Hi, Thanks for your reply. I'm running this as a user, and not as root. And I am using /tmp/blast, this is my confg file. /mnt/pvfs /tmp/blast /opt/BioBrew/NCBI/6.1.0/data Anything else that I can try? As for the links you had provided me with, I've been to http://scalableinformatics.com/run_mpiblast.html just that I have not really been able to understand what it means. Thanks alot. >From: Joe Landman <landman@scalableinformatics.com> >Reply-To: bioclusters@bioinformatics.org >To: biocluster <bioclusters@bioinformatics.org> >Subject: Re: [Bioclusters] re: how to run mpiblast >Date: Wed, 14 Jul 2004 23:44:14 -0400 > >You might want to use our run_mpiblast script. It handles the details >of existence and permissions testing, and could help you debug this >better. > >Looking at the output, I would guess: > >1) write permissions. It looks like you should probably be running this >as a user, and not as root. > >2) You should probably be working in a temporary directory. > >What basically happened is a typical error cascade. When you get these, >ignore the ones at the end. They are the result of the ones at the >beginning. > >I would suggest running this as a user, and not as root. I would also >suggest getting http://scalableinformatics.com/run_mpiblast.html and the >script http://downloads.scalableinformatics.com/downloads/run_mpiblast >and the rc file >http://downloads.scalableinformatics.com/downloads/run_mpiblastrc . > >Joe > >On Wed, 2004-07-14 at 23:25, kenix y wrote: > > Hi, I tried to run mpiblast with this command : > > mpirun -np 2 /opt/BioBrew/NCBI/6.1.0/bin/mpiblast > > --config-file=/opt/BioBrew/NCBI/6.1.0/etc/mpiblast.conf -p blastn -d > > ecoli.nt -i /root/test.fas -o blast_results.txt > > > > But it gave me this error: > > mv: cannot stat '/root/blast/ecoli.ntChNsWp': No such file or directory > > cp: cannot create regular file '/root/blast/ecoli.nt.00.nhr': Permission > > denied > > cp: cannot create regular file '/root/blast/ecoli.nt.00.nin': Permission > > denied > > cp: cannot create regular file '/root/blast/ecoli.nt.00.nsq': Permission > > denied > > cp: cannot create regular file '/root/blast/ecoli.nt.00.nnd': Permission > > denied > > cp: cannot create regular file '/root/blast/ecoli.nt.00.nni': Permission > > denied > > cp: cannot create regular file '/root/blast/ecoli.nt.00.nsd': Permission > > denied > > cp: cannot create regular file '/root/blast/ecoli.nt.00.nsi': Permission > > denied > > Error opening /root/blast/ecoli.ntChNsWp.nal > > > > With mpirun -v -np 2 /opt/BioBrew/NCBI/6.1.0/bin/mpiblast --debug > > --config-file=/opt/BioBrew/NCBI/6.1.0/etc/mpiblast.conf -p blastn -d > > ecoli.nt -i /root/test.fas -o blast_results.txt > > > > 24491 /opt/BioBrew/NCBI/6.1.0/bin/mpiblast running on n0 (o) > > 18435 /opt/BioBrew/NCBI/6.1.0/bin/mpiblast running on n1 > > blastall -p blastn -i /root/test.fas -o blast_test.txt -d >/mnt/pvfs/ecoli.nt > > [blastall] FATAL ERROR: blast: Unable to open output file >blast_results.txt > > > > Temp name base: /tmp/blast/ecoli.ntXXXXXX > > Got temp name: /tmp/blast/ecoli.ntrZvzGm > > mv: Cannot stat '/tmp/blast/ecoli.ntrZvzGm': No such file or directory > > Temp name base: /tmp/blast/blast_results.txt.1XXXXXX > > Got temp name: /tmp/blast/blast_results.txt.1E6sMMp > > Temp name base: /tmp/blast/test.fas.XXXXXX > > Got temp name: /tmp/blast/test.fas.B9Y1Ss > > blastall -p blastn -z 4652914 -i /tmp/blast/test.fasB9Y1Ss -0 > > /tmp/blast/blast_results.txt.1E6sMMp -d /tmp/blast/ecoli.ntrZvzGm -J -o > > /dev/null Sending 0 fragments. > > Fragment list sent. > > waiting for file size broadcast > > MPI_Recv: process in local group is dead (rank 1, MPI_COMM_WORLD) > > RANK ( 1, MPI_COMM_WORLD): call stack withinLAM: > > RANK ( 1, MPI_COMM_WORLD): - MPI_Recv() > > RANK ( 1, MPI_COMM_WORLD): - MPI_BCast() > > RANK ( 1, MPI_COMM_WORLD): - main() > > > > Does anyone knows what is the problem with it? > > Thank you > > > > _________________________________________________________________ > > Get 10mb of inbox space with MSN Hotmail Extra Storage > > http://join.msn.com/?pgmarket=en-sg > > > > _______________________________________________ > > Bioclusters maillist - Bioclusters@bioinformatics.org > > https://bioinformatics.org/mailman/listinfo/bioclusters >-- >Joseph Landman, Ph.D >Scalable Informatics LLC, >email: landman@scalableinformatics.com >web : http://scalableinformatics.com >phone: +1 734 612 4615 > >_______________________________________________ >Bioclusters maillist - Bioclusters@bioinformatics.org >https://bioinformatics.org/mailman/listinfo/bioclusters _________________________________________________________________ Download games, logos, wallpapers and lots more at MSN Mobile! http://www.msn.com.sg/mobile/