Building OpenSim 4.0 with static libraries

[clnsmith]

Hi All,

I am working on getting 4.0 running on a linux computing cluster. I have been able to build the source from the master branch on Scientific Linux 6.

Ideally, OpenSim does not need to be installed on the "worker" nodes (as these are random computers in labs across campus). I currently have it setup where I can run a simulation on a "worker" node by sending the executable (ie cmc), input files and the shared opensim libraries (.so). Ideally, I would like to build OpenSim with static libraries, so the executables are stand alone and I don't need to transfer the .so libraries for every simulation.

Do you anticipate any problems with building OpenSim with static libraries? Am I correct that I should be able to do this by editing the CMakeLists.txt files?

Thanks,
Colin

[chrisdembia]

On Linux, there should be no problem. On Windows, there will be an issue related to the OSIMCOMMON_EXPORTS macros (this problem can also be solved; it's just annoying).

Remove the SHARED from this line.

I'm not sure Simbody's SimbodyConfig.cmake will include the static libraries...you might have to change OpenSim's CMakeLists to link to SimTKcommon_static or whatever the names of the Simbody static targets are.

[chrisdembia]

@aymanhab mentioned that there might be issues with the python/java bindings, but I don't think there will be. I think the shared libraries for the wrapping can link to the static osimCommon, etc. However, the shared libraries for the wrapping will need to remain as shared libraries (I'm talking about osimJavaJNI, _common, _simulation, etc.)

[clnsmith]

OK great thanks, I'll give it a try.

For my current application the potential python/java bindings and windows issues wouldn't be a problem anyways. I'll let you know what I find.

[clnsmith]

I am getting the following errors by changing the line Chris suggested (on Scientific Linux 6, GCC 5.2.1, not building the python/java bindings)

I'm trying to build without the tests right now.

[ 63%] Linking CXX executable ../../../testMarkerData
../../../libosimCommon.a(MarkerData.cpp.o): In function getPeakRSS()': MarkerData.cpp:(.text+0x40): multiple definition ofgetPeakRSS()'
CMakeFiles/testMarkerData.dir/testMarkerData.cpp.o:testMarkerData.cpp:(.text+0x90): first defined here
../../../libosimCommon.a(MarkerData.cpp.o): In function getCurrentRSS()': MarkerData.cpp:(.text+0x70): multiple definition ofgetCurrentRSS()'
CMakeFiles/testMarkerData.dir/testMarkerData.cpp.o:testMarkerData.cpp:(.text+0xc0): first defined here
../../../libosimCommon.a(MarkerData.cpp.o): In function CHECK_STORAGE_AGAINST_STANDARD(OpenSim::Storage const&, OpenSim::Storage const&, std::vector<double, std::allocator<double> > const&, std::string const&, int, std::string const&)': MarkerData.cpp:(.text+0xd20): multiple definition ofCHECK_STORAGE_AGAINST_STANDARD(OpenSim::Storage const&, OpenSim::Storage const&, std::vector<double, std::allocator > const&, std::string const&, int, std::string const&)'
CMakeFiles/testMarkerData.dir/testMarkerData.cpp.o:testMarkerData.cpp:(.text+0x140): first defined here
../../../libosimCommon.a(MarkerData.cpp.o): In function validateMemoryUseEstimates(unsigned long)': MarkerData.cpp:(.text+0x45d0): multiple definition ofvalidateMemoryUseEstimates(unsigned long)'
CMakeFiles/testMarkerData.dir/testMarkerData.cpp.o:testMarkerData.cpp:(.text+0x710): first defined here
../../../libosimCommon.a(MarkerData.cpp.o): In function randomize(OpenSim::Object*)': MarkerData.cpp:(.text+0x5e10): multiple definition ofrandomize(OpenSim::Object_)'
CMakeFiles/testMarkerData.dir/testMarkerData.cpp.o:testMarkerData.cpp:(.text+0x1f50): first defined here
collect2: error: ld returned 1 exit status
make[2]: *_* [testMarkerData] Error 1
make[1]: *** [OpenSim/Common/Test/CMakeFiles/testMarkerData.dir/all] Error 2
make: *** [all] Error 2

[clnsmith]

I get the following error if I build without tests. No errors if I build without tests and examples.
However, the analyze executable is still looking for the simbody dynamic libraries, so I will dig through the CMakeLists to make it link against the static simbody libraries

[ 94%] Linking CXX shared library ../../../libexampleExpressionReporterPlugin.so
/opt/rh/devtoolset-4/root/usr/libexec/gcc/x86_64-redhat-linux/5.2.1/ld: ../../../libosimSimulation.a(RegisterTypes_osimSimulation.cpp.o): relocation R_X86_64_32 against `__pthread_key_create' can not be used when making a shared object; recompile with -fPIC
../../../libosimSimulation.a: error adding symbols: Bad value
collect2: error: ld returned 1 exit status
make[2]: *** [libexampleExpressionReporterPlugin.so] Error 1
make[1]: *** [OpenSim/Examples/SymbolicExpressionReporter/CMakeFiles/exampleExpressionReporterPlugin.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....

[chrisdembia]

For the earlier multiple-definition errors, you can declare the problematic functions as inline; those functions are located here: https://github.com/opensim-org/opensim-core/tree/master/OpenSim/Auxiliary.

The latter error is saying to compile with the -fPIC flag. I don't know too much about that, but you could try adding that flag to CMAKE_CXX_FLAGS.

To use Simbody static libraries, edit this line and other similar lines to use ${Simbody_STATIC_LIBRARIES} instead of ${Simbody_LIBRARIES}.

[mitkof6]

I tried to do something similar on linux. My conclusions are:

Simobdy builds static libraries, but unfortunately, there is a lapack and blas dependency. So the simbody static libraries have a .so reference if you look into SimbodyTargets-[RelWithDebInfo].cmake. I tried to enforce linking only static libraries but wasn't able (issue).

For OpenSim I was able to compile static libraries with some modifications to the CMakeLists files. At the end you will not get a pure static executable if you don't manage to solve the static linking of lapack and blas.