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Re: How to start running Firefly on computer cluster?

Solntsev Pasha
solntsev@univ.kiev.ua


On our cluster i use this command (under pbs system):

export TMP_DIR=/mnt/work/solntsev/$PBS_JOBID
export FFHOME=/home/solntsev/bin
export WORK_DIR=$PBS_O_WORKDIR
export NCPUS=3 # total number of CPU!

mpirun -np $NCPUS $FFHOME/firefly -r -f -p -stdext -ex $FFHOME -i $WORK_DIR/job40.inp -o $WORK_DIR/job40.out -t $TMP_DIR

rm -rf $TMP_DIR

may be you also need add some library to the LD_LIBRARY_PATH.






On Fri Mar 5 '10 12:43pm, Olga wrote
------------------------------------
>Hi!
>I’m a student of Petrozavodsk University, and I use FF for my work. Now I have the opportunity to use computer cluster of Karelian Branch of RAS (http://cluster.krc.karelia.ru/http://cluster.krc.karelia.ru/) for my tasks. Cluster has 10 nodes, each of which has 2 CPU Quad-Core Intel Xeon 5430, OS - SuSE Linux Enterprise Server 10 with Cleo Job Manager. Number of nodes, free to use with Firefly, changes from run to run. I hope to use about 2-5 nodes. At the end of each run I must to delete "traces of my stay" on compute nodes.

>Please, help me to run my task for the first time. After studying tutorials I have made the following plan of starting. What you think about it?
>     Assume I have 2 nodes for my task (4 processors, 16 cores).
>a) I create 3 work directories – on master node and on each compute nodes with the same name, e. g. mywork/home_ff.
>b) Then I put into each of them FF binaries. Preliminary I copy corresponding file from BINDINGS folder into installation directory and rename it to mpibind.dll.
>Q.1: Here I have my first question: on the cluster there are the several mpi libraries, specifically, openmpi v. 1.3 (not v. 1.2!) and mvapich-1.1.0, mvapich2-1.2p1. What of them is better for using?
>Q.2: What dll from BINDINGS folder is suitable for OpenMPI?
>copy the appropriate dll from BINDINGS folder into the PC GAMESS installation directory and rename it to mpibind.dll
>c) After that I create a command line for FF run in batch_file placed in my_work/inputs directory where there is input file also:
>mpirun -np 4 /mywork/home_ff/pcgamess -r -f -p -i ./bench01.inp -o /my_work/outs/bench01.out -ex /mywork/home_ff -t /tmp/run_ff
>d) Finally I run batch_file from Cleo job manager…
>Q.3: What is incorrect here?
>Q.4: Is the np 4 parameter correctly set? Does FF use all 16 cores for calculation?
>Q.5: In what directory the -ex option copies the fastdiag.ex and pcgp2p.ex files? Into /tmp/run_ff?
>Q.6: If I'll receive for run one of nodes not entirely (but one processor only), what I should change in this case?
>Thanks in advance!

>


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