Entering edit mode
5.8 years ago
I installed MPI-BLAST in linux (ubuntu 16.04) , but while running query its generates an error, which may be pointed towards DATABASE.
to create database i ran this query:
$mpiformatdb -N 16 -i /home/ntm/Downloads/MPI_BLAST_MTB_ASM/all_ASM.fna -o /home/ntm/mpiblast/mtb_ASM
result was:
Reading input file
111Done, read 86563441 lines
Database type unspecified, assuming nucleotide
Breaking all_ASM.fna into 16 fragments
Executing: formatdb -i /home/ntm/Downloads/MPI_BLAST_MTB_ASM/all_ASM.fna -p F -N 16 -o T
Created 16 fragments.
<<< Please make sure the formatted database fragments are placed in /home/ntm/mpiblast/ before executing mpiblast. >>>
i ran this query:
$mpiexec -n 18 mpiblast -p blastn -d mpiblast/all.fna -i /home/ntm/samples/test_data/100/100.fasta -o /home/ntm/samples/test_data/100/r_100.txt
and get this error:
Error opening /home/ntm/mpiblast/mpiblast/all.fna.mbf
open: No such file or directory
Fatal Error:
Unable to access fragment list file
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 17 in communicator MPI_COMM_WORLD
with errorcode -1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
4 0.00846505 Bailing out with signal 15
5 0.0102329 Bailing out with signal 15
6 0.023458 Bailing out with signal 15
7 0.0255911 Bailing out with signal 15
8 0.032532 Bailing out with signal 15
9 0.03491 Bailing out with signal 15
10 0.035645 Bailing out with signal 15
11 0.0363281 Bailing out with signal 15
12 0.038064 Bailing out with signal 15
13 0.039439 Bailing out with signal 15
14 0.0391941 Bailing out with signal 15
15 0.0411971 Bailing out with signal 15
16 0.0412331 Bailing out with signal 15
0 0.00338316 Bailing out with signal 15
1 0.00537801 Bailing out with signal 15
2 0.00614786 Bailing out with signal 15
3 0.00781703 Bailing out with signal 15
[ablab:06080] 17 more processes have sent help message help-mpi-api.txt / mpi-abort
[ablab:06080] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
how can i remove this error?
Hello genious.kalia.141198,
Please use the formatting bar (especially the
codeoption) to present your post better. I've done it for you this time.Thank you!
Have you done this part?
yes, i did. just after my formatted database get ready i copied all the files to the location you mentioned.
Is
/home/ntm/mpiblast/mpiblast/all.fna.mbfpresent and readable from all nodes? The error say that the file could not be read.yeah, i resolved this.. but MPI-BLAST still generating errors.mpiexec -n 3 mpiblast -p blastn -d mpiblast/all_ASM.fna -i /home/ntm/samples/test_data/100/100.fasta -o /home/ntm/samples/test_data/100/r_100.txt
[blastall] WARNING: NZ_CP009614.1_0000000001: Unable to open all_ASM.fna.000.nin
[blastall] WARNING: NZ_CP009614.1_0000000001: Unable to open all_ASM.fna.000.nin
[blastall] WARNING: NZ_CP009614.1_0000000001: Unable to open all_ASM.fnaABL4KB.nin
[blastall] WARNING: NZ_CP009614.1_0000000001: Unable to open all_ASM.fna.000.nin
[blastall] WARNING: NZ_CP009614.1_0000000001: Unable to open all_ASM.fna.000.nin
[blastall] WARNING: NZ_CP009614.1_0000000001: Unable to open all_ASM.fnaABL4KB.nin
[blastall] FATAL ERROR: NZ_CP009614.1_0000000001: Database /home/ntm/mpiblast/mpiblast /all_ASM.fnaABL4KB was not found or does not exist
1 0.052954 Bailing out with signal -1
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 0.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
2 0.054822 Bailing out with signal 15
0 0.0540459 Bailing out with signal 15
[ablab:17905] 2 more processes have sent help message help-mpi-api.txt / mpi-abort
[ablab:17905] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages