Simbody Build Error in Ubuntu 12.04

Simbody is useful for internal coordinate and coarse grained molecule modeling, large scale mechanical models like skeletons, and anything else that can be modeled as bodies interconnected by joints, acted upon by forces, and restricted by constraints.
User avatar
Rishabh Katiyar
Posts: 2
Joined: Mon Jun 10, 2013 12:08 pm

Simbody Build Error in Ubuntu 12.04

Post by Rishabh Katiyar » Fri Jun 14, 2013 4:58 pm

Hi,

I'm trying to build (Debug mode) Simbody 3.0 from source in linux (Ubuntu 12.04 32 bit) and I get the following error while executing the make command. I'm following the documentation provide in the simbody repository. It seems that the compiler is not able to link to the math libraries. Could you please provide suggestions on how I could proceed with the install?

Thanks,
Priyanshu

Scanning dependencies of target PlatformFiles
[ 0%] Copy /home/reneu-glados/Projects/mysimbody/Simbody3.0/Platform/Linux/lib_x86/libSimTKlapack.so -> /home/reneu-glados/Projects/mysimbody/build_d/./libSimTKlapack.so
[ 1%] Copy /home/reneu-glados/Projects/mysimbody/Simbody3.0/Platform/Linux/lib_x86/libSimTKAtlas_Lin_Opt.so -> /home/reneu-glados/Projects/mysimbody/build_d/./libSimTKAtlas_Lin_Opt.so
[ 1%] Copy /home/reneu-glados/Projects/mysimbody/Simbody3.0/Platform/Linux/lib_x86/libSimTKAtlas_Lin_P4E_64_SSE3.so -> /home/reneu-glados/Projects/mysimbody/build_d/./libSimTKAtlas_Lin_P4E_64_SSE3.so
[ 1%] Copy /home/reneu-glados/Projects/mysimbody/Simbody3.0/Platform/Linux/lib_x86/libSimTKAtlas_Lin_generic.so -> /home/reneu-glados/Projects/mysimbody/build_d/./libSimTKAtlas_Lin_generic.so
[ 1%] Copy /home/reneu-glados/Projects/mysimbody/Simbody3.0/Platform/Linux/lib_x86/libSimTKAtlas_Lin_P4.so -> /home/reneu-glados/Projects/mysimbody/build_d/./libSimTKAtlas_Lin_P4.so
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[ 9%] Building CXX object SimTKcommon/sharedTarget/CMakeFiles/SimTKcommon_d.dir/__/Simulation/src/Event.cpp.o
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[ 11%] Building CXX object SimTKcommon/sharedTarget/CMakeFiles/SimTKcommon_d.dir/__/Polynomial/src/cpoly.cpp.o
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[ 12%] Building CXX object SimTKcommon/sharedTarget/CMakeFiles/SimTKcommon_d.dir/__/Polynomial/src/PolynomialRootFinder.cpp.o
Linking CXX shared library ../../libSimTKcommon_d.so
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Linking CXX executable ../../SpatialAlgebraTest
[ 14%] Built target SpatialAlgebraTest
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[ 14%] Building CXX object SimTKcommon/tests/CMakeFiles/StateTest.dir/StateTest.cpp.o
Linking CXX executable ../../StateTest
[ 14%] Built target StateTest
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Linking CXX executable ../../TestArray
[ 14%] Built target TestArray
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[ 15%] Built target TestAtomicInteger
Scanning dependencies of target TestBigMatrix
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Linking CXX executable ../../TestBigMatrix
[ 15%] Built target TestBigMatrix
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[ 15%] Building CXX object SimTKcommon/tests/CMakeFiles/TestFunction.dir/TestFunction.cpp.o
Linking CXX executable ../../TestFunction
[ 15%] Built target TestFunction
Scanning dependencies of target TestMassProperties
[ 15%] Building CXX object SimTKcommon/tests/CMakeFiles/TestMassProperties.dir/TestMassProperties.cpp.o
Linking CXX executable ../../TestMassProperties
[ 15%] Built target TestMassProperties
Scanning dependencies of target TestParallel2DExecutor
[ 15%] Building CXX object SimTKcommon/tests/CMakeFiles/TestParallel2DExecutor.dir/TestParallel2DExecutor.cpp.o
Linking CXX executable ../../TestParallel2DExecutor
[ 15%] Built target TestParallel2DExecutor
Scanning dependencies of target TestParallelExecutor
[ 15%] Building CXX object SimTKcommon/tests/CMakeFiles/TestParallelExecutor.dir/TestParallelExecutor.cpp.o
Linking CXX executable ../../TestParallelExecutor
[ 15%] Built target TestParallelExecutor
Scanning dependencies of target TestParallelWorkQueue
[ 16%] Building CXX object SimTKcommon/tests/CMakeFiles/TestParallelWorkQueue.dir/TestParallelWorkQueue.cpp.o
Linking CXX executable ../../TestParallelWorkQueue
[ 16%] Built target TestParallelWorkQueue
Scanning dependencies of target TestPlugin
[ 16%] Building CXX object SimTKcommon/tests/CMakeFiles/TestPlugin.dir/TestPlugin.cpp.o
Linking CXX executable ../../TestPlugin
[ 16%] Built target TestPlugin
