Re: [gmx-users] Error in Installing gromacs4.6.3 with mpi
No idea if it's causing your problem, but you need all the Ds in -DBUILD_SHARED_LIBS=no Mark On Wed, Sep 11, 2013 at 6:15 AM, Qin Qiao qiaoqi...@gmail.com wrote: Dear all, I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster and got the following error in step 'make': /usr/bin/ld: /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation R_X86_64_32 against `.bss' can not be used when making a shared object; recompile with -fPIC /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a: could not read symbols: Bad value I was using command cmake ../ -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/.../gromacs-4.6.3/ -DGMX_BUILD_OWN_FFTW=ON -BUILD_SHARED_LIBS='no' and I thought the mvapich is compiled with --enable-shared... Could you give me some advice if possible? Thanks in advance. Best Qin -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Error in Installing gromacs4.6.3 with mpi
On Wed, Sep 11, 2013 at 3:08 PM, Mark Abraham mark.j.abra...@gmail.comwrote: No idea if it's causing your problem, but you need all the Ds in -DBUILD_SHARED_LIBS=no Mark On Wed, Sep 11, 2013 at 6:15 AM, Qin Qiao qiaoqi...@gmail.com wrote: Dear all, I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster and got the following error in step 'make': /usr/bin/ld: /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation R_X86_64_32 against `.bss' can not be used when making a shared object; recompile with -fPIC /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a: could not read symbols: Bad value I was using command cmake ../ -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/.../gromacs-4.6.3/ -DGMX_BUILD_OWN_FFTW=ON -BUILD_SHARED_LIBS='no' Thanks, Mark! I get to know -D is a must for cmake to define variables. Best Qin and I thought the mvapich is compiled with --enable-shared... Could you give me some advice if possible? Thanks in advance. Best Qin -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Error in Installing gromacs4.6.3 with mpi
Dear all, I'm trying to install gromacs4.6.3 with mvapich2-1.9a on a local cluster and got the following error in step 'make': /usr/bin/ld: /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a(mvapich_malloc.o): relocation R_X86_64_32 against `.bss' can not be used when making a shared object; recompile with -fPIC /usr/local/mvapich2-1.9a-gcc/lib/libmpich.a: could not read symbols: Bad value I was using command cmake ../ -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=/.../gromacs-4.6.3/ -DGMX_BUILD_OWN_FFTW=ON -BUILD_SHARED_LIBS='no' and I thought the mvapich is compiled with --enable-shared... Could you give me some advice if possible? Thanks in advance. Best Qin -- gmx-users mailing listgmx-users@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-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
