Re: [gmx-users] error sharing libraries...gromacs error
Hi, That command doesn't compile with the gcc compiler, does it? I already suggested what to do ;-) Mark On Tue, Sep 12, 2017 at 2:28 PM Vidya R wrote: > Hi, > > I now use > > export MPIRUN="/usr/mpi/gcc/openmpi-1.2.8/bin" > > But, how to fix that error? > > Thanks, > Vidya.R > > On Tue, Sep 12, 2017 at 5:42 PM, Mark Abraham > wrote: > > > Hi, > > > > If you're trying to use the PGI compilers, then please don't because the > > C++ performance is very poor. We recommend latest gcc or intel. > > > > Otherwise, configure GROMACS so that it uses the wrapper compilers when > > buildling, e.g. cmake -DCMAKE_C_COMPILER=mpicc > -DCMAKE_CXX_COMPILER=mpic++ > > etc. Organizing this stuff is their job. > > > > Mark > > > > On Tue, Sep 12, 2017 at 1:46 PM Vidya R wrote: > > > > > Hi, > > > > > > I give these commands > > > > > > PATH=$PATH:"/usr/local/gromacs/bin/" > > > export GMXLIB=/usr/local/gromacs/share/gromacs/top > > > export LD_LIBRARY_PATH=/usr/lib > > > export MPIRUN="/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun" > > > export > > > > > > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/ansys_inc/v140/CFX/ > > tools/icemcfd-12.0-post-3/lib/linux-amd64 > > > > > > > > > before these > > > > > > gmx grompp -f mdp/min.mdp -o min -pp min -po min > > > g_tune_pme -np 4 -s min.tpr -launch > > > > > > > > > > > > But, I am getting this error > > > > > > /usr/mpi/pgi/openmpi-1.2.8/bin/mpirun: error while loading shared > > > libraries: libpgc.so: cannot open shared object file: No such file or > > > directory > > > > > > > > > But libpgc.so is in > > > /usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64 > > > > > > What to do? > > > > > > Can someone help me with the commands? > > > > > > Thanks, > > > Vidya.R > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > posting! > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > * For (un)subscribe requests visit > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > -- > > Gromacs Users mailing list > > > > * Please search the archive at http://www.gromacs.org/ > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error sharing libraries...gromacs error
Hi, I now use export MPIRUN="/usr/mpi/gcc/openmpi-1.2.8/bin" But, how to fix that error? Thanks, Vidya.R On Tue, Sep 12, 2017 at 5:42 PM, Mark Abraham wrote: > Hi, > > If you're trying to use the PGI compilers, then please don't because the > C++ performance is very poor. We recommend latest gcc or intel. > > Otherwise, configure GROMACS so that it uses the wrapper compilers when > buildling, e.g. cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ > etc. Organizing this stuff is their job. > > Mark > > On Tue, Sep 12, 2017 at 1:46 PM Vidya R wrote: > > > Hi, > > > > I give these commands > > > > PATH=$PATH:"/usr/local/gromacs/bin/" > > export GMXLIB=/usr/local/gromacs/share/gromacs/top > > export LD_LIBRARY_PATH=/usr/lib > > export MPIRUN="/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun" > > export > > > > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/ansys_inc/v140/CFX/ > tools/icemcfd-12.0-post-3/lib/linux-amd64 > > > > > > before these > > > > gmx grompp -f mdp/min.mdp -o min -pp min -po min > > g_tune_pme -np 4 -s min.tpr -launch > > > > > > > > But, I am getting this error > > > > /usr/mpi/pgi/openmpi-1.2.8/bin/mpirun: error while loading shared > > libraries: libpgc.so: cannot open shared object file: No such file or > > directory > > > > > > But libpgc.so is in > > /usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64 > > > > What to do? > > > > Can someone help me with the commands? > > > > Thanks, > > Vidya.R > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] error sharing libraries...gromacs error
Hi, If you're trying to use the PGI compilers, then please don't because the C++ performance is very poor. We recommend latest gcc or intel. Otherwise, configure GROMACS so that it uses the wrapper compilers when buildling, e.g. cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpic++ etc. Organizing this stuff is their job. Mark On Tue, Sep 12, 2017 at 1:46 PM Vidya R wrote: > Hi, > > I give these commands > > PATH=$PATH:"/usr/local/gromacs/bin/" > export GMXLIB=/usr/local/gromacs/share/gromacs/top > export LD_LIBRARY_PATH=/usr/lib > export MPIRUN="/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun" > export > > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64 > > > before these > > gmx grompp -f mdp/min.mdp -o min -pp min -po min > g_tune_pme -np 4 -s min.tpr -launch > > > > But, I am getting this error > > /usr/mpi/pgi/openmpi-1.2.8/bin/mpirun: error while loading shared > libraries: libpgc.so: cannot open shared object file: No such file or > directory > > > But libpgc.so is in > /usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64 > > What to do? > > Can someone help me with the commands? > > Thanks, > Vidya.R > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] error sharing libraries...gromacs error
Hi, I give these commands PATH=$PATH:"/usr/local/gromacs/bin/" export GMXLIB=/usr/local/gromacs/share/gromacs/top export LD_LIBRARY_PATH=/usr/lib export MPIRUN="/usr/mpi/pgi/openmpi-1.2.8/bin/mpirun" export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64 before these gmx grompp -f mdp/min.mdp -o min -pp min -po min g_tune_pme -np 4 -s min.tpr -launch But, I am getting this error /usr/mpi/pgi/openmpi-1.2.8/bin/mpirun: error while loading shared libraries: libpgc.so: cannot open shared object file: No such file or directory But libpgc.so is in /usr/ansys_inc/v140/CFX/tools/icemcfd-12.0-post-3/lib/linux-amd64 What to do? Can someone help me with the commands? Thanks, Vidya.R -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
