Re: [gmx-users] mpi enabled gromacs
Hi, I think you need to recompile your mpi library. See the "recompile with -fPIC"? You need to recompile your mpi library with that option. At least that is what I did last time when I install GROMACS. On Oct 22, 2012 5:04 PM, "Rajiv Gandhi" wrote: > Dear Gromacs users, > > I have been trying to install mpi enabled gromacs in my cluster. I have > followed the exact procedure which is described in gromacs manual by > giving following command line. > > ./configure --program-suffix=_mpi --enable-mpi > > I get only this following error after i command " make mdrun " > > usr/bin/ld: /home/rajiv/lam/lib/libmpi.a(csize.o): relocation R_X86_64_32 > against `lam_mpi_comm_world' can not be used when making a shared object; > recompile with -fPIC > /home/rajiv/lam/lib/libmpi.a: could not read symbols: Bad value > collect2: error: ld returned 1 exit status > mpicc: No such file or directory > make[2]: *** [libgmx_mpi.la] Error 1 > make[2]: Leaving directory `/home/rajiv/gromacs-4.5.5/src/gmxlib' > make[1]: *** [install-recursive] Error 1 > make[1]: Leaving directory `/home/rajiv/gromacs-4.5.5/src/gmxlib' > (cd ./src/mdlib && make install ; exit 0) > make[1]: Entering directory `/home/rajiv/gromacs-4.5.5/src/mdlib' > make[1]: *** No rule to make target `../gmxlib/libgmx_mpi.la', needed by ` > libmd_mpi.la'. Stop. > make[1]: Leaving directory `/home/rajiv/gromacs-4.5.5/src/mdlib' > (cd ./src/kernel && make install-libLTLIBRARIES ; exit 0) > make[1]: Entering directory `/home/rajiv/gromacs-4.5.5/src/kernel' > /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 > -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 > -funroll-all-loops -std=gnu99 -fexcess-precision=fast -no-undefined > -version-info 6:0:0 -L/home/rajiv/fftw/lib -o > libgmxpreprocess_mpi.la-rpath /home/rajiv/gmx/lib add_par.lo > compute_io.lo convparm.lo > fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo > gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo > readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo > topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo > vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm > libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or > unhandled > argument `../mdlib/libmd_mpi.la' > make[1]: *** [libgmxpreprocess_mpi.la] Error 1 > make[1]: Leaving directory `/home/rajiv/gromacs-4.5.5/src/kernel' > (cd ./src/kernel && make install-mdrun ; exit 0) > make[1]: Entering directory `/home/rajiv/gromacs-4.5.5/src/kernel' > /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 > -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 > -funroll-all-loops -std=gnu99 -fexcess-precision=fast -no-undefined > -version-info 6:0:0 -L/home/rajiv/fftw/lib -o > libgmxpreprocess_mpi.la-rpath /home/rajiv/gmx/lib add_par.lo > compute_io.lo convparm.lo > fflibutil.lo gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo > gpp_bond_atomtype.lo h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo > readir.lo readpull.lo resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo > topdirs.lo topexcl.lo topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo > vsite_parm.lo xlate.lo ../mdlib/libmd_mpi.la -lnsl -lm > libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or > unhandled > argument `../mdlib/libmd_mpi.la' > make[1]: *** [libgmxpreprocess_mpi.la] Error 1 > make[1]: Leaving directory `/home/rajiv/gromacs-4.5.5/src/kernel' > [root@masters gromacs-4.5.5]# > > > Please advice me how do i install mpi based gromacs without having any > error? Thanks in advance. > > > > Regards > > Rajiv > -- > 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] MPI installation
Hi, I had similar problem. Still did not manage to compile GROMACS with MPICH2 but OpenMPI works fine. You might want to try that instead. On Mon, Apr 9, 2012 at 11:11 AM, Mark Abraham wrote: > On 8/04/2012 12:41 PM, bharat gupta wrote: > > Hi, > > I am trying to enable mpi fro mdrun in an already installed gromacs-4.5.5. > > > Using a freshly unpacked tarball will eliminate some sources of problems. > Shouldn't be necessary, of course, but since nobody can warrant something > hasn't been broken accidentally... > > But while executing the command make mdrun , I am getting the following > errorn:- > mv -f .deps/xlate.Tpo .deps/xlate.Plo > /bin/sh ../../libtool --tag=CC --mode=link mpicc -O3 > -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 > -funroll-all-loops -std=gnu99 -fexcess-precision=fast -no-undefined > -version-info 6:0:0 -o libgmxpreprocess_mpi.la -rpath > /usr/local/gromacs/lib add_par.lo compute_io.lo convparm.lo fflibutil.lo > gen_ad.lo gen_vsite.lo genhydro.lo gpp_atomtype.lo gpp_bond_atomtype.lo > h_db.lo hackblock.lo hizzie.lo pdb2top.lo pgutil.lo readir.lo readpull.lo > resall.lo sorting.lo specbond.lo ter_db.lo tomorse.lo topdirs.lo topexcl.lo > topio.lo toppush.lo topshake.lo toputil.lo tpbcmp.lo vsite_parm.lo xlate.lo > ../mdlib/libmd_mpi.la -lnsl -lm > libtool: link: cannot find the library `../mdlib/libmd_mpi.la' or > unhandled argument `../mdlib/libmd_mpi.la' > make[1]: *** [libgmxpreprocess_mpi.la] Error 1 > make[1]: Leaving directory `/usr/local/gromacs-4.5.5/src/kernel' > > > The original error occurred earlier - this error is triggered by libmd not > being built earlier because of some other problem. > > > I used this command to configure , before issuing make mdrun : > ./configure --enable-mpi --program-suffix=_mpi --with-fft=fftw3. Also I > have mpich2 installed in my system. So, what could be reason for this error > ?? > > > Unknown at this stage. > > Mark > > -- > 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 > -- Regards, THChew -- 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] mpirun
Where did you install your Gromacs? Most likely the executables are not in the PATH. On Thu, Mar 29, 2012 at 5:09 PM, cuong nguyen wrote: > Dear Gromacs Users, > > as in the manual, I tried to run the simulation on 4 processors and used > the command as follow: > *mpirun -np 4 mdrun_mpi -s NVT_50ns -o NVT_50ns -c NVT_50ns.g96 -x > NVT_50ns -e NVT_50ns -g NVT_50ns -v* > > Then I got the error: > *mpirun was unable to launch the specified application as it could not > find an executable: > > Executable: mdrun_mpi* > Please help me to deal with this problem. > > Best regards, > > > Nguyen Van Cuong > PhD student - Curtin University of Technology > Mobile: (+61) 452213981 > > > > -- > 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 > -- Regards, THChew -- 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] Gromacs 4.5.5 GPU Error
Hi all, I am trying to get the GPU version of gromacs running. I manage to install OpenMM, compile and install mdrun-gpu. However when I ran mdrun-gpu on any of the benchmark files, I got this: ./run.sh: line 2: 14224 Floating point exception/usr/local/gromacs-4.5.5-cuda/bin/mdrun-gpu -v Any idea what goes wrong here? -- Regards, THChew -- 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
