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mpiblast [2017/09/12 21:39]
jokinsey
mpiblast [2017/10/10 18:07]
jokinsey Changed PBS script to run in /scratch
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-==== mpiBlast ​====+==== mpiBLAST ​====  
 +{{ :​mpiblast.png?​nolink&​200|}}
  
 mpiBlast is a freely available, opensource, parallel implementation of NCBI Blast. mpiBlast takes advantage of shared parallel computign resources, i.e. a cluster this gives it access to more avaliable resources unlike NCBI blast which only can take advantage of shared-memory multi-processors(SMP'​s). mpiBlast is a freely available, opensource, parallel implementation of NCBI Blast. mpiBlast takes advantage of shared parallel computign resources, i.e. a cluster this gives it access to more avaliable resources unlike NCBI blast which only can take advantage of shared-memory multi-processors(SMP'​s).
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 #PBS -j oe #PBS -j oe
 #PBS -m abe #PBS -m abe
-#PBS -M YourUserName@uark.edu+#PBS -M jokinsey@uark.edu
 #PBS -o MPIBLAST.$PBS_JOBID #PBS -o MPIBLAST.$PBS_JOBID
 #PBS -l nodes=1:​ppn=12 #PBS -l nodes=1:​ppn=12
 #PBS -l walltime=02:​00:​00 #PBS -l walltime=02:​00:​00
 +
  
 cd "​$PBS_O_WORKDIR"​ cd "​$PBS_O_WORKDIR"​
 +cp input /​scratch/​$PBS_JOBID
 +cd /​scratch/​$PBS_JOBID
  
-mpirun -np 12 mpiblast -p blastn -d mito.nt -i /​home/​YourUserName/​testing/​input -o /​home/​YourUserName/​testing/​output+mpirun -np 12 mpiblast -p blastn -d mito.nt -i input -o $HOME/​testing/​output
 </​code>​ </​code>​
  
-Notice ​the line ''​cd "​$PBS_O_WORKDIR"​'' ​this is saying ​we want to start running ​the job from the current ​directory.+In the ''​PBS'' ​script first we copy our input file to the directory ​we will be working in ''/​scratch/​$PBS_JOBID''​Then we go into that directory to run the computation and send the output to ''​$HOME/​testing/​output''​
  
 Then submit the job. Then submit the job.
  
 <​code>​ <​code>​
-razor-l1:​jokinsey:​~/​SCHED_PLACE$ qsub /​home/​YourUserName/​testing/​mpiBlastTest.pbs ​+razor-l3:​jokinsey:​~/​testing$ qsub mpiBlastTest.pbs ​
 </​code>​ </​code>​
  
mpiblast.txt · Last modified: 2017/10/10 18:07 by jokinsey