[gmx-users] Gromac4.6.7 installation problem

Mark Abraham mark.j.abraham at gmail.com
Fri Mar 3 08:20:03 CET 2017 

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 ...*
> --
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