[gmx-users] Gromac4.6.7 installation problem

Mark Abraham mark.j.abraham at gmail.com
Sat Mar 4 02:32:32 CET 2017 

Hi,

For the record, with GROMACS 4.6.7, the gcc 5.4.0 in ubuntu 16.04.2 with
CUDA 8.0 installed and past tests perfectly for me on a 24-core AMD
dual-GPU node, with and without the own-fftw option. So something about
your machine looks fishy. You should not need to provide linker flags, but
they shouldn't be the problem either.

Mark

On Fri, Mar 3, 2017 at 7:51 PM Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> So that means your gcc 4.9 works, but something about the cuda or build
> system doesn't work right in such an old (and slow) version of Gromacs.
> Ubuntu 16.04 ships a new version of glibc which could also be a problem.
>
> The error is probably not a problem, but we would be interested to see
> mdrun.out from a failing case. We'd only fix an issue on our end in a
> supported version, however.
>
> Mark
>
> On Fri, 3 Mar 2017 18:21 Mohsen Ramezanpour <ramezanpour.mohsen at gmail.com>
> wrote:
>
> Thanks Mark.
>
> I tried gcc 4.9 and used it as follows:
>
> cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> -DGMX_GPU=ON  -DCMAKE_INSTALL_PREFIX=/home/mohsen/programs-mohsen
> -DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/4.9
> -L/usr/lib/gcc/x86_64-linux-gnu/4.9"
>
>
> I tried simple make for both  -DGMX_GPU=ON and -DGMX_GPU=off
>
> for -DGMX_GPU=ON it failed and the same problem happened, although I used
> gcc 4.9
>
> When I made -DGMX_GPU=off, it said:
>
> -- Configuring done
> -- Generating done
> CMake Warning:
>   Manually-specified variables *were not used* by the project:
>
>     *CMAKE_CXX_LINK_FLAGS*
>
> again, some of the previous errors happened.
> for instance:
>
> CMake Warning (dev) at cmake/gmxSetBuildInformation.cmake:156 (set):
>   Policy CMP0053 is not set: Simplify variable reference and escape
> sequence
>   evaluation.  Run "cmake --help-policy CMP0053" for policy details.  Use
> the
>   cmake_policy command to set the policy and suppress this warning.
>
>   For input:
>
>     '@OUTPUT_CPU_FEATURES@'
>
>   the old evaluation rules produce:
>
>     'aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma htt lahf_lm mmx msr
> nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3
> sse4.1 sse4.2 ssse3 tdt x2apic'
>
>   but the new evaluation rules produce:
>
>     '@OUTPUT_CPU_FEATURES@'
>
>   Using the old result for compatibility since the policy is not set.
>
> The, I did a make check, and I got this.
> [  1%] Built target fftwBuild
> [ 64%] Built target gmx
> [ 83%] Built target md
> [ 94%] Built target gmxana
> [ 94%] Built target editconf
> [ 98%] Built target gmxpreprocess
> [100%] Built target mdrun
> [100%] Built target pdb2gmx
> [100%] Built target gmxcheck
> [100%] Built target grompp
> Scanning dependencies of target gmxtests
> [100%] Built target gmxtests
> Scanning dependencies of target check
> Test project /home/mohsen/Downloads/gromacs-4.6.7/build
>     Start 1: regressiontests/simple
> 1/6 Test #1: regressiontests/simple ...........   Passed    1.17 sec
>     Start 2: regressiontests/complex
> 2/6 Test #2: regressiontests/complex ..........   Passed    2.84 sec
>     Start 3: regressiontests/kernel
> 3/6 Test #3: regressiontests/kernel ...........   Passed   26.26 sec
>     Start 4: regressiontests/freeenergy
> 4/6 Test #4: regressiontests/freeenergy .......***Failed    4.83 sec
> Mdrun cannot use the requested (or automatic) number of cores, retrying
> with 8.
> Mdrun cannot use the requested (or automatic) number of cores, retrying
> with 8.
> Mdrun cannot use the requested (or automatic) number of cores, retrying
> with 8.
> FAILED. Check checkpot.out (18 errors) files in relative
> Mdrun cannot use the requested (or automatic) number of cores, retrying
> with 8.
> 1 out of 9 freeenergy tests FAILED
>
>     Start 5: regressiontests/pdb2gmx
> 5/6 Test #5: regressiontests/pdb2gmx ..........   Passed   11.53 sec
>     Start 6: regressiontests/rotation
> 6/6 Test #6: regressiontests/rotation .........   Passed    1.87 sec
>
> 83% tests passed, 1 tests failed out of 6
>
> Total Test time (real) =  48.50 sec
>
> The following tests FAILED:
>       4 - regressiontests/freeenergy (Failed)
> Errors while running CTest
> CMakeFiles/check.dir/build.make:57: recipe for target 'CMakeFiles/check'
> failed
> make[3]: *** [CMakeFiles/check] Error 8
> CMakeFiles/Makefile2:131: recipe for target 'CMakeFiles/check.dir/all'
> failed
> make[2]: *** [CMakeFiles/check.dir/all] Error 2
> CMakeFiles/Makefile2:138: recipe for target 'CMakeFiles/check.dir/rule'
> failed
> make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> Makefile:221: recipe for target 'check' failed
