[BioBrew Users] FW: Re: [Bioclusters] re: how to run mpiblast

[Glen Otero]

On Jul 15, 2004, at 8:13 PM, kenix y wrote:

> mpiBLAST is ready to run in BioBrew.
>
> 1)I had set up .ncbirc
>
> [NCBI]
> Data=/opt/BioBrew/NCBI/6.1.0/data
> [BLAST]
> BLASTDB=/tmp/blast
>
> 2) and mpiblast.conf
>
> /mnt/pvfs
> /tmp/blast
> /opt/BioBrew/NCBI/6.1.0/bin
>
> 3) edit my /etc/profile
>> export BLASTPATH=/opt/BioBrew/NCBI/6.1.0/bin
>> export MPIBLASTCONFIG=/home/build/mpiblast.conf
>> export MPIRUN=/opt/mpich-vmi-2.0-gcc/bin/mpirun

You can't use the values I was using--they were set up for my 
environment, which uses mpich-vmi and for user glen. You need to set 
these for regular mpich and user bigcpuguest
>
> 4) my $HOME/machines contains
> comp-pvfs-0-0
>
> But this command gave me the mpirun helpfile
> $MPIRUN -np 2 -machinefile $HOME/machines $BLASTPATH/mpiblast
> config-file=$MPIBLASTCONFIG -p blastn -d ecoli.nt -i test.fas -o 
> blast.txt
>
> and this command
> mpirun -np 2 -machinefile $HOME/machines $BLASTPATH/mpiblast
> config-file=$MPIBLASTCONFIG -p blastn -d ecoli.nt -i 
> /tmp/blast/test.fas -o /tmp/blast/blast_results.txt
>
> gave me
> 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
>
> Can anyone tell if it's my configuration or was it my command that's 
> wrong?

It looks like the ecoli db is in /root and probably owned by root, but 
you're running the job as bigcpuguest which causes the permissions 
problem. Move the data into a directory that can be read by 
bigcpuguest, like /home/bigcpuguest and change permissions on it so 
bigcpuguest can read the file.

Glen

>
> Thank you
>
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Glen Otero, Ph.D.
Linux Prophet
619.917.1772