[gmx-developers] Gromacs 4.6.1 ATLAS/CUDA detection problems...

Christoph Junghans junghans at votca.org
Wed Mar 6 20:08:01 CET 2013 

Hi Evren,

please post these kind of questions on the users list as they are not
really related to the development of gromacs.

Concerning your question below, can you please post your cmake
configure command line?

Christoph

2013/3/6 Evren Yurtesen IB <eyurtese at abo.fi>:
> Sorry for the double post. I tried to post it from web and it said the post
> was not accepted to mailing list but then it arrived anyway.
>
> In addition the manual mentions setting CMAKE_INSTALL_PREFIX however this
> does not work when it is "set" it only works when given to cmake as a
> parameter with -DCMAKE_INSTALL_PREFIX=/something
> http://www.gromacs.org/Documentation/Installation_Instructions#4.3._CMake_advanced_options
>
> When I do an 'export CMAKE_INSTALL_PREFIX=/something' this is does not seem
> to propagate to configuration files, interestingly 'export
> CMAKE_PREFIX_PATH=/libpaths' seem to have the desired effect.
>
> Thanks,
> Evren
>
>
> On Wed, 6 Mar 2013, Evren Yurtesen IB wrote:
>
>> Hello,
>>
>> I am not exactly sure if this is a bug but I realized that cmake system of
>> gromacs couldnt find my ATLAS libraries. First problem was that it needed
>> -lgfortran (and then -lcblas also) for compiling with gcc. The error I found
>> in cmake error file can be found below.
>>
>> In addition while documentation suggests latest GCC versions, the only
>> compatible version of GCC with CUDA 5.0 is GCC 4.6 but there doesnt seem to
>> be any checks for this.
>>
>> Run Build Command:/usr/bin/gmake "cmTryCompileExec3752895534/fast"
>> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec3752895534.dir/build.make
>> CMakeFiles/cmTryCompileExec3752895534.dir/build
>> gmake[1]: Entering directory
>> `/home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp'
>> /usr/bin/cmake -E cmake_progress_report
>> /home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp/CMakeFiles
>> 1
>> Building C object
>> CMakeFiles/cmTryCompileExec3752895534.dir/CheckFunctionExists.c.o
>> /export/modules/compilers/gnu/gcc/4.7.2/bin/gcc   -Wextra
>> -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused
>> -Wunused-value  -march=native -mtune=native -DCHECK_FUNCTION_EXISTS=dgemm_
>> -o CMakeFiles/cmTryCompileExec3752895534.dir/CheckFunctionExists.c.o   -c
>> /usr/share/cmake/Modules/CheckFunctionExists.c
>> Linking C executable cmTryCompileExec3752895534
>> /usr/bin/cmake -E cmake_link_script
>> CMakeFiles/cmTryCompileExec3752895534.dir/link.txt --verbose=1
>> /export/modules/compilers/gnu/gcc/4.7.2/bin/gcc   -Wextra
>> -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused
>> -Wunused-value  -march=native -mtune=native -DCHECK_FUNCTION_EXISTS=dgemm_
>> CMakeFiles/cmTryCompileExec3752895534.dir/CheckFunctionExists.c.o  -o
>> cmTryCompileExec3752895534 -rdynamic -Wl,-Bstatic -lf77blas -latlas
>> -Wl,-Bdynamic
>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/libf77blas.a(xerbla.o): In
>> function `xerbla_':
>> xerbla.f:(.text+0x4a): undefined reference to `_gfortran_st_write'
>> xerbla.f:(.text+0x5a): undefined reference to
>> `_gfortran_transfer_character_write'
>> xerbla.f:(.text+0x6a): undefined reference to
>> `_gfortran_transfer_integer_write'
>> xerbla.f:(.text+0x72): undefined reference to `_gfortran_st_write_done'
>> xerbla.f:(.text+0x7b): undefined reference to `_gfortran_stop_string'
>> collect2: error: ld returned 1 exit status
>> gmake[1]: *** [cmTryCompileExec3752895534] Error 1
>> gmake[1]: Leaving directory
>> `/home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp'
>> gmake: *** [cmTryCompileExec3752895534/fast] Error 2
>>
>>
>> After this the -lcblas was missing. Which caused the following errors.
>>
>> Run Build Command:/usr/bin/gmake "cmTryCompileExec2027137673/fast"
>> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec2027137673.dir/build.make
>> CMakeFiles/cmTryCompileExec2027137673.dir/build
>> gmake[1]: Entering directory
>> `/home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp'
>> /usr/bin/cmake -E cmake_progress_report
>> /home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp/CMakeFiles
>> 1
>> Building C object
>> CMakeFiles/cmTryCompileExec2027137673.dir/CheckFunctionExists.c.o
>> /export/modules/compilers/gnu/gcc/4.7.2/bin/gcc   -Wextra
>> -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused
>> -Wunused-value  -march=native -mtune=native -DCHECK_FUNCTION_EXISTS=cheev_
>> -o CMakeFiles/cmTryCompileExec2027137673.dir/CheckFunctionExists.c.o   -c
>> /usr/share/cmake/Modules/CheckFunctionExists.c
>> Linking C executable cmTryCompileExec2027137673
>> /usr/bin/cmake -E cmake_link_script
>> CMakeFiles/cmTryCompileExec2027137673.dir/link.txt --verbose=1
>> /export/modules/compilers/gnu/gcc/4.7.2/bin/gcc   -Wextra
>> -Wno-missing-field-initializers -Wno-sign-compare -Wall -Wno-unused
>> -Wunused-value  -march=native -mtune=native -DCHECK_FUNCTION_EXISTS=cheev_
>> CMakeFiles/cmTryCompileExec2027137673.dir/CheckFunctionExists.c.o  -o
>> cmTryCompileExec2027137673 -rdynamic -Wl,-Bstatic -llapack -lf77blas -latlas
>> -Wl,-Bdynamic -lgfortran
>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarfb.o): In
>> function `ATL_clarfb':
>> ATL_larfb.c:(.text+0x160): undefined reference to `cblas_ccopy'
>> ATL_larfb.c:(.text+0x1fe): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x263): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x2b9): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x400): undefined reference to `cblas_ccopy'
>> ATL_larfb.c:(.text+0x4a4): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x509): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x55f): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x670): undefined reference to `cblas_ccopy'
>> ATL_larfb.c:(.text+0x6f4): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x759): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x7b2): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x8b8): undefined reference to `cblas_ccopy'
>> ATL_larfb.c:(.text+0x93f): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x9a4): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x9fd): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0xb04): undefined reference to `cblas_ccopy'
