[gmx-users] Problem configuring openMPI
Nicolas
nsapay at ucalgary.ca
Tue Mar 3 19:58:02 CET 2009
Manik Mayur a écrit :
>
>
> On Tue, Mar 3, 2009 at 11:47 PM, Nicolas <nsapay at ucalgary.ca
> <mailto:nsapay at 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\
CC=/path/to/gcc
CPPFLAGS=-I/path/to/fftw/include/\
LDFLAGS=-L/path/to/fftw/lib/
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 <nsapay at ucalgary.ca
> <mailto:nsapay at ucalgary.ca> <mailto:nsapay at ucalgary.ca
> <mailto:nsapay at 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
>
> ------------------------------------------------------------------------
>
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> --
> Graduate student
> Microfluidics Lab
> Dept. of Mechanical Engg.
> IIT Kharagpur
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>
> --
> Graduate student
> Microfluidics Lab
> Dept. of Mechanical Engg.
> IIT Kharagpur
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