Scanning dependencies of target TestPolygonalMesh
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[ 16%] Built target TestPolygonalMesh
Scanning dependencies of target TestPrivateImplementation
[ 17%] Building CXX object SimTKcommon/tests/CMakeFiles/TestPrivateImplementation.dir/TestPrivateImplementation.cpp.o
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[ 17%] Built target TestPrivateImplementation
Scanning dependencies of target TestScalar
[ 17%] Building CXX object SimTKcommon/tests/CMakeFiles/TestScalar.dir/TestScalar.cpp.o
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[ 17%] Built target TestScalar
Scanning dependencies of target TestSimulation
[ 18%] Building CXX object SimTKcommon/tests/CMakeFiles/TestSimulation.dir/TestSimulation.cpp.o
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[ 18%] Built target TestSimulation
Scanning dependencies of target TestSmallMatrix
[ 18%] Building CXX object SimTKcommon/tests/CMakeFiles/TestSmallMatrix.dir/TestSmallMatrix.cpp.o
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[ 18%] Building CXX object SimTKcommon/tests/CMakeFiles/TestXml.dir/TestXml.cpp.o
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Scanning dependencies of target BigMatrixTest
[ 18%] Building CXX object SimTKcommon/tests/adhoc/CMakeFiles/BigMatrixTest.dir/BigMatrixTest.cpp.o
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[ 18%] Built target BigMatrixTest
Scanning dependencies of target SimTKmath_d
[ 18%] Building CXX object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/LinearAlgebra/src/FactorQTZ.cpp.o
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[ 19%] Building CXX object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/LinearAlgebra/src/FactorSVD.cpp.o
[ 19%] Building CXX object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/LinearAlgebra/src/LapackInterface.cpp.o
[ 19%] Building CXX object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/LinearAlgebra/src/LapackConvert.cpp.o
[ 19%] Building CXX object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/LinearAlgebra/src/Eigen.cpp.o
[ 20%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/sundials/sundials_spbcgs.c.o
[ 20%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/sundials/sundials_spgmr.c.o
[ 20%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/sundials/sundials_dense.c.o
[ 20%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/sundials/sundials_lapack.c.o
[ 21%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/sundials/sundials_sptfqmr.c.o
[ 21%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/sundials/sundials_nvector.c.o
[ 21%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/sundials/sundials_band.c.o
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[ 23%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/cpodes/cpodes_lapack.c.o
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[ 24%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/cpodes/cpodes_io.c.o
[ 24%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/cpodes/cpodes_sptfqmr.c.o
[ 24%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/cpodes/cpodes_direct.c.o
[ 25%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/cpodes/cpodes.c.o
[ 25%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/cpodes/cpodes_band.c.o
[ 25%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/cpodes/cpodes_bandpre.c.o
[ 26%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/cpodes/cpodes_spgmr.c.o
[ 26%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/cpodes/cpodes_proj.c.o
[ 26%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/cpodes/cpodes_spbcgs.c.o
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[ 27%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/nvec_ser/fnvector_serial.c.o
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[ 27%] Building CXX object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/nvector_SimTK.cpp.o
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[ 28%] Building CXX object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/RungeKuttaMersonIntegrator.cpp.o
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User avatar
Michael Sherman
Posts: 807
Joined: Fri Apr 01, 2005 6:05 pm

Re: Simbody Build Error in Ubuntu 12.04

Post by Michael Sherman » Fri Jun 14, 2013 10:31 pm

Hi, Rishabh. We have built Simbody 3.1 successfully on Ubuntu 12.04 but have not tried Simbody 3.0. Please use the Simbody3.1 branch instead of 3.0 and post again if you are still seeing the problem or have any other trouble building it.

