF versions.

          + +

          I will be skipping all the introductions about polynomial regression and jumping straight to the code. Personally, I prefer using scikit-learn for this task.

          + +

          Position vs Salary Dataset

          + +

          Again, we will be using https://drive.google.com/file/d/1tNL4jxZEfpaP4oflfSn6pIHJX7Pachm9/view (Salary vs Position Dataset)

          + +

          If you are in a Python Notebook environment like Kaggle or Google Colaboratory, you can simply run:

          + +
          +
          !wget --no-check-certificate 'https://docs.google.com/uc?export=download&id=1tNL4jxZEfpaP4oflfSn6pIHJX7Pachm9' -O data.csv
+
          +
          + +

          Code

          + +

          If you just want to copy-paste the code, scroll to the bottom for the entire snippet. Here I will try and walk through setting up code for a 3rd-degree (cubic) polynomial

          + +

          Imports

          + +
          +
          import pandas as pd
+import tensorflow as tf
+import matplotlib.pyplot as plt
+import numpy as np
+
          +
          + +

          Reading the Dataset

          + +
          +
          df = pd.read_csv("data.csv")
+
          +
          + +

          Variables and Constants

          + +

          Here, we initialize the X and Y values as constants, since they are not going to change. The coefficients are defined as variables.

          + +
          +
          X = tf.constant(df["Level"], dtype=tf.float32)
+Y = tf.constant(df["Salary"], dtype=tf.float32)
+
+coefficients = [tf.Variable(np.random.randn() * 0.01, dtype=tf.float32) for _ in range(4)]
+
          +
          + +

          Here, X and Y are the values from our dataset. We initialize the coefficients for the equations as small random values.

          + +

          These coefficients are evaluated by Tensorflow's tf.math.poyval function which returns the n-th order polynomial based on how many coefficients are passed. Since our list of coefficients contains 4 different variables, it will be evaluated as:

          + +
          y = (x**3)*coefficients[3] + (x**2)*coefficients[2] + (x**1)*coefficients[1] (x**0)*coefficients[0]
+
          + +

          Which is equivalent to the general cubic equation:

          + +

          + +$$ +y = ax^3 + bx^2 + cx + d +$$ + +### Optimizer Selection & Training +

          + +
          optimizer = tf.keras.optimizers.Adam(learning_rate=0.3)
+num_epochs = 10_000
+
+for epoch in range(num_epochs):
+    with tf.GradientTape() as tape:
+        y_pred = tf.math.polyval(coefficients, X)
+        loss = tf.reduce_mean(tf.square(y - y_pred))
+    grads = tape.gradient(loss, coefficients)
+    optimizer.apply_gradients(zip(grads, coefficients))
+    if (epoch+1) % 1000 == 0:
+        print(f"Epoch: {epoch+1}, Loss: {loss.numpy()}"
+
          + +
          + + +In TensorFlow 1, we would have been using `tf.Session` instead. + +Here we are using `GradientTape()` instead, to keep track of the loss evaluation and coefficients. This is crucial, as our optimizer needs these gradients to be able to optimize our coefficients. + +Our loss function is Mean Squared Error (MSE) + +$$ += \frac{1}{n}\sum_{i=1}^{n} (Y_i - \^{Y_i}) +$$ + +Where $\^{Y_i}$ is the predicted value and $Y_i$ is the actual value + +### Plotting Final Coefficients +
          + +
          final_coefficients = [c.numpy() for c in coefficients]
+print("Final Coefficients:", final_coefficients)
+
+plt.plot(df["Level"], df["Salary"], label="Original Data")
+plt.plot(df["Level"],[tf.math.polyval(final_coefficients, tf.constant(x, dtype=tf.float32)).numpy() for x in df["Level"]])
+plt.ylabel('Salary')
+plt.xlabel('Position')
+plt.title("Salary vs Position")
+plt.show()
+
          + +
          + + + +## Code Snippet for a Polynomial of Degree N + +### Using Gradient Tape + +This should work regardless of the Keras backend version (2 or 3) +
          + +
          import tensorflow as tf
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+
+df = pd.read_csv("data.csv")
+
+############################
+## Change Parameters Here ##
+############################
+x_column = "Level"         #
+y_column = "Salary"        #
+degree = 2                 #
+learning_rate = 0.3        #
+num_epochs = 25_000        #
+############################
+
+X = tf.constant(df[x_column], dtype=tf.float32)
+Y = tf.constant(df[y_column], dtype=tf.float32)
+
+coefficients = [tf.Variable(np.random.randn() * 0.01, dtype=tf.float32) for _ in range(degree + 1)]
+
+optimizer = tf.keras.optimizers.Adam(learning_rate=learning_rate)
+
+for epoch in range(num_epochs):
+    with tf.GradientTape() as tape:
+        y_pred = tf.math.polyval(coefficients, X)
+        loss = tf.reduce_mean(tf.square(Y - y_pred))
+    grads = tape.gradient(loss, coefficients)
+    optimizer.apply_gradients(zip(grads, coefficients))
+    if (epoch+1) % 1000 == 0:
+        print(f"Epoch: {epoch+1}, Loss: {loss.numpy()}")
+
+final_coefficients = [c.numpy() for c in coefficients]
+print("Final Coefficients:", final_coefficients)
+
+print("Final Equation:", end=" ")
+for i in range(degree+1):
+  print(f"{final_coefficients[i]} * x^{degree-i}", end=" + " if i < degree else "\n")
+
+plt.plot(X, Y, label="Original Data")
+plt.plot(X,[tf.math.polyval(final_coefficients, tf.constant(x, dtype=tf.float32)).numpy() for x in df[x_column]]), label="Our Poynomial"
+plt.ylabel(y_column)
+plt.xlabel(x_column)
+plt.title(f"{x_column} vs {y_column}")
+plt.legend()
+plt.show()
+
          + +
          + + +### Without Gradient Tape + +This relies on the Optimizer's `minimize` function and uses the `var_list` parameter to update the variables. + +This will not work with Keras 3 backend in TF 2.16.0 and above unless you switch to the legacy backend. +
          + +
          import tensorflow as tf
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+
+df = pd.read_csv("data.csv")
+
+############################
+## Change Parameters Here ##
+############################
+x_column = "Level"         #
+y_column = "Salary"        #
+degree = 2                 #
+learning_rate = 0.3        #
+num_epochs = 25_000        #
+############################
+
+X = tf.constant(df[x_column], dtype=tf.float32)
+Y = tf.constant(df[y_column], dtype=tf.float32)
+
+coefficients = [tf.Variable(np.random.randn() * 0.01, dtype=tf.float32) for _ in range(degree + 1)]
+
+optimizer = tf.keras.optimizers.Adam(learning_rate=learning_rate)
+
+def loss_function():
+  pred_y = tf.math.polyval(coefficients, X)
+  return tf.reduce_mean(tf.square(pred_y - Y))
+
+for epoch in range(num_epochs):
+    optimizer.minimize(loss_function, var_list=coefficients)
+    if (epoch+1) % 1000 == 0:
+        current_loss = loss_function().numpy()
+        print(f"Epoch {epoch+1}: Training Loss: {current_loss}")
+
+final_coefficients = coefficients.numpy()
+print("Final Coefficients:", final_coefficients)
+
+print("Final Equation:", end=" ")
+for i in range(degree+1):
+  print(f"{final_coefficients[i]} * x^{degree-i}", end=" + " if i < degree else "\n")
+
+plt.plot(X, Y, label="Original Data")
+plt.plot(X,[tf.math.polyval(final_coefficients, tf.constant(x, dtype=tf.float32)).numpy() for x in df[x_column]], label="Our Polynomial")
+plt.ylabel(y_column)
+plt.xlabel(x_column)
+plt.legend()
+plt.title(f"{x_column} vs {y_column}")
+plt.show()
+
          + +
          + + + +As always, remember to tweak the parameters and choose the correct model for the job. A polynomial regression model might not even be the best model for this particular dataset. + +## Further Programming + +How would you modify this code to use another type of nonlinear regression? Say, $ y = ab^x $ + +Hint: Your loss calculation would be similar to: +
          + +
          bx = tf.pow(coefficients[1], X)
+pred_y = tf.math.multiply(coefficients[0], bx)
+loss = tf.reduce_mean(tf.square(pred_y - Y))
+
          + +

          +]]>           +           + https://web.navan.dev/posts/hello-world.html diff --git a/docs/images/opengraph/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.png b/docs/images/opengraph/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.png new file mode 100644 index 0000000..0dbdd08 Binary files /dev/null and b/docs/images/opengraph/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.png differ diff --git a/docs/index.html b/docs/index.html index f6a4942..0a3070a 100644 --- a/docs/index.html +++ b/docs/index.html @@ -50,6 +50,21 @@

          Recent Posts

          For all posts go to Posts diff --git a/docs/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.html b/docs/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.html new file mode 100644 index 0000000..c1a4ae4 --- /dev/null +++ b/docs/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.html @@ -0,0 +1,311 @@ + + + + + + + + + Polynomial Regression Using TensorFlow 2.x + + + + + + + + + + + + + + + + + + + + + +
          +
          + +
          + +

          Polynomial Regression Using TensorFlow 2.x

          + +

          I have a similar post titled Polynomial Regression Using Tensorflow that used tensorflow.compat.v1 (Which still works as of TF 2.16). But, I thought it would be nicer to redo it with newer TF versions.

          + +

          I will be skipping all the introductions about polynomial regression and jumping straight to the code. Personally, I prefer using scikit-learn for this task.

          + +

          Position vs Salary Dataset

          + +

          Again, we will be using https://drive.google.com/file/d/1tNL4jxZEfpaP4oflfSn6pIHJX7Pachm9/view (Salary vs Position Dataset)

          + +

          If you are in a Python Notebook environment like Kaggle or Google Colaboratory, you can simply run:

          + +
          +
          !wget --no-check-certificate 'https://docs.google.com/uc?export=download&id=1tNL4jxZEfpaP4oflfSn6pIHJX7Pachm9' -O data.csv
+
          +
          + +

          Code

          + +

          If you just want to copy-paste the code, scroll to the bottom for the entire snippet. Here I will try and walk through setting up code for a 3rd-degree (cubic) polynomial

          + +

          Imports

          + +
          +
          import pandas as pd
+import tensorflow as tf
+import matplotlib.pyplot as plt
+import numpy as np
+
          +
          + +

          Reading the Dataset

          + +
          +
          df = pd.read_csv("data.csv")
+
          +
          + +

          Variables and Constants

          + +

          Here, we initialize the X and Y values as constants, since they are not going to change. The coefficients are defined as variables.

          + +
          +
          X = tf.constant(df["Level"], dtype=tf.float32)
+Y = tf.constant(df["Salary"], dtype=tf.float32)
+
+coefficients = [tf.Variable(np.random.randn() * 0.01, dtype=tf.float32) for _ in range(4)]
+
          +
          + +

          Here, X and Y are the values from our dataset. We initialize the coefficients for the equations as small random values.

