[GE users] PVM tight integration

davide cittaro daweonline at gmail.com
Tue Apr 11 13:48:21 BST 2006


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I can remove it, but then it happens that a program I will use (hmmer)
can't find another executable (hmmersearch-pvm).

Let's see...
[10 minutes later]

No, it doesn't work. It seems to me that the PVM_DPATH cannot be
passed correctly... slave nodes cannot start pvm. How can I solve this
if neither "env" in the rsh wrapper doesn't work?

d

On 4/11/06, Reuti <reuti at staff.uni-marburg.de> wrote:
> Can it be, that:
>
> -ep /usr/bin
>
> will bypass the rsh-wrapper - can you remove it?
>
> ...more below
>
> Am 11.04.2006 um 14:03 schrieb davide cittaro:
>
> > On 4/11/06, Reuti <reuti at staff.uni-marburg.de> wrote:
> >> I put all in .bashrc according to my location of the files:
> >>
> >> export PVM_ROOT=$HOME/pvm3
> >> export PATH=$PVM_ROOT/bin/LINUX:$PVM_ROOT/lib/LINUX:$PATH
> >
> > I'm going to try.
> >
> >>
> >> What is the output of the .po and .pe are the started pvmds counted
> >> correctly?
> >
> > $ cat tester_tight.sh.po39641
> > -ep /usr/bin -catch_rsh
> > /opt/n1ge6/omix/spool/node6/active_jobs/39641.1/pe_hostfile
> > node6.sge.ifom-ieo-campus.it /usr/share/pvm3
> > /tmp/pvmtmp017402.0
> > startpvm.sh: startup failed - invoking cleanup script
> > -catch_rsh /opt/n1ge6/omix/spool/node6/active_jobs/39641.1/pe_hostfile
> > node6.sge.ifom-ieo-campus.it
> > -catch_rsh /opt/n1ge6/omix/spool/node6/active_jobs/39641.1/pe_hostfile
> > node6.sge.ifom-ieo-campus.it
> >
> > $ cat tester_tight.sh.pe39641
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399]: pvm_mytid(): Can't contact local daemon
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399]: pvm_mytid(): Can't contact local daemon
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399]: pvm_mytid(): Can't contact local daemon
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399]: pvm_mytid(): Can't contact local daemon
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399]: pvm_mytid(): Can't contact local daemon
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399]: pvm_mytid(): Can't contact local daemon
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399]: pvm_mytid(): Can't contact local daemon
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399]: pvm_mytid(): Can't contact local daemon
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399]: pvm_mytid(): Can't contact local daemon
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17399]: pvm_mytid(): Can't contact local daemon
> > start_pvm: Couldn't enroll to pvm
> > libpvm [pid17430] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17430] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17430]: pvm_halt(): Can't contact local daemon
> > rm: cannot remove `/tmp/39641.1.bofh.q/hostfile': No such file or
> > directory
> > rm: cannot remove `/tmp/39641.1.bofh.q/rsh': No such file or directory
>
> So, here is the problem: why are the files "hostfile" and (the link)
> "rsh" not created in the intended location? Something is not working
> with your start_proc_args. Are you setting TMPDIR by hand in any of
> your login scripts which supersedes the SGE setting of it? - Reuti
>
> > libpvm [pid17435] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17435] /tmp/39641.1.bofh.q/pvmd.2486: No such file or
> > directory
> > libpvm [pid17435]: pvm_halt(): Can't contact local daemon
> >
> >
> >>
> >>> but still the headnode can't start slavenodes...
> >>> Also, if I delete a job with qdel, pvm doesn't stop on the head
> >>> node,
> >>> and I have to enter to pvm console and manually halt it.
> >>> Any hint on this?
> >>>
> >>
> >> This shouldn't work, unless you set also PVM_TMP by hand before
> >> entering the console, as inside PVM_TMP the special files are
> >> created. Where are they in your cluster placed?
> >
> > the default is in /tmp (pvmd.ID, pvml.ID and the socket)
> >
> > d
> >
> >>
> >> -- Reuti
> >>
> >>
> >>> Thanks again
> >>>
> >>> --
> >>> dawe
> >>> http://dawe.ilbello.com
> >>> ---
> >>> "Prediction is very difficult, especially if it's about the
> >>> future." -
> >>> Niels Bohr
> >>>
> >>> --------------------------------------------------------------------
> >>> -
> >>> To unsubscribe, e-mail: users-unsubscribe at gridengine.sunsource.net
> >>> For additional commands, e-mail: users-help at gridengine.sunsource.net
> >>>
> >>
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> >>
> >>
> >
> >
> > --
> > dawe
> > http://dawe.ilbello.com
> > ---
> > "Prediction is very difficult, especially if it's about the future." -
> > Niels Bohr
> >
> > ---------------------------------------------------------------------
> > To unsubscribe, e-mail: users-unsubscribe at gridengine.sunsource.net
> > For additional commands, e-mail: users-help at gridengine.sunsource.net
> >
>
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>


--
dawe
http://dawe.ilbello.com
---
"Prediction is very difficult, especially if it's about the future." -
Niels Bohr

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