[BiO BB] Re: your mail

Joe Landman landman at scalableinformatics.com
Sat May 21 09:00:28 EDT 2005

Hi Sravan:

   Dont use an absolute or relative path for the directory entry.  mpiblast 
handles this for you (e.g. your -d /full/path/to/database should be -d 


On Sat, 21 May 2005, sravan  sravan wrote:

> Dear Sir,
         Thanks for your asisstance. During the compilation of lam version I have got this error message. Kindly let me know the solution.
1. Compilation of NCBI-2.2.10-5.x86_64.rpm: creates: /usr/share/ncbi/data. and /usr/bin/exes.
2. Compilation of mpiblast-1.3.0-2LAM.x86_64.rpm : created exes in /usr/local/bin.
3. .ncbirc file has been set up in each node at ~sravan/.ncbirc:
BLASTDB=/apps/Databases/blastdb        BLASTMAT=/apps/Databases/ncbi/data
Shared=/apps/Databases/blastdb ( full permission)
Local=/tmp/mpiblast(full permission)
4. formatdb -N 20 -i /home/sravan/demorun/blast/silkcds -p F : has created a shared blastable parsed dataset fragments in /apps/Databases/blastdb(drwxrwxrwx): but the files are created as user. So their permissions are: -rw-r--r--.
5. script:
/usr/local/lam/bin/mpirun -np 5 /usr/local/bin/mpiblast -p blastn -i /home/sravan/demorun/blast/SWseq -d /apps/Databases/blastdb/silkcds -e 10 -v 5 -b 5 -o /home/sravan/demorun/blast/mpiblast.out --debug=mpiblastlog.
Error Message I got:
Sat May 21 11:09:14 IST 2005
(0) Error opening: /apps/Databases/blastdb///apps/Databases/blastdb/silkcds.dbs
Fatal Error:
db_spec.cpp(DbSpecFile): Unable to open file
One of the processes started by mpirun has exited with a nonzero exit
code.  This typically indicates that the process finished in error.
If your process did not finish in error, be sure to include a "return
0" or "exit(0)" in your C code before exiting the application.

PID 15092 failed on node n0 ( with exit status 1.
MPI_Recv: process in local group is dead (rank 1, SSI:coll:smp:local comm for CID 0)
Rank (3, MPI_COMM_WORLD): Call stack within LAM:
Rank (3, MPI_COMM_WORLD):  - MPI_Recv()
Rank (3, MPI_COMM_WORLD):  - MPI_Recv()
Sat May 21 11:09:16 IST 2005

Thank you very much.

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