          + +

          These coefficients are evaluated by Tensorflow's tf.math.poyval function which returns the n-th order polynomial based on how many coefficients are passed. Since our list of coefficients contains 4 different variables, it will be evaluated as:

          + +
          y = (x**3)*coefficients[3] + (x**2)*coefficients[2] + (x**1)*coefficients[1] (x**0)*coefficients[0]
+
          + +

          Which is equivalent to the general cubic equation:

          + +

          + +$$ +y = ax^3 + bx^2 + cx + d +$$ + +### Optimizer Selection & Training +

          + +
          optimizer = tf.keras.optimizers.Adam(learning_rate=0.3)
+num_epochs = 10_000
+
+for epoch in range(num_epochs):
+    with tf.GradientTape() as tape:
+        y_pred = tf.math.polyval(coefficients, X)
+        loss = tf.reduce_mean(tf.square(y - y_pred))
+    grads = tape.gradient(loss, coefficients)
+    optimizer.apply_gradients(zip(grads, coefficients))
+    if (epoch+1) % 1000 == 0:
+        print(f"Epoch: {epoch+1}, Loss: {loss.numpy()}"
+
          + +
          + + +In TensorFlow 1, we would have been using `tf.Session` instead. + +Here we are using `GradientTape()` instead, to keep track of the loss evaluation and coefficients. This is crucial, as our optimizer needs these gradients to be able to optimize our coefficients. + +Our loss function is Mean Squared Error (MSE) + +$$ += \frac{1}{n}\sum_{i=1}^{n} (Y_i - \^{Y_i}) +$$ + +Where $\^{Y_i}$ is the predicted value and $Y_i$ is the actual value + +### Plotting Final Coefficients +
          + +
          final_coefficients = [c.numpy() for c in coefficients]
+print("Final Coefficients:", final_coefficients)
+
+plt.plot(df["Level"], df["Salary"], label="Original Data")
+plt.plot(df["Level"],[tf.math.polyval(final_coefficients, tf.constant(x, dtype=tf.float32)).numpy() for x in df["Level"]])
+plt.ylabel('Salary')
+plt.xlabel('Position')
+plt.title("Salary vs Position")
+plt.show()
+
          + +
          + + + +## Code Snippet for a Polynomial of Degree N + +### Using Gradient Tape + +This should work regardless of the Keras backend version (2 or 3) +
          + +
          import tensorflow as tf
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+
+df = pd.read_csv("data.csv")
+
+############################
+## Change Parameters Here ##
+############################
+x_column = "Level"         #
+y_column = "Salary"        #
+degree = 2                 #
+learning_rate = 0.3        #
+num_epochs = 25_000        #
+############################
+
+X = tf.constant(df[x_column], dtype=tf.float32)
+Y = tf.constant(df[y_column], dtype=tf.float32)
+
+coefficients = [tf.Variable(np.random.randn() * 0.01, dtype=tf.float32) for _ in range(degree + 1)]
+
+optimizer = tf.keras.optimizers.Adam(learning_rate=learning_rate)
+
+for epoch in range(num_epochs):
+    with tf.GradientTape() as tape:
+        y_pred = tf.math.polyval(coefficients, X)
+        loss = tf.reduce_mean(tf.square(Y - y_pred))
+    grads = tape.gradient(loss, coefficients)
+    optimizer.apply_gradients(zip(grads, coefficients))
+    if (epoch+1) % 1000 == 0:
+        print(f"Epoch: {epoch+1}, Loss: {loss.numpy()}")
+
+final_coefficients = [c.numpy() for c in coefficients]
+print("Final Coefficients:", final_coefficients)
+
+print("Final Equation:", end=" ")
+for i in range(degree+1):
+  print(f"{final_coefficients[i]} * x^{degree-i}", end=" + " if i < degree else "\n")
+
+plt.plot(X, Y, label="Original Data")
+plt.plot(X,[tf.math.polyval(final_coefficients, tf.constant(x, dtype=tf.float32)).numpy() for x in df[x_column]]), label="Our Poynomial"
+plt.ylabel(y_column)
+plt.xlabel(x_column)
+plt.title(f"{x_column} vs {y_column}")
+plt.legend()
+plt.show()
+
          + +
          + + +### Without Gradient Tape + +This relies on the Optimizer's `minimize` function and uses the `var_list` parameter to update the variables. + +This will not work with Keras 3 backend in TF 2.16.0 and above unless you switch to the legacy backend. +
          + +
          import tensorflow as tf
+import numpy as np
+import pandas as pd
+import matplotlib.pyplot as plt
+
+df = pd.read_csv("data.csv")
+
+############################
+## Change Parameters Here ##
+############################
+x_column = "Level"         #
+y_column = "Salary"        #
+degree = 2                 #
+learning_rate = 0.3        #
+num_epochs = 25_000        #
+############################
+
+X = tf.constant(df[x_column], dtype=tf.float32)
+Y = tf.constant(df[y_column], dtype=tf.float32)
+
+coefficients = [tf.Variable(np.random.randn() * 0.01, dtype=tf.float32) for _ in range(degree + 1)]
+
+optimizer = tf.keras.optimizers.Adam(learning_rate=learning_rate)
+
+def loss_function():
+  pred_y = tf.math.polyval(coefficients, X)
+  return tf.reduce_mean(tf.square(pred_y - Y))
+
+for epoch in range(num_epochs):
+    optimizer.minimize(loss_function, var_list=coefficients)
+    if (epoch+1) % 1000 == 0:
+        current_loss = loss_function().numpy()
+        print(f"Epoch {epoch+1}: Training Loss: {current_loss}")
+
+final_coefficients = coefficients.numpy()
+print("Final Coefficients:", final_coefficients)
+
+print("Final Equation:", end=" ")
+for i in range(degree+1):
+  print(f"{final_coefficients[i]} * x^{degree-i}", end=" + " if i < degree else "\n")
+
+plt.plot(X, Y, label="Original Data")
+plt.plot(X,[tf.math.polyval(final_coefficients, tf.constant(x, dtype=tf.float32)).numpy() for x in df[x_column]], label="Our Polynomial")
+plt.ylabel(y_column)
+plt.xlabel(x_column)
+plt.legend()
+plt.title(f"{x_column} vs {y_column}")
+plt.show()
+
          + +
          + + + +As always, remember to tweak the parameters and choose the correct model for the job. A polynomial regression model might not even be the best model for this particular dataset. + +## Further Programming + +How would you modify this code to use another type of nonlinear regression? Say, $ y = ab^x $ + +Hint: Your loss calculation would be similar to: +
          + +
          bx = tf.pow(coefficients[1], X)
+pred_y = tf.math.multiply(coefficients[0], bx)
+loss = tf.reduce_mean(tf.square(pred_y - Y))
+
          + +

          + +
          If you have scrolled this far, consider subscribing to my mailing list here. You can subscribe to either a specific type of post you are interested in, or subscribe to everything with the "Everything" list.
          + +
          + +
          +
          + + + + + \ No newline at end of file diff --git a/docs/posts/index.html b/docs/posts/index.html index 2d9d613..d886b19 100644 --- a/docs/posts/index.html +++ b/docs/posts/index.html @@ -52,6 +52,21 @@
            +
          • Polynomial Regression Using TensorFlow 2.x
            • +
              +
            • Predicting n-th degree polynomials using TensorFlow 2.x
              • +
            • Published On: 2024-03-21 12:46
              • +
            • Tags: + + Tutorial, + + Tensorflow, + + Colab + +
            + +
          • Cross-Compiling Hello World for DOS on macOS
            • This goes through compiling Open Watcom 2 and creating simple hello-world exampls
              • diff --git a/docs/tags/Colab.html b/docs/tags/Colab.html index a3721a7..fd8ef08 100644 --- a/docs/tags/Colab.html +++ b/docs/tags/Colab.html @@ -49,6 +49,21 @@
                +
              • Polynomial Regression Using TensorFlow 2.x
                • +
                  +
                • Predicting n-th degree polynomials using TensorFlow 2.x
                  • +
                • Published On: 2024-03-21 12:46
                  • +
                • Tags: + + Tutorial, + + Tensorflow, + + Colab + +
                + +
              • Installing RDKit on Google Colab
                • Install RDKit on Google Colab with one code snippet.
                  • diff --git a/docs/tags/Tensorflow.html b/docs/tags/Tensorflow.html index 3bcb911..04006bb 100644 --- a/docs/tags/Tensorflow.html +++ b/docs/tags/Tensorflow.html @@ -49,6 +49,21 @@
                    +
                  • Polynomial Regression Using TensorFlow 2.x
                    • +
                      +
                    • Predicting n-th degree polynomials using TensorFlow 2.x
                      • +
                    • Published On: 2024-03-21 12:46
                      • +
                    • Tags: + + Tutorial, + + Tensorflow, + + Colab + +
                    + +
                  • Polynomial Regression Using TensorFlow
                    • Polynomial regression using TensorFlow
                      • -- cgit v1.2.3 From 37661080a111768e565ae53299c4796ebe711a71 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Thu, 21 Mar 2024 14:29:50 -0600 Subject: fix mathjax stuff --- ...-03-21-Polynomial-Regression-in-TensorFlow-2.md | 17 +++--- docs/feed.rss | 66 +++++++++------------- ...3-21-Polynomial-Regression-in-TensorFlow-2.html | 62 +++++++++----------- 3 files changed, 63 insertions(+), 82 deletions(-) (limited to 'Content/posts') diff --git a/Content/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.md b/Content/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.md index 4341f09..6317175 100644 --- a/Content/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.md +++ b/Content/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.md @@ -59,9 +59,8 @@ y = (x**3)*coefficients[3] + (x**2)*coefficients[2] + (x**1)*coefficients[1] (x* Which is equivalent to the general cubic equation: - + + $$ y = ax^3 + bx^2 + cx + d @@ -85,15 +84,15 @@ for epoch in range(num_epochs): In TensorFlow 1, we would have been using `tf.Session` instead. -Here we are using `GradientTape()` instead, to keep track of the loss evaluation and coefficients. This is crucial, as our optimizer needs these gradients to be able to optimize our coefficients. +Here we are using `GradientTape()` instead, to keep track of the loss evaluation and coefficients. This is crucial, as our optimizer needs these gradients to be able to optimize our coefficients. -Our loss function is Mean Squared Error (MSE) +Our loss function is Mean Squared Error (MSE): $$ -= \frac{1}{n}\sum_{i=1}^{n} (Y_i - \^{Y_i}) += \frac{1}{n} \sum_{i=1}^{n}{(Y\_i - \hat{Y\_i})^2} $$ -Where $\^{Y_i}$ is the predicted value and $Y_i$ is the actual value +Where Yi^ is the predicted value and Yi is the actual value ### Plotting Final Coefficients @@ -228,7 +227,9 @@ As always, remember to tweak the parameters and choose the correct model for the ## Further Programming -How would you modify this code to use another type of nonlinear regression? Say, $ y = ab^x $ +How would you modify this code to use another type of nonlinear regression? Say, + +$$ y = ab^x $$ Hint: Your loss calculation would be similar to: diff --git a/docs/feed.rss b/docs/feed.rss index df334a3..12e9f8d 100644 --- a/docs/feed.rss +++ b/docs/feed.rss @@ -4,8 +4,8 @@ Navan's Archive Rare Tips, Tricks and Posts https://web.navan.dev/en - Thu, 21 Mar 2024 13:54:34 -0000 - Thu, 21 Mar 2024 13:54:34 -0000 + Thu, 21 Mar 2024 14:27:28 -0000 + Thu, 21 Mar 2024 14:27:28 -0000 250 @@ -553,18 +553,17 @@ creating a DOS Which is equivalent to the general cubic equation:

                      -

                      - + -$$ +

                      $$ y = ax^3 + bx^2 + cx + d -$$ +$$

                      -### Optimizer Selection & Training -
                      +

                      Optimizer Selection & Training

                      +
                      optimizer = tf.keras.optimizers.Adam(learning_rate=0.3)
 num_epochs = 10_000
 
@@ -577,25 +576,23 @@ $$
     if (epoch+1) % 1000 == 0:
         print(f"Epoch: {epoch+1}, Loss: {loss.numpy()}"
                      -
                      +

                      In TensorFlow 1, we would have been using tf.Session instead.

                      -In TensorFlow 1, we would have been using `tf.Session` instead. +

                      Here we are using GradientTape() instead, to keep track of the loss evaluation and coefficients. This is crucial, as our optimizer needs these gradients to be able to optimize our coefficients.

                      -Here we are using `GradientTape()` instead, to keep track of the loss evaluation and coefficients. This is crucial, as our optimizer needs these gradients to be able to optimize our coefficients. +

                      Our loss function is Mean Squared Error (MSE):

                      -Our loss function is Mean Squared Error (MSE) +

                      $$ += \frac{1}{n} \sum_{i=1}^{n}{(Y_i - \hat{Y_i})^2} +$$

                      -$$ -= \frac{1}{n}\sum_{i=1}^{n} (Y_i - \^{Y_i}) -$$ +

                      Where Yi^ is the predicted value and Yi is the actual value

                      -Where $\^{Y_i}$ is the predicted value and $Y_i$ is the actual value +

                      Plotting Final Coefficients

                      -### Plotting Final Coefficients
                      - 
                      final_coefficients = [c.numpy() for c in coefficients]
 print("Final Coefficients:", final_coefficients)
 
@@ -606,18 +603,15 @@ Where $\^{Y_i}$ is the predicted value and $Y_i$ is the actual value
 plt.title("Salary vs Position")
 plt.show()
                      -
                      +

                      Code Snippet for a Polynomial of Degree N

                      +

                      Using Gradient Tape

                      -## Code Snippet for a Polynomial of Degree N - -### Using Gradient Tape +

                      This should work regardless of the Keras backend version (2 or 3)

                      -This should work regardless of the Keras backend version (2 or 3)
                      - 
                      import tensorflow as tf
 import numpy as np
 import pandas as pd
@@ -666,17 +660,15 @@ This should work regardless of the Keras backend version (2 or 3)
 plt.legend()
 plt.show()
                      -
                      +

                      Without Gradient Tape

                      -### Without Gradient Tape +

                      This relies on the Optimizer's minimize function and uses the var_list parameter to update the variables.

