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+---
+date: 2020-05-31 23:30
+description: Compiling Open Babel on iOS
+tags: iOS, Jailbreak, Cheminformatics, Open-Babel
+---
+
+# Compiling 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 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 
+
+```
+scp -r /Applications/Xcode.app/Contents/Developer/Platforms/iPhoneOS.platform/Developer/SDKs/iPhoneOS.sdk root@192.168.1.8:/var/sdks/
+```
+
+Them I told cmake that this is the location for my SDK 😠. Successful! 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:
+/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
+```
+
+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.
+
+
+!["Open-Babel running on my iPad"](/assets/posts/open-babel/s1.png)
+
+
+## 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 successful but when I tried `obabel` it just aborted.
+
+
+!["Open Babel crashing"](/assets/posts/open-babel/s2.jpg)
+
+
+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: `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.
+
+!["Open Babel Plugin Error"](/assets/posts/open-babel/s3.jpg)
+
+So I just copied the entire build folder from my iPad to my phone and tried running it. Oops, Apple Sandbox Error, Oh no!
+
+I spent 2 hours around this problem, only to see the documentation and realise 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.
+
+Edit 1: Added Screenshots, had to replicate the errors.
+