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quast [2017/10/12 18:30]
jokinsey Corrected the serial job running location
quast [2017/10/12 18:37]
jokinsey Corrected the job running location in the parallel example
Line 72: Line 72:
  
 cd $PBS_O_WORKDIR cd $PBS_O_WORKDIR
 +cp -r test_data/ /​scratch/​$PBS_JOBID
 +cd /​scratch/​$PBS_JOBID
  
-python /​share/​apps/​quast/​quast-3.1/​quast.py --threads ​48 test_data/​contigs_1.fasta test_data/​contigs_2.fasta -R test_data/​reference.fasta.gz -G test_data/​genes.gff+python /​share/​apps/​quast/​quast-3.1/​quast.py --threads ​12 test_data/​contigs_1.fasta test_data/​contigs_2.fasta -R test_data/​reference.fasta.gz -G test_data/​genes.gff 
 +mv /​scratch/​$PBS_JOBID/​quast_results/​results* $PBS_O_WORKDIR/​quast_results/​
 </​code>​ </​code>​
  
-This sets the max thread count at 48 for out set value of 12 virtual processors. You can evaluate the speedup by comparing the completion times of job running in serial job and a job running in parallel ​with the change above.+This changes ​the maximum ​thread count to 12 as we don't want to run more threads on node than their are cores on that node, because ​with hyper-threading turned off any more would kill efficiency.
   ​   ​
  
  
quast.txt · Last modified: 2017/10/12 18:37 by jokinsey