mpiBlast

Description
	mpiBLAST is a parallelization of NCBI BLAST. mpiBLAST segments the BLAST database and distributes it across cluster nodes, permitting BLAST queries to be processed on many nodes simultaneously.
Site	Version (Latest: v1.5.0-PIO)	Notes
ngs.rl.ac.uk	v1.4.0	No Parallel IO. Compiled using GNU Compilers & ScaliMPI

License

mpiBLAST version 1.5.0-PIO is licensed to the public under the terms of the GNU Public License (GPL) version 2 See further licensing details from the mpiBLAST web site.

Users of this application should credit the code authors and the NGS accordingly and where applicable the specific site where the code is installed, when publishing work using NGS resources.

Running mpiBLAST on the NGS

The input file used for the following examples, aadnafra.fsa can be found at

gsiftp://ngs.rl.ac.uk:2811/apps/mpi_blast/examples/aadnafra.fsa

• Submission Using the UI/WMS

  To submit an mpiBLAST job via the WMS, login to the UI and create a JDL file as below, replacing your ngs ID on the UI for ngsxxxx, then submit using:

  glite-wms-job-submit -o jobIDs -a abc.jdl

  Type = "Job";
  JobType = "mpich";
  CpuNumber = 22;
  Executable = "/usr/ngs/MPI-BLAST";
  Arguments = "mpiblast -p blastn -d est -i aadnafra.fsa --removedb";
  Environment = {"DB=EBI_N"};
  StdOutput = "mpiBlast.out";
  StdError = "mpiBlast.err";
  Myproxyserver= "myproxy.ngs.ac.uk";
  InputSandbox = {"aadnafra.fsa"};
  InputSandboxBaseURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngs0055/mpiblast";
  OutputSandbox = {"mpiBlast.out","mpiBlast.err"};
  OutputSandboxBaseDestURI = "gsiftp://ngsui03.ngs.ac.uk:2811/home/ngs0055/mpiblast";
  Requirements = (
       member("NGS-UEE-MPI-BLAST", other.GlueHostApplicationSoftwareRunTimeEnvironment)
  );
  ShallowRetryCount = -1;

   

• NGS Web Portal Submission

  After logging in to the NGS portal, select the "mpiBlast" template under the " BioInformatics" category and make the amendments appropriate for your specific job. Read the description page of the template for further details.

• Submission Using Globus

  Eg To submit an mpiBLAST job use the following command (one line. You should not include the backslashes):

  globusrun -b -r ngs.rl.ac.uk/jobmanager-lsf \ '&(executable=/usr/ngs/MPI-BLAST_1_4_0) \ (arguments= mpiblast -p blastn -d est -i aadnafra.fsa --removedb) \ (jobType=mpi)(count=22)(environment = (DB EBI_N)) \ (stdout=mpiBlast.out)(stderr=mpiBlast.err)'

  • This runs the specific 1.4.0 version. To run any available option on any site use MPI-BLAST instead of MPI-BLAST_1_4_0.
  • stdout and stderr are set to 'mpiBlast.out' and 'mpiBlast.err' respectively.
  • The first argument must be the program we want to run. ( mpiblast in this case)
  • The input files must be given as an argument and not as stdin .
  • (count=22) must always be set to 22 (20+2), as the databases have already been fragmented into 20 sets (unless you are using your own fragmented database).
  • To perform a search across the EBI_NUCLEOTINE database, the environment variable DB should be set to EBI_N , whilst a search across the EBI_PROTEIN database requires DB to be set to EBI_P . If DB is set to any other value or is left unset, it is assumed that you are searching your own database in mpiblast format, and thus have an appropriate .ncbirc file in your working directory.
  • For more information about the available databases formatted fotr mpiblast searches, see here and here for the EBI NUCLEOTIDE and EBI PROTEIN databases in mpi-blast format respectively. More information about the databases available on the NGS can be found here

   

Further Information

• An Online Reference Manual for mpiBLAST.
• mpiBLAST: Open-Source Parallel BLAST
• mpiBLAST Mailing Lists