[gmx-users] Fw: About MPIRUN (Chuanjie Wu) Errors

[David]

On Fri, 2005-05-27 at 09:01 +0800, chuanjiewu at 126.com wrote:
> 
>  
> Hi, 
>  
> I have lamboot our Cluster with
>  
> lamboot -v hostfile
>  
> Then the job as follows works on distributed computer nodes:
>  
> $HOME/grotest/bin/grompp_mpi -np 9 -shuffle -sort -v -f full -o full -
> c after_pr -p speptide >& grompp.info &
> $MPI_DIR/bin/mpirun n0-8 /home/test0/grotest/bin/mdrun_mpi -v -s full
> -o full -c after_full -g speptide.log >& pro.info &
> 
> However, if I use the following commands:
>  
> $MPI_DIR/bin/mpirun -np 9 /home/test0/grotest/bin/mdrun_mpi -v -s full
> -o full -c after_full -g speptide.log >& pro.info &
> 
> An error will prompt as:
>  
> -----------------------------------------------------------------------------
> The selected RPI failed to initialize during MPI_INIT.  This is a
> fatal error; I must abort.
>  
> This occurred on host compute-0-0.local (n1).
> The PID of failed process was 29396 (MPI_COMM_WORLD rank: 2)
> -----------------------------------------------------------------------------
> -----------------------------------------------------------------------------
> One of the processes started by mpirun has exited with a nonzero exit
> code.  This typically indicates that the process finished in error.
> If your process did not finish in error, be sure to include a "return
> 0" or "exit(0)" in your C code before exiting the application.
>  
> PID 4448 failed on node n0 (202.120.51.87) with exit status 1.
> -----------------------------------------------------------------------------
> 
> The difference between the two commands is that "n0-8" was changed
> into "-np 9".
This is a LAM issue. Basically they changed the syntax for mpirun.

> I have tested the command with "n0-x" by changing the nodes number,
> and I did not find the parallel brought faster calculation than the
> unparalleled jobs.
Depends on your job size and run parameters.


>  
> I wonder what is the problem?
>  
> Best wishes,
>  
> Chuanjie Wu
>  
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++