Regards,
Sherm

User avatar
Rishabh Katiyar
Posts: 2
Joined: Mon Jun 10, 2013 12:08 pm

Re: Simbody Build Error in Ubuntu 12.04

Post by Rishabh Katiyar » Sat Jun 15, 2013 2:36 pm

Hi Michael,

Thanks so much for replying. I did a fresh checkout of the Simbody 3.1 branch. However, I still see the exact same error. Just to make sure, I'm using 32 bit Ubuntu. Though we are able to build Simbody 3.0 on a 64 bit Ubuntu 12.04 without any problems. Is it a bug in the 32 bit version? Any suggestions on what might be going wrong would help.

Thanks.

User avatar
Michael Sherman
Posts: 807
Joined: Fri Apr 01, 2005 6:05 pm

Re: Simbody Build Error in Ubuntu 12.04

Post by Michael Sherman » Sat Jun 15, 2013 5:21 pm

My Ubuntu 12.04 is 64 bit and builds with no problem. I will try to dig up a 32 bit Ubuntu and see if I can reproduce the problem you're having.

Sherm

User avatar
Priyanshu Agarwal
Posts: 39
Joined: Tue Jun 08, 2010 10:08 am

Re: Simbody Build Error in Ubuntu 12.04

Post by Priyanshu Agarwal » Sat Jun 15, 2013 10:23 pm

Thanks so much Michael. That will be really helpful.

Regards,
Priyanshu

User avatar
Michael Sherman
Posts: 807
Joined: Fri Apr 01, 2005 6:05 pm

Re: Simbody Build Error in Ubuntu 12.04

Post by Michael Sherman » Sun Jun 16, 2013 12:47 pm

I built a new 32 bit Ubuntu 12.04 VM and tried building Simbody 3.1. Everything compiled fine -- I did not see the error you reported. That makes me think you might be using a different compiler. I installed the Ubuntu-supplied gcc, which is version 4.6.3. If I type "c++ --version" it outputs: c++ (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3. What compiler are you using?

After the successful build I ran "make test" and saw 2 test failures out of the 92 regression tests. I do not see these with the same version of the compiler in 64 bit. I'm not sure what to make of that.

Sherm

User avatar
Priyanshu Agarwal
Posts: 39
Joined: Tue Jun 08, 2010 10:08 am

Re: Simbody Build Error in Ubuntu 12.04

Post by Priyanshu Agarwal » Mon Jun 17, 2013 12:59 pm

Thanks Michael. We have the exact same compiler. May be it has to do with setting some flag while generating the make file. We edited the "link.txt" files in following directories to add -lm flag

/mysimbody/build_d/SimTKmath/Integrators/src/CPodes/sundials/tests/CMakeFiles

After making these chages it complied cleanly. We also saw the following 2 tests failing in Release build, but none in Debug.

The following tests FAILED:
20 - BNTTest (Failed)
70 - TestGeo (Failed)
Errors while running CTest
make: *** [test] Error 8

Regards,
Priyanshu

User avatar
Michael Sherman
Posts: 807
Joined: Fri Apr 01, 2005 6:05 pm

Re: Simbody Build Error in Ubuntu 12.04

Post by Michael Sherman » Mon Jun 17, 2013 1:29 pm

I'm mystified as to why you had to set that flag and I did not.

But those are the same two test failures I saw so we are probably getting the same builds now. I believe those are 32-bit gcc 4.6.3 optimizer bugs. The 64 bit code generator doesn't seem to have the same problem. Hopefully the bugs are being triggered by the test code itself (which can be somewhat extreme). That appears to be the case for BNTTest (and I've seen compilers fail on that before), but I'm not as sure about TestGeo.

Sherm

User avatar
Priyanshu Agarwal
Posts: 39
Joined: Tue Jun 08, 2010 10:08 am

Re: Simbody Build Error in Ubuntu 12.04

Post by Priyanshu Agarwal » Tue Jun 18, 2013 9:19 pm

Yes, figuring out where to add the flags took some time. We were wondering if the same could be achieve by adding the flag in the CMakeLists.txt. Yes, none of the tests failed for the 64 bit code generator for us as well.

Thanks so much for your help.

Regards,
Priyanshu

User avatar
Michael Sherman
Posts: 807
Joined: Fri Apr 01, 2005 6:05 pm

Re: Simbody Build Error in Ubuntu 12.04

Post by Michael Sherman » Tue Jun 18, 2013 9:43 pm

Hi, Priyanshu. Well, I still don't understand why you needed to add -lm explicitly, but you can add flags within the CMake GUI (either ccmake or cmake-gui) if you toggle the "adanced" mode. Then you have access to CMake variables like CMAKE_MODULE_LINKER_FLAGS where I believe you can add "-lm". After that it will be append to the link line for all shared objects. There is a separate linker flags variables for executables. You should never have to edit the CMake-generated makefiles, which are a mess and not fit for human consumption.

Regards,
Sherm

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