[gmx-users] Problem configuring openMPI

[Manik Mayur]

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).

Thanks,
Manik

On Tue, Mar 3, 2009 at 10:58 PM, Nicolas <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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