                      -This relies on the Optimizer's `minimize` function and uses the `var_list` parameter to update the variables. +

                      This will not work with Keras 3 backend in TF 2.16.0 and above unless you switch to the legacy backend.

                      -This will not work with Keras 3 backend in TF 2.16.0 and above unless you switch to the legacy backend.
                      - 
                      import tensorflow as tf
 import numpy as np
 import pandas as pd
@@ -726,26 +718,24 @@ This will not work with Keras 3 backend in TF 2.16.0 and above unless you switch
 plt.title(f"{x_column} vs {y_column}")
 plt.show()
                      -
                      +

                      As always, remember to tweak the parameters and choose the correct model for the job. A polynomial regression model might not even be the best model for this particular dataset.

                      +

                      Further Programming

                      -As always, remember to tweak the parameters and choose the correct model for the job. A polynomial regression model might not even be the best model for this particular dataset. +

                      How would you modify this code to use another type of nonlinear regression? Say,

                      -## Further Programming +

                      $$ y = ab^x $$

                      -How would you modify this code to use another type of nonlinear regression? Say, $ y = ab^x $ +

                      Hint: Your loss calculation would be similar to:

                      -Hint: Your loss calculation would be similar to:
                      - 
                      bx = tf.pow(coefficients[1], X)
 pred_y = tf.math.multiply(coefficients[0], bx)
 loss = tf.reduce_mean(tf.square(pred_y - Y))
                      - -

                      +
                      ]]> diff --git a/docs/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.html b/docs/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.html index c1a4ae4..7a25daf 100644 --- a/docs/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.html +++ b/docs/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.html @@ -103,18 +103,17 @@

                      Which is equivalent to the general cubic equation:

                      -

                      - + -$$ +

                      $$ y = ax^3 + bx^2 + cx + d -$$ +$$

                      -### Optimizer Selection & Training -
                      +

                      Optimizer Selection & Training

                      +
                      optimizer = tf.keras.optimizers.Adam(learning_rate=0.3)
 num_epochs = 10_000
 
@@ -127,25 +126,23 @@ $$
     if (epoch+1) % 1000 == 0:
         print(f"Epoch: {epoch+1}, Loss: {loss.numpy()}"
                      -
                      +

                      In TensorFlow 1, we would have been using tf.Session instead.

                      -In TensorFlow 1, we would have been using `tf.Session` instead. +

                      Here we are using GradientTape() instead, to keep track of the loss evaluation and coefficients. This is crucial, as our optimizer needs these gradients to be able to optimize our coefficients.

                      -Here we are using `GradientTape()` instead, to keep track of the loss evaluation and coefficients. This is crucial, as our optimizer needs these gradients to be able to optimize our coefficients. +

                      Our loss function is Mean Squared Error (MSE):

                      -Our loss function is Mean Squared Error (MSE) +

                      $$ += \frac{1}{n} \sum_{i=1}^{n}{(Y_i - \hat{Y_i})^2} +$$

                      -$$ -= \frac{1}{n}\sum_{i=1}^{n} (Y_i - \^{Y_i}) -$$ +

                      Where Yi^ is the predicted value and Yi is the actual value

                      -Where $\^{Y_i}$ is the predicted value and $Y_i$ is the actual value +

                      Plotting Final Coefficients

                      -### Plotting Final Coefficients
                      - 
                      final_coefficients = [c.numpy() for c in coefficients]
 print("Final Coefficients:", final_coefficients)
 
@@ -156,18 +153,15 @@ Where $\^{Y_i}$ is the predicted value and $Y_i$ is the actual value
 plt.title("Salary vs Position")
 plt.show()
                      -
                      +

                      Code Snippet for a Polynomial of Degree N

                      +

                      Using Gradient Tape

                      -## Code Snippet for a Polynomial of Degree N - -### Using Gradient Tape +

                      This should work regardless of the Keras backend version (2 or 3)

                      -This should work regardless of the Keras backend version (2 or 3)
                      - 
                      import tensorflow as tf
 import numpy as np
 import pandas as pd
@@ -216,17 +210,15 @@ This should work regardless of the Keras backend version (2 or 3)
 plt.legend()
 plt.show()
                      -
                      +

                      Without Gradient Tape

                      -### Without Gradient Tape +

                      This relies on the Optimizer's minimize function and uses the var_list parameter to update the variables.

                      -This relies on the Optimizer's `minimize` function and uses the `var_list` parameter to update the variables. +

                      This will not work with Keras 3 backend in TF 2.16.0 and above unless you switch to the legacy backend.

                      -This will not work with Keras 3 backend in TF 2.16.0 and above unless you switch to the legacy backend.
                      - 
                      import tensorflow as tf
 import numpy as np
 import pandas as pd
@@ -276,26 +268,24 @@ This will not work with Keras 3 backend in TF 2.16.0 and above unless you switch
 plt.title(f"{x_column} vs {y_column}")
 plt.show()
                      -
                      +

                      As always, remember to tweak the parameters and choose the correct model for the job. A polynomial regression model might not even be the best model for this particular dataset.

                      +

                      Further Programming

                      -As always, remember to tweak the parameters and choose the correct model for the job. A polynomial regression model might not even be the best model for this particular dataset. +

                      How would you modify this code to use another type of nonlinear regression? Say,

                      -## Further Programming +

                      $$ y = ab^x $$

                      -How would you modify this code to use another type of nonlinear regression? Say, $ y = ab^x $ +

                      Hint: Your loss calculation would be similar to:

                      -Hint: Your loss calculation would be similar to:
                      - 
                      bx = tf.pow(coefficients[1], X)
 pred_y = tf.math.multiply(coefficients[0], bx)
 loss = tf.reduce_mean(tf.square(pred_y - Y))
                      - -

                      +
                      If you have scrolled this far, consider subscribing to my mailing list here. You can subscribe to either a specific type of post you are interested in, or subscribe to everything with the "Everything" list.
                      -

                      $$ -y = ax^3 + bx^2 + cx + d -$$

                      +y=ax3+bx2+cx+d

                      Optimizer Selection & Training

                      @@ -584,9 +582,7 @@ $$

                      Our loss function is Mean Squared Error (MSE):

                      -

                      $$ -= \frac{1}{n} \sum_{i=1}^{n}{(Y_i - \hat{Y_i})^2} -$$

                      +=1n∑i=1n(Y_i−Y_i^)2

                      Where Yi^ is the predicted value and Yi is the actual value

                      @@ -726,7 +722,7 @@ $$

                      How would you modify this code to use another type of nonlinear regression? Say,

                      -

                      $$ y = ab^x $$

                      +y=abx

                      Hint: Your loss calculation would be similar to:

                      @@ -3186,6 +3182,52 @@ values using the X values. We then plot it to compare the actual data and predic ]]> + + + https://web.navan.dev/posts/2024-03-26-Derivation-of-the-Quadratic-Equation.html + + + Quadratic Formula Derivation + + + Quick derivation of the quadratic equation by completing the square + + https://web.navan.dev/posts/2024-03-26-Derivation-of-the-Quadratic-Equation.html + Tue, 26 Mar 2024 15:36:00 -0000 + Quadratic Formula Derivation + +

                      The standard form of a quadratic equation is:

                      + +ax2+bx+c=0 + +

                      Here, a,b,c∈ℝ, and a≠0

                      + +

                      We begin by first dividing both sides by the coefficient a

                      + +⟹x2+bax+ca=0 + +

                      We can rearrange the equation:

                      + +x2+bax=−ca + +

                      We can then use the method of completing the square. (Maths is Fun has a really good explanation for this technique)

                      + +x2+bax+(b2a)2=−ca+(b2a)2 + +

                      On our LHS, we can clearly recognize that it is the expanded form of (x+d)2 i.e x2+2x·d+d2

                      + +⟹(x+b2a)2=−ca+b24a2=−4ac+b24a2 + +

                      Taking the square root of both sides

                      + +x+b2a=−4ac+b22ax=±−4ac+b2−b2a=−b±b2−4ac2a + +

                      This gives you the world famous quadratic formula:

                      + +x=−b±b2−4ac2a +]]>                       +                       + https://web.navan.dev/posts/2022-08-05-Why-You-No-Host.html diff --git a/docs/images/opengraph/posts/2024-03-26-Derivation-of-the-Quadratic-Equation.png b/docs/images/opengraph/posts/2024-03-26-Derivation-of-the-Quadratic-Equation.png new file mode 100644 index 0000000..2464364 Binary files /dev/null and b/docs/images/opengraph/posts/2024-03-26-Derivation-of-the-Quadratic-Equation.png differ diff --git a/docs/index.html b/docs/index.html index 0a3070a..c462f4b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -50,6 +50,17 @@

                      Recent Posts

                      For all posts go to Posts diff --git a/docs/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.html b/docs/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.html index 7a25daf..ab46ec7 100644 --- a/docs/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.html +++ b/docs/posts/2024-03-21-Polynomial-Regression-in-TensorFlow-2.html @@ -107,9 +107,7 @@ -

                      $$ -y = ax^3 + bx^2 + cx + d -$$

                      +y=ax3+bx2+cx+d

                      Optimizer Selection & Training

                      @@ -134,9 +132,7 @@ $$

                      Our loss function is Mean Squared Error (MSE):

                      -

                      $$ -= \frac{1}{n} \sum_{i=1}^{n}{(Y_i - \hat{Y_i})^2} -$$

                      +=1n∑i=1n(Y_i−Y_i^)2

                      Where Yi^ is the predicted value and Yi is the actual value

                      @@ -276,7 +272,7 @@ $$

                      How would you modify this code to use another type of nonlinear regression? Say,

                      -

                      $$ y = ab^x $$

                      +y=abx

                      Hint: Your loss calculation would be similar to:

                      diff --git a/docs/posts/2024-03-26-Derivation-of-the-Quadratic-Equation.html b/docs/posts/2024-03-26-Derivation-of-the-Quadratic-Equation.html new file mode 100644 index 0000000..6f02f7c --- /dev/null +++ b/docs/posts/2024-03-26-Derivation-of-the-Quadratic-Equation.html @@ -0,0 +1,90 @@ + + + + + + + + + Quadratic Formula Derivation + + + + + + + + + + + + + + + + + + + + + +
                      +
                      + +
                      + +

                      Quadratic Formula Derivation

                      + +

                      The standard form of a quadratic equation is:

                      + +ax2+bx+c=0 + +

                      Here, a,b,c∈ℝ, and a≠0

                      + +

                      We begin by first dividing both sides by the coefficient a

                      + +⟹x2+bax+ca=0 + +

                      We can rearrange the equation:

                      + +x2+bax=−ca + +

                      We can then use the method of completing the square. (Maths is Fun has a really good explanation for this technique)

                      + +x2+bax+(b2a)2=−ca+(b2a)2 + +

                      On our LHS, we can clearly recognize that it is the expanded form of (x+d)2 i.e x2+2x·d+d2

                      + +⟹(x+b2a)2=−ca+b24a2=−4ac+b24a2 + +

                      Taking the square root of both sides

                      + +x+b2a=−4ac+b22ax=±−4ac+b2−b2a=−b±b2−4ac2a + +

                      This gives you the world famous quadratic formula:

