[Bioclusters] re: how to run mpiblast

[Joe Landman]

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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-- 
Joseph Landman, Ph.D
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://scalableinformatics.com
phone: +1 734 612 4615