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diff --git a/docs/posts/2020-05-31-compiling-open-babel-on-ios.html b/docs/posts/2020-05-31-compiling-open-babel-on-ios.html new file mode 100644 index 0000000..bccab0e --- /dev/null +++ b/docs/posts/2020-05-31-compiling-open-babel-on-ios.html @@ -0,0 +1,147 @@ +<!DOCTYPE html> +<html lang="en"> +<head> + + <link rel="stylesheet" href="/assets/main.css" /> + <link rel="stylesheet" href="/assets/sakura.css" /> + <meta charset="utf-8"> + <meta name="viewport" content="width=device-width, initial-scale=1.0"> + <title>Hey - Post</title> + +</head> +<body> + <nav style="display: block;"> +| +<a href="/">home</a> | +<a href="/about/">about/links</a> | +<a href="/posts/">posts</a> | +<a href="/publications/">publications</a> | +<a href="/repo/">iOS repo</a> | +<a href="/feed.rss">RSS Feed</a> | +</nav> + +<main> + <h1>Compiling Open Babel on iOS</h1> + +<p>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.</p> + +<p>I am running the Checkr1n jailbreak on my iPad and the Unc0ver jailbreak on my phone.</p> + +<h2>But Why?</h2> + +<p>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.</p> + +<h2>Let's Go!</h2> + +<p>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 <code>cmake</code> to build and the <code>make</code> to install.</p> + +<p>It is 11 AM in the morning. I install <code>clang, cmake and make</code> from the Sam Bingner's repository, fired up ssh, downloaded the source code and ran the build command.`clang</p> + +<h3>Fail No. 1</h3> + +<p>I couldn't even get cmake to run, I did a little digging around StackOverflow and founf that I needed the iOS SDK, sure no problem. I waited for Xcode to update and transferred the SDKs to my iPad </p> + +<pre><code>scp -r /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk root@192.168.1.8:/var/sdks/ +</code></pre> + +<p>Them I told cmake that this is the location for my SDK 😠. Successful! Now I just needed to use make.</p> + +<h3>Fail No. 2</h3> + +<p>It was giving the error that thread-local-storage was not supported on this device.</p> + +<pre><code>[ 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: +/var/root/obabel/ob-src/include/openbabel/typer.h:70:1: error: thread-local storage is not supported for the current target +THREAD_LOCAL OB_EXTERN OBAtomTyper atomtyper; +^ +/var/root/obabel/ob-src/include/openbabel/mol.h:35:24: note: expanded from macro 'THREAD_LOCAL' +# define THREAD_LOCAL thread_local + ^ +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: +/var/root/obabel/ob-src/include/openbabel/typer.h:84:1: error: thread-local storage is not supported for the current target +THREAD_LOCAL OB_EXTERN OBAromaticTyper aromtyper; +^ +/var/root/obabel/ob-src/include/openbabel/mol.h:35:24: note: expanded from macro 'THREAD_LOCAL' +# define THREAD_LOCAL thread_local + ^ +/var/root/obabel/ob-src/src/atom.cpp:107:10: error: thread-local storage is not supported for the current target + extern THREAD_LOCAL OBAromaticTyper aromtyper; + ^ +/var/root/obabel/ob-src/include/openbabel/mol.h:35:24: note: expanded from macro 'THREAD_LOCAL' +# define THREAD_LOCAL thread_local + ^ +/var/root/obabel/ob-src/src/atom.cpp:108:10: error: thread-local storage is not supported for the current target + extern THREAD_LOCAL OBAtomTyper atomtyper; + ^ +/var/root/obabel/ob-src/include/openbabel/mol.h:35:24: note: expanded from macro 'THREAD_LOCAL' +# define THREAD_LOCAL thread_local + ^ +/var/root/obabel/ob-src/src/atom.cpp:109:10: error: thread-local storage is not supported for the current target + extern THREAD_LOCAL OBPhModel phmodel; + ^ +/var/root/obabel/ob-src/include/openbabel/mol.h:35:24: note: expanded from macro 'THREAD_LOCAL' +# define THREAD_LOCAL thread_local + ^ +5 errors generated. +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 +</code></pre> + +<p>Strange but it is alright, there is nothing that hasn't been answered on the internet.</p> + +<p>I did a little digging around and could not find a solution 😔</p> + +<p>As a temporary fix, I disabled multithreading by going and commenting the lines in the source code.</p> + +<p><img src="/assets/posts/open-babel/s1.png" alt=""Open-Babel running on my iPad"" /></p> + +<h2>Packaging as a deb</h2> + +<p>This was pretty straight forward, I tried installing it on my iPad and it was working pretty smoothly.</p> + +<h2>Moment of Truth</h2> + +<p>So I airdropped the .deb to my phone and tried installing it, the installation was successful but when I tried <code>obabel</code> it just aborted.</p> + +<p><img src="/assets/posts/open-babel/s2.jpg" alt=""Open Babel crashing"" /></p> + +<p>Turns out because I had created an install target of a separate folder while compiling, the binaries were referencing 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: <code>install_name_tool -change /var/root/obabel/ob-build/lib/libopenbabel.7.dylib /usr/lib/libopenbabel.7.dylib</code> for all the executables and then signed them using jtool</p> + +<p>I then installed it and everything went smoothly, I even ran <code>obabel</code> and it executed perfectly, showing the version number 3.1.0 ✌️ Ahh, smooth victory.</p> + +<p>Nope. When I tried converting from SMILES to pdbqt, it gave an error saying plugin not found. This was weird.</p> + +<p><img src="/assets/posts/open-babel/s3.jpg" alt=""Open Babel Plugin Error"" /></p> + +<p>So I just copied the entire build folder from my iPad to my phone and tried running it. Oops, Apple Sandbox Error, Oh no!</p> + +<p>I spent 2 hours around this problem, only to see the documentation and realise I hadn't setup the environment variable 🤦♂️</p> + +<h2>The Final Fix ( For Now )</h2> + +<pre><code>export BABEL_DATADIR="/usr/share/openbabel/3.1.0" +export BABEL_LIBDIR="/usr/lib/openbabel/3.1.0" +</code></pre> + +<p>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.</p> + +<p>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.</p> + +<p>Hopefully, I add some more screenshots to this post.</p> + +<p>Edit 1: Added Screenshots, had to replicate the errors.</p> + +</main> + + +<script src="assets/manup.min.js"></script> +<script src="/pwabuilder-sw-register.js"></script> +</body> +</html>
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