On Tue, Mar 3, 2009 at 11:47 PM, Nicolas <nsa...@ucalgary.ca> wrote: > Manik Mayur a écrit : > >> Hi, >> >> If I have 2 mpi environments, namely LAM and openMPI, and I want gromacs >> to use openMPI of the two, what extra option should I pass during the >> ./configure step? In my case openMPI is installed locally(in my /home >> folder). >> > Sorry, I've misunderstood your message. Anyway, I would first check twice > the paths to the binaries in my script. Then, I would check my environment > variables, especially PATH, LD_LIBRARY_PATH and LD_RUN_PATH. You might need > to modify them to make sure any Lam-related stuff is loaded by default in > your environment. >
ok, is there any specific option or environment variable through which I can make gromacs aware of openMPI and not LAM while installation? If I carry on the default --enable-mpi thing, upon executing the following: $/home/openmpi/bin/mpirun -np 4 mdrun_mpi -s eql_mpi.tpr -o eql_mpi.trr I get the following error: ------------------------------------------------ It seems that there is no lamd running on this host, which indicates that the LAM/MPI runtime environment is not operating. The LAM/MPI runtime environment is necessary for MPI programs to run (the MPI program tired to invoke the "MPI_Init" function). Please run the "lamboot" command the start the LAM/MPI runtime environment. See the LAM/MPI documentation for how to invoke "lamboot" across multiple machines. ----------------------------------------------------------------------------- so it is like mdrun_mpi was configured with LAM and hence it is looking for it. I've tried to use a local installation of openMPI myself, but finally asked > my sysadmin to install it for all users. I had many problems with libraries > that couldn't be loaded properly. > > Cheers, > Nicolas > >> >> Thanks, >> Manik >> >> >> On Tue, Mar 3, 2009 at 10:58 PM, Nicolas <nsa...@ucalgary.ca <mailto: >> nsa...@ucalgary.ca>> wrote: >> >> Hi, >> >> As mentioned by the error message: >> >> >> Please run the "lamboot" command the start the LAM/MPI runtime >> >> Before using Lam, you have to boot it. In my scripts, I've got >> something like: >> >> lamboot -v $PBS_NODEFILE >> lamrun -v -np $NPROC mdrun mdargs >> lamhalt >> >> I don't use Lam often, though, you might need to use different Lam >> options. >> >> Nicolas >> >> Manik Mayur a écrit : >> >> Hi, >> >> I have till now successfully used openMPI and gromacs >> together. Recently I got a cluster where I tried to install >> openMPI and gromacs locally as I donot have root priviledges >> on it. But it turns out that it already has MPI environment on >> it (LAM) which I donot want to use (as the version is quite >> old.. the cluster still has gcc-3.2.3!). >> So after installing openMPI 1.3 and gromacs 4.0.4 on it (in my >> /home folder), I tried to execute: >> >> $/home/openmpi/bin/mpirun -np 4 mdrun_4_mpi -s eql_mpi.tpr -o >> eql_mpi.trr >> >> It gives the following error: >> >> >> >> ----------------------------------------------------------------------------- >> It seems that there is no lamd running on this host, which >> indicates >> that the LAM/MPI runtime environment is not operating. The >> LAM/MPI >> runtime environment is necessary for MPI programs to run (the MPI >> program tired to invoke the "MPI_Init" function). >> >> Please run the "lamboot" command the start the LAM/MPI runtime >> environment. See the LAM/MPI documentation for how to invoke >> "lamboot" across multiple machines. >> >> >> ----------------------------------------------------------------------------- >> >> My question is - Why it still tries to look for LAM >> environment or lamd? I will be extremely thankful if somebody >> gives a hint. >> >> -Manik >> -- Graduate student >> Microfluidics Lab >> Dept. of Mechanical Engg. >> IIT Kharagpur >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> Graduate student >> Microfluidics Lab >> Dept. of Mechanical Engg. >> IIT Kharagpur >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php >> > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Graduate student Microfluidics Lab Dept. of Mechanical Engg. IIT Kharagpur
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php