[gmx-users] Gromacs installation fails in CentOS 6.5

Szilárd Páll pall.szilard at gmail.com
Sat Jul 8 00:53:17 CEST 2017 

Good that it worked out. You might have changes something in your
environment (path?) perhaps between last time and now.

On Fri, Jul 7, 2017 at 10:57 PM, Seyed Mostafa Razavi <sr87 at zips.uakron.edu>
wrote:

> Strangely enough, I could install this time,and I do not know why. I
> followed exact same procedure except running make VERBOSE=1
>
> Btw, here is the libgromacs_LIB_DEPENDS line in CMakeCache.txt if you want
> to know:
> libgromacs_LIB_DEPENDS:STATIC=general;/usr/lib64/libz.so;gen
> eral;dl;general;rt;general;m;general;gmxfftw;general;-lpthr
> ead;general;-fopenmp;
>

Yeah, that's what I was expecting to see there, so not sure what was wrong.


>
>
> S. Mostafa Razavi
> Graduate Research Assistant
> Molecular Simulation Lab
> Department of Chemical and Biomolecular Engineering
> The University of Akron, OH, USA
>
> On Fri, Jul 7, 2017 at 2:36 PM, Szilárd Páll <pall.szilard at gmail.com>
> wrote:
>
> > Strange. That means the GROAMCS build system somehow does not get the
> final
> > link command right. Without investigating deeper, I'm not sure what would
> > be the solution.
> >
> > I'd look a the actual link command that fails (make VERBOSE=1) and try to
> > see what and why is missing.
> >
> > BTW, cmake should know that libgromacs.so is linked against the OpenMP
> > library, can you check what's in the libgromacs_LIB_DEPENDS variable in
> > CMakeCache.txt?
> >
> >
> > --
> > Szilárd
> >
> > On Fri, Jul 7, 2017 at 8:13 PM, Seyed Mostafa Razavi <
> sr87 at zips.uakron.edu
> > >
> > wrote:
> >
> > > Here is what I did:
> > >
> > > $ gcc -o omp_helloc -fopenmp omp_hello.c
> > > $ ./omp_helloc
> > > Hello World from thread = 0
> > > Number of threads = 4
> > > Hello World from thread = 3
> > > Hello World from thread = 1
> > > Hello World from thread = 2
> > >
> > >
> > >
> > >
> > > Thank you,
> > >
> > > S. Mostafa Razavi
> > >
> > >
> > > On Fri, Jul 7, 2017 at 9:12 AM, Szilárd Páll <pall.szilard at gmail.com>
> > > wrote:
> > >
> > > > Hi,
> > > >
> > > > That looks weird. Can you compile a sample OpenMP code, e.g. this
> > > > https://computing.llnl.gov/tutorials/openMP/samples/C/omp_hello.c
> > > >
> > > > --
> > > > Szilárd
> > > >
> > > > On Fri, Jul 7, 2017 at 11:59 AM, Seyed Mostafa Razavi <
> > > > sr87 at zips.uakron.edu>
> > > > wrote:
> > > >
> > > > > Hello,
> > > > >
> > > > > I'm trying to install Gromacs (gromacs-2016.3) on my CentOS 6.5
> > > system. I
> > > > > exactly follow the installation instruction in
> > > > http://manual.gromacs.org/
> > > > > documentation/2016.3/install-guide/index.html. After I run "make",
> > the
> > > > > installation process starts and proceeds to %97, then it gives me
> an
> > > > error.
> > > > >
> > > > > [Ahmad at chem30 build]$ make
> > > > >
> > > > > .
> > > > > .(lots of output)
> > > > > .
> > > > >
> > > > > [ 97%] Building C object src/gromacs/CMakeFiles/
> > > > > libgromacs.dir/__/external/
> > > > > tng_io/src/lib/tng_io.c.o
> > > > > [ 97%] Building C object src/gromacs/CMakeFiles/
> > > > > libgromacs.dir/__/external/
> > > > > tng_io/src/lib/md5.c.o
> > > > > [ 97%] Building CXX object src/gromacs/CMakeFiles/
> > > > > libgromacs.dir/__/external/lmfit/lmmin.cpp.o
> > > > > [ 97%] Building C object src/gromacs/CMakeFiles/
> > > libgromacs.dir/utility/
