Hi Darling,
Thank you so much, for your help.
Now it's working very nice.
I was mountin the database on server machine.
Anything I will back to call you.
Thanks,
Daniel Xavier - PUC-Rio Brasil
> ----- Mensagem original ----
> De: Aaron Darling <[EMAIL PROTECTED]>
> Para: [email protected]
> Enviadas: Quinta-feira, 2 de Novembro de 2006 1:25:37
> Assunto: Re: [Mpiblast-users] Problem to execut MPIBLAST
>
> 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="">> >
> > [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
> <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
> <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
>
>
> ------------------------------------------------------------------------
> 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/>
Thank you so much, for your help.
Now it's working very nice.
I was mountin the database on server machine.
Anything I will back to call you.
Thanks,
Daniel Xavier - PUC-Rio Brasil
> ----- Mensagem original ----
> De: Aaron Darling <[EMAIL PROTECTED]>
> Para: [email protected]
> Enviadas: Quinta-feira, 2 de Novembro de 2006 1:25:37
> Assunto: Re: [Mpiblast-users] Problem to execut MPIBLAST
>
> 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="">> >
> > [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
> <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
> <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
>
>
> ------------------------------------------------------------------------
> 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/>
Novidade no Yahoo! Mail: receba alertas de novas mensagens no seu celular. Registre seu aparelho agora!
------------------------------------------------------------------------- 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
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