[Bioclusters] re: how to run mpiblast

[Joe Landman]

What does your .ncbirc look like?  Somewhere you are getting a
/root/blast in there, and that might be it.

Joe

On Thu, 2004-07-15 at 01:26, kenix y wrote:
> Hi,
> 
> I've moved my data out of /root.
> Now my command looks like this :
> 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 /tmp/blast/test.fas -o /tmp/blast/blast_results.txt
> 
> The output is :
> Master got message with tag -32766 from node -32766
> 
> And it goes on till I ctrl c it.
> 
> Is there something wrong with my command?
> 
> Without the -v and --debug all it shows is :
> 
> 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
> 
> What else can I do?
> 
> >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: Thu, 15 Jul 2004 00:43:52 -0400
> >
> >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
> >
> >_______________________________________________
> >Bioclusters maillist  -  Bioclusters@bioinformatics.org
> >https://bioinformatics.org/mailman/listinfo/bioclusters
> 
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> 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