Simcenter_clusters_excises

Tutorials and training excises for using simcenter clusters

ts117 job runs

ssh [email protected]

$ module load sge
$ qsub *.pbs

HaoboGuo: You can also use
$ qavail #For available cores
$ qatatus -all #For checking status of running jobs, etc.

If you are using GPU and hope the entire node is used for your job (1 GPU+27CPU), you can use
$ qsub -excl=true job.pbs

sample PBS for R

-bash-4.2$ cat ts_yeastPIN_job1.pbs
#!/bin/bash -l
#$ -S /bin/bash
#$ -N yPIN.Dang.001.col4
#$ -cwd
. /etc/profile.d/modules.sh
module load shared
module load R/3.4.3
cmd="R -f yeast_Zscore_GO-DangCR.R"
$cmd

sample PBS with taks ID

#!/bin/bash -l
#$ -S /bin/bash
#$ -N somejobs
#$ -cwd
#$ -t 1-100
. /etc/profile.d/modules.sh
module load shared
cmd=" somecommand $SGE_TASK_ID "
$cmd

sample PBS for Python Anaconda (Enviroment 'grib' is Hong Qin's enviroment for PyGRIB

#!/bin/bash -l
#$ -S /bin/bash
#$ -N somejobs
#$ -cwd
. /etc/profile.d/modules.sh
module load shared
module load anaconda
source activate grib
cmd=" somecommand "
$cmd

QBERT job runs

todo here

Lookout job runs

todo here

redhat open stack

to do here