From 22ec209b97c2ebf015be46d6b1d07bb123390656 Mon Sep 17 00:00:00 2001 From: Navan Chauhan Date: Mon, 1 Jun 2020 00:48:39 +0530 Subject: Publish deploy 2020-06-01 00:48 --- assets/posts/open-babel/s2.jpg | Bin 0 -> 132781 bytes assets/posts/open-babel/s3.jpg | Bin 0 -> 314900 bytes feed.rss | 6 +++--- .../2020-05-31-compiling-open-babel-on-ios/index.html | 4 ++-- 4 files changed, 5 insertions(+), 5 deletions(-) create mode 100644 assets/posts/open-babel/s2.jpg create mode 100644 assets/posts/open-babel/s3.jpg diff --git a/assets/posts/open-babel/s2.jpg b/assets/posts/open-babel/s2.jpg new file mode 100644 index 0000000..7ece652 Binary files /dev/null and b/assets/posts/open-babel/s2.jpg differ diff --git a/assets/posts/open-babel/s3.jpg b/assets/posts/open-babel/s3.jpg new file mode 100644 index 0000000..5803e97 Binary files /dev/null and b/assets/posts/open-babel/s3.jpg differ diff --git a/feed.rss b/feed.rss index 4e5aa1e..a8f147d 100644 --- a/feed.rss +++ b/feed.rss @@ -1,4 +1,4 @@ -Navan ChauhanWelcome to my personal fragment of the internet. Majority of the posts should be complete.https://navanchauhan.github.io/enMon, 1 Jun 2020 00:41:37 +0530Mon, 1 Jun 2020 00:41:37 +0530250https://navanchauhan.github.io/posts/2020-05-31-compiling-open-babel-on-iosCompiling Open Babel on iOSCompiling Open Babel on iOShttps://navanchauhan.github.io/posts/2020-05-31-compiling-open-babel-on-iosSun, 31 May 2020 11:30:00 +0530Compiling Open Babel on iOS

Due to the fact that my summer vacations started today, I had the brilliant idea of trying to run open babel on my iPad. To give a little background, I had tried to compile AutoDock Vina using a cross-compiler but I had miserably failed.

I am running the Checkr1n jailbreak on my iPad and the Unc0ver jailbreak on my phone.

But Why?

Well, just because I can. This is literally the only reason I tried compiling it and also partially because in the long run I want to compile AutoDock Vina so I can do Molecular Docking on the go.

Let's Go!

How hard can it be to compile open babel right? It is just a simple software with clear and concise build instructions. I just need to use cmake to build and the make to install.

It is 11 AM in the morning. I install clang, cmake and make from the Sam Bingner's repository, fired up ssh, downloaded the source code and ran the build command.`clang

Fail No. 1

I couldn't even get cmake to run, I did a little digging arond StackOverflow and founf that I needed the iOS SDK, sure no problem. I waited for Xcode to update and transfered the /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk to /var/sdks/ on my iPad

Them I told cmake that this is the location for my SDK 😠. Succesful! Now I just needed to use make.

Fail No. 2

It was giving the error that thread-local-storage was not supported on this device.

