[Bioclusters] re: how to run mpiblast

[Joe Landman]

Try moving your data out of ~root.  All your input and output is being
done there: -i /root/test.fas -o blast_results.txt

Regular users do not have read or write permission to /root unless
something is badly broken.


On Thu, 2004-07-15 at 00:03, kenix y wrote:
> 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
> > >
> > > _________________________________________________________________
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> > >
> > > _______________________________________________
> > > 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
> 
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> _______________________________________________
> 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