Hello, I'm having difficulty running mpiblast using the code pasted below. The goal is to run the blast search in parallel on 3 different nodes (2 processors, 8 CPU cores, and 24 GB RAM per node). Whenever I run mpiexec without the -n parameter I get the error message: "Sorry, mpiBLAST must be run on 3 or more nodes". Whenever I run mpiexec and pass it "-n 24" the job runs, but it takes and excessive amount of time (>8h to search 10 records) and only one of the three designated nodes is active (memory usage, cpu %, network I/O) during the job while the other allocated nodes are quiet.
What am I doing wrong here? It seems as though mpiexec isn't getting the relevant info about number of allocated nodes and/or the identities of the specific hosts from the PBS scheduler. Can anyone help me out with this? Much appreciated! ---------------------------- Greg Cary, Ph.D. Carnegie Mellon University Dept. of Biological Sciences Hinman Lab 412-268-9290 #!/bin/sh #PBS -N MPI_BLAST -e error_log.txt #PBS -l nodes=3:ppn=8 -n #PBS -l walltime=24:00:00 #PBS -M gregc...@andrew.cmu.edu -m abe #PBS -q pool1 mpiexec\ mpiblast -p blastp -d nr -e 1e-5 -m 7 -v 10000\ --removedb\ --time-profile=time-profile_1.txt\ -i ~/fasta_files/test2.fa\ -o ~/fasta_files/blast_results/mpi_test1_10recs.xml
