[gmx-users] Gromac4.6.7 installation problem

[Mohsen Ramezanpour]

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 ...*