[gridengine users] help

Reuti reuti at staff.uni-marburg.de
Thu Nov 22 13:26:04 UTC 2012


Am 22.11.2012 um 12:30 schrieb jan roels:

> Hi,
> 
> qstat -j <jobid> didn't show the full error message, this one is the full error message:
> 
> 11/22/2012 12:26:11|  main|camilla|E|shepherd of job 76.226 exited with exit status = 27
> 11/22/2012 12:26:11|  main|camilla|E|can't open usage file "active_jobs/76.226/usage" for job 76.226: No such file or directory
> 11/22/2012 12:26:11|  main|camilla|E|11/22/2012 12:26:10 [0:11412]: execvlp(/var/spool/gridengine/execd/camilla/job_scripts/76, "/var/spool/gridengine/execd/camilla/job_scripts/76") failed: No such file or directory

Could be a permission problem. Everyone needs read-access to this directory as the jobscript is executed from there.

-- Reuti


> 
> 
> 2012/11/22 jan roels <janroels at gmail.com>
> Hi,
> 
> Do you guys now what this error could be:
> 
> error reason    2:          11/22/2012 11:12:25 [0:31220]: execvlp(/var/spool/gridengine/execd/node0/job_scripts/69, "/var/spool
> error reason    3:          11/22/2012 11:12:25 [0:31221]: execvlp(/var/spool/gridengine/execd/node0/job_scripts/69, "/var/spool
> 
> this goes on as long as iets running... and my state went to:
> 
>      69 0.50000 SA         root         Eqw   11/22/2012 09:12:05     1 1-500:1
>      69 0.00000 SA         root         qw    11/22/2012 09:12:05     1 501-4200:1
> 
> This is the script i was running:
> 
> #!/bin/bash
> #$-cwd
> #$-N SA
> #$-t 1-4200:1
> 
> /var/software/packages/Mathematica/7.0/Executables/math -run "teller=$SGE_TASK_ID;<< ModelCaCO31.m"
> 
> Hope somebody can fix the problem.
> 
> Kind Regards
> 
> 
> 2012/11/14 Reuti <reuti at staff.uni-marburg.de>
> Am 14.11.2012 um 10:08 schrieb jan roels:
> 
> > I got it working again, there was already a proces of execd running that needed to be killed and then restart the services.
> >
> > I'm trying to run a script now:
> >
> >
> > #!/bin/bash
> > #$-cwd
> > #$-N SA
> > #$-S /bin/sh
> > #$-t 1-4200:
> 
> Don't run scripts at root. If something goes wring it might trash your machine(s).
> 
> 
> > /var/software/packages/Mathematica/7.0/Executables/math -run "teller=$SGE_TASK_ID;<< ModelCaCO31.m"
> >
> > but it gives the following output:
> >
> > stdin: is not a tty
> 
> It's just a warning - unless someone complains I would suggest to ignore it.
> 
> 
> > and this is the output of my qstat -f:
> >
> > queuename                      qtype resv/used/tot. load_avg arch          states
> > ---------------------------------------------------------------------------------
> > main.q at camilla.UGent.be        BIP   0/1/1          0.70     lx26-amd64
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 1
> > ---------------------------------------------------------------------------------
> > main.q at node0                   BIP   0/24/24        27.71    lx26-amd64
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 2
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 3
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 4
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 5
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 6
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 7
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 8
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 9
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 10
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 11
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 12
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 13
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 14
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 15
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 16
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 17
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 18
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 19
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 20
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 21
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 22
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 23
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 24
> >      35 0.50000 SA         root         r     11/14/2012 09:57:47     1 25
> >
> > ############################################################################
> >  - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS - PENDING JOBS
> > ############################################################################
> >      35 0.50000 SA         root         qw    11/14/2012 09:57:38     1 26-4200:1
> >
> >
> > root at camilla:/nfs/share/sge#  qstat -explain c -j 35
