[BiO BB] mpiblast error ObjMgrNextAvailEntityID failed
Mike Muratet
muratem at eng.uah.edu
Mon Dec 19 13:34:29 EST 2005
Greetings
This question appears to have come up before on these 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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