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 <[email protected]>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 < > [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 > > -- > 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 > > > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- 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
