User Tools

Site Tools


mpiblast

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
mpiblast [2017/09/12 21:26]
jokinsey
mpiblast [2017/10/10 18:07] (current)
jokinsey Changed PBS script to run in /scratch
Line 1: Line 1:
-==== 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).
Line 14: Line 15:
 module load mpiblast/​1.6.0 module load mpiblast/​1.6.0
 </​code>​ </​code>​
 +
 +You may have to logout and log back in for the modules to load. You can check with the command ''​module list'',​ which should also be displayed on login.
  
 Make a directory to contain the FASTA database that will be fragmented. Download the database and decompress it. Make a directory to contain the FASTA database that will be fragmented. Download the database and decompress it.
Line 78: Line 81:
 #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.1505251612.txt.gz · Last modified: 2017/09/12 21:26 by jokinsey