[Bioclusters] re: how to run mpiblast

[kenix y]

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/