[gmx-users] gromacs 4.6 installation error

Fri Feb 1 15:40:45 CET 2013

Hi,

make sure to run
source /opt/intel/bin/iccvars.sh intel64
before compiling.

Roland

On Fri, Feb 1, 2013 at 9:06 AM, Fernando Favela <ffavela at fis.cinvestav.mx>wrote:

> Hi justin,
>
> this is the other error message:
> [ 56%] Building C object src/mdlib/CMakeFiles/md.dir/genborn_allvsall.c.o
> [ 56%] [ 56%] [ 56%] Building C object
> src/mdlib/CMakeFiles/md.dir/mvxvf.c.o
> Building C object src/mdlib/CMakeFiles/md.dir/qm_mopac.c.o
> Building C object src/mdlib/CMakeFiles/md.dir/csettle.c.o
> Building C object src/mdlib/CMakeFiles/md.dir/ebin.c.o
> Building C object src/mdlib/CMakeFiles/md.dir/genborn.c.o
> [ 56%] Building C object
> src/mdlib/CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o
> ld: warning: libimf.so, needed by ../../src/gmxlib/libgmx.so.6, not found
> (try using -rpath or -rpath-link)
> ld: warning: libsvml.so, needed by ../../src/gmxlib/libgmx.so.6, not found
> (try using -rpath or -rpath-link)
> ld: warning: libirng.so, needed by ../../src/gmxlib/libgmx.so.6, not found
> (try using -rpath or -rpath-link)
> ld: warning: libintlc.so.5, needed by ../../src/gmxlib/libgmx.so.6, not
> found (try using -rpath or -rpath-link)
> [ 56%] Building C object src/mdlib/CMakeFiles/md.dir/pme.c.o
> ld: template: hidden symbol `__intel_cpu_indicator_init' in
> /opt/intel/composer_xe_2013.1.117/compiler/lib/intel64/libirc.a(cpu_disp.o)
> is referenced by DSO
> ld: final link failed: Bad value
> make[2]: *** [share/template/template] Error 1
> make[1]: *** [share/template/CMakeFiles/template.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs….
>
> then
> ...
> [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o
> [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o
> Linking CXX shared library libmd.so
> [ 65%] Built target md
> make: *** [all] Error 2
>
> That's all.
>
> Thanks,
>
> Fernando.
>
> On Feb 1, 2013, at 7:38 AM, Justin Lemkul wrote:
>
> >
> >
> > On 2/1/13 8:35 AM, Fernando Favela wrote:
> >> Dear Mark Abraham,
> >>
> >> without the sudo, the problem is still there:
> >> ...
> >> …
> >> ...
> >> [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/ewald.c.o
> >> [ 65%] Building C object src/mdlib/CMakeFiles/md.dir/calcvir.c.o
> >> Linking CXX shared library libmd.so
> >> [ 65%] Built target md
> >> make: *** [all] Error 2
> >>
> >> It could be possible that after a previous gromacs installation
> (removed) there's still a linked library or something?
> >>
> >
> > Not likely, but you still haven't posted the original error.  Error 2
> says that somewhere higher up there is an Error 1.  We need that
> information.
> >
> > -Justin
> >
> >> Thanks in advance.
> >>
> >> Fernando.
> >>
> >> On Feb 1, 2013, at 2:11 AM, Mark Abraham wrote:
> >>
> >>> On Fri, Feb 1, 2013 at 2:18 AM, Fernando Favela <
> ffavela at fis.cinvestav.mx>wrote:
> >>>
> >>>> Dear Gromacs users,
> >>>>
> >>>> I'm trying to install GMX 4.6 in a 64 Bit Machine with Nvidia GTX 680
> >>>> cards, I've already installed the intel compilers, cuda 5 and openmpi.
> >>>>
> >>>> I do the following procedure:
