Hi Mike,
Can you try using the latest CVS snapshot?
Unfortunately sourceforge seems to have silently deleted the cron job
that updates the cvs snapshot and it hadn't been updated since May(!).
That should be fixed now and the current snapshot is available from:
http://mpiblast.sf.net/mpiblast-latest.tar.gz
You will need to run
aclocal && autoheader && automake -a && autoconf
prior to running ./configure because the cvs snapshots don't include the
complete build system.
Also, does using the -b and -v options to limit the number of results
have any effect on whether the error appears?
-Aaron
Mike Muratet wrote:
Greetings
This question appears to have come up before on other lists, but I
don't see an answer. I recall we've posted about this problem before
but I don't think we ever got the problem resovled. I created two
databases using the commands below from the Ensembl human and mouse
databases. I tried to run a query with:
setenv data_root /scratch/uahmam
setenv blast_root /opt/asn/apps/mpiBlast_1.3.0/latest/bin
setenv MPI_REQUEST_MAX 128000
setenv MPI_TYPE_MAX 128000
echo "blast_root is "$blast_root
echo "data_root is "$data_root
cd /scratch/uahmam
time /usr/bin/mpirun -np 8 $blast_root/mpiblast --remove -p blastn -d
Homo_sapiens.NCBI35.nov.cdna.fa -i novel_v11.fa -W 9 -r 1 -q -1
-G 1 -E 3 -o novel_v_Hsen.blast
where my .ncbirc file is as below:
[mpiBLAST]
Shared=/scratch/uahmam
Local=/scratch/uahmam
[NCBI]
Data= /opt/asn/apps/ncbi_6.1/data
[BLAST]
BLASTDB=/scratch/uahmam
BLATMAT=/opt/asn/apps/ncbi_6.1/data
mpiformatdb --nfrags=6 -t enHs -i Homo_sapiens.NCBI35.nov.cdna.fa -p F
-n enHs
mpiformatdb --nfrags=6 -t enMm -i Mus_musculus.NCBIM34.nov.cdna.fa -p
F -n enMm
I get nothing but a million+ lines of:
ObjMgrNextAvailEntityID failed with idx 2048
It fills up my disk quota and crashes so I get nothing else.
I have found this line in the source code, but I can't figure out
what's going on from that.
mpiblast seems to work OK for other databases/queries.
Can anybody offer any suggestions?
Thanks
Mike
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