On Tue, Mar 3, 2009 at 11:47 PM, Nicolas <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:
$/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>> 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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>
>
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--
Graduate student
Microfluidics Lab
Dept. of Mechanical Engg.
IIT Kharagpur
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