=> Did some test and editing on byte, and transfer files to Gordon using Globus.
Sat Jan 2 22:26:12 PST 2016, Try a testing pbs
[hongqin@gordon-ln3 1.ori.ginppi.2015Oct]$ cat ori_aging_loopgordon.pbs
#!/bin/bash
#PBS -l nodes=1:ppn=16
#PBS -l walltime=07:00:00:00
module load R
echo hostname
cd /oasis/scratch/hongqin/temp_project/mactower-network-failure-simulation/1.ori.ginppi.2015Oct
pwd
#for p in 1.0 0.98 0.95 0.94 0.93 0.92 0.9 0.89 0.88 0.87 0.86 0.85 0.82 0.8
for p in 1.0 0.98
do
#for LOne in 0.003 0.0035 0.004 0.0045 0.005 0.0055 0.006 0.0065 0.007 0.0075 0.008
for LOne in 0.003 0.035
do
echo "$p $LOne"
#R --vanilla --slave -f 20151101-net-sim-ginppi.R --args $LOne 0.0002 5 $p 1000
Rscript netwk_aging_sim.v0.1b.R -if1 merged_PPIGIN_Factorized2015Oct132Cols.csv -if2 essentialGeneLookupTable_20151013.csv -l1 $LOne -l2 0 -dt 4 -p $p -n 49 -op ginppi -od ginppi.ori.out -iC 4 -d 1 -h /oasis/scratch/hongqin/temp_project/mactower-network-failure-simulation/1.ori.ginppi.2015Oct
done
done
[hongqin@gordon-ln3 1.ori.ginppi.2015Oct]$ date
Sat Jan 2 22:27:30 PST 2016
[hongqin@gordon-ln3 1.ori.ginppi.2015Oct]$ qsub ori_aging_loopgordon.pbs
2391092.gordon-fe2.local
[hongqin@gordon-ln3 1.ori.ginppi.2015Oct]$ qstat -u hongqin
gordon-fe2.local:
Req'd Req'd Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
----------------------- ----------- -------- ---------------- ------ ----- ------ ------ --------- - ---------
2390576.gordon-fe2.loc hongqin normal grid_aging_loopg 110732 1 16 -- 168:00:00 R 06:25:40
2391092.gordon-fe2.loc hongqin normal ori_aging_loopgo 81499 1 16 -- 168:00:00 R 00:00:02
This pbs works.
[hongqin@gordon-ln3 1.ori.ginppi.2015Oct]$ date
Sat Jan 2 22:31:48 PST 2016
[hongqin@gordon-ln3 1.ori.ginppi.2015Oct]$ cat ori_aging_loopgordon.pbs
#!/bin/bash
#PBS -l nodes=1:ppn=16
#PBS -l walltime=07:00:00:00
module load R
echo hostname
cd /oasis/scratch/hongqin/temp_project/mactower-network-failure-simulation/1.ori.ginppi.2015Oct
pwd
for p in 1.0 0.98 0.95 0.94 0.93 0.92 0.9 0.89 0.88 0.87 0.86 0.85 0.82 0.8
do
for LOne in 0.002 0.0021 0.0022 0.0023 0.0024 0.0025 0.0026 0.0028 0.0028 0.0029 0.003 0.0035 0.004 0.0045
do
echo "$p $LOne"
Rscript netwk_aging_sim.v0.1b.R -if1 merged_PPIGIN_Factorized2015Oct132Cols.csv -if2 essentialGeneLookupTable_20151013.csv -l1 $LOne -l2 0 -dt 4 -p $p -n 5000 -op ginppi -od ginppi.ori.out -iC 16 -d 1 -h /oasis/scratch/hongqin/temp_project/mactower-network-failure-simulation/1.ori.ginppi.2015Oct
done
done
[hongqin@gordon-ln3 1.ori.ginppi.2015Oct]$ date
Sat Jan 2 22:32:07 PST 2016
[hongqin@gordon-ln3 1.ori.ginppi.2015Oct]$ qsub ori_aging_loopgordon.pbs
2391118.gordon-fe2.local
This job run from 22:34 to 10:30am PST for a total of 12 hours for 197 runs.
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