                      + +x=−b±b2−4ac2a + +
                      If you have scrolled this far, consider subscribing to my mailing list here. You can subscribe to either a specific type of post you are interested in, or subscribe to everything with the "Everything" list.
                      + +
                      + +
                      +
                      + + + + + \ No newline at end of file diff --git a/docs/posts/index.html b/docs/posts/index.html index d886b19..40b6a92 100644 --- a/docs/posts/index.html +++ b/docs/posts/index.html @@ -52,6 +52,17 @@
                        +
                      • Quadratic Formula Derivation
                        • +
                          +
                        • Quick derivation of the quadratic equation by completing the square
                          • +
                        • Published On: 2024-03-26 15:36
                          • +
                        • Tags: + + mathematics + +
                        + +
                      • Polynomial Regression Using TensorFlow 2.x
                        • Predicting n-th degree polynomials using TensorFlow 2.x
                          • diff --git a/docs/tags/mathematics.html b/docs/tags/mathematics.html index b948423..eb5201c 100644 --- a/docs/tags/mathematics.html +++ b/docs/tags/mathematics.html @@ -49,6 +49,17 @@
                            +
                          • Quadratic Formula Derivation
                            • +
                              +
                            • Quick derivation of the quadratic equation by completing the square
                              • +
                            • Published On: 2024-03-26 15:36
                              • +
                            • Tags: + + mathematics + +
                            + +
                          • n-body solution generator
                            • n-body solution generator and solver
                              • -- cgit v1.2.3 From fdf67099dbe882b50444a42e4bbd024394cfb548 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Thu, 28 Mar 2024 21:28:46 -0600 Subject: adfrsuite --- .../2024-03-28-Running-ADFRSuite-on-arm64-Macs.md | 379 ++++++++++++++++ .../2024-03-28-Running-ADFRSuite-on-arm64-Macs.png | Bin 0 -> 26043 bytes docs/feed.rss | 412 +++++++++++++++++- .../2024-03-28-Running-ADFRSuite-on-arm64-Macs.png | Bin 0 -> 26043 bytes docs/index.html | 26 +- ...2024-03-28-Running-ADFRSuite-on-arm64-Macs.html | 484 +++++++++++++++++++++ docs/posts/index.html | 13 + docs/tags/Cheminformatics.html | 13 + docs/tags/macOS.html | 13 + 9 files changed, 1325 insertions(+), 15 deletions(-) create mode 100644 Content/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.md create mode 100644 Resources/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png create mode 100644 docs/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png create mode 100644 docs/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html (limited to 'Content/posts') diff --git a/Content/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.md b/Content/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.md new file mode 100644 index 0000000..f43f15c --- /dev/null +++ b/Content/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.md @@ -0,0 +1,379 @@ +--- +date: 2024-03-28 20:12 +description: Fixing ADFRsuite on M1/MX chip Macs - CLI Tools +tags: macOS, Cheminformatics +--- + +# Fixing ADFRSuite for Apple Silicon + +We are going to be running everything through Rosetta 2. I am confident that if I had access to the original source code, I could find a way to run everything natively. + +These are the following issues that we will be fixing in this part: + +* “python2.7” cannot be opened because the developer cannot be verified. +* OpenBabel Error +* Segmentation fault while running the [redocking tutorial](https://ccsb.scripps.edu/adcp/tutorial-redocking/) + +For the sake of simplicity, I am assuming that I am running all these commands in the folder `~/Developer/scrippstuff/` + +## Installing Rosetta 2 + +We are going to run all of these steps in the terminal + +```bash +/usr/sbin/softwareupdate --install-rosetta --agree-to-license +``` + +### Install Homebrew for x86 + +Both versions of homebrew (x86 and arm64) can peacefully coexist on your system. + +From now on, every command should be run in a terminal session that starts with this as the first command: + +```bash +arch -x86_64 zsh +``` + +Now, we can install homebrew: + +```bash +/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" +``` + +Here is my output: + +``` bash +➜ scrippstuff uname -a +Darwin Navans-MacBook-Pro.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:31:00 PST 2023; root:xnu-10002.81.5~7/RELEASE_ARM64_T6020 x86_64 +➜ scrippstuff /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)" +==> Checking for `sudo` access (which may request your password)... +Password: +==> This script will install: +/usr/local/bin/brew +/usr/local/share/doc/homebrew +/usr/local/share/man/man1/brew.1 +/usr/local/share/zsh/site-functions/_brew +/usr/local/etc/bash_completion.d/brew +/usr/local/Homebrew +==> The following new directories will be created: +/usr/local/Cellar +/usr/local/Caskroom + +Press RETURN/ENTER to continue or any other key to abort: +==> /usr/bin/sudo /bin/mkdir -p /usr/local/Cellar /usr/local/Caskroom +==> /usr/bin/sudo /bin/chmod ug=rwx /usr/local/Cellar /usr/local/Caskroom +==> /usr/bin/sudo /usr/sbin/chown navanchauhan /usr/local/Cellar /usr/local/Caskroom +==> /usr/bin/sudo /usr/bin/chgrp admin /usr/local/Cellar /usr/local/Caskroom +==> /usr/bin/sudo /usr/sbin/chown -R navanchauhan:admin /usr/local/Homebrew +==> /usr/bin/sudo /bin/mkdir -p /Users/navanchauhan/Library/Caches/Homebrew +==> /usr/bin/sudo /bin/chmod g+rwx /Users/navanchauhan/Library/Caches/Homebrew +==> /usr/bin/sudo /usr/sbin/chown -R navanchauhan /Users/navanchauhan/Library/Caches/Homebrew +==> Downloading and installing Homebrew... +remote: Enumerating objects: 47, done. +remote: Counting objects: 100% (47/47), done. +remote: Compressing objects: 100% (19/19), done. +remote: Total 47 (delta 28), reused 47 (delta 28), pack-reused 0 +Unpacking objects: 100% (47/47), 6.11 KiB | 223.00 KiB/s, done. +From https://github.com/Homebrew/brew + + 18ebdd8c8f...67a096fcbb tapioca-compiler-for-tty-rbi -> origin/tapioca-compiler-for-tty-rbi (forced update) +Switched to and reset branch 'stable' +==> Updating Homebrew... +==> Installation successful! + +==> Homebrew has enabled anonymous aggregate formulae and cask analytics. +Read the analytics documentation (and how to opt-out) here: + https://docs.brew.sh/Analytics +No analytics data has been sent yet (nor will any be during this install run). + +==> Homebrew is run entirely by unpaid volunteers. Please consider donating: + https://github.com/Homebrew/brew#donations + +==> Next steps: +- Run these two commands in your terminal to add Homebrew to your PATH: + (echo; echo 'eval "$(/usr/local/bin/brew shellenv)"') >> /Users/navanchauhan/.zprofile + eval "$(/usr/local/bin/brew shellenv)" +- Run brew help to get started +- Further documentation: + https://docs.brew.sh +``` + +At this point, you don't need to edit your `zshrc` or `zsh_profile`. + +### Install pyenv + +The reason we are installing pyenv is because it is easier to build Python 2.7.18 from scratch than messing around with codesigning and quarantine bs on macOS. + +```bash +➜ scrippstuff brew install pyenv +==> Downloading https://ghcr.io/v2/homebrew/core/pyenv/manifests/2.3.36 +############################################################################################################################################################### 100.0% +==> Fetching dependencies for pyenv: m4, autoconf, ca-certificates, openssl@3, pkg-config and readline +==> Downloading https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19 +############################################################################################################################################################### 100.0% +==> Fetching m4 +==> Downloading https://ghcr.io/v2/homebrew/core/m4/blobs/sha256:8434a67a4383836b2531a6180e068640c5b482ee6781b673d65712e4fc86ca76 +############################################################################################################################################################### 100.0% +==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72 +############################################################################################################################################################### 100.0% +==> Fetching autoconf +==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/blobs/sha256:12368e33b89d221550ba9e261b0c6ece0b0e89250fb4c95169d09081e0ebb2dd +############################################################################################################################################################### 100.0% +==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11 +############################################################################################################################################################### 100.0% +==> Fetching ca-certificates +==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/blobs/sha256:cab828953672906e00a8f25db751977b8dc4115f021f8dfe82b644ade03dacdb +############################################################################################################################################################### 100.0% +==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1 +############################################################################################################################################################### 100.0% +==> Fetching openssl@3 +==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/blobs/sha256:ef8211c5115fc85f01261037f8fea76cc432b92b4fb23bc87bbf41e9198fcc0f +############################################################################################################################################################### 100.0% +==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3 +############################################################################################################################################################### 100.0% +==> Fetching pkg-config +==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/blobs/sha256:421571f340277c62c5cc6fd68737bd7c4e085de113452ea49b33bcd46509bb12 +############################################################################################################################################################### 100.0% +==> Downloading https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10 +############################################################################################################################################################### 100.0% +==> Fetching readline +==> Downloading https://ghcr.io/v2/homebrew/core/readline/blobs/sha256:9796e0ff1cc29ae7e75d8fc1a3e2c5e8ae2aeade8d9d59a16363306bf6c5b8f4 +############################################################################################################################################################### 100.0% +==> Fetching pyenv +==> Downloading https://ghcr.io/v2/homebrew/core/pyenv/blobs/sha256:d117a99ed53502aff29109bfa366693ca623f2326e1e6b4db68fef7b7f63eeba +############################################################################################################################################################### 100.0% +==> Installing dependencies for pyenv: m4, autoconf, ca-certificates, openssl@3, pkg-config and readline +==> Installing pyenv dependency: m4 +==> Downloading https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19 +Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/5b2a7f715487b7377e409e8ca58569040cd89f33859f691210c58d94410fd33b--m4-1.4.19.bottle_manifest.json +==> Pouring m4--1.4.19.sonoma.bottle.tar.gz +🍺 /usr/local/Cellar/m4/1.4.19: 13 files, 739.9KB +==> Installing pyenv dependency: autoconf +==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72 +Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/b73cdb320c4261bbf8d02d03e50dc755c869c5859c1d4e93616898fc7cd939ff--autoconf-2.72.bottle_manifest.json +==> Pouring autoconf--2.72.sonoma.bottle.tar.gz +🍺 /usr/local/Cellar/autoconf/2.72: 71 files, 3.6MB +==> Installing pyenv dependency: ca-certificates +==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11 +Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/c431e0186df2ccc2ea942b34a3c26c2cebebec8e07ad6abdae48447a52c5f506--ca-certificates-2024-03-11.bottle_manifest.json +==> Pouring ca-certificates--2024-03-11.all.bottle.tar.gz +==> Regenerating CA certificate bundle from keychain, this may take a while... +🍺 /usr/local/Cellar/ca-certificates/2024-03-11: 3 files, 229.6KB +==> Installing pyenv dependency: openssl@3 +==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1 +Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/f7b6e249843882452d784a8cbc4e19231186230b9e485a2a284d5c1952a95ec2--openssl@3-3.2.1-1.bottle_manifest.json +==> Pouring openssl@3--3.2.1.sonoma.bottle.1.tar.gz +🍺 /usr/local/Cellar/openssl@3/3.2.1: 6,874 files, 32.5MB +==> Installing pyenv dependency: pkg-config +==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3 +Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/ac691fc7ab8ecffba32a837e7197101d271474a3a84cfddcc30c9fd6763ab3c6--pkg-config-0.29.2_3.bottle_manifest.json +==> Pouring pkg-config--0.29.2_3.sonoma.bottle.tar.gz +🍺 /usr/local/Cellar/pkg-config/0.29.2_3: 11 files, 656.4KB +==> Installing pyenv dependency: readline +==> Downloading https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10 +Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/4ddd52803319828799f1932d4c7fa8d11c667049b20a56341c0c19246a1be93b--readline-8.2.10.bottle_manifest.json +==> Pouring readline--8.2.10.sonoma.bottle.tar.gz +🍺 /usr/local/Cellar/readline/8.2.10: 50 files, 1.7MB +==> Installing pyenv +==> Pouring pyenv--2.3.36.sonoma.bottle.tar.gz +🍺 /usr/local/Cellar/pyenv/2.3.36: 1,158 files, 3.4MB +==> Running `brew cleanup pyenv`... +Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP. +Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`). +``` + +And, build the last version of Python 2.7 + +```bash +➜ scrippstuff PYENV_ROOT="~/Developer/scrippstuff" pyenv install 2.7.18 +python-build: use openssl from homebrew +python-build: use readline from homebrew +Downloading Python-2.7.18.tar.xz... +-> https://www.python.org/ftp/python/2.7.18/Python-2.7.18.tar.xz +Installing Python-2.7.18... +patching file configure +patching file configure.ac +patching file setup.py +patching file 'Mac/Tools/pythonw.c' +patching file setup.py +patching file 'Doc/library/ctypes.rst' +patching file 'Lib/test/test_str.py' +patching file 'Lib/test/test_unicode.py' +patching file 'Modules/_ctypes/_ctypes.c' +patching file 'Modules/_ctypes/callproc.c' +patching file 'Modules/_ctypes/ctypes.h' +patching file 'Modules/_ctypes/callproc.c' +patching file setup.py +patching file 'Mac/Modules/qt/setup.py' +patching file setup.py +python-build: use readline from homebrew +python-build: use zlib from xcode sdk +Installed Python-2.7.18 to /Users/navanchauhan/Developer/scrippstuff/~/Developer/scrippstuff/versions/2.7.18 +``` + +Test the new installation: + +```bash +➜ scrippstuff ~/Developer/scrippstuff/\~/Developer/scrippstuff/versions/2.7.18/bin/python2.7 +Python 2.7.18 (default, Mar 28 2024, 20:47:13) +[GCC Apple LLVM 15.0.0 (clang-1500.1.0.2.5)] on darwin +Type "help", "copyright", "credits" or "license" for more information. +>>> from random import randint +>>> randint(0,10) +6 +>>> exit() +``` + +Now, we can compress this newly created Python version into a `tar.gz` file to replace the one provided in ADFRsuite_x86_64Darwin_1.0.tar.gz. Don't forget the `.` at the end + +```bash +➜ scrippstuff tar -C ./\~/Developer/scrippstuff/versions/2.7.18 -czf new.tar.gz . +``` + +## Install ADFRsuite + +If you don't already have the tarball, you can download it by: + +```bash +$ curl -o adfr.tar.gz https://ccsb.scripps.edu/adfr/download/1033/ +``` + +Uncompress it + +```bash +$ tar -xvzf adfr.tar.gz +``` + +Replace the provided Python archive with the one we created: + +```bash +$ cd ADFRsuite_x86_64Darwin_1.0 +$ mv new.tar.gz Python2.7.tar.gz +``` + +Note: For some reason simply copying it doesn't work and you need to use `mv` + +Just to not mess with anything else, I will be installing everything in a folder called `clean_install` + +```bash +$ mkdir clean_install +$ ./install.sh -d clean_install +... + ADFRsuite installation complete. +To run agfr, agfrgui, adfr, autosite, about, pythonsh scripts located at: +/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin +add /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin to the path environment variable in .cshrc or .bashrc: +.cshrc: +set path = (/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin $path) + +.bashrc: +export PATH=/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:$PATH +``` + +Now, to test `agfr`, first run the command (replacing `navanchauhan` with yout username) + +```bash +$ export PATH=/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:$PATH +$ agfr +➜ ADFRsuite_x86_64Darwin_1.0 agfr +============================== +*** Open Babel Error in openLib + /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so did not load properly. + Error: dlopen(/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so, 0x0009): Library not loaded: /opt/X11/lib/libcairo.2.dylib + Referenced from: <24174F3E-2670-79AC-4F26-F8B49774194A> /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so + Reason: tried: '/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libcairo.2.dylib' (no such file), '/opt/X11/lib/libcairo.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libcairo.2.dylib' (no such file), '/opt/X11/lib/libcairo.2.dylib' (no such file), '/usr/local/lib/libcairo.2.dylib' (no such file), '/usr/lib/libcairo.2.dylib' (no such file, not in dyld cache) +============================== +``` + + +## Fixing `Open Babel Error` + +```bash +$ brew install cairo +``` + +## Completing the re-docking tutorial + +### Dowbloading the dataset + +```bash +$ curl -o tutorial-data.zip https://ccsb.scripps.edu/adcp/download/1063/ +$ unzip tutorial-data.zip +$ cd ADCP_tutorial_data/3Q47 +``` + +### Conversion to PDBQT + +```bash +$ reduce 3Q47_rec.pdb > 3Q47_recH.pdb +$ reduce 3Q47_pep.pdb > 3Q47_pepH.pdb +``` + +### Preparing Receptor + +``` +$ prepare_receptor -r 3Q47_recH.pdb +$ prepare_ligand -l 3Q47_pepH.pdb +``` + +### Generate Target File + +```bash +$ agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47 +➜ 3Q47 agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47 +Traceback (most recent call last): + File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/bin/runAGFR.py", line 36, in + from ADFR.utils.runAGFR import runAGFR + File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/runAGFR.py", line 41, in + from ADFR.utils.maps import flexResStr2flexRes + File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/maps.py", line 35, in + from ADFRcc.adfr import GridMap + File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/__init__.py", line 34, in + from ADFRcc.adfr import Parameters + File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfr.py", line 43, in + import ADFRcc.adfrcc as CPP + File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py", line 28, in + _adfrcc = swig_import_helper() + File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py", line 24, in swig_import_helper + _mod = imp.load_module('_adfrcc', fp, pathname, description) +ImportError: dlopen(/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so, 0x0002): Library not loaded: /Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib + Referenced from: <424BF61E-BF0F-351E-B546-E82EBBD8FBF5> /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so + Reason: tried: '/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libgomp.1.dylib' (no such file), '/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/usr/local/lib/libgomp.1.dylib' (no such file), '/usr/lib/libgomp.1.dylib' (no such file, not in dyld cache) +➜ 3Q47 +``` + +Sometimes this error is simply outputted as a segmentation fault. But, it is because it cannot find the `libgomp.1.dylib`. I haven't tested using a newer version of GCC to make it work. Building GCC 8 yourself is absolutely painful. We are going to use a copy generated by the homebrew team. + +```bash +$ cd ../../ +$ pwd +/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0 +$ curl -L -H "Authorization: Bearer QQ==" -o gcc8amd64.tar.gz https://ghcr.io/v2/homebrew/core/gcc/8/blobs/sha256:438d5902e5f21a5e8acb5920f1f5684ecfe0c645247d46c8d44c2bbe435966b2 +$ tar -xzf gcc8amd64.tar.gz +$ cp -r gcc@8/8.5.0/lib/gcc/8/* clean_install/lib/ +``` + +Now, we should be able to go back and run the target generation command: + +```bash +$ cd ADCP_tutorial_data/3Q47 +$ agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47 +################################################################# +# If you used AGFR in your work, please cite: # +# # +# P.A. Ravindranath S. Forli, D.S. Goodsell, A.J. Olson and # +# M.F. Sanner # +# AutoDockFR: Advances in Protein-Ligand Docking with # +... +``` + +### Docking Peptide + +```bash +$ adcp -t 3Q47.trg -s npisdvd -N 20 -n 1000000 -o 3Q47_redocking -ref 3Q47_pepH.pdb +``` + +There you have it. Running ADCP on the newest macOS version against all odds. + +I haven't yet looked into fixing/patching `agfrgui` as I don't use the software. But, if someone reallllly needs to run it on Apple Silicon, I am happy to take a look at monkeypatching it. + +In case years down the line the prebuilt version of GCC 8 is not available, let me know so I can replace the link with my mirror. diff --git a/Resources/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png b/Resources/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png new file mode 100644 index 0000000..4b1bad2 Binary files /dev/null and b/Resources/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png differ diff --git a/docs/feed.rss b/docs/feed.rss index 2cb2370..d4cd27c 100644 --- a/docs/feed.rss +++ b/docs/feed.rss @@ -4,8 +4,8 @@ Navan's Archive Rare Tips, Tricks and Posts https://web.navan.dev/en - Wed, 27 Mar 2024 23:45:05 -0000 - Wed, 27 Mar 2024 23:45:05 -0000 + Thu, 28 Mar 2024 21:27:46 -0000 + Thu, 28 Mar 2024 21:27:46 -0000 250 @@ -1953,6 +1953,414 @@ Serving HTTP on 0.0.0.0 port 8000 ... ]]> + + + https://web.navan.dev/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html + + + Fixing ADFRSuite for Apple Silicon + + + Fixing ADFRsuite on M1/MX chip Macs - CLI Tools + + https://web.navan.dev/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html + Thu, 28 Mar 2024 20:12:00 -0000 + Fixing ADFRSuite for Apple Silicon + +