>> ATL_larfb.c:(.text+0xb97): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0xbfd): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0xc4e): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0xd54): undefined reference to `cblas_ccopy'
>> ATL_larfb.c:(.text+0xded): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0xe53): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0xea4): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0xf70): undefined reference to `cblas_ccopy'
>> ATL_larfb.c:(.text+0xff8): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x105e): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x10b7): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x1180): undefined reference to `cblas_ccopy'
>> ATL_larfb.c:(.text+0x1208): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x126e): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x12c7): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x13a7): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x140c): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x1464): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x14d0): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x1521): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x15b8): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x161d): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x1675): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x16e1): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x1732): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x17d2): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x1837): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x188e): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x18fb): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x1951): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x19eb): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x1a50): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x1aa7): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x1b14): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x1b6a): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x1bdf): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x1c78): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x1ccf): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x1d3c): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x1d95): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x1e09): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x1e8e): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x1ee6): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x1f4e): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x1fa7): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x201c): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x20b0): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x2108): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x2170): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x21c9): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x2240): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x22dc): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x2333): undefined reference to `cblas_ctrmm'
>> ATL_larfb.c:(.text+0x23a0): undefined reference to `cblas_cgemm'
>> ATL_larfb.c:(.text+0x23f9): undefined reference to `cblas_ctrmm'
>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In
>> function `ATL_clarft_blockFC':
>> ATL_larft.c:(.text+0x152): undefined reference to `cblas_ctrmm'
>> ATL_larft.c:(.text+0x1c3): undefined reference to `cblas_cgemm'
>> ATL_larft.c:(.text+0x211): undefined reference to `cblas_ctrmm'
>> ATL_larft.c:(.text+0x254): undefined reference to `cblas_ctrmm'
>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In
>> function `ATL_clarft_blockFR':
>> ATL_larft.c:(.text+0x3bd): undefined reference to `cblas_ctrmm'
>> ATL_larft.c:(.text+0x433): undefined reference to `cblas_cgemm'
>> ATL_larft.c:(.text+0x481): undefined reference to `cblas_ctrmm'
>> ATL_larft.c:(.text+0x4c4): undefined reference to `cblas_ctrmm'
>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In
>> function `ATL_clarft_blockBC':
>> ATL_larft.c:(.text+0x643): undefined reference to `cblas_ctrmm'
>> ATL_larft.c:(.text+0x69d): undefined reference to `cblas_cgemm'
>> ATL_larft.c:(.text+0x6e8): undefined reference to `cblas_ctrmm'
>> ATL_larft.c:(.text+0x72e): undefined reference to `cblas_ctrmm'
>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In
>> function `ATL_clarft_blockBR':
>> ATL_larft.c:(.text+0x8c8): undefined reference to `cblas_ctrmm'
>> ATL_larft.c:(.text+0x920): undefined reference to `cblas_cgemm'
>> ATL_larft.c:(.text+0x96b): undefined reference to `cblas_ctrmm'
>> ATL_larft.c:(.text+0x9b1): undefined reference to `cblas_ctrmm'
>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In
>> function `ATL_clarftFC':
>> ATL_larft.c:(.text+0xcfb): undefined reference to `cblas_cdotc_sub'
>> ATL_larft.c:(.text+0xdb3): undefined reference to `cblas_cdotu_sub'
>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In
>> function `ATL_clarftBC':
>> ATL_larft.c:(.text+0xffd): undefined reference to `cblas_cdotc_sub'
>> ATL_larft.c:(.text+0x10a9): undefined reference to `cblas_cdotu_sub'
>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In
>> function `ATL_clarftFR':
>> ATL_larft.c:(.text+0x1368): undefined reference to `cblas_cdotc_sub'
>> ATL_larft.c:(.text+0x1422): undefined reference to `cblas_cdotu_sub'
>> /export/modules/devel/ATLAS/3.10.1/gnu/lib/liblapack.a(ATL_clarft.o): In
>> function `ATL_clarftBR':
>> ATL_larft.c:(.text+0x165d): undefined reference to `cblas_cdotc_sub'
>> ATL_larft.c:(.text+0x1713): undefined reference to `cblas_cdotu_sub'
>> collect2: error: ld returned 1 exit status
>> gmake[1]: *** [cmTryCompileExec2027137673] Error 1
>> gmake[1]: Leaving directory
>> `/home/eyurtese/tmp/gromacs-4.6.1/build-cmake/CMakeFiles/CMakeTmp'
>> gmake: *** [cmTryCompileExec2027137673/fast] Error 2
>>
>>
>>
>> Thanks,
>> Evren
>> --
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>>
> --
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--
Christoph Junghans
Web: http://www.compphys.de

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