[gmx-users] Problem configuring openMPI

Manik Mayur manik.mayur at gmail.com
Tue Mar 3 19:36:28 CET 2009 

On Tue, Mar 3, 2009 at 11:47 PM, Nicolas <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:

     $/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>> 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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>>
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>>
>>
>>
>> --
>> Graduate student
>> Microfluidics Lab
>> Dept. of Mechanical Engg.
>> IIT Kharagpur
>> ------------------------------------------------------------------------
>>
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>
>
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-- 
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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