                              We are going to be running everything through Rosetta 2. I am confident that if I had access to the original source code, I could find a way to run everything natively.

                              + +

                              These are the following issues that we will be fixing in this part:

                              + +
                                +
                              • “python2.7” cannot be opened because the developer cannot be verified.
                                • +
                              • OpenBabel Error
                                • +
                              • Segmentation fault while running the redocking tutorial
                                • +
                              + +

                              For the sake of simplicity, I am assuming that I am running all these commands in the folder ~/Developer/scrippstuff/

                              + +

                              Installing Rosetta 2

                              + +

                              We are going to run all of these steps in the terminal

                              + +
                              +
                              /usr/sbin/softwareupdate --install-rosetta --agree-to-license
+
                              +
                              + +

                              Install Homebrew for x86

                              + +

                              Both versions of homebrew (x86 and arm64) can peacefully coexist on your system.

                              + +

                              From now on, every command should be run in a terminal session that starts with this as the first command:

                              + +
                              +
                              arch -x86_64 zsh
+
                              +
                              + +

                              Now, we can install homebrew:

                              + +
                              +
                              /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+
                              +
                              + +

                              Here is my output:

                              + +
                              +
                              ➜  scrippstuff uname -a
+Darwin Navans-MacBook-Pro.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:31:00 PST 2023; root:xnu-10002.81.5~7/RELEASE_ARM64_T6020 x86_64
+➜  scrippstuff /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+==> Checking for `sudo` access (which may request your password)...
+Password:
+==> This script will install:
+/usr/local/bin/brew
+/usr/local/share/doc/homebrew
+/usr/local/share/man/man1/brew.1
+/usr/local/share/zsh/site-functions/_brew
+/usr/local/etc/bash_completion.d/brew
+/usr/local/Homebrew
+==> The following new directories will be created:
+/usr/local/Cellar
+/usr/local/Caskroom
+
+Press RETURN/ENTER to continue or any other key to abort:
+==> /usr/bin/sudo /bin/mkdir -p /usr/local/Cellar /usr/local/Caskroom
+==> /usr/bin/sudo /bin/chmod ug=rwx /usr/local/Cellar /usr/local/Caskroom
+==> /usr/bin/sudo /usr/sbin/chown navanchauhan /usr/local/Cellar /usr/local/Caskroom
+==> /usr/bin/sudo /usr/bin/chgrp admin /usr/local/Cellar /usr/local/Caskroom
+==> /usr/bin/sudo /usr/sbin/chown -R navanchauhan:admin /usr/local/Homebrew
+==> /usr/bin/sudo /bin/mkdir -p /Users/navanchauhan/Library/Caches/Homebrew
+==> /usr/bin/sudo /bin/chmod g+rwx /Users/navanchauhan/Library/Caches/Homebrew
+==> /usr/bin/sudo /usr/sbin/chown -R navanchauhan /Users/navanchauhan/Library/Caches/Homebrew
+==> Downloading and installing Homebrew...
+remote: Enumerating objects: 47, done.
+remote: Counting objects: 100% (47/47), done.
+remote: Compressing objects: 100% (19/19), done.
+remote: Total 47 (delta 28), reused 47 (delta 28), pack-reused 0
+Unpacking objects: 100% (47/47), 6.11 KiB | 223.00 KiB/s, done.
+From https://github.com/Homebrew/brew
+ + 18ebdd8c8f...67a096fcbb tapioca-compiler-for-tty-rbi -> origin/tapioca-compiler-for-tty-rbi  (forced update)
+Switched to and reset branch 'stable'
+==> Updating Homebrew...
+==> Installation successful!
+
+==> Homebrew has enabled anonymous aggregate formulae and cask analytics.
+Read the analytics documentation (and how to opt-out) here:
+  https://docs.brew.sh/Analytics
+No analytics data has been sent yet (nor will any be during this install run).
+
+==> Homebrew is run entirely by unpaid volunteers. Please consider donating:
+  https://github.com/Homebrew/brew#donations
+
+==> Next steps:
+- Run these two commands in your terminal to add Homebrew to your PATH:
+    (echo; echo 'eval "$(/usr/local/bin/brew shellenv)"') >> /Users/navanchauhan/.zprofile
+    eval "$(/usr/local/bin/brew shellenv)"
+- Run brew help to get started
+- Further documentation:
+    https://docs.brew.sh
+
                              +
                              + +

                              At this point, you don't need to edit your zshrc or zsh_profile.

                              + +

                              Install pyenv

                              + +

                              The reason we are installing pyenv is because it is easier to build Python 2.7.18 from scratch than messing around with codesigning and quarantine bs on macOS.

