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

[Evren Yurtesen IB]

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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