Hello Daniel, You may want to check whether the .pal file, which should be called something like /home/server/b0220445/DB_mpiBlast/ecoli.aa.pal has the correct paths to each database fragment. The .pal file is an blast database alias file used to aggregate several database files (fragments) into a single virtual database. Incorrect paths in that file could result in the bad mpiblast behavior you are observing. To solve the problem, either change the paths or reformat the database.
Another thing to check is whether each worker process may be reading different copies of .ncbirc. If .ncbirc is not located on shared storage then it is important to maintain consistency among each copy of the file. -Aaron Daniel Xavier de Sousa wrote: > Hi for all, > > Please, I have one problem when try execute mpiBlast. > I configured the file .ncbirc, like this: > > [NCBI] > Data=/home/server/b0220445/ncbi/data > > [BLAST] > BLASTDB=/home/server/b0220445/DB_mpiBlast > BLASTMAT=/home/local/b0220445/ncbi/data > > [mpiBLAST] > Shared=/home/server/b0220445/DB_mpiBlast > Local=/home/local/b0220445/mpiblast-1.4.0/storageLocal > > I put my databases in /home/server/b0220445/DB_mpiBlast > But de mpiBLAST show me this out: > > [blastall] WARNING: NCU10034.1: Could not find index files for > database /home/local/b0220445/DB_mpiBlast/ecoli.aa.000 > [blastall] WARNING: NCU10034.1: Could not find index files for > database /home/local/b0220445/DB_mpiBlast/ecoli.aa.001 > [blastall] WARNING: NCU10034.1: Could not find index files for > database /home/local/b0220445/DB_mpiBlast/ecoli.aa.002 > [blastall] WARNING: NCU10034.1: Could not find index files for > database /home/local/b0220445/DB_mpiBlast/ecoli.aa.003 > [blastall] WARNING: NCU10034.1: Could not find index files for > database /home/server/b0220445/DB_mpiBlast/ecoli.aa > [blastall] WARNING: NCU10034.1: Could not find index files for > database /home/local/b0220445/DB_mpiBlast/ecoli.aa.000 > [blastall] WARNING: NCU10034.1: Could not find index files for > database /home/local/b0220445/DB_mpiBlast/ecoli.aa.001 > [blastall] WARNING: NCU10034.1: Could not find index files for > database /home/local/b0220445/DB_mpiBlast/ecoli.aa.002 > [blastall] WARNING: NCU10034.1: Could not find index files for > database /home/local/b0220445/DB_mpiBlast/ecoli.aa.003 > [blastall] WARNING: NCU10034.1: Could not find index files for > database /home/server/b0220445/DB_mpiBlast/ecoli.aa > [blastall] FATAL ERROR: NCU10034.1: Database > /home/server/b0220445/DB_mpiBlast/ecoli.aa was not found or does not exist > MPI_Recv: process in local group is dead (rank 1, comm 3) > MPI_Recv: process in local group is dead (rank 2, comm 3) > > I don't know why it show this address > :/home/local/b0220445/DB_mpiBlast/ecoli.aa.003, as local storage. > Why it isn't working? > OBS: I have confirmed if directories there are. > > Thanks > Daniel > > > ------------------------------------------------------------------------ > Novidade no Yahoo! Mail: receba alertas de novas mensagens no seu > celular. Registre seu aparelho agora! > <http://us.rd.yahoo.com/mail/br/tagline/mobile_alerts/*http://br.mobile.yahoo.com/mailalertas/> > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > ------------------------------------------------------------------------ > > _______________________________________________ > Mpiblast-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/mpiblast-users > ------------------------------------------------------------------------- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 _______________________________________________ Mpiblast-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mpiblast-users
