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

Sean Davis sdavis2 at mail.nih.gov
Fri Dec 28 23:11:40 GMT 2007


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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
12/28/2007 16:06:54 [0:25961]: forked "job" with pid 0
12/28/2007 16:06:54 [0:25961]: child: job - pid: 0
12/28/2007 16:06:54 [0:25961]: wait3 returned -1
12/28/2007 16:06:54 [0:25961]: can't open file /tmp/285.1.all.q/pid: No such
file or directory
12/28/2007 16:06:54 [0:25961]: write_to_qrsh - data = 1:can't open file
/tmp/285.1.all.q/pid: No such file or directory
12/28/2007 16:06:54 [0:25961]: write_to_qrsh - address =
shakespeare<http://shakespeare.nci.nih.gov/>
12/28/2007 16:06:54 [0:25961]: illegal value for qrsh_control_port: "
shakespeare <http://shakespeare.nci.nih.gov/>". Should be host:port
12/28/2007 16:06:54 [10020:25958]: wait3 returned 25961 (status: 2816;
WIFSIGNALED: 0,  WIFEXITED: 1, WEXITSTATUS: 11)
12/28/2007 16:06:54 [10020:25958]: job exited with exit status 11
12/28/2007 16:06:54 [10020:25958]: reaped "job" with pid 25961
12/28/2007 16:06:54 [10020:25958]: job exited not due to signal
12/28/2007 16:06:54 [10020:25958]: job exited with status 11
12/28/2007 16:06:54 [0:25958]: can't open file /tmp/285.1.all.q/pid: No such
file or directory
12/28/2007 16:06:54 [0:25958]: write_to_qrsh - data = 1:can't open file
/tmp/285.1.all.q/pid: No such file or directory
12/28/2007 16:06:54 [0:25958]: write_to_qrsh - address =
shakespeare:44242<http://shakespeare.nci.nih.gov:44242/>
12/28/2007 16:06:54 [0:25958]: write_to_qrsh - host =
shakespeare<http://shakespeare.nci.nih.gov/>,
port = 44242

Any other ideas?

Thanks again,
Sean



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