> make: *** [check] Error 2
>
>
> Is this critical or I can continue installing?
>
> Thanks in advance for your reply and help
>
> Cheers
> Mohsen
>
>
> -- Build files have been written to:
> /home/mohsen/Downloads/gromacs-4.6.7/build
>
>
> The problem still exist.
> Cheers
> Mohsen
>
> On Fri, Mar 3, 2017 at 12:19 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
> > Hi,
> >
> > Using parallel make obscures problems when they exist, so run again with
> > simple make. Probably cuda does not support your compiler, so you will
> run
> > into problems later. I suggest gcc 4.9
> >
> > Mark
> >
> > On Thu, 2 Mar 2017 06:58 Mohsen Ramezanpour <
> ramezanpour.mohsen at gmail.com>
> > wrote:
> >
> > > Dear Gromacs users,
> > >
> > > I am trying to install gromacs 4.6.7 on Ubuntu 16.04.
> > > Unfortunately, I get an Error which I do not know how to solve it.
> > >
> > > After
> > > mkdir build
> > > cd build
> > >
> > > *I use:*
> > > cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON
> > -DGMX_GPU=ON
> > > -DCMAKE_INSTALL_PREFIX=/home/mohsen/programs
> > > -DCMAKE_CXX_LINK_FLAGS="-Wl,-rpath,/usr/lib/gcc/x86_64-linux-gnu/5
> > > -L/usr/lib/gcc/x86_64-linux-gnu/5"
> > >
> > > *I get this:*
> > > -- The C compiler identification is GNU 5.4.0
> > > -- Check for working C compiler: /usr/bin/cc
> > > -- Check for working C compiler: /usr/bin/cc -- works
> > > -- Detecting C compiler ABI info
> > > -- Detecting C compiler ABI info - done
> > > -- Detecting C compile features
> > > -- Detecting C compile features - done
> > > -- Looking for NVIDIA GPUs present in the system
> > > -- Number of NVIDIA GPUs detected: 1
> > > -- Looking for pthread.h
> > > -- Looking for pthread.h - found
> > > -- Looking for pthread_create
> > > -- Looking for pthread_create - not found
> > > -- Looking for pthread_create in pthreads
> > > -- Looking for pthread_create in pthreads - not found
> > > -- Looking for pthread_create in pthread
> > > -- Looking for pthread_create in pthread - found
> > > -- Found Threads: TRUE
> > > -- Found CUDA: /usr (found suitable version "7.5", minimum required is
> > > "3.2")
> > > -- The CXX compiler identification is GNU 5.4.0
> > > -- Check for working CXX compiler: /usr/bin/c++
> > > -- Check for working CXX compiler: /usr/bin/c++ -- works
> > > -- Detecting CXX compiler ABI info
> > > -- Detecting CXX compiler ABI info - done
> > > -- Detecting CXX compile features
> > > -- Detecting CXX compile features - done
> > > -- Checking for GCC x86 inline asm
> > > -- Checking for GCC x86 inline asm - supported
> > > -- Detecting best acceleration for this CPU
> > > CMake Warning (dev) at cmake/gmxDetectAcceleration.cmake:65 (set):
> > >   Policy CMP0053 is not set: Simplify variable reference and escape
> > > sequence
> > >   evaluation.  Run "cmake --help-policy CMP0053" for policy details.
> Use
> > > the
> > >   cmake_policy command to set the policy and suppress this warning.
> > >
> > >   For input:
> > >
> > >     '@GCC_INLINE_ASM_DEFINE@ -I${CMAKE_SOURCE_DIR}/include
> > > -DGMX_CPUID_STANDALONE'
> > >
> > >   the old evaluation rules produce:
> > >
> > >     '-DGMX_X86_GCC_INLINE_ASM
> > > -I/home/mohsen/Downloads/gromacs-4.6.7/include -DGMX_CPUID_STANDALONE'
> > >
> > >   but the new evaluation rules produce:
> > >
> > >     '@GCC_INLINE_ASM_DEFINE@
> > > -I/home/mohsen/Downloads/gromacs-4.6.7/include
> > > -DGMX_CPUID_STANDALONE'
> > >
> > >   Using the old result for compatibility since the policy is not set.
> > > Call Stack (most recent call first):
> > >   cmake/gmxDetectAcceleration.cmake:98 (gmx_suggest_x86_acceleration)
> > >   CMakeLists.txt:184 (gmx_detect_acceleration)
> > > This warning is for project developers.  Use -Wno-dev to suppress it.
> > >
> > >
> > >
> > >
> > > *and similar blocks like this again and again.*
> > >
> > >
> > > *it ends up with:*.
> > > .
> > > .
> > > -- [download 96% complete]
> > > -- [download 97% complete]
> > > -- [download 98% complete]
> > > -- [download 99% complete]
> > > -- [download 100% complete]
> > > -- Configuring done
> > > -- Generating done
> > > -- Build files have been written to:
> > > /home/mohsen/Downloads/gromacs-4.6.7/build
> > >
> > >
> > >
> > >
> > >
> > > *So, I use:*
> > > *make -j 16*
> > >
> > > *and I get lots of lines which end with:*
> > >
> > > .
> > > .
> > > .
> > > Making install in neon
> > > Making install in reodft
> > > Making install in api
> > >  /usr/bin/install -c -m 644
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/src/fftwBuild/api/fftw3.h
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/src/fftwBuild/api/fftw3.f