                              + +
                              +
                              ➜  scrippstuff brew install pyenv
+==> Downloading https://ghcr.io/v2/homebrew/core/pyenv/manifests/2.3.36
+############################################################################################################################################################### 100.0%
+==> Fetching dependencies for pyenv: m4, autoconf, ca-certificates, openssl@3, pkg-config and readline
+==> Downloading https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19
+############################################################################################################################################################### 100.0%
+==> Fetching m4
+==> Downloading https://ghcr.io/v2/homebrew/core/m4/blobs/sha256:8434a67a4383836b2531a6180e068640c5b482ee6781b673d65712e4fc86ca76
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72
+############################################################################################################################################################### 100.0%
+==> Fetching autoconf
+==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/blobs/sha256:12368e33b89d221550ba9e261b0c6ece0b0e89250fb4c95169d09081e0ebb2dd
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11
+############################################################################################################################################################### 100.0%
+==> Fetching ca-certificates
+==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/blobs/sha256:cab828953672906e00a8f25db751977b8dc4115f021f8dfe82b644ade03dacdb
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1
+############################################################################################################################################################### 100.0%
+==> Fetching openssl@3
+==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/blobs/sha256:ef8211c5115fc85f01261037f8fea76cc432b92b4fb23bc87bbf41e9198fcc0f
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3
+############################################################################################################################################################### 100.0%
+==> Fetching pkg-config
+==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/blobs/sha256:421571f340277c62c5cc6fd68737bd7c4e085de113452ea49b33bcd46509bb12
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10
+############################################################################################################################################################### 100.0%
+==> Fetching readline
+==> Downloading https://ghcr.io/v2/homebrew/core/readline/blobs/sha256:9796e0ff1cc29ae7e75d8fc1a3e2c5e8ae2aeade8d9d59a16363306bf6c5b8f4
+############################################################################################################################################################### 100.0%
+==> Fetching pyenv
+==> Downloading https://ghcr.io/v2/homebrew/core/pyenv/blobs/sha256:d117a99ed53502aff29109bfa366693ca623f2326e1e6b4db68fef7b7f63eeba
+############################################################################################################################################################### 100.0%
+==> Installing dependencies for pyenv: m4, autoconf, ca-certificates, openssl@3, pkg-config and readline
+==> Installing pyenv dependency: m4
+==> Downloading https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/5b2a7f715487b7377e409e8ca58569040cd89f33859f691210c58d94410fd33b--m4-1.4.19.bottle_manifest.json
+==> Pouring m4--1.4.19.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/m4/1.4.19: 13 files, 739.9KB
+==> Installing pyenv dependency: autoconf
+==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/b73cdb320c4261bbf8d02d03e50dc755c869c5859c1d4e93616898fc7cd939ff--autoconf-2.72.bottle_manifest.json
+==> Pouring autoconf--2.72.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/autoconf/2.72: 71 files, 3.6MB
+==> Installing pyenv dependency: ca-certificates
+==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/c431e0186df2ccc2ea942b34a3c26c2cebebec8e07ad6abdae48447a52c5f506--ca-certificates-2024-03-11.bottle_manifest.json
+==> Pouring ca-certificates--2024-03-11.all.bottle.tar.gz
+==> Regenerating CA certificate bundle from keychain, this may take a while...
+🍺  /usr/local/Cellar/ca-certificates/2024-03-11: 3 files, 229.6KB
+==> Installing pyenv dependency: openssl@3
+==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/f7b6e249843882452d784a8cbc4e19231186230b9e485a2a284d5c1952a95ec2--openssl@3-3.2.1-1.bottle_manifest.json
+==> Pouring openssl@3--3.2.1.sonoma.bottle.1.tar.gz
+🍺  /usr/local/Cellar/openssl@3/3.2.1: 6,874 files, 32.5MB
+==> Installing pyenv dependency: pkg-config
+==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/ac691fc7ab8ecffba32a837e7197101d271474a3a84cfddcc30c9fd6763ab3c6--pkg-config-0.29.2_3.bottle_manifest.json
+==> Pouring pkg-config--0.29.2_3.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/pkg-config/0.29.2_3: 11 files, 656.4KB
+==> Installing pyenv dependency: readline
+==> Downloading https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/4ddd52803319828799f1932d4c7fa8d11c667049b20a56341c0c19246a1be93b--readline-8.2.10.bottle_manifest.json
+==> Pouring readline--8.2.10.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/readline/8.2.10: 50 files, 1.7MB
+==> Installing pyenv
+==> Pouring pyenv--2.3.36.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/pyenv/2.3.36: 1,158 files, 3.4MB
+==> Running `brew cleanup pyenv`...
+Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP.
+Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`).
+
                              +
                              + +

                              And, build the last version of Python 2.7

                              + +
                              +
                              ➜  scrippstuff PYENV_ROOT="~/Developer/scrippstuff" pyenv install 2.7.18
+python-build: use openssl from homebrew
+python-build: use readline from homebrew
+Downloading Python-2.7.18.tar.xz...
+-> https://www.python.org/ftp/python/2.7.18/Python-2.7.18.tar.xz
+Installing Python-2.7.18...
+patching file configure
+patching file configure.ac
+patching file setup.py
+patching file 'Mac/Tools/pythonw.c'
+patching file setup.py
+patching file 'Doc/library/ctypes.rst'
+patching file 'Lib/test/test_str.py'
+patching file 'Lib/test/test_unicode.py'
+patching file 'Modules/_ctypes/_ctypes.c'
+patching file 'Modules/_ctypes/callproc.c'
+patching file 'Modules/_ctypes/ctypes.h'
+patching file 'Modules/_ctypes/callproc.c'
+patching file setup.py
+patching file 'Mac/Modules/qt/setup.py'
+patching file setup.py
+python-build: use readline from homebrew
+python-build: use zlib from xcode sdk
+Installed Python-2.7.18 to /Users/navanchauhan/Developer/scrippstuff/~/Developer/scrippstuff/versions/2.7.18
+
                              +
                              + +

                              Test the new installation:

                              + +
                              +
                              ➜  scrippstuff ~/Developer/scrippstuff/\~/Developer/scrippstuff/versions/2.7.18/bin/python2.7
+Python 2.7.18 (default, Mar 28 2024, 20:47:13)
+[GCC Apple LLVM 15.0.0 (clang-1500.1.0.2.5)] on darwin
+Type "help", "copyright", "credits" or "license" for more information.
+>>> from random import randint
+>>> randint(0,10)
+6
+>>> exit()
+
                              +
                              + +

                              Now, we can compress this newly created Python version into a tar.gz file to replace the one provided in ADFRsuitex8664Darwin_1.0.tar.gz. Don't forget the . at the end

                              + +
                              +
                              ➜  scrippstuff tar -C ./\~/Developer/scrippstuff/versions/2.7.18 -czf new.tar.gz .
+
                              +
                              + +

                              Install ADFRsuite

                              + +

                              If you don't already have the tarball, you can download it by:

                              + +
                              +
                              $ curl -o adfr.tar.gz https://ccsb.scripps.edu/adfr/download/1033/
+
                              +
                              + +

                              Uncompress it

                              + +
                              +
                              $ tar -xvzf adfr.tar.gz
+
                              +
                              + +

                              Replace the provided Python archive with the one we created:

                              + +
                              +
                              $ cd ADFRsuite_x86_64Darwin_1.0
+$ mv new.tar.gz Python2.7.tar.gz
+
                              +
                              + +

                              Note: For some reason simply copying it doesn't work and you need to use mv

                              + +

                              Just to not mess with anything else, I will be installing everything in a folder called clean_install

                              + +
                              +
                              $ mkdir clean_install
+$ ./install.sh -d clean_install
+...
+ ADFRsuite installation complete.
+To run agfr, agfrgui, adfr, autosite, about, pythonsh scripts located at:
+/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin
+add  /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin to the path environment variable in .cshrc or .bashrc:
+.cshrc:
+set path = (/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin $path)
+
+.bashrc:
+export PATH=/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:$PATH
+
                              +
                              + +

                              Now, to test agfr, first run the command (replacing navanchauhan with yout username)

                              + +
                              +
                              $ export PATH=/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:$PATH
+$ agfr
+➜  ADFRsuite_x86_64Darwin_1.0 agfr
+==============================
+*** Open Babel Error  in openLib
+  /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so did not load properly.
+ Error: dlopen(/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so, 0x0009): Library not loaded: /opt/X11/lib/libcairo.2.dylib
+  Referenced from: <24174F3E-2670-79AC-4F26-F8B49774194A> /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so
+  Reason: tried: '/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libcairo.2.dylib' (no such file), '/opt/X11/lib/libcairo.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libcairo.2.dylib' (no such file), '/opt/X11/lib/libcairo.2.dylib' (no such file), '/usr/local/lib/libcairo.2.dylib' (no such file), '/usr/lib/libcairo.2.dylib' (no such file, not in dyld cache)
+==============================
+
                              +
                              + +

                              Fixing Open Babel Error

                              + +
                              +
                              $ brew install cairo
+
                              +
                              + +

                              Completing the re-docking tutorial

                              + +

                              Dowbloading the dataset

                              + +
                              +
                              $ curl -o tutorial-data.zip https://ccsb.scripps.edu/adcp/download/1063/
+$ unzip tutorial-data.zip
+$ cd ADCP_tutorial_data/3Q47
+
                              +
                              + +

                              Conversion to PDBQT

                              + +
                              +
                              $ reduce 3Q47_rec.pdb > 3Q47_recH.pdb
+$ reduce 3Q47_pep.pdb > 3Q47_pepH.pdb
+
                              +
                              + +

                              Preparing Receptor

                              + +
                              $ prepare_receptor -r 3Q47_recH.pdb
+$ prepare_ligand -l 3Q47_pepH.pdb
+
                              + +

                              Generate Target File

                              + +
                              +
                              $ agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47
+➜  3Q47 agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47
+Traceback (most recent call last):
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/bin/runAGFR.py", line 36, in <module>
+    from ADFR.utils.runAGFR import runAGFR
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/runAGFR.py", line 41, in <module>
+    from ADFR.utils.maps import flexResStr2flexRes
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/maps.py", line 35, in <module>
+    from ADFRcc.adfr import GridMap
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/__init__.py", line 34, in <module>
+    from ADFRcc.adfr import Parameters
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfr.py", line 43, in <module>
+    import ADFRcc.adfrcc as CPP
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py", line 28, in <module>
+    _adfrcc = swig_import_helper()
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py", line 24, in swig_import_helper
+    _mod = imp.load_module('_adfrcc', fp, pathname, description)
+ImportError: dlopen(/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so, 0x0002): Library not loaded: /Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib
+  Referenced from: <424BF61E-BF0F-351E-B546-E82EBBD8FBF5> /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so
+  Reason: tried: '/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libgomp.1.dylib' (no such file), '/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/usr/local/lib/libgomp.1.dylib' (no such file), '/usr/lib/libgomp.1.dylib' (no such file, not in dyld cache)
+➜  3Q47
+
                              +
                              + +

                              Sometimes this error is simply outputted as a segmentation fault. But, it is because it cannot find the libgomp.1.dylib. I haven't tested using a newer version of GCC to make it work. Building GCC 8 yourself is absolutely painful. We are going to use a copy generated by the homebrew team.

                              + +
                              +
                              $ cd ../../
+$ pwd
+/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0
+$ curl -L -H "Authorization: Bearer QQ==" -o gcc8amd64.tar.gz https://ghcr.io/v2/homebrew/core/gcc/8/blobs/sha256:438d5902e5f21a5e8acb5920f1f5684ecfe0c645247d46c8d44c2bbe435966b2
+$ tar -xzf gcc8amd64.tar.gz
+$ cp -r gcc@8/8.5.0/lib/gcc/8/* clean_install/lib/
+
                              +
                              + +

                              Now, we should be able to go back and run the target generation command:

                              + +
                              +
                              $ cd ADCP_tutorial_data/3Q47
+$ agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47
+#################################################################
+# If you used AGFR in your work, please cite:                   #
+#                                                               #
+# P.A. Ravindranath S. Forli, D.S. Goodsell, A.J. Olson and     #
+# M.F. Sanner                                                   #
+# AutoDockFR: Advances in Protein-Ligand Docking with           #
+...
+
                              +
                              + +

                              Docking Peptide

                              + +
                              +
                              $ adcp -t 3Q47.trg -s npisdvd -N 20 -n 1000000 -o 3Q47_redocking -ref 3Q47_pepH.pdb
+
                              +
                              + +

                              There you have it. Running ADCP on the newest macOS version against all odds.

                              + +

                              I haven't yet looked into fixing/patching agfrgui as I don't use the software. But, if someone reallllly needs to run it on Apple Silicon, I am happy to take a look at monkeypatching it.

                              + +

                              In case years down the line the prebuilt version of GCC 8 is not available, let me know so I can replace the link with my mirror.

                              +]]>                               +                               + https://web.navan.dev/posts/2022-11-07-a-new-method-to-blog.html diff --git a/docs/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png b/docs/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png new file mode 100644 index 0000000..4b1bad2 Binary files /dev/null and b/docs/images/opengraph/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.png differ diff --git a/docs/index.html b/docs/index.html index da5e542..7b1f66c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -88,6 +88,19 @@ lead.innerText = new_phrase;

                              Recent Posts

                              For all posts go to Posts diff --git a/docs/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html b/docs/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html new file mode 100644 index 0000000..5b59fa1 --- /dev/null +++ b/docs/posts/2024-03-28-Running-ADFRSuite-on-arm64-Macs.html @@ -0,0 +1,484 @@ + + + + + + + + + + Fixing ADFRSuite for Apple Silicon + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
                              +
                              +
                              +

                              Navan

                              +

                              Alea iacta est.

