[gmx-users] Gromac4.6.7 installation problem
Mohsen Ramezanpour
ramezanpour.mohsen at gmail.com
Fri Mar 3 18:20:51 CET 2017
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
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
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> >
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> >
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