Thanks for your help. Now i can run my program mpiblast. But still i have question why mpiblast is not run on all machines? I have 12 Sun fire v20z machines and each has two processors. But when i am running my my job for 24 processors than it execute randomaly not on all machines. It used hardely 8-9 processors at one time.
I used lam-mpi 7.0. Is there any problem with lam environment for mpiblast?
Lucas Carey <[EMAIL PROTECTED]> wrote:
Hi Ankit,
Could you post the conents of your .ncbicr file?
Also, you can try passing them as environment variables:
mpirun -np 24 -x MPIBLAST_SHARED=/where/ever,MPIBLAST_LOCAL=/local/storage mpirun
-Lucas
On Sunday, April 09, 2006 at 23:39 -0700, ankit patel wrote:
> i think i have a problem to set the environment
> variable for mpiblast. MPIBLAST_SHARED and
> MPIBLAST_LOCAL. I am already set in .ncbirc file
> created by me at home directory as well as in ncbi
> directory but i failed to get output. so can u tell me
> when i have to make .ncbirc file and what i have to
> write in it.
>
> With Best Regards,
>
> Ankit Patel
>
> __________________________________________________
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Content-Description: 1897716519-error_mpiblast.txt
> $ mpirun -np 24 mpiblast -p blastn -d mm_ref_chr_intergenic.db -i ..1G/hs_ref_chr01.IG -o mpi_hs_ref_chr01.txt
> FaFatal Error:
> Unable to read mpiBLAST shared storage path from either .ncbirc or the MPIBLAST_SHARED environment variable.
> The mpiBLAST configuration in .ncbirc should look like:
> [mpiBLAST]
> Shared=/path/to/shared/storage
> Local=/path/to/local/storage
> tal Error:F
> FUnablFatal Error:e to raead tFatal Error:
> Unable to read mpiBLAST shared
> Unable to read mpiBLAST shared storage path from eitherFatal Error:
> Fatal Error:Fatal Error:Unable to re
> Unable to read mp
> Unable to read mpiBLAST Fatal Error:
> shared storage path frUnable to reaaFatal Error:Fatal Error:
> Unable to read mp
> Unable to riBLAST shared storaead mpiBLAST shared l storage path from either .ncbirc or the MPI .ncbirc or the MPIBLAST_SHARED environment vFatal Error:
> Unable to read mpiBLAST shared storage path from either .ncbirc or the MPIBLAST_SHARED environment variable.
> The mpiBLAST configuration in .ncbirc should look like:
> [mpiBLAST]
> Shared=/path/to/shared/storage
> Local=/path/to/local/storage
> ariable.
> The mpiBLAST conFatal Error:
> Unable to read mpiBLAST shared storage path from either .ncbirc or the MPIBLAST_SHARED environment variable.
> The mpiBLAST configuration in .ncbirc should look like:
> [mpiBLAST]
> Shared=/path/to/Fatal Error:
> Unable to read mpiBLAST shared storage path from either .ncbirc or the MPIBLAST_SHARED environment variable.
> The mpiBLAST configuration in .ncbirc should look like:
> [mpiBLAST]
> Shared=/path/to/shared/storage
> Local=/path/to/local/storage
> BLAST_SHARED environment variable.
> The mpiBLAST coad mpiBLAST shared storaFatal Error:
> Unable to read mpiBLAST shared storage path from either .ncbirc or the MPIBLAST_SHARED environment variable.
> The mpiBLAST configuration in .ncbirc should look like:
> [mpiBLAST]
> Shared=/path/to/ge path from eitheiBLAST shared storagom either .ncbirc or the MPIBLAST_SHARED enr .ncbirc or the e path from either .ncbirc or the d mpiBLAST shared storage path from either .ncbirc or Evironmentge path from eitherstorage path from either .n .ncbirc or thcbie MPIBLASrc or the MPIBLAST_SHAREr variable.
> The mpiBLAST configuration in .ncbirc should lofiguration in .ncbirc should lrook like:
> [mpiBLAST]
> nfiguration in .ncbirc should lShared=/path/to/shared/storage
> Local=/pathshared/storage
> Local=/path/to/local/storage
> shared/storage
> Local=/path/to/local/storage
> ook like:
> [mpiBLAST]
> ShareMPIBLAST_SHARED environment MPIBLAST_SHAok like:
> [mpiBLAST]
> Shared=/path/to/shared/storage
> Local=variable.
> TRED environment varithe MPIBLAST_SHARED environment variable.
