[torqueusers] Any one have experience of testing mpiBLAST through PBS

James J Coyle jjc at iastate.edu
Thu Apr 17 09:04:26 MDT 2008


Xin,

   It's not finding a file, so my guess is that you are in the
wrong directory, probably your home directory.  
Placing the command pwd in the script that you submit would confirm this.

   I'd try inserting the command 
cd $PBS_O_WORDIR
after the #PBS lines in the script 
and before the mpirun command.

   This will place you in the directory from which you issued 
qsub.

-- 
 James Coyle, PhD
 High Performance Computing Group     
 235 Durham Center            
 Iowa State Univ.           phone: (515)-294-2099
 Ames, Iowa 50011           web: http://www.public.iastate.edu/~jjc

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> Hello All,
> 
> I compile mpiBLAST on our linux-rhel4-x86_64 cluster. The test on interacti=
> ve nodes runs well. However, I get error message with no debug file that we=
> re generated. I have no clue but guess it has something to do with PBS. I a=
> ppreciate any hint on it.
> 
> Best,
> Xin
> 
> xinhong at Quarry: /N/gpfsbr/xinhong/mpiblast/test> more testPBS.e282564
> logging to pio.debug.0
> logging to logging to pio.debug.1
> logging to pio.debug.2
> **io No such file or directoryError opening "quarry.fasta"
> Fatal Error:
> mpiblast_util.cpp(MpiBlast::broadcastFile): Unable to open file
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
>     p4_error: latest msg from perror: No such file or directory
> Killed by signal 2.
> Killed by signal 2.
> Killed by signal 2.
> 
> 
> xinhong at Quarry: /N/gpfsbr/xinhong/mpiblast/test> more testPBS.o282564
> mpirun mpiblast exit code ( 0 is normal):
> p0_19748:  p4_error: : -1
> 1
> Done!
> 
> xinhong at Quarry: /N/gpfsbr/xinhong/mpiblast/test> more testPBS
> #PBS -l nodes=3D2:ppn=3D2,walltime=3D1:00:00
> #PBS -m ae
> #PBS -N testPBS
> echo "mpirun mpiblast exit code ( 0 is normal):"
> mpirun -np 4 -machinefile $PBS_NODEFILE /N/soft/linux-rhel4-x86_64/mpiblast=
> -1.5.0-pio/bin/mpiblast -p blastn -d mito.nt -i quarry.fasta  -o noninter
> active4.out --use-parallel-write --debug=3Dpio.debug
> echo $?
> echo "Done!"
> 
> 
> 
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> <div class=3DSection1>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>Hello All,<o:p></o:p></span></font></p=
> >
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>I compile mpiBLAST on our linux-rhel4-=
> x86_64
> cluster. The test on interactive nodes runs well. However, I get error mess=
> age with
> no debug file that were generated. I have no clue but guess it has somethin=
> g to
> do with PBS. I appreciate any hint on it.<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>Best,<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>Xin<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>xinhong at Quarry:
> /N/gpfsbr/xinhong/mpiblast/test&gt; more testPBS.e282564<o:p></o:p></span><=
> /font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>logging to pio.debug.0<o:p></o:p></spa=
> n></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>logging to logging to pio.debug.1<o:p>=
> </o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>logging to pio.debug.2<o:p></o:p></spa=
> n></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>**io No such file or directoryError
> opening &quot;quarry.fasta&quot;<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>Fatal Error:<o:p></o:p></span></font><=
> /p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>mpiblast_util.cpp(MpiBlast::broadcastF=
> ile):
> Unable to open file<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>[0] MPI Abort by user Aborting program=
>  !<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>[0] Aborting program!<o:p></o:p></span=
> ></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>&nbsp;&nbsp;&nbsp; p4_error: latest ms=
> g
> from perror: No such file or directory<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>Killed by signal 2.<o:p></o:p></span><=
> /font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>Killed by signal 2.<o:p></o:p></span><=
> /font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>Killed by signal 2.<o:p></o:p></span><=
> /font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>xinhong at Quarry:
> /N/gpfsbr/xinhong/mpiblast/test&gt; more testPBS.o282564<o:p></o:p></span><=
> /font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>mpirun mpiblast exit code ( 0 is norma=
> l):<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>p0_19748:&nbsp; p4_error: : -1<o:p></o=
> :p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>1<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>Done!<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>xinhong at Quarry:
> /N/gpfsbr/xinhong/mpiblast/test&gt; more testPBS<o:p></o:p></span></font></=
> p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>#PBS -l nodes=3D2:ppn=3D2,walltime=3D1=
> :00:00<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>#PBS -m ae<o:p></o:p></span></font></p=
> >
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>#PBS -N testPBS<o:p></o:p></span></fon=
> t></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>echo &quot;mpirun mpiblast exit code (=
>  0
> is normal):&quot;<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>mpirun -np 4 -machinefile $PBS_NODEFIL=
> E
> /N/soft/linux-rhel4-x86_64/mpiblast-1.5.0-pio/bin/mpiblast -p blastn -d mit=
> o.nt
> -i quarry.fasta&nbsp; -o noninter<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>active4.out --use-parallel-write
> --debug=3Dpio.debug<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>echo $?<o:p></o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'>echo &quot;Done!&quot;<o:p></o:p></spa=
> n></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>
> 
> <p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span style=
> =3D'font-size:
> 10.0pt;font-family:Arial;color:navy'><o:p>&nbsp;</o:p></span></font></p>
> 
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