                              +
                              + + +

                              © 2019-2024. Navan Chauhan
                              RSS

                              +
                              +
                              + + +
                              + +
                              +

                              Fixing ADFRSuite for Apple Silicon

                              + +

                              We are going to be running everything through Rosetta 2. I am confident that if I had access to the original source code, I could find a way to run everything natively.

                              + +

                              These are the following issues that we will be fixing in this part:

                              + +
                                +
                              • “python2.7” cannot be opened because the developer cannot be verified.
                                • +
                              • OpenBabel Error
                                • +
                              • Segmentation fault while running the redocking tutorial
                                • +
                              + +

                              For the sake of simplicity, I am assuming that I am running all these commands in the folder ~/Developer/scrippstuff/

                              + +

                              Installing Rosetta 2

                              + +

                              We are going to run all of these steps in the terminal

                              + +
                              +
                              /usr/sbin/softwareupdate --install-rosetta --agree-to-license
+
                              +
                              + +

                              Install Homebrew for x86

                              + +

                              Both versions of homebrew (x86 and arm64) can peacefully coexist on your system.

                              + +

                              From now on, every command should be run in a terminal session that starts with this as the first command:

                              + +
                              +
                              arch -x86_64 zsh
+
                              +
                              + +

                              Now, we can install homebrew:

                              + +
                              +
                              /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+
                              +
                              + +

                              Here is my output:

                              + +
                              +
                              ➜  scrippstuff uname -a
+Darwin Navans-MacBook-Pro.local 23.3.0 Darwin Kernel Version 23.3.0: Wed Dec 20 21:31:00 PST 2023; root:xnu-10002.81.5~7/RELEASE_ARM64_T6020 x86_64
+➜  scrippstuff /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+==> Checking for `sudo` access (which may request your password)...
+Password:
+==> This script will install:
+/usr/local/bin/brew
+/usr/local/share/doc/homebrew
+/usr/local/share/man/man1/brew.1
+/usr/local/share/zsh/site-functions/_brew
+/usr/local/etc/bash_completion.d/brew
+/usr/local/Homebrew
+==> The following new directories will be created:
+/usr/local/Cellar
+/usr/local/Caskroom
+
+Press RETURN/ENTER to continue or any other key to abort:
+==> /usr/bin/sudo /bin/mkdir -p /usr/local/Cellar /usr/local/Caskroom
+==> /usr/bin/sudo /bin/chmod ug=rwx /usr/local/Cellar /usr/local/Caskroom
+==> /usr/bin/sudo /usr/sbin/chown navanchauhan /usr/local/Cellar /usr/local/Caskroom
+==> /usr/bin/sudo /usr/bin/chgrp admin /usr/local/Cellar /usr/local/Caskroom
+==> /usr/bin/sudo /usr/sbin/chown -R navanchauhan:admin /usr/local/Homebrew
+==> /usr/bin/sudo /bin/mkdir -p /Users/navanchauhan/Library/Caches/Homebrew
+==> /usr/bin/sudo /bin/chmod g+rwx /Users/navanchauhan/Library/Caches/Homebrew
+==> /usr/bin/sudo /usr/sbin/chown -R navanchauhan /Users/navanchauhan/Library/Caches/Homebrew
+==> Downloading and installing Homebrew...
+remote: Enumerating objects: 47, done.
+remote: Counting objects: 100% (47/47), done.
+remote: Compressing objects: 100% (19/19), done.
+remote: Total 47 (delta 28), reused 47 (delta 28), pack-reused 0
+Unpacking objects: 100% (47/47), 6.11 KiB | 223.00 KiB/s, done.
+From https://github.com/Homebrew/brew
+ + 18ebdd8c8f...67a096fcbb tapioca-compiler-for-tty-rbi -> origin/tapioca-compiler-for-tty-rbi  (forced update)
+Switched to and reset branch 'stable'
+==> Updating Homebrew...
+==> Installation successful!
+
+==> Homebrew has enabled anonymous aggregate formulae and cask analytics.
+Read the analytics documentation (and how to opt-out) here:
+  https://docs.brew.sh/Analytics
+No analytics data has been sent yet (nor will any be during this install run).
+
+==> Homebrew is run entirely by unpaid volunteers. Please consider donating:
+  https://github.com/Homebrew/brew#donations
+
+==> Next steps:
+- Run these two commands in your terminal to add Homebrew to your PATH:
+    (echo; echo 'eval "$(/usr/local/bin/brew shellenv)"') >> /Users/navanchauhan/.zprofile
+    eval "$(/usr/local/bin/brew shellenv)"
+- Run brew help to get started
+- Further documentation:
+    https://docs.brew.sh
+
                              +
                              + +

                              At this point, you don't need to edit your zshrc or zsh_profile.

                              + +

                              Install pyenv

                              + +

                              The reason we are installing pyenv is because it is easier to build Python 2.7.18 from scratch than messing around with codesigning and quarantine bs on macOS.

                              + +
                              +
                              ➜  scrippstuff brew install pyenv
+==> Downloading https://ghcr.io/v2/homebrew/core/pyenv/manifests/2.3.36
+############################################################################################################################################################### 100.0%
+==> Fetching dependencies for pyenv: m4, autoconf, ca-certificates, openssl@3, pkg-config and readline
+==> Downloading https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19
+############################################################################################################################################################### 100.0%
+==> Fetching m4
+==> Downloading https://ghcr.io/v2/homebrew/core/m4/blobs/sha256:8434a67a4383836b2531a6180e068640c5b482ee6781b673d65712e4fc86ca76
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72
+############################################################################################################################################################### 100.0%
+==> Fetching autoconf
+==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/blobs/sha256:12368e33b89d221550ba9e261b0c6ece0b0e89250fb4c95169d09081e0ebb2dd
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11
+############################################################################################################################################################### 100.0%
+==> Fetching ca-certificates
+==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/blobs/sha256:cab828953672906e00a8f25db751977b8dc4115f021f8dfe82b644ade03dacdb
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1
+############################################################################################################################################################### 100.0%
+==> Fetching openssl@3
+==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/blobs/sha256:ef8211c5115fc85f01261037f8fea76cc432b92b4fb23bc87bbf41e9198fcc0f
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3
+############################################################################################################################################################### 100.0%
+==> Fetching pkg-config
+==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/blobs/sha256:421571f340277c62c5cc6fd68737bd7c4e085de113452ea49b33bcd46509bb12
+############################################################################################################################################################### 100.0%
+==> Downloading https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10
+############################################################################################################################################################### 100.0%
+==> Fetching readline
+==> Downloading https://ghcr.io/v2/homebrew/core/readline/blobs/sha256:9796e0ff1cc29ae7e75d8fc1a3e2c5e8ae2aeade8d9d59a16363306bf6c5b8f4
+############################################################################################################################################################### 100.0%
+==> Fetching pyenv
+==> Downloading https://ghcr.io/v2/homebrew/core/pyenv/blobs/sha256:d117a99ed53502aff29109bfa366693ca623f2326e1e6b4db68fef7b7f63eeba
+############################################################################################################################################################### 100.0%
+==> Installing dependencies for pyenv: m4, autoconf, ca-certificates, openssl@3, pkg-config and readline
+==> Installing pyenv dependency: m4
+==> Downloading https://ghcr.io/v2/homebrew/core/m4/manifests/1.4.19
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/5b2a7f715487b7377e409e8ca58569040cd89f33859f691210c58d94410fd33b--m4-1.4.19.bottle_manifest.json
+==> Pouring m4--1.4.19.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/m4/1.4.19: 13 files, 739.9KB
+==> Installing pyenv dependency: autoconf
+==> Downloading https://ghcr.io/v2/homebrew/core/autoconf/manifests/2.72
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/b73cdb320c4261bbf8d02d03e50dc755c869c5859c1d4e93616898fc7cd939ff--autoconf-2.72.bottle_manifest.json
+==> Pouring autoconf--2.72.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/autoconf/2.72: 71 files, 3.6MB
+==> Installing pyenv dependency: ca-certificates
+==> Downloading https://ghcr.io/v2/homebrew/core/ca-certificates/manifests/2024-03-11
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/c431e0186df2ccc2ea942b34a3c26c2cebebec8e07ad6abdae48447a52c5f506--ca-certificates-2024-03-11.bottle_manifest.json
+==> Pouring ca-certificates--2024-03-11.all.bottle.tar.gz
+==> Regenerating CA certificate bundle from keychain, this may take a while...
+🍺  /usr/local/Cellar/ca-certificates/2024-03-11: 3 files, 229.6KB
+==> Installing pyenv dependency: openssl@3
+==> Downloading https://ghcr.io/v2/homebrew/core/openssl/3/manifests/3.2.1-1
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/f7b6e249843882452d784a8cbc4e19231186230b9e485a2a284d5c1952a95ec2--openssl@3-3.2.1-1.bottle_manifest.json
+==> Pouring openssl@3--3.2.1.sonoma.bottle.1.tar.gz
+🍺  /usr/local/Cellar/openssl@3/3.2.1: 6,874 files, 32.5MB
+==> Installing pyenv dependency: pkg-config
+==> Downloading https://ghcr.io/v2/homebrew/core/pkg-config/manifests/0.29.2_3
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/ac691fc7ab8ecffba32a837e7197101d271474a3a84cfddcc30c9fd6763ab3c6--pkg-config-0.29.2_3.bottle_manifest.json
+==> Pouring pkg-config--0.29.2_3.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/pkg-config/0.29.2_3: 11 files, 656.4KB
+==> Installing pyenv dependency: readline
+==> Downloading https://ghcr.io/v2/homebrew/core/readline/manifests/8.2.10
+Already downloaded: /Users/navanchauhan/Library/Caches/Homebrew/downloads/4ddd52803319828799f1932d4c7fa8d11c667049b20a56341c0c19246a1be93b--readline-8.2.10.bottle_manifest.json
+==> Pouring readline--8.2.10.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/readline/8.2.10: 50 files, 1.7MB
+==> Installing pyenv
+==> Pouring pyenv--2.3.36.sonoma.bottle.tar.gz
+🍺  /usr/local/Cellar/pyenv/2.3.36: 1,158 files, 3.4MB
+==> Running `brew cleanup pyenv`...
+Disable this behaviour by setting HOMEBREW_NO_INSTALL_CLEANUP.
+Hide these hints with HOMEBREW_NO_ENV_HINTS (see `man brew`).
+
                              +
                              + +

                              And, build the last version of Python 2.7

                              + +
                              +
                              ➜  scrippstuff PYENV_ROOT="~/Developer/scrippstuff" pyenv install 2.7.18
+python-build: use openssl from homebrew
+python-build: use readline from homebrew
+Downloading Python-2.7.18.tar.xz...
+-> https://www.python.org/ftp/python/2.7.18/Python-2.7.18.tar.xz
+Installing Python-2.7.18...
+patching file configure
+patching file configure.ac
+patching file setup.py
+patching file 'Mac/Tools/pythonw.c'
+patching file setup.py
+patching file 'Doc/library/ctypes.rst'
+patching file 'Lib/test/test_str.py'
+patching file 'Lib/test/test_unicode.py'
+patching file 'Modules/_ctypes/_ctypes.c'
+patching file 'Modules/_ctypes/callproc.c'
+patching file 'Modules/_ctypes/ctypes.h'
+patching file 'Modules/_ctypes/callproc.c'
+patching file setup.py
+patching file 'Mac/Modules/qt/setup.py'
+patching file setup.py
+python-build: use readline from homebrew
+python-build: use zlib from xcode sdk
+Installed Python-2.7.18 to /Users/navanchauhan/Developer/scrippstuff/~/Developer/scrippstuff/versions/2.7.18
+
                              +
                              + +

                              Test the new installation:

                              + +
                              +
                              ➜  scrippstuff ~/Developer/scrippstuff/\~/Developer/scrippstuff/versions/2.7.18/bin/python2.7
+Python 2.7.18 (default, Mar 28 2024, 20:47:13)
+[GCC Apple LLVM 15.0.0 (clang-1500.1.0.2.5)] on darwin
+Type "help", "copyright", "credits" or "license" for more information.
+>>> from random import randint
+>>> randint(0,10)
+6
+>>> exit()
+
                              +
                              + +