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/src/fftwBuild/api/fftw3l.f03
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/src/fftwBuild/api/fftw3q.f03
> > >
> > > '/home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/include'
> > >  /usr/bin/install -c -m 644 fftw3.f03
> > >
> > > '/home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/include'
> > > Making install in libbench2
> > > Making install in .
> > >  /bin/bash ./libtool   --mode=install /usr/bin/install -c
> libfftw3f.la
> > >
> > > '/home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/lib'
> > >  /usr/bin/install -c -m 644 fftw3f.pc
> > >
> > > '/home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/lib/pkgconfig'
> > > libtool: install: /usr/bin/install -c .libs/libfftw3f.lai
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/lib/
> > > libfftw3f.la
> > > libtool: install: /usr/bin/install -c .libs/libfftw3f.a
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/lib/libfftw3f.a
> > > libtool: install: chmod 644
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/lib/libfftw3f.a
> > > libtool: install: ranlib
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/lib/libfftw3f.a
> > > libtool: finish:
> > >
> > > PATH="/home/mohsen/bin:/home/mohsen/.local/bin:/usr/local/
> > sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/
> > games:/usr/local/games:/snap/bin:/sbin"
> > > ldconfig -n
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/lib
> > > ----------------------------------------------------------------------
> > > Libraries have been installed in:
> > >
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/lib
> > >
> > > If you ever happen to want to link against installed libraries
> > > in a given directory, LIBDIR, you must either use libtool, and
> > > specify the full pathname of the library, or use the `-LLIBDIR'
> > > flag during linking and do at least one of the following:
> > >    - add LIBDIR to the `LD_LIBRARY_PATH' environment variable
> > >      during execution
> > >    - add LIBDIR to the `LD_RUN_PATH' environment variable
> > >      during linking
> > >    - use the `-Wl,-rpath -Wl,LIBDIR' linker flag
> > >    - have your system administrator add LIBDIR to `/etc/ld.so.conf'
> > >
> > > See any operating system documentation about shared libraries for
> > > more information, such as the ld(1) and ld.so(8) manual pages.
> > > ----------------------------------------------------------------------
> > > Making install in threads
> > > Making install in tests
> > > Making install in mpi
> > > Making install in doc
> > > Making install in FAQ
> > >  /usr/bin/install -c -m 644
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/
> > > fftw3.info
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/fftw3.info-1
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/src/fftwBuild/doc/fftw3.info-2
> > >
> > > '/home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/share/info'
> > >  install-info
> > >
> > > --info-dir='/home/mohsen/Downloads/gromacs-4.6.7/build/
> > src/contrib/fftw/fftwBuild-prefix/share/info'
> > >
> > > '/home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/share/info/
> > > fftw3.info'
> > > Making install in tools
> > >  /usr/bin/install -c fftw-wisdom-to-conf
> > >
> > > '/home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/bin'
> > >   /bin/bash ../libtool   --mode=install /usr/bin/install -c
> fftwf-wisdom
> > >
> > > '/home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/bin'
> > >  /usr/bin/install -c -m 644
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/src/fftwBuild/tools/fftw-wisdom-to-conf.1
> > > fftwf-wisdom.1
> > >
> > > '/home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/share/man/man1'
> > > libtool: install: /usr/bin/install -c fftwf-wisdom
> > >
> > > /home/mohsen/Downloads/gromacs-4.6.7/build/src/
> > contrib/fftw/fftwBuild-prefix/bin/fftwf-wisdom
> > > Making install in m4
> > > [  1%] Completed 'fftwBuild'
> > > [  1%] Built target fftwBuild
> > > Makefile:160: recipe for target 'all' failed
> > > make: *** [all] Error 2
> > >
> > >
> > > *No idea why this is happening :-)*
> > >
> > > Based on this, I tried:
> > >
> > > export LD_LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/5
> > >
> > > But this did not solve the problem neither.
> > >
> > > Any suggestion is highly appreciated in advance.
> > >
> > > Cheers
> > > Mohsen
> > >
> > >
> > >
> > > --
> > > *Rewards work better than punishment ...*
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
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> > > posting!
> > >
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>
>
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