[GE users] qmake job and errors: pid: No such file or directory

Sean Davis sdavis2 at mail.nih.gov
Sat Dec 29 14:05:10 GMT 2007


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On Dec 29, 2007 7:58 AM, Reuti <reuti at staff.uni-marburg.de> wrote:

> Am 29.12.2007 um 00:11 schrieb Sean Davis:
>
> On Dec 28, 2007 5:16 PM, Reuti < reuti at staff.uni-marburg.de> wrote:
>
> > Hi,
> >
> > Am 28.12.2007 um 22:15 schrieb Sean Davis:
> >
> > > I am trying to run qmake on the Solexa analysis pipeline (probably
> > > not important, but....).  When I run this command, I get the
> > > following error:
> > >
> > > can't open file /tmp/285.1.all.q/pid: No such file or directory
> > >
> > > I have the shepherd trace available, also.  Does this problem ring
> > > any bells for anyone?
> > >
> > > As for details of our setup, we have several linux boxes running
> > > the lx24-amd64 binaries (though they are intel machines).  All are
> > > using ssh for communication.  None has a firewall enabled.  They
> > > are using shared home directories, but /tmp, etc., are local to the
> > > machines.  Qlogin, qrsh, and qsh seem to be working.  We have
> > > openmpi installed, also.
> > >
> > > I know the question is pretty vague.  I am pretty new to SGE, so
> > > debugging these issues is pretty new also.  Any guidance is
> > > appreciated.
> >
> > usually the 'pid' file should go to a spool directory like:
> >
> > $SGE_ROOT/spool/sge/<node>/active_jobs/<job_id>.<task_id>
> >
> > or better:
> >
> > /var/spool/sge/<node>/active_jobs/<job_id>.<task_id>
> >
> > and not the local tmp directory for the job. Where is the spool
> > directory for the node: local or on the NFS server? Best would be to
> > have it local on all nodes:
> >
> > http://gridengine.sunsource.net/howto/nfsreduce.html
> >
>
> Thanks, Reuti and John.
>
> The /tmp directory is world read and write, just to make certain.
>
> How can I set the location of the pid file?  Is there a convenient way to
> check where the local spooling for each node is located?
>
> Here is a bit of the shepherd trace, as it seems like the local spool
> directory is used, but also the tmp directory on the qmaster:
>
> 2/28/2007 16:05:54 [10020:25961]: setting environment
> 12/28/2007 16:05:54 [10020:25961]: Initializing error file
> 12/28/2007 16:05:54 [10020:25958]: forked "job" with pid 25961
> 12/28/2007 16:05:54 [10020:25958]: child: job - pid: 25961
> 12/28/2007 16:05:54 [10020:25961]: switching to intermediate/target user
> 12/28/2007 16:05:54 [10005:25961]: closing all filedescriptors
> 12/28/2007 16:05:54 [10005:25961]: further messages are in "error" and
> "trace"
> 12/28/2007 16:05:54 [0:25961]: now running with uid=0, euid=0
> 12/28/2007 16:05:54 [0:25961]: start qlogin
> 12/28/2007 16:05:54 [0:25961]: calling qlogin_starter(/var/spool/sge /local/pressa/active_jobs/285.1,
> /usr/sbin/sshd -i);
> 12/28/2007 16:05:54 [0:25961]: uid = 0, euid = 0, gid = 0, egid = 0
> 12/28/2007 16:05:54 [0:25961]: using sfd 1
> 12/28/2007 16:05:54 [0:25961]: bound to port 54613
> 12/28/2007 16:05:54 [0:25961]: write_to_qrsh - data =
> 0:54613:/usr/local/sge/utilbin/lx24-amd64:/var/spool/sge/local/pressa/active_jobs/285.1:
> pressa <http://pressa.nci.nih.gov/>
> 12/28/2007 16:05:54 [0:25961]: write_to_qrsh - address = shakespeare:44242<http://shakespeare.nci.nih.gov:44242/>
> 12/28/2007 16:05:54 [0:25961]: write_to_qrsh - host = shakespeare<http://shakespeare.nci.nih.gov/>,
> port = 44242
> 12/28/2007 16:05:54 [0:25961]: waiting for connection.
> 12/28/2007 16:06:54 [0:25961]: nobody connected to the socket
>
>
> What are the protections of your var/spool/sge/local/pressa/active_jobs
> and who is the owner? Who is the admin user of your SGE installation (the
> one who owns /usr/local/sge)?
>

Reuti,

root owns /usr/local/sge--this could be a problem, since the partition is
mounted with root-squash.  However, sgeadmin is the admin user (the user
under which sge_execd, sge_qmaster, etc. run).  As for
/var/spool/sge/local/pressa/active_jobs, the owner is sgeadmin; everyone can
r-x, owner can rwx.

I have changed the ownership of /usr/local/sge to sgeadmin, but the problem
seems to remain.

Thanks again,
Sean



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