[  0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.cpp.o
+Navan ChauhanWelcome to my personal fragment of the internet. Majority of the posts should be complete.https://navanchauhan.github.io/enMon, 1 Jun 2020 00:48:18 +0530Mon, 1 Jun 2020 00:48:18 +0530250https://navanchauhan.github.io/posts/2020-05-31-compiling-open-babel-on-iosCompiling Open Babel on iOSCompiling Open Babel on iOShttps://navanchauhan.github.io/posts/2020-05-31-compiling-open-babel-on-iosSun, 31 May 2020 11:30:00 +0530Compiling Open Babel on iOS
Due to the fact that my summer vacations started today, I had the brilliant idea of trying to run open babel on my iPad. To give a little background, I had tried to compile AutoDock Vina using a cross-compiler but I had miserably failed.
I am running the Checkr1n jailbreak on my iPad and the Unc0ver jailbreak on my phone.
But Why?
Well, just because I can. This is literally the only reason I tried compiling it and also partially because in the long run I want to compile AutoDock Vina so I can do Molecular Docking on the go.
Let's Go!
How hard can it be to compile open babel right? It is just a simple software with clear and concise build instructions. I just need to use cmake to build and the make to install.
It is 11 AM in the morning. I install clang, cmake and make from the Sam Bingner's repository, fired up ssh, downloaded the source code and ran the build command.`clang
Fail No. 1
I couldn't even get cmake to run, I did a little digging arond StackOverflow and founf that I needed the iOS SDK, sure no problem. I waited for Xcode to update and transfered the /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk to /var/sdks/ on my iPad
Them I told cmake that this is the location for my SDK 😠. Succesful! Now I just needed to use make.
Fail No. 2
It was giving the error that thread-local-storage was not supported on this device.
[  0%] Building CXX object src/CMakeFiles/openbabel.dir/alias.cpp.o
 [  1%] Building CXX object src/CMakeFiles/openbabel.dir/atom.cpp.o
 In file included from /var/root/obabel/ob-src/src/atom.cpp:28:
 In file included from /var/root/obabel/ob-src/include/openbabel/ring.h:29:
@@ -38,9 +38,9 @@ THREAD_LOCAL OB_EXTERN OBAromaticTyper  aromtyper;
 make[2]: *** [src/CMakeFiles/openbabel.dir/build.make:76: src/CMakeFiles/openbabel.dir/atom.cpp.o] Error 1
 make[1]: *** [CMakeFiles/Makefile2:1085: src/CMakeFiles/openbabel.dir/all] Error 2
 make: *** [Makefile:129: all] Error 2
-
Strange but it is alright, there is nothing that hasn't been answered on the internet.
I did a little digging around and could not find a solution 😔
As a temporary fix, I disabled multithreading by going and commenting the lines in the source code.
Packaging as a deb
This was pretty straight forward, I tried installing it on my iPad and it was working pretty smoothly.
Moment of Truth
So I airdropped the .deb to my phone and tried installing it, the installation was succesful but when I tried obabel it just abborted with syscall 9
Turns out because I had created an install target of a seprate folder while compiling, the binaries were refferencing a non-existing dylib rather than those in the /usr/lib folder. As a quick workaround I transferred the deb folder to my laptop and used otool and install_name tool: install_name_tool -change /var/root/obabel/ob-build/lib/libopenbabel.7.dylib /usr/lib/libopenbabel.7.dylib for all the executables and then signed them using jtool
I then installed it and everything went smoothly, I even ran obabel and it executed perfectly, showing the version number 3.1.0 ✌️ Ahh, smooth victory.
Nope. When I tried converting from SMILES to pdbqt, it gave an error saying plugin not found. This was weird. So I just copied the entire build folder from my iPad to my phone and tried runnig it. Oops, Apple Sandbox Error, Oh no!
I spent 2 hours around this problem, only to see the documentation and relaise I hadn't setup the environment variable 🤦‍♂️
The Final Fix ( For Now )
export BABEL_DATADIR="/usr/share/openbabel/3.1.0"
+
Strange but it is alright, there is nothing that hasn't been answered on the internet.
I did a little digging around and could not find a solution 😔
As a temporary fix, I disabled multithreading by going and commenting the lines in the source code.
Packaging as a deb
This was pretty straight forward, I tried installing it on my iPad and it was working pretty smoothly.
Moment of Truth
