[gmx-users] Problem configuring openMPI

Nicolas nsapay at ucalgary.ca
Tue Mar 3 18:28:56 CET 2009


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 

    lamboot -v $PBS_NODEFILE
    lamrun -v -np $NPROC mdrun mdargs

I don't use Lam often, though, you might need to use different Lam options.


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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