Simbody Build Error in Ubuntu 12.04

[Rishabh Katiyar]

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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[ 20%] Building C object SimTKmath/sharedTarget/CMakeFiles/SimTKmath_d.dir/__/Integrators/src/CPodes/sundials/src/sundials/sundials_spbcgs.c.o
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[ 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
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[Michael Sherman]

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

[Rishabh Katiyar]

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.

[Michael Sherman]

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

[Priyanshu Agarwal]

Thanks so much Michael. That will be really helpful.

Regards,
Priyanshu

[Michael Sherman]

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

[Priyanshu Agarwal]

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

[Michael Sherman]

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

[Priyanshu Agarwal]

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

[Michael Sherman]

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