[gmx-users] Problem in mdrun_mpi using MPICH

[Alok]

Hello Dr. David,
                        Thanks for your kind reply. Can you guide me how 
can I compile it with MPICH, previously I used --enable mpi  flag for 
both fftw & groamacs 3.3.
Thanking you,
Best Regards,
Alok

David van der Spoel wrote:

>On Wed, 2005-10-19 at 18:55 +0530, Alok wrote:
>  
>
>>Greeting to All,
>>
>>sorry for very silly question.I have very limited knowledge of parallel
>>computing.
>>
>>I am trying to install parallel version of gromacs 3.3 in SUN Cluster.I
>>compiled  fftw,binutis & gromacs 3.3 without any error.
>>
>>MPICH was already installed on the SUN Cluster.
>>    
>>
>
>But you compiled it with LAM.
>
>That won't work. 
>
>  
>
>>when i run grompp_mpi for 2 node it ran fine and generated the *.tpr file
>>for two processors.
>>
>>But i tried to  mdrun_mpi -h it gave following message.
>>
>>-----------------------------------------------------------------------------
>>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.
>>-----------------------------------------------------------------------------
>>
>>
>>
>>Due to boundation of out computer center rules i could not use the
>>"lamboot" command. I have to submit the job by using following script
>>(provided by our system administrator)
>>
>>
>>
>>
>>---------------------------------------------------------------------------
>>
>>#!/bin/csh -f
>>#
>>#
>># (c) 2004 Sun Microsystems, Inc. Use is subject to license terms.
>>
>># ---------------------------
>># our name
>>#$ -N MPI_Job
>>#
>># pe request
>>#$ -pe mpich* 2-20
>>#
>># MPIR_HOME from submitting environment
>>#$ -v MPIR_HOME=/opt/mpichdefault-1.2.6
>># ---------------------------
>>
>>#
>># needs in
>>#   $NSLOTS
>>#       the number of tasks to be used
>>#   $TMPDIR/machines
>>#       a valid machine file to be passed to mpirun
>>
>>echo "Got $NSLOTS slots."
>>
>># enables $TMPDIR/rsh to catch rsh calls if available
>>set path=($TMPDIR $path)
>>
>>$MPIR_HOME/bin/mpirun -np $NSLOTS -machinefile $TMPDIR/machines -nolocal *
>>
>>---------------------------------------------------------------------------
>>
>>
>>and start the job by using following command.
>>qsub -pe mpichpar <no of nodes> -q par.q <script_name>
>>
>>where * is Path of the input file including parallel program name (in my
>>case it is /users/alokjain/mdrun_mpi -s full.tpr -o full -x full -c
>>after_full -e full -g full)
>>
>>but it is not recognizing the mdrun_mpi command.(I already set the path)
>>
>>can some one help me to overcome this problem?
>>Is there some problem in installation or in the script?
>>
>>Thanking you,
>>Best regards,
>>Alok Jain
>>
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>>    
>>

-- 
--------------------------------------------
Alok Jain
Graduate Student
C/o Dr. R. Sankararamakrishnan
Bioinformatics & Biomolecular Simulation Lab
Dept. of Biological Sciences & Bioengineering
Indian Institute of Technology,
Kanpur (U.P.)- India
Lab:- +91-512-259-4025
Cell:- 9415540594
http://www.iitk.ac.in/bsbe/
---------------------------------------------