So I airdropped the .deb to my phone and tried installing it, the installation was succesful but when I tried obabel it just abborted.
Turns out because I had created an install target of a seprate folder while compiling, the binaries were refferencing a non-existing dylib rather than those in the /usr/lib folder. As a quick workaround I transferred the deb folder to my laptop and used otool and install_name tool: install_name_tool -change /var/root/obabel/ob-build/lib/libopenbabel.7.dylib /usr/lib/libopenbabel.7.dylib for all the executables and then signed them using jtool
I then installed it and everything went smoothly, I even ran obabel and it executed perfectly, showing the version number 3.1.0 ✌️ Ahh, smooth victory.
Nope. When I tried converting from SMILES to pdbqt, it gave an error saying plugin not found. This was weird.
So I just copied the entire build folder from my iPad to my phone and tried runnig it. Oops, Apple Sandbox Error, Oh no!
I spent 2 hours around this problem, only to see the documentation and relaise I hadn't setup the environment variable 🤦‍♂️
The Final Fix ( For Now )
export BABEL_DATADIR="/usr/share/openbabel/3.1.0"
 export BABEL_LIBDIR="/usr/lib/openbabel/3.1.0"
-
This was the tragedy of trying to compile something without knowing enough about compiling. It is 11:30 as of writing this. Something as trivial as this should not have taken me so long. Am I going to try to compile AutoDock Vina next? 🤔 Maybe.
Also, if you want to try Open Babel on you jailbroken iDevice, install the package from my repository ( You, need to run the above mentioned final fix :p ). This was tested on iOS 13.5, I cannot tell if it will work on others or not.
Hopefully, I add some more screenshots to this post.
]]>https://navanchauhan.github.io/posts/2020-04-13-Fixing-X11-Error-AmberTools-macOSFixing X11 Error on macOS Catalina for AmberTools 18/19Fixing Could not find the X11 libraries; you may need to edit config.h, AmberTools macOS Catalinahttps://navanchauhan.github.io/posts/2020-04-13-Fixing-X11-Error-AmberTools-macOSMon, 13 Apr 2020 11:41:00 +0530Fixing X11 Error on macOS Catalina for AmberTools 18/19
I was trying to install AmberTools on my macOS Catalina Installation. Running ./configure -macAccelerate clang gave me an error that it could not find X11 libraries, even though locate libXt showed that my installation was correct.
Error:
Could not find the X11 libraries; you may need to edit config.h
+
This was the tragedy of trying to compile something without knowing enough about compiling. It is 11:30 as of writing this. Something as trivial as this should not have taken me so long. Am I going to try to compile AutoDock Vina next? 🤔 Maybe.
Also, if you want to try Open Babel on you jailbroken iDevice, install the package from my repository ( You, need to run the above mentioned final fix :p ). This was tested on iOS 13.5, I cannot tell if it will work on others or not.
Hopefully, I add some more screenshots to this post.
Edit 1: Added Screenshots, had to replicate the errors.
]]>https://navanchauhan.github.io/posts/2020-04-13-Fixing-X11-Error-AmberTools-macOSFixing X11 Error on macOS Catalina for AmberTools 18/19Fixing Could not find the X11 libraries; you may need to edit config.h, AmberTools macOS Catalinahttps://navanchauhan.github.io/posts/2020-04-13-Fixing-X11-Error-AmberTools-macOSMon, 13 Apr 2020 11:41:00 +0530Fixing X11 Error on macOS Catalina for AmberTools 18/19
I was trying to install AmberTools on my macOS Catalina Installation. Running ./configure -macAccelerate clang gave me an error that it could not find X11 libraries, even though locate libXt showed that my installation was correct.
Error:
Could not find the X11 libraries; you may need to edit config.h
    to set the XHOME and XLIBS variables.
 Error: The X11 libraries are not in the usual location !
        To search for them try the command: locate libXt
diff --git a/posts/2020-05-31-compiling-open-babel-on-ios/index.html b/posts/2020-05-31-compiling-open-babel-on-ios/index.html
index be8f4fc..5ead530 100644
--- a/posts/2020-05-31-compiling-open-babel-on-ios/index.html
+++ b/posts/2020-05-31-compiling-open-babel-on-ios/index.html
@@ -38,6 +38,6 @@ THREAD_LOCAL OB_EXTERN OBAromaticTyper  aromtyper;
 make[2]: *** [src/CMakeFiles/openbabel.dir/build.make:76: src/CMakeFiles/openbabel.dir/atom.cpp.o] Error 1
 make[1]: *** [CMakeFiles/Makefile2:1085: src/CMakeFiles/openbabel.dir/all] Error 2
