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

[Christoph Junghans]

2013/3/6 Evren Yurtesen IB <eyurtese at abo.fi>:
> Hi Christoph,
>
> I thought problems in the compilation is more related to devs than users.
> But I sure can send mail first to users list in future.
Thanks.

>
> I used the following to get it working.
>
> mkdir build_cmake
> cd build_cmake
> cmake .. -DCMAKE_INSTALL_PREFIX=/export/modules/apps/gromacs/4.6.1/mvapich2
>
> This does not seem to work
>
> mkdir build_cmake
> cd build_cmake
> export CMAKE_INSTALL_PREFIX=/export/modules/apps/gromacs/4.6.1/mvapich2
> cmake ..
>
> Was this the information you were looking for?
That looks ok.

I had a another look at the issue and I guess cmake's blas detention
is a bit flaky, when it comes to static libraries.
You are using liblapack.a, which has no link information, with
liblapack.so it should have worked.
Anyhow, thanks for reporting the issue.

Christoph
>
> Thanks
> Evren
>
>
>
>
> On Wed, 6 Mar 2013, Christoph Junghans wrote:
>
>> 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
>>>> --
>>>> gmx-developers mailing list
>>>> gmx-developers at gromacs.org
>>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>>> Please don't post (un)subscribe requests to the list. Use the www
>>>> interface or send it to gmx-developers-request at gromacs.org.
>>>>
>>> --
>>> gmx-developers mailing list
>>> gmx-developers at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-developers
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface
>>> or send it to gmx-developers-request at gromacs.org.
>>
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>>
>



--
Christoph Junghans
Web: http://www.compphys.de