                              Now, we can compress this newly created Python version into a tar.gz file to replace the one provided in ADFRsuitex8664Darwin_1.0.tar.gz. Don't forget the . at the end

                              + +
                              +
                              ➜  scrippstuff tar -C ./\~/Developer/scrippstuff/versions/2.7.18 -czf new.tar.gz .
+
                              +
                              + +

                              Install ADFRsuite

                              + +

                              If you don't already have the tarball, you can download it by:

                              + +
                              +
                              $ curl -o adfr.tar.gz https://ccsb.scripps.edu/adfr/download/1033/
+
                              +
                              + +

                              Uncompress it

                              + +
                              +
                              $ tar -xvzf adfr.tar.gz
+
                              +
                              + +

                              Replace the provided Python archive with the one we created:

                              + +
                              +
                              $ cd ADFRsuite_x86_64Darwin_1.0
+$ mv new.tar.gz Python2.7.tar.gz
+
                              +
                              + +

                              Note: For some reason simply copying it doesn't work and you need to use mv

                              + +

                              Just to not mess with anything else, I will be installing everything in a folder called clean_install

                              + +
                              +
                              $ mkdir clean_install
+$ ./install.sh -d clean_install
+...
+ ADFRsuite installation complete.
+To run agfr, agfrgui, adfr, autosite, about, pythonsh scripts located at:
+/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin
+add  /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin to the path environment variable in .cshrc or .bashrc:
+.cshrc:
+set path = (/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin $path)
+
+.bashrc:
+export PATH=/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:$PATH
+
                              +
                              + +

                              Now, to test agfr, first run the command (replacing navanchauhan with yout username)

                              + +
                              +
                              $ export PATH=/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/bin:$PATH
+$ agfr
+➜  ADFRsuite_x86_64Darwin_1.0 agfr
+==============================
+*** Open Babel Error  in openLib
+  /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so did not load properly.
+ Error: dlopen(/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so, 0x0009): Library not loaded: /opt/X11/lib/libcairo.2.dylib
+  Referenced from: <24174F3E-2670-79AC-4F26-F8B49774194A> /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/openbabel/2.4.1/acesformat.so
+  Reason: tried: '/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libcairo.2.dylib' (no such file), '/opt/X11/lib/libcairo.2.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/opt/X11/lib/libcairo.2.dylib' (no such file), '/opt/X11/lib/libcairo.2.dylib' (no such file), '/usr/local/lib/libcairo.2.dylib' (no such file), '/usr/lib/libcairo.2.dylib' (no such file, not in dyld cache)
+==============================
+
                              +
                              + +

                              Fixing Open Babel Error

                              + +
                              +
                              $ brew install cairo
+
                              +
                              + +

                              Completing the re-docking tutorial

                              + +

                              Dowbloading the dataset

                              + +
                              +
                              $ curl -o tutorial-data.zip https://ccsb.scripps.edu/adcp/download/1063/
+$ unzip tutorial-data.zip
+$ cd ADCP_tutorial_data/3Q47
+
                              +
                              + +

                              Conversion to PDBQT

                              + +
                              +
                              $ reduce 3Q47_rec.pdb > 3Q47_recH.pdb
+$ reduce 3Q47_pep.pdb > 3Q47_pepH.pdb
+
                              +
                              + +

                              Preparing Receptor

                              + +
                              $ prepare_receptor -r 3Q47_recH.pdb
+$ prepare_ligand -l 3Q47_pepH.pdb
+
                              + +

                              Generate Target File

                              + +
                              +
                              $ agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47
+➜  3Q47 agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47
+Traceback (most recent call last):
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/bin/runAGFR.py", line 36, in <module>
+    from ADFR.utils.runAGFR import runAGFR
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/runAGFR.py", line 41, in <module>
+    from ADFR.utils.maps import flexResStr2flexRes
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFR/utils/maps.py", line 35, in <module>
+    from ADFRcc.adfr import GridMap
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/__init__.py", line 34, in <module>
+    from ADFRcc.adfr import Parameters
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfr.py", line 43, in <module>
+    import ADFRcc.adfrcc as CPP
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py", line 28, in <module>
+    _adfrcc = swig_import_helper()
+  File "/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/adfrcc.py", line 24, in swig_import_helper
+    _mod = imp.load_module('_adfrcc', fp, pathname, description)
+ImportError: dlopen(/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so, 0x0002): Library not loaded: /Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib
+  Referenced from: <424BF61E-BF0F-351E-B546-E82EBBD8FBF5> /Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/CCSBpckgs/ADFRcc/_adfrcc.so
+  Reason: tried: '/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0/clean_install/lib/libgomp.1.dylib' (no such file), '/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/Users/Shared/mgltoolsDev/src/homebrew/opt/gcc/lib/gcc/8/libgomp.1.dylib' (no such file), '/usr/local/lib/libgomp.1.dylib' (no such file), '/usr/lib/libgomp.1.dylib' (no such file, not in dyld cache)
+➜  3Q47
+
                              +
                              + +

                              Sometimes this error is simply outputted as a segmentation fault. But, it is because it cannot find the libgomp.1.dylib. I haven't tested using a newer version of GCC to make it work. Building GCC 8 yourself is absolutely painful. We are going to use a copy generated by the homebrew team.

                              + +
                              +
                              $ cd ../../
+$ pwd
+/Users/navanchauhan/Developer/scrippstuff/ADFRsuite_x86_64Darwin_1.0
+$ curl -L -H "Authorization: Bearer QQ==" -o gcc8amd64.tar.gz https://ghcr.io/v2/homebrew/core/gcc/8/blobs/sha256:438d5902e5f21a5e8acb5920f1f5684ecfe0c645247d46c8d44c2bbe435966b2
+$ tar -xzf gcc8amd64.tar.gz
+$ cp -r gcc@8/8.5.0/lib/gcc/8/* clean_install/lib/
+
                              +
                              + +

                              Now, we should be able to go back and run the target generation command:

                              + +
                              +
                              $ cd ADCP_tutorial_data/3Q47
+$ agfr -r 3Q47_recH.pdbqt -l 3Q47_pepH.pdbqt -asv 1.1 -o 3Q47
+#################################################################
+# If you used AGFR in your work, please cite:                   #
+#                                                               #
+# P.A. Ravindranath S. Forli, D.S. Goodsell, A.J. Olson and     #
+# M.F. Sanner                                                   #
+# AutoDockFR: Advances in Protein-Ligand Docking with           #
+...
+
                              +
                              + +

                              Docking Peptide

                              + +
                              +
                              $ adcp -t 3Q47.trg -s npisdvd -N 20 -n 1000000 -o 3Q47_redocking -ref 3Q47_pepH.pdb
+
                              +
                              + +

                              There you have it. Running ADCP on the newest macOS version against all odds.

                              + +

                              I haven't yet looked into fixing/patching agfrgui as I don't use the software. But, if someone reallllly needs to run it on Apple Silicon, I am happy to take a look at monkeypatching it.

                              + +

                              In case years down the line the prebuilt version of GCC 8 is not available, let me know so I can replace the link with my mirror.

                              + +
                              +
                              If you have scrolled this far, consider subscribing to my mailing list here. You can subscribe to either a specific type of post you are interested in, or subscribe to everything with the "Everything" list.
                              + +
                              + +
                              + +
                              + + + + \ No newline at end of file diff --git a/docs/posts/index.html b/docs/posts/index.html index a64a79a..ef630d7 100644 --- a/docs/posts/index.html +++ b/docs/posts/index.html @@ -84,6 +84,19 @@ lead.innerText = new_phrase;
                                +
                              • Fixing ADFRSuite for Apple Silicon
                                • +
                                  +
                                • Fixing ADFRsuite on M1/MX chip Macs - CLI Tools
                                  • +
                                • Published On: 2024-03-28 20:12
                                  • +
                                • Tags: + + macOS, + + Cheminformatics + +
                                + +
                              • Quadratic Formula Derivation
                                • Quick derivation of the quadratic equation by completing the square
                                  • diff --git a/docs/tags/Cheminformatics.html b/docs/tags/Cheminformatics.html index c686c20..6a98f75 100644 --- a/docs/tags/Cheminformatics.html +++ b/docs/tags/Cheminformatics.html @@ -81,6 +81,19 @@ lead.innerText = new_phrase;
                                    +
                                  • Fixing ADFRSuite for Apple Silicon
                                    • +
                                      +
                                    • Fixing ADFRsuite on M1/MX chip Macs - CLI Tools
                                      • +
                                    • Published On: 2024-03-28 20:12
                                      • +
                                    • Tags: + + macOS, + + Cheminformatics + +
                                    + +
                                  • Cheminformatics on the Web (2021)
                                    • Summarising Cheminformatics on the web in 2021.
                                      • diff --git a/docs/tags/macOS.html b/docs/tags/macOS.html index 1fa2569..124d64b 100644 --- a/docs/tags/macOS.html +++ b/docs/tags/macOS.html @@ -81,6 +81,19 @@ lead.innerText = new_phrase;
                                        +
                                      • Fixing ADFRSuite for Apple Silicon
                                        • +
                                          +
                                        • Fixing ADFRsuite on M1/MX chip Macs - CLI Tools
                                          • +
                                        • Published On: 2024-03-28 20:12
                                          • +
                                        • Tags: + + macOS, + + Cheminformatics + +
                                        + +
                                      • Cross-Compiling Hello World for DOS on macOS
                                        • This goes through compiling Open Watcom 2 and creating simple hello-world exampls
                                          • -- cgit v1.2.3 From 6e1296ef714e2931b41364219585d31e84ba6d9a Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Sun, 31 Mar 2024 13:34:13 -0600 Subject: update colab-rdkit post --- Content/posts/2020-07-01-Install-rdkit-colab.md | 10 ++++++++++ docs/feed.rss | 13 +++++++++++-- docs/posts/2020-07-01-Install-rdkit-colab.html | 9 +++++++++ 3 files changed, 30 insertions(+), 2 deletions(-) (limited to 'Content/posts') diff --git a/Content/posts/2020-07-01-Install-rdkit-colab.md b/Content/posts/2020-07-01-Install-rdkit-colab.md index ff5da1e..4a87bf1 100644 --- a/Content/posts/2020-07-01-Install-rdkit-colab.md +++ b/Content/posts/2020-07-01-Install-rdkit-colab.md @@ -6,6 +6,16 @@ tags: Tutorial, Code-Snippet, Colab # Installing RDKit on Google Colab +**Update: March 2024** + +`rdkit-pypi` has been deprecated in favour of `rdkit` + +You can simply run: + +``` +!pip install rdkit +``` + **EDIT:** Try installing RDKit using pip ``` diff --git a/docs/feed.rss b/docs/feed.rss index d4cd27c..38509ac 100644 --- a/docs/feed.rss +++ b/docs/feed.rss @@ -4,8 +4,8 @@ Navan's Archive Rare Tips, Tricks and Posts https://web.navan.dev/en - Thu, 28 Mar 2024 21:27:46 -0000 - Thu, 28 Mar 2024 21:27:46 -0000 + Sun, 31 Mar 2024 13:33:29 -0000 + Sun, 31 Mar 2024 13:33:29 -0000 250 @@ -4715,6 +4715,15 @@ A box with 200px height and 300px width Wed, 01 Jul 2020 14:23:00 -0000 Installing RDKit on Google Colab +

                                          Update: March 2024

                                          + +

                                          rdkit-pypi has been deprecated in favour of rdkit

                                          + +

                                          You can simply run:

                                          + +
                                          !pip install rdkit
+
                                          +

                                          EDIT: Try installing RDKit using pip

                                          !pip install rdkit-pypi
diff --git a/docs/posts/2020-07-01-Install-rdkit-colab.html b/docs/posts/2020-07-01-Install-rdkit-colab.html
index 9f5c507..68372d0 100644
--- a/docs/posts/2020-07-01-Install-rdkit-colab.html
+++ b/docs/posts/2020-07-01-Install-rdkit-colab.html
@@ -77,6 +77,15 @@ lead.innerText = new_phrase;
 	
                                          
 	
                                          Installing RDKit on Google Colab
                                          
 
+
                                          Update: March 2024 
                                          
+
+
                                          rdkit-pypi has been deprecated in favour of rdkit
                                          
+
+
                                          You can simply run:
                                          
+
+
                                          !pip install rdkit
+
                                          
+
 
                                          EDIT: Try installing RDKit using pip
                                          
 
 
                                          !pip install rdkit-pypi
-- 
cgit v1.2.3