tar backup byte laptop

lapphy-pc1:~ hqin$ cat backup.byte.sh 

date

 echo "Back up Byte laptop  now"

 time perl /Users/hqin/perl/backup4.pl /Volumes/bear/byte > /tmp/_backup.hqin.txt 

date

lapphy-pc1:~ hqin$ sh backup.byte.sh 

Wed Jan 20 20:23:37 EST 2016

Back up Byte laptop  now

defined(%hash) is deprecated at /Users/hqin/lib/perl/Util.pm line 610.

(Maybe you should just omit the defined()?)

du: Library/Saved Application State/com.adobe.flashplayer.installmanager.savedState: Permission denied

tar: wdijk-112507/trash: Couldn't visit directory: Permission denied

tar: wdijk-112507/doc: Couldn't visit directory: Permission denied

tar: day2.tab: could not open file: Permission denied

tar: day3.tab: could not open file: Permission denied

tar: day4.tab: could not open file: Permission denied

tar: Error exit delayed from previous errors.

tar: Google: Cannot stat: No such file or directory

tar: Error exit delayed from previous errors.

real 82m9.817s

user 0m9.009s

sys 5m13.683s

Wed Jan 20 21:45:47 EST 2016

How fast is Gordon? 2.6GHz 2x8 cores, compare with Byte Intel core i7 6 cores

@Byte, simulate aging for 1000 cells using 4 cores.
11:02am -11:05
time Rscript netwk_aging_sim.v0.1b.R -if1 merged_PPIGIN_Factorized2015Oct132Cols.csv -if2 essentialGeneLookupTable_20151013.csv -l1 0.0023 -l2 0 -dt 4 -p 0.9 -n 1000  -op __TEST -od tmp -iC 4 -d 1 -h /Users/hqin/github/mactower-network-failure-simulation/1.ori.ginppi.2015Oct

real 2m23.106s

user 8m25.295s

sys 0m37.280s

@gordon,  job with 16 cores

[hongqin@gordon-ln2 1.ori.ginppi.2015Oct]$ cat ori_aging_loopgordon.3.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 0.99 0.98 0.97 0.96 0.95 0.94 0.93 0.92 0.91 0.9 0.89 0.88 0.87 0.86 0.85 0.82 0.8 

for p in 1.0 0.99 0.98 0.97 0.96 0.95 0.94 0.93 0.92 0.91 0.9

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

   for LOne in 0.001 0.0011 0.0012 0.0013 0.0014 0.0015 00016 0.0017 0.0018 0.0019 0.002

   do

      echo "$p $LOne"

 time Rscript netwk_aging_sim.v0.1b.R -if1 merged_PPIGIN_Factorized2015Oct132Cols.csv -if2 essentialGeneLookupTable_20151013.csv -l1 $LOne -l2 0 -dt 5 -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

real    3m35.381s

user    54m18.786s

sys     0m50.109s

[hongqin@gordon-ln1 1.ori.ginppi.2015Oct]$ cat ori_aging_loopgordon.3.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 0.99 0.98 0.97 0.96 0.95 0.94 0.93 0.92 0.91 0.9 0.89 0.88 0.87 0.86 0.85 0.82 0.8 

for p in 0.99 0.98 

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

   for LOne in 0.001 0.0011

   do

      echo "$p $LOne"

 time Rscript netwk_aging_sim.v0.1b.R -if1 merged_PPIGIN_Factorized2015Oct132Cols.csv -if2 essentialGeneLookupTable_20151013.csv -l1 $LOne -l2 0 -dt 5 -p $p -n 1000 -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

real    0m45.861s

user    11m8.614s

sys     0m10.168s

Conclusions: Gordon single core seems to be similar or even slower than Byte. However, its numbers of cores saves time.

"Each compute node contains two 8-core 2.6 GHz Intel EM64T Xeon E5 (Sandy Bridge) processors and 64 GB of DDR3-1333 memory. " By is Intel 2.6 GHz Corei7 (6 cores?)