> The mpiBLAST o/path/to/loT_SHARED environmD environment variabent variable.
> Thele.
> The mpiBLAST conf mpiBLAST coniguration in .rcal/storage
> /to/local/storage
> :atal Error:d=/pa
> Unable to read mpiBLAST th/to/shared/storage
> Local=/path/to/local/storage
> Fatal he mpiBLAST configurable.
> TheFatal Error:ation in . mpiBLAST configuconfiguration in .ncbirc should loo
>
> Unfiguration inncbirc should .ncbirc shlook like:ould look l
> [mpiBLASUable to readshared stornage path from either .nEcbirc or the MPIBLAST_SHARED environrror:
> ncbirc should lookration in mpiBLAST like:.ncbirc should lok like:
> [mpiBLAST]
> Shared=/path/to/shara shared ike:
> [mpiBLAST]
> SharedT]
> Shared=/pa=/path/to/th/to/shared/shared/ststorage
> Local=/bstoragment variable.
> Tlhe mpiBLAST configuration in .ncUnable birc shouto read mpiBLAST shared storage
> [mpiBLAST]
> Shared=/pathok like:
> [e path from either .ncbirc or the MPIBLAST_SHARED environ/to/sharedmpiBLAST]
> Shared=/pathed/storage
> Local=/path/to/local/storage
> Fatal Error:ement variable.
> The mpiBLAST configuration in .ncbirc should loooragpath/to/loce
> Local=/pal/storage
> ath/to/locaFatal E k like:
> [mpiBLAST]
> Shared=/path/to/shared/storageld look likte:
> [mpiBLAST]
> path frShared=/pom either ./storage
> Loca/to/s
> Local=/path/tl=/path/hared/storage
> Unable to reaoo/local/storage
> l/storage
> rror:Fatal E
> rror:Unable to ath/to/shared/storagre
> Local=/pncbiath/to/local/storage
> rc or the MPIBLAST_SHARED eto/local/storage
> Local=/path/to/loc
> al/storage
> d mpiBLAST shared storage path from either .ncbirc or the MPIBLAST_SHARED environment variable.
> The mpiBLAST configuratione
> Uread mnable to repiBLAST ad mshared storage path from eithadnvironment variable.
> The mpiFatal Error:Fatal Error:
> U
> in .ncbirc should look like:
> [mpiBLAST piBLAST shared ster .ncbir]
> Shared=/path/to/shared/sorage path from either .ncbirc or the MPIBLc or the AST_SHMPIBLASTmpBLAST configuration in .ncbirc shouldnable to read mpiBLAUnable to rST sharead mpiBLAtorage
> Local=/path/to/local/storage
> iARED envir_SHAonment variable.
> The mpiBLAST configuration in RED envi.ncbirronment variable.
> The mpiBLASTBL look like:
> [mpiBLAST]
> Shaed storage path froST shared storagem either .ncb path from either .ncAc should configuralook like:
> [mpiBLAST]
> Shared=/path/to/shared/tion in storage
> .ncbSTred=/path/irc or thto/shared/storage
> Local=/path/to/local/se MPbirc or the MPIBLAST_SHARED environmeIBLAST_SHARnt variab Lirc shoulocal=/pathd look like:
> [mpiBLAST]
> Shared/to/local/storage
> =/path/toshtorage
> ED environment varile.
> The mpiBLAST configuration in .ncbirc should look able.
> The mpiBLAST confilike:
> [mpa/shared/storage
> Local=reguration in iBLAST]
> Shared=/p.ncbircdath/to/shared/stora/path/to/local/storage
> s shge
> Local=/path/to/local/storage
> ould look like:
> [mptoriBLAST]
> Shared=/path/to/shared/storage
> Loagecal=/path/to/local/storage
> path from either .ncbirc or the MPIBLAST_SHARED environment variable.
> The mpiBLAST configuration in .ncbirc should look like:
> [mpiBLAST]
> Shared=/path/to/shared/storage
> Local=/path/to/local/stor-----------------------------------------------------------------------------
> age
> 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.
>
> FPID 5953 failed on node n0 (10.10.0.1) with exit status 1.
> -----------------------------------------------------------------------------
> atal Error:
> Unable to read mpiBLAST shared storage path from either .ncbirc or the MPIBLAST_SHARED environment variable.
> The mpiBLAST configuration in .ncbirc should look like:
> [mpiBLAST]
> Shared=/path/to/shared/storage
> Local=/path/to/local/storage
>
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With Best Regards,
Ankit Patel
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