I hope this is a better post to the list :) To put a long story short, Joe Landman of ScalableInformatics kindly coached me to setup a mpiblast.conf file which contains 3 lines: ------------------------------ /raid/pub/ncbi/blast/mpidb /tmp /home/src/ncbi/data ------------------------------ My .ncbirc contains: ------------------------- [NCBI] Data="/home/src/ncbi/data" [BLAST] BLASTDB="/raid/pub/ncbi/blast/mpidb" BLASTMAT="/home/src/ncbi/data" [mpiBLAST] Shared="/raid/pub/ncbi/blast/mpidb" Local="/tmp" ----------------------- I ran MPIblast using OpenMPI v.1.2.3 as in: bash> /opt/openmpi.gcc/bin/mpirun -np 3 -machinefile ./machines /home/local/bin/mpiblast --config-file=/home/zhu/.mpiblast.conf -p blastp -i ./bait.fasta -d ecoli.aa and got following errors: [blastall] ERROR: gi|1786184|gb|AAC73114.1|: BlastKarlinBlkGappedCalc: P is not a supported matrix [blastall] ERROR: gi|1786184|gb|AAC73114.1|: BlastKarlinBlkGappedCalc: BLOSUM80 is a supported matrix [blastall] ERROR: gi|1786184|gb|AAC73114.1|: BlastKarlinBlkGappedCalc: BLOSUM62 is a supported matrix [blastall] ERROR: gi|1786184|gb|AAC73114.1|: BlastKarlinBlkGappedCalc: BLOSUM50 is a supported matrix [blastall] ERROR: gi|1786184|gb|AAC73114.1|: BlastKarlinBlkGappedCalc: BLOSUM45 is a supported matrix [blastall] ERROR: gi|1786184|gb|AAC73114.1|: BlastKarlinBlkGappedCalc: PAM250 is a supported matrix [blastall] ERROR: gi|1786184|gb|AAC73114.1|: BlastKarlinBlkGappedCalc: BLOSUM62_20 is a supported matrix [blastall] ERROR: gi|1786184|gb|AAC73114.1|: BlastKarlinBlkGappedCalc: BLOSUM90 is a supported matrix [blastall] ERROR: gi|1786184|gb|AAC73114.1|: BlastKarlinBlkGappedCalc: PAM30 is a supported matrix [blastall] ERROR: gi|1786184|gb|AAC73114.1|: BlastKarlinBlkGappedCalc: PAM70 is a supported matrix 2 0.149567 Bailing out with signal 11 [node002:24414] MPI_ABORT invoked on rank 2 in communicator MPI_COMM_WORLD with errorcode 0 --- It hangs here for hours although I had only a few query sequences against a very small database (4000 sequences). I had to ctr-C or kill the job. To be sure, I have also put in my .bashrc following lines: export BLASTMAT="/home/src/ncbi/data" and did "source ~/.bashrc", then re-run the mpiblast, and got the same error. I have also googled for "[blastall] ERROR: BlastKarlinBlkGappedCalc: BLOSUM62 is a supported matrix", didn't get much useful information on my case. Also, very strangely, when I tried to use the mvapich (v.0.9.9) to run: bash> /opt/openmpi.gcc/bin/mpirun -np 5 -machinefile ./machines /home/local/bin/mpiblast --debug --config-file=/home/.mpiblast.conf -p blastp -i ./bait.fasta -d ecoli.aa I got simply one line error: "End of file reached on hostfile at 4 of 9 hostnames" Any hint? Thanks in advance! Zhiliang