> > > > > baseversion-gen.c.o
> > > > > [ 97%] Linking CXX shared library ../../lib/libgromacs.so
> > > > > [ 97%] Built target libgromacs
> > > > > Scanning dependencies of target template
> > > > > [ 97%] Building CXX object share/template/CMakeFiles/
> > > > > template.dir/template.cpp.o
> > > > > [ 97%] Linking CXX executable ../../bin/template
> > > > > ../../lib/libgromacs.so.2.3.0: undefined reference to
> `GOMP_parallel'
> > > > > collect2: error: ld returned 1 exit status
> > > > > make[2]: *** [bin/template] Error 1
> > > > > make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> > > > > make: *** [all] Error 2
> > > > >
> > > > > "make check" command gives me the following output:
> > > > >
> > > > > [Ahmad at chem30 build]$ make check
> > > > > Scanning dependencies of target mdrun_objlib
> > > > > [  0%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > > objlib.dir/mdrun/md.cpp.o
> > > > > [  0%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > > objlib.dir/mdrun/resource-division.cpp.o
> > > > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > > objlib.dir/mdrun/runner.cpp.o
> > > > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > > objlib.dir/mdrun/repl_ex.cpp.o
> > > > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > > objlib.dir/mdrun/mdrun.cpp.o
> > > > > [  1%] Building CXX object src/programs/CMakeFiles/mdrun_
> > > > > objlib.dir/mdrun/membed.cpp.o
> > > > > [  1%] Built target mdrun_objlib
> > > > > [  2%] Built target fftwBuild
> > > > > [ 87%] Built target libgromacs
> > > > > Scanning dependencies of target view_objlib
> > > > > [ 87%] Building CXX object src/programs/CMakeFiles/view_
> > > > > objlib.dir/view/view.cpp.o
> > > > > [ 87%] Built target view_objlib
> > > > > Scanning dependencies of target gmx
> > > > > [ 88%] Building CXX object src/programs/CMakeFiles/gmx.
> dir/gmx.cpp.o
> > > > > [ 88%] Building CXX object src/programs/CMakeFiles/gmx.
> > > > > dir/legacymodules.cpp.o
> > > > > [ 88%] Linking CXX executable ../../bin/gmx
> > > > > ../../lib/libgromacs.so.2.3.0: undefined reference to
> `GOMP_parallel'
> > > > > collect2: error: ld returned 1 exit status
> > > > > make[3]: *** [bin/gmx] Error 1
> > > > > make[2]: *** [src/programs/CMakeFiles/gmx.dir/all] Error 2
> > > > > make[1]: *** [CMakeFiles/check.dir/rule] Error 2
> > > > > make: *** [check] Error 2
> > > > >
> > > > >
> > > > > Here are some other information about my system:
> > > > >
> > > > > [Ahmad at chem30 Downloads]$ cat /etc/centos-release
> > > > > CentOS release 6.5 (Final)
> > > > >
> > > > > [Ahmad at chem30 Downloads]$ echo |cpp -fopenmp -dM |grep -i open
> > > > > #define _OPENMP 200805
> > > > >
> > > > >
> > > > > [Ahmad at chem30 Downloads]$ cmake --version
> > > > > cmake version 3.5.0
> > > > >
> > > > > [Ahmad at chem30 Downloads]$ gcc --version
> > > > > gcc (GCC) 5.3.1 20160406 (Red Hat 5.3.1-6)
> > > > > Copyright (C) 2010 Free Software Foundation, Inc.
> > > > > This is free software; see the source for copying conditions.
> There
> > is
> > > > NO
> > > > > warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
> > > > PURPOSE.
> > > > >
> > > > > ------------------------------------------------------------
> > > > > ------------------------
> > > > > Thank you,
> > > > > S. Mostafa Razavi
> > > > > --
> > > > > Gromacs Users mailing list
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