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 <[email protected]>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 [email protected]
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 [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list [email protected]
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 [email protected].
* 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 [email protected]
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 [email protected].
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