> >>>> CC=/opt/intel/bin/icc CXX=/opt/intel/bin/icpc cmake ..
> >>>>
> >>>> then
> >>>>
> >>>> sudo make -j 12
> >>>>
> >>>
> >>> Don't use sudo before make. Consider using sudo before "make install",
> per
> >>> the installation instructions.
> >>>
> >>> There's no error message in the output file you posted. I suspect you
> might
> >>> running "sudo make", and then "make" and running into file permissions
> >>> problems because of it. Remove your whole build directory (which will
> >>> probably need sudo) and start again.
> >>>
> >>> Mark
> >>>
> >>>
> >>>>
> >>>> and I get this error:
> >>>>
> >>>> Linking CXX shared library libmd.so
> >>>> cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib &&
> >>>> /usr/bin/cmake -E cmake_link_script CMakeFiles/md.dir/link.txt
> --verbose=1
> >>>> /opt/intel/bin/icpc -fPIC -mavx -Wall -ip -funroll-all-loops -O3
> -DNDEBUG
> >>>> -shared -Wl,-soname,libmd.so.6 -o libmd.so.6
> >>>> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_gpu_ref.c.o
> >>>> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_4xn.c.o
> >>>> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_common.c.o
> >>>> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_simd_2xnn.c.o
> >>>> CMakeFiles/md.dir/nbnxn_kernels/nbnxn_kernel_ref.c.o
> >>>> CMakeFiles/md.dir/genborn_allvsall.c.o CMakeFiles/md.dir/qm_mopac.c.o
> >>>> CMakeFiles/md.dir/mvxvf.c.o CMakeFiles/md.dir/genborn.c.o
> >>>> CMakeFiles/md.dir/ebin.c.o CMakeFiles/md.dir/csettle.c.o
> >>>> CMakeFiles/md.dir/genborn_allvsall_sse2_single.c.o
> >>>> CMakeFiles/md.dir/pme.c.o CMakeFiles/md.dir/gmx_fft.c.o
> >>>> CMakeFiles/md.dir/force.c.o CMakeFiles/md.dir/qm_gaussian.c.o
> >>>> CMakeFiles/md.dir/qm_orca.c.o CMakeFiles/md.dir/mdatom.c.o
> >>>> CMakeFiles/md.dir/stat.c.o CMakeFiles/md.dir/perf_est.c.o
> >>>> CMakeFiles/md.dir/domdec_network.c.o CMakeFiles/md.dir/pme_pp.c.o
> >>>> CMakeFiles/md.dir/calcmu.c.o CMakeFiles/md.dir/shakef.c.o
> >>>> CMakeFiles/md.dir/fft5d.c.o CMakeFiles/md.dir/tables.c.o
> >>>> CMakeFiles/md.dir/qmmm.c.o CMakeFiles/md.dir/domdec_con.c.o
> >>>> CMakeFiles/md.dir/clincs.c.o CMakeFiles/md.dir/domdec_setup.c.o
> >>>> CMakeFiles/md.dir/gmx_wallcycle.c.o
> CMakeFiles/md.dir/gmx_fft_fftw3.c.o
> >>>> CMakeFiles/md.dir/partdec.c.o CMakeFiles/md.dir/domdec.c.o
> >>>> CMakeFiles/md.dir/genborn_allvsall_sse2_double.c.o
> >>>> CMakeFiles/md.dir/md_support.c.o CMakeFiles/md.dir/vsite.c.o
> >>>> CMakeFiles/md.dir/groupcoord.c.o CMakeFiles/md.dir/mdebin.c.o
> >>>> CMakeFiles/md.dir/gmx_fft_fftpack.c.o CMakeFiles/md.dir/tgroup.c.o
> >>>> CMakeFiles/md.dir/vcm.c.o CMakeFiles/md.dir/nsgrid.c.o
> >>>> CMakeFiles/md.dir/nbnxn_search.c.o CMakeFiles/md.dir/constr.c.o
> >>>> CMakeFiles/md.dir/shellfc.c.o
> CMakeFiles/md.dir/iteratedconstraints.c.o
> >>>> CMakeFiles/md.dir/rf_util.c.o CMakeFiles/md.dir/update.c.o
> >>>> CMakeFiles/md.dir/genborn_sse2_double.c.o
> CMakeFiles/md.dir/forcerec.c.o
> >>>> CMakeFiles/md.dir/nbnxn_atomdata.c.o
> >>>> CMakeFiles/md.dir/genborn_sse2_single.c.o
> CMakeFiles/md.dir/gmx_fft_mkl.c.o
> >>>> CMakeFiles/md.dir/pull.c.o CMakeFiles/md.dir/domdec_box.c.o
