[gmx-users] Problem configuring openMPI

[Nicolas]

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.

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>> 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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