bsub
an example of job script job.sh
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#!/bin/bash
#BSUB -J HS[1-96] # job name in a job array, needs to start from 1
#BSUB -n 1 # use 1 node
#BSUB -W 24:00 # wall time 24 hours
#BSUB -o job.out # output job status; otherwise will be sent to email
cd $PWD
# run the command
./exe > output
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bsub bash job.sh
job arrays
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#!/bin/bash
#BSUB -J HS[1-96] # job name in a job array, needs to start from 1
#BSUB -n 1 # use 1 node
#BSUB -W 24:00 # wall time 24 hours
#BSUB -o job.out # output job status; otherwise will be sent to email
cd $PWD
# run the command
sed -n "${LSB_JOBINDEX}p" TaskList | /bin/bash
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where TaskList contains lines of executive command ./HSMD jobnumber
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./HSMD 0 >> outputHS_0
./HSMD 1 >> outputHS_1
./HSMD 2 >> outputHS_2
./HSMD 3 >> outputHS_3
... ... ... ...
./HSMD 94 >> outputHS_94
./HSMD 95 >> outputHS_95
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# submit jobs
bsub < job.sh
-q gerstein
-q interactive
-q shared
-q long
# monitor jobs
bjobs
bjobs -A
bjobs -l jobid # job details
bjobs -u all
JOBID USER STAT QUEUE FROM_HOST EXEC_HOST JOB_NAME SUBMIT_TIME
13606 vaccaro RUN long grace0 20*c04n08 *DZ_OptNO2 Jun 15 02:52
15856 yc467 RUN shared grace0 c02n12 *0142_2_00 Jun 18 02:22
15881 yc467 RUN shared grace0 c02n12 *0002_1_00 Jun 18 03:30
... ... ... ...
qstat
# delete jobs
bkill jobid
bqueues # list of queues available on the cluster
QUEUE_NAME PRIO STATUS MAX JL/U JL/P JL/H NJOBS PEND RUN SUSP
gerstein 100 Open:Active 80 - - - 0 0 0 0
interactive 30 Open:Active - 1 - - 0 0 0 0
shared 20 Open:Active - - - - 10253 9022 1231 0
long 10 Open:Active 160 20 - - 46 0 46 0
bqueues -l
blimits
lshosts # list of cluster resources
HOST_NAME type model cpuf ncpus maxmem maxswp server RESOURCES
mgt1 X86_64 Intel_EM 60.0 8 63.9G 7.9G Yes (mg)
c06n12 X86_64 Intel_EM 60.0 20 127.9G 3.9G Yes ()
c06n11 X86_64 Intel_EM 60.0 20 127.9G 3.9G Yes ()
c01n01 X86_64 Intel_EM 60.0 20 127.9G 3.9G Yes (mg)
c01n02 X86_64 Intel_EM 60.0 20 127.9G 3.9G Yes ()
... ... ... ...
c06n09 X86_64 Intel_EM 60.0 20 127.9G 3.9G Yes ()
c06n10 X86_64 Intel_EM 60.0 20 127.9G 3.9G Yes ()
grace0 X86_64 Intel_EM 60.0 - - - No ()
grace1 X86_64 Intel_EM 60.0 - - - No ()
columbus X86_64 Intel_EM 60.0 - - - No ()