 make: *** [Makefile:129: all] Error 2
-
Strange but it is alright, there is nothing that hasn't been answered on the internet.
I did a little digging around and could not find a solution 😔
As a temporary fix, I disabled multithreading by going and commenting the lines in the source code.
Packaging as a deb
This was pretty straight forward, I tried installing it on my iPad and it was working pretty smoothly.
Moment of Truth
So I airdropped the .deb to my phone and tried installing it, the installation was succesful but when I tried obabel it just abborted with syscall 9
Turns out because I had created an install target of a seprate folder while compiling, the binaries were refferencing a non-existing dylib rather than those in the /usr/lib folder. As a quick workaround I transferred the deb folder to my laptop and used otool and install_name tool: install_name_tool -change /var/root/obabel/ob-build/lib/libopenbabel.7.dylib /usr/lib/libopenbabel.7.dylib for all the executables and then signed them using jtool
I then installed it and everything went smoothly, I even ran obabel and it executed perfectly, showing the version number 3.1.0 ✌️ Ahh, smooth victory.
Nope. When I tried converting from SMILES to pdbqt, it gave an error saying plugin not found. This was weird. So I just copied the entire build folder from my iPad to my phone and tried runnig it. Oops, Apple Sandbox Error, Oh no!
I spent 2 hours around this problem, only to see the documentation and relaise I hadn't setup the environment variable 🤦‍♂️
The Final Fix ( For Now )
export BABEL_DATADIR="/usr/share/openbabel/3.1.0"
+
Strange but it is alright, there is nothing that hasn't been answered on the internet.
I did a little digging around and could not find a solution 😔
As a temporary fix, I disabled multithreading by going and commenting the lines in the source code.
Packaging as a deb
This was pretty straight forward, I tried installing it on my iPad and it was working pretty smoothly.
Moment of Truth
So I airdropped the .deb to my phone and tried installing it, the installation was succesful but when I tried obabel it just abborted.
Turns out because I had created an install target of a seprate folder while compiling, the binaries were refferencing a non-existing dylib rather than those in the /usr/lib folder. As a quick workaround I transferred the deb folder to my laptop and used otool and install_name tool: install_name_tool -change /var/root/obabel/ob-build/lib/libopenbabel.7.dylib /usr/lib/libopenbabel.7.dylib for all the executables and then signed them using jtool
I then installed it and everything went smoothly, I even ran obabel and it executed perfectly, showing the version number 3.1.0 ✌️ Ahh, smooth victory.
Nope. When I tried converting from SMILES to pdbqt, it gave an error saying plugin not found. This was weird.
So I just copied the entire build folder from my iPad to my phone and tried runnig it. Oops, Apple Sandbox Error, Oh no!
I spent 2 hours around this problem, only to see the documentation and relaise I hadn't setup the environment variable 🤦‍♂️
The Final Fix ( For Now )
export BABEL_DATADIR="/usr/share/openbabel/3.1.0"
 export BABEL_LIBDIR="/usr/lib/openbabel/3.1.0"
-
This was the tragedy of trying to compile something without knowing enough about compiling. It is 11:30 as of writing this. Something as trivial as this should not have taken me so long. Am I going to try to compile AutoDock Vina next? 🤔 Maybe.
Also, if you want to try Open Babel on you jailbroken iDevice, install the package from my repository ( You, need to run the above mentioned final fix :p ). This was tested on iOS 13.5, I cannot tell if it will work on others or not.
Hopefully, I add some more screenshots to this post.
Tagged with: 

\ No newline at end of file
+

This was the tragedy of trying to compile something without knowing enough about compiling. It is 11:30 as of writing this. Something as trivial as this should not have taken me so long. Am I going to try to compile AutoDock Vina next? 🤔 Maybe.

Also, if you want to try Open Babel on you jailbroken iDevice, install the package from my repository ( You, need to run the above mentioned final fix :p ). This was tested on iOS 13.5, I cannot tell if it will work on others or not.

Hopefully, I add some more screenshots to this post.

Edit 1: Added Screenshots, had to replicate the errors.

Tagged with:
\ No newline at end of file -- cgit v1.2.3