greenfield, netaging simulation test run, 8SU for each file generated with 2000 cells

[hqin2@greenfield ms02GINPPI]$ cat netagingd.pbs 

#!/bin/bash

# Request 15 cores

#PBS -l nodes=1:ppn=15

#  Request 6 days of cpu time

#PBS -l walltime=6:00:00:00

module load R/3.2.1-mkl

echo hostname

pwd

cd /crucible/mc48o9p/hqin2/mactower-network-failure-simulation-master/ms02GINPPI

pwd

R --vanilla --slave -f net-aging-sim-2014Sep7.R

[hqin2@greenfield ms02GINPPI]$ qstat

Job ID                    Name             User            Time Use S Queue

------------------------- ---------------- --------------- -------- - -----

1816.greenfield            newRunNew.job    ismini          132:07:5 R batch          

1985.greenfield            run_idba_ud.bash sczyrba         170:42:1 R batch          

1999.greenfield            netaging.pbs     hqin2           00:00:41 R batch    

1pm. problem. Local run of net-aging-sim-2014Sep7b.R works, but pbs does not.

[hqin2@greenfield ms02GINPPI]$ R -f net-aging-sim-2014Sep7b.R --args 105 106 

by 1:10pm, I removed old files and cleaned up the directory. Everything seems to work now. Perhaps I probably qsub a wrong file. 

[hqin2@greenfield ms02GINPPI]$ cat netagingd.pbs 

#!/bin/bash

# Request 15 cores

#PBS -l nodes=1:ppn=15

#  Request 7days of cpu time

#PBS -l walltime=7:00:00:00

module load R/3.2.1-mkl

echo hostname

pwd

cd /crucible/mc48o9p/hqin2/mactower-network-failure-simulation-master/ms02GINPPI

pwd

numactl -C +0 R --vanilla --slave -f net-aging-sim-2014Sep7b.R --args 90 90

numactl -C +1 R --vanilla --slave -f net-aging-sim-2014Sep7b.R --args 91 91

numactl -C +2 R --vanilla --slave -f net-aging-sim-2014Sep7b.R --args 92 92

[hqin2@greenfield ms02GINPPI]$ qstat 

Job ID                    Name             User            Time Use S Queue

------------------------- ---------------- --------------- -------- - -----

1816.greenfield            newRunNew.job    ismini          137:17:5 R batch          

1985.greenfield            run_idba_ud.bash sczyrba         245:35:3 R batch          

2007.greenfield            netagingc.pbs    hqin2           03:30:22 R batch          

2011.greenfield            netagingd.pbs    hqin2                  0 R batch 

20150915Monday, Note that the three jobs were run in sequential, not in parallel! 

[hqin2@greenfield ms02GINPPI]$ ll -t dipgin.ms02.output/90/popages/

total 142

-rw-r--r-- 1 hqin2 mc48o9p 33803 Sep 10 05:17 cutoff.4.p.1.lambda.0.02.popsize.2000.time.2015Sep10_051711.txt

-rw-r--r-- 1 hqin2 mc48o9p 33790 Sep  9 22:12 cutoff.4.p.0.9.lambda.0.02.popsize.2000.time.2015Sep09_221225.txt

-rw-r--r-- 1 hqin2 mc48o9p 33815 Sep  9 15:04 cutoff.4.p.0.8.lambda.0.02.popsize.2000.time.2015Sep09_150443.txt

-rw-r--r-- 1 hqin2 mc48o9p 33885 Sep  9 07:49 cutoff.4.p.0.7.lambda.0.02.popsize.2000.time.2015Sep09_074906.txt

-rw-r--r-- 1 hqin2 mc48o9p 33802 Sep  8 23:27 cutoff.4.p.1.lambda.0.01.popsize.2000.time.2015Sep08_232736.txt

-rw-r--r-- 1 hqin2 mc48o9p 33779 Sep  8 16:21 cutoff.4.p.0.9.lambda.0.01.popsize.2000.time.2015Sep08_162114.txt

-rw-r--r-- 1 hqin2 mc48o9p 33827 Sep  8 09:15 cutoff.4.p.0.8.lambda.0.01.popsize.2000.time.2015Sep08_091521.txt

-rw-r--r-- 1 hqin2 mc48o9p 33814 Sep  8 02:01 cutoff.4.p.0.7.lambda.0.01.popsize.2000.time.2015Sep08_020109.txt

[hqin2@greenfield ms02GINPPI]$ ll -t dipgin.ms02.output/91/popages/

total 142

-rw-r--r-- 1 hqin2 mc48o9p 33795 Sep 12 17:34 cutoff.4.p.1.lambda.0.02.popsize.2000.time.2015Sep12_173458.txt

-rw-r--r-- 1 hqin2 mc48o9p 33788 Sep 12 10:25 cutoff.4.p.0.9.lambda.0.02.popsize.2000.time.2015Sep12_102544.txt

-rw-r--r-- 1 hqin2 mc48o9p 33840 Sep 12 03:16 cutoff.4.p.0.8.lambda.0.02.popsize.2000.time.2015Sep12_031655.txt

-rw-r--r-- 1 hqin2 mc48o9p 33886 Sep 11 19:57 cutoff.4.p.0.7.lambda.0.02.popsize.2000.time.2015Sep11_195758.txt

-rw-r--r-- 1 hqin2 mc48o9p 33776 Sep 11 11:31 cutoff.4.p.1.lambda.0.01.popsize.2000.time.2015Sep11_113115.txt

-rw-r--r-- 1 hqin2 mc48o9p 33778 Sep 11 04:18 cutoff.4.p.0.9.lambda.0.01.popsize.2000.time.2015Sep11_041814.txt

-rw-r--r-- 1 hqin2 mc48o9p 33778 Sep 10 21:08 cutoff.4.p.0.8.lambda.0.01.popsize.2000.time.2015Sep10_210855.txt

-rw-r--r-- 1 hqin2 mc48o9p 33808 Sep 10 13:51 cutoff.4.p.0.7.lambda.0.01.popsize.2000.time.2015Sep10_135103.txt

[hqin2@greenfield ms02GINPPI]$ ll -t dipgin.ms02.output/92/popages/

total 107

-rw-r--r-- 1 hqin2 mc48o9p 33761 Sep 13 16:43 cutoff.4.p.0.9.lambda.0.01.popsize.2000.time.2015Sep13_164355.txt

-rw-r--r-- 1 hqin2 mc48o9p 33801 Sep 13 09:33 cutoff.4.p.0.8.lambda.0.01.popsize.2000.time.2015Sep13_093348.txt

-rw-r--r-- 1 hqin2 mc48o9p 33822 Sep 13 02:17 cutoff.4.p.0.7.lambda.0.01.popsize.2000.time.2015Sep13_021713.txt

Conclusions: Each run took 7-8 hours for popSize=2000.