[Bioclusters] re: how to run mpiblast
kenix y
bioclusters@bioinformatics.org
Thu, 15 Jul 2004 13:26:16 +0800
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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