If there any possibility to support IBM LSF system?

[crazyzlj]

Hi,
I have developed my algorithm using DEAP with SCOOP and tested on our little cluster using PBS system. Now, I want to run on our big cluster which installed IBM LSF. Since I cannot specify the accessible hosts, I found SCOOP cannot detect the LSF system.
Then, I found the following instruction.

SCOOP natively supports Sun Grid Engine (SGE), Torque (PBS-compatible, Moab, Maui) and SLURM. That means that a minimum launch file is needed while the framework recognizes automatically the nodes assigned to your task.

So, I wonder if there any possibility to support IBM LSF system?

Thank you very much!

[crazyzlj]

After some try-and-trial, finally, I find out the solution. The key point is creating hostfile dynamically.
Here is the step-by-step and hope it helpful for others.

• Create a job script file deap_scoop_lsf_demo.lsf.

#!/bin/sh
#BSUB -J TEST_SCOOP
#BSUB -q rhel6normal

source ~/.bash_profile
# Path to executable
cd /wps/home/zhulj/demo/scoop_test
# Add local python installation paht
export PATH=/home/zhulj/soft/python-2.7.13/bin:$PATH
# start a new host file from scratch
SCOOPHOST_FILE=hosts_$LSB_JOBID
rm -f $SCOOPHOST_FILE
touch $SCOOPHOST_FILE
echo "# SCOOP hostfile created by LSF on `date`"
# check if we were able to start writing the conf file
if [ -f $SCOOPHOST_FILE ]; then
    :
else
    echo "$0: can't create $SCOOPHOST_FILE"
    exit 1
fi
HOST=""
NUM_PROC=""
FLAG=""
TOTAL_CPUS=0
for TOKEN in $LSB_MCPU_HOSTS
    do
        if [ -z "$FLAG" ]; then # -z means string is empty
            HOST="$TOKEN"
            FLAG="0"
        else
            NUM_PROC="$TOKEN"
            FLAG="1"
        fi
        if [ "$FLAG" = "1" ]; then
            _x=0
            if [ $_x -lt $NUM_PROC ]; then
                TOTAL_CPUS=`expr "$TOTAL_CPUS" + "$NUM_PROC"`
                echo "$HOST $NUM_PROC" >> $SCOOPHOST_FILE
            fi
            # get ready for the next host
            FLAG=""
            HOST=""
            NUM_PROC=""
        fi
    done
echo "Your SCOOP boot hostfile looks like:"
echo "TOTAL_CPUS: ${TOTAL_CPUS}"
# Python script
script=onemax_island_scoop.py
# SCOOP command
python -m scoop --debug --hostfile $SCOOPHOST_FILE $script > testscoop_$LSB_JOBID.stdout.log

• cd to the directory of deap_scoop_lsf_demo.lsf.
• Submit job by bsub with the specification of processor number.

  $ bsub -n 48 ./deap_scoop_lsf_demo.lsf

The hostfile created is something like this. Be caution, no other lines should be existed in this file.

b10n07.cluster.com 12
b06n03.cluster.com 12
b07n12.cluster.com 8
b07n06.cluster.com 12
b07n03.cluster.com 4

[louisabraham]

It would still be great to support LSF! Can this issue be reopened?

[crazyzlj]

It would still be great to support LSF! Can this issue be reopened?

Currently, the above solution I posted can work. It would be great if SCOOP can support LSF natively.