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<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>
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