How to run the PC GAMESS/Firefly in parallel - Linux/MPICH case:

To run Linux/MPICH version of the PC GAMESS/Firefly in parallel you'll need:

How to run the PC GAMESS/Firefly in parallel?

Create or procgrp file that is suitable for your environment. Please read the MPICH documentation for information on how this file should be organized. This file must reside on the computer where the master PC GAMESS/Firefly copy will run.

The simplest command line for the parallel PC GAMESS/Firefly run is as follows:

      ./pcgamess DIR0 DIR1 DIR2 ... DIRN < MPICH options >

Here, DIR0, DIR1, DIR2, etc... are the working directories of the master PC GAMESS/Firefly process (i.e., of MPI RANK=0), second instance of PC GAMESS/Firefly (MPI RANK=1), third instance, and so on. Only absolute paths are allowed.

< MPICH options > are the optional MPICH-specific options (see MPICH documentation for the list).

For example, you can use something like following:

      ./pcgamess /home/me/mydir/wrk0 /home/me/mydir/wrk1 "/home/me/my dir/wrk2" -p4pg /home/me/procgrp

Depending on the cluster topology used, the three directories above must exist prior to PC GAMESS/Firefly execution either on the single computer, two different computers, or three different computers. The input file must be in the master working directory (i.e., in the /home/me/mydir/wrk0 for the example above).

Alternatively, instead of creation of custom procgrp files and passing them as an argument directly to the PC GAMESS/Firefly binaries, you can use the mpirun command to launch the PC GAMESS/Firefly in parallel.

Assume you have two nodes, e.g., node pb1 (master node) and node pb2 (slave). Assume you want to use /scratch/pcgamess on pb1 and /tmp/pcgamess on pb2 to store temporary working files, and on both systems the PC GAMESS/Firefly binaries reside in /home/peter/bin (with /home most likely being mounted via NFS or so on both systems).

Then you should:

  1. Put input file into the /scratch/pcgamess on pb1

  2. Put fastdiag.ex, pcgp2p.ex, and p4stuff.ex (if any) into /scratch/pcgamess on pb1 and into /tmp/pcgamess on pb2

  3. Run pc gamess from pb1 by either typing:

       mpirun -np 2 /home/peter/bin/pcgamess /scratch/pcgamess /tmp/pcgamess

    to get output on stdout, or

       mpirun -np 2 /home/peter/bin/pcgamess -o /home/peter/test.out /scratch/pcgamess /tmp/pcgamess

    to redirect output into the /home/peter/test.out on pb1

    Another way is:

       /home/peter/bin/pcgamess -o /home/peter/test.out /scratch/pcgamess /tmp/pcgamess -p4pg /home/peter/procgrp

    with /home/peter/procgrp file like this (assuming pb1 is a master):

    local 0
    pb2   1 /home/peter/bin/pcgamess

A couple of useful hints

Known issues and problems

  1. While running PC GAMESS/Firefly in parallel using standalone SMP system, the performance degradation is possible because of simultaneous I/O operations. In this case, the use of high-quality RAID or separate physical disks can help. If the problem persist, for dual- (and more, 4, 8, for example)-CPUs/cores SMP/multicore systems the better solution is probably to switch to the direct computation methods which require much less disk I/O.

  2. The default value for AOINTS is DUP. It is probably optimal for low-speed networks (10 and 100 Mbps Ethernet). On the other hand, for faster networks and SMP systems the optimal value could be AOINTS=DIST. You can change the default by using the AOINTS keyword in the $SYSTEM group. So, you can check what is the faster way for your systems.

  3. There are four keywords in the $SYSTEM group which can help in the case of MPI-related problems. Do not modify the default values unless you are absolutely sure that you need to do this. They are as follows:

            MXBCST (integer) - the maximum size (in DP words) of the message
                               used in broadcast operation. Default is 32768.
                               You can change it to see whether this helps
            MPISNC (logical) - activates the strategy when the call of the
                               broadcast operation will periodically
                               synchronize all MPI processes, thus freeing
                               wp4 global memory pool.
                               Default is false. Setting it to true should
                               resolve most buffer-overflow problems by the
                               cost of somewhat reduced performance.
            MXBNUM (integer) - the maximum number of broadcast operations
                               which can be performed before the global
                               synchronization call is done.
                               Relevant if MPISNC=.true. Default is 100.
            LENSNC (integer) - the maximum total length (in DP words) of all
                               messages which can be broadcasted before the
                               global synchronization call is done.
                               Relevant if MPISNC=.true. Default is dependent
                               on the number of processes used (meaningful values
                               vary from 20000 to, say, 262144 or even more).

See also:

Last updated: March 18, 2009