On Wed, Mar 4, 2009 at 12:28 AM, Nicolas <nsa...@ucalgary.ca> wrote: > Manik Mayur a écrit : > >> >> >> On Tue, Mar 3, 2009 at 11:47 PM, Nicolas <nsa...@ucalgary.ca <mailto: >> 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: >> > Just a silly question: Did you recompile Gromacs with openMPI? If not, you > should with the correct CPPFLAGS, LDFLAGS and MPICC. Typically, you should > have something like: > > ./configure\ > --prefix /home/local/gromacs\ > --enable-mpi\ > --program-suffix="_mpi"\ > --without-x\ > --disable-nice\ > MPICC=/path/to/mpicc\
thanks, I think that is what I needed. Let me try and then I will let you know. > CC=/path/to/gcc > CPPFLAGS=-I/path/to/fftw/include/\ > LDFLAGS=-L/path/to/fftw/lib/ > Why is FFTW necessary? In all my gromacs installations till now, I have avoided this package (out of ignorance). > mpicc is located in the bin/ directory of openMPI. gcc is the regular gcc > installation (gcc 3). As I said, your issue is probably due to a path > uncorrectly pointing to Lam. So check/modify your environment variables, > especially the paths to loaded libraries. > > >> $/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> <mailto: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> >> <mailto: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> >> <mailto: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> >> <mailto: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> >> <mailto: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 >> <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
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