> >>>> CMakeFiles/md.dir/domdec_top.c.o CMakeFiles/md.dir/mdebin_bar.c.o
> >>>> CMakeFiles/md.dir/nlistheuristics.c.o CMakeFiles/md.dir/qm_gamess.c.o
> >>>> CMakeFiles/md.dir/coupling.c.o CMakeFiles/md.dir/adress.c.o
> >>>> CMakeFiles/md.dir/init.c.o CMakeFiles/md.dir/wnblist.c.o
> >>>> CMakeFiles/md.dir/expanded.c.o CMakeFiles/md.dir/wall.c.o
> >>>> CMakeFiles/md.dir/ns.c.o CMakeFiles/md.dir/minimize.c.o
> >>>> CMakeFiles/md.dir/sim_util.c.o CMakeFiles/md.dir/pullutil.c.o
> >>>> CMakeFiles/md.dir/gmx_parallel_3dfft.c.o CMakeFiles/md.dir/edsam.c.o
> >>>> CMakeFiles/md.dir/pull_rotation.c.o CMakeFiles/md.dir/gmx_fft_acml.c.o
> >>>> CMakeFiles/md.dir/tpi.c.o CMakeFiles/md.dir/ewald.c.o
> >>>> CMakeFiles/md.dir/calcvir.c.o nbnxn_cuda/libnbnxn_cuda.a
> >>>> ../gmxlib/libgmx.so.6 /usr/lib/libblas.so.3gf
> /usr/lib/liblapack.so.3gf
> >>>> /usr/lib/libblas.so.3gf -ldl -lm -lfftw3f -openmp
> /usr/lib/liblapack.so.3gf
> >>>> -ldl -lm -lfftw3f ../gmxlib/gpu_utils/libgpu_utils.a
> >>>> ../gmxlib/cuda_tools/libcuda_tools.a
> /usr/local/cuda/lib64/libcudart.so
> >>>> -lcuda -lpthread
> >>>>
> -Wl,-rpath,/home/ffavela/Downloads/gromacs-4.6/build-cmake/src/gmxlib:/usr/local/cuda/lib64:
> >>>> cd /home/ffavela/Downloads/gromacs-4.6/build-cmake/src/mdlib &&
> >>>> /usr/bin/cmake -E cmake_symlink_library libmd.so.6 libmd.so.6 libmd.so
> >>>> make[2]: Leaving directory
> >>>> `/home/ffavela/Downloads/gromacs-4.6/build-cmake'
> >>>> /usr/bin/cmake -E cmake_progress_report
> >>>> /home/ffavela/Downloads/gromacs-4.6/build-cmake/CMakeFiles 89 90 91
> 92 93
> >>>> 94 95 96 97
> >>>> [ 65%] Built target md
> >>>> make[1]: Leaving directory
> >>>> `/home/ffavela/Downloads/gromacs-4.6/build-cmake'
> >>>> make: *** [all] Error 2
> >>>>
> >>>> I think this issue must be related with the compilers because if I
> use the
> >>>> default gnu compilers the problem disappear.
> >>>>
> >>>> Could anybody help me please?
> >>>>
> >>>> Thanks in advance.
> >>>>
> >>>> Fernando.
> >>>>
> >>>> NOTE: after an eventual successful installation, where can I find
> >>>> information of how to get the benefits of gromacs-gpu? --
> >>>> gmx-users mailing list    gmx-users at gromacs.org
> >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>>> * Please search the archive at
> >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>>> * Please don't post (un)subscribe requests to the list. Use the
> >>>> www interface or send it to gmx-users-request at gromacs.org.
> >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>>>
> >>> --
> >>> gmx-users mailing list    gmx-users at gromacs.org
> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users
> >>> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> >>> * Please don't post (un)subscribe requests to the list. Use the
> >>> www interface or send it to gmx-users-request at gromacs.org.
> >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >>
> >
> > --
> > ========================================
> >
> > Justin A. Lemkul, Ph.D.
> > Research Scientist
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
>
>
>
>

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