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diff --git a/Content/posts/2020-05-31-compiling-open-babel-on-ios.md b/Content/posts/2020-05-31-compiling-open-babel-on-ios.md new file mode 100644 index 0000000..6da19c6 --- /dev/null +++ b/Content/posts/2020-05-31-compiling-open-babel-on-ios.md @@ -0,0 +1,138 @@ +--- +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. + + + + + +## 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. + + + + + +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. + + + +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. + |