> > ==============================================================
> > job_number:                 35
> > exec_file:                  job_scripts/35
> > submission_time:            Wed Nov 14 09:57:38 2012
> > owner:                      root
> > uid:                        0
> > group:                      root
> > gid:                        0
> > sge_o_home:                 /root
> > sge_o_log_name:             root
> > sge_o_path:                 /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
> > sge_o_shell:                /bin/bash
> > sge_o_workdir:              /nfs/share/sge
> > sge_o_host:                 camilla
> > account:                    sge
> > cwd:                        /nfs/share/sge
> > mail_list:                  root at camilla
> > notify:                     FALSE
> > job_name:                   SA
> > jobshare:                   0
> > shell_list:                 NONE:/bin/sh
> > env_list:
> > script_file:                HistDisCaCO31.sh
> > job-array tasks:            1-4200:1
> > usage    1:                 cpu=00:05:20, mem=105.16135 GBs, io=0.01537, vmem=1.110G, maxvmem=1.110G
> > usage    2:                 cpu=00:04:17, mem=179.44371 GBs, io=0.01395, vmem=3.643G, maxvmem=3.643G
> > usage    3:                 cpu=00:04:37, mem=191.69532 GBs, io=0.01394, vmem=3.657G, maxvmem=3.657G
> > usage    4:                 cpu=00:04:34, mem=188.12645 GBs, io=0.01394, vmem=3.655G, maxvmem=3.655G
> > usage    5:                 cpu=00:04:16, mem=180.18292 GBs, io=0.01394, vmem=3.636G, maxvmem=3.636G
> > usage    6:                 cpu=00:04:22, mem=183.47616 GBs, io=0.01394, vmem=3.644G, maxvmem=3.644G
> > usage    7:                 cpu=00:04:15, mem=179.89624 GBs, io=0.01400, vmem=3.640G, maxvmem=3.640G
> > usage    8:                 cpu=00:04:55, mem=207.28643 GBs, io=0.01394, vmem=3.669G, maxvmem=3.669G
> > usage    9:                 cpu=00:04:27, mem=184.86707 GBs, io=0.01394, vmem=3.653G, maxvmem=3.653G
> > usage   10:                 cpu=00:04:14, mem=179.09446 GBs, io=0.01394, vmem=3.635G, maxvmem=3.635G
> > usage   11:                 cpu=00:04:47, mem=195.80372 GBs, io=0.01400, vmem=3.668G, maxvmem=3.668G
> > usage   12:                 cpu=00:04:49, mem=203.43895 GBs, io=0.01394, vmem=3.665G, maxvmem=3.665G
> > usage   13:                 cpu=00:04:45, mem=196.67175 GBs, io=0.01394, vmem=3.663G, maxvmem=3.663G
> > usage   14:                 cpu=00:04:24, mem=185.68047 GBs, io=0.01400, vmem=3.648G, maxvmem=3.648G
> > usage   15:                 cpu=00:04:40, mem=195.96253 GBs, io=0.01394, vmem=3.656G, maxvmem=3.656G
> > usage   16:                 cpu=00:04:11, mem=179.84016 GBs, io=0.01394, vmem=3.633G, maxvmem=3.633G
> > usage   17:                 cpu=00:04:43, mem=196.21689 GBs, io=0.01394, vmem=3.662G, maxvmem=3.662G
> > usage   18:                 cpu=00:04:37, mem=197.39875 GBs, io=0.01394, vmem=3.653G, maxvmem=3.653G
> > usage   19:                 cpu=00:04:35, mem=191.55982 GBs, io=0.01394, vmem=3.653G, maxvmem=3.653G
> > usage   20:                 cpu=00:04:26, mem=191.62928 GBs, io=0.01394, vmem=3.643G, maxvmem=3.643G
> > usage   21:                 cpu=00:04:42, mem=197.87398 GBs, io=0.01394, vmem=3.660G, maxvmem=3.660G
> > usage   22:                 cpu=00:04:36, mem=193.43107 GBs, io=0.01394, vmem=3.652G, maxvmem=3.652G
> > usage   23:                 cpu=00:04:32, mem=193.12103 GBs, io=0.01394, vmem=3.652G, maxvmem=3.652G
> > usage   24:                 cpu=00:04:25, mem=186.56485 GBs, io=0.01400, vmem=3.644G, maxvmem=3.644G
> > usage   25:                 cpu=00:04:51, mem=201.81706 GBs, io=0.01400, vmem=3.669G, maxvmem=3.669G
> > scheduling info:            queue instance "main.q at camilla" dropped because it is full
> >                             queue instance "main.q at node0" dropped because it is full
> >                             All queues dropped because of overload or full
> >                             not all array task may be started due to 'max_aj_instances'
> 
> The machine is just full.
> 
> -- Reuti
> 
> 
> > You guys know how this can be solved?
> >
> >
> >
> > 2012/11/13 Reuti <reuti at staff.uni-marburg.de>
> > Am 13.11.2012 um 13:42 schrieb jan roels:
> >
> > > Hi,
> > >
> > > I followed the following tutorial:
> > >
> > > http://verahill.blogspot.be/2012/06/setting-up-sun-grid-engine-with-three.html on how to install the SGE. It all went fine on my masternode but on my exec node i have some troubles.
> > >
> > > First it gave the following error:
> > >
> > > 11/13/2012 13:44:43|  main|node0|E|communication error for "node0/execd/1" running on port 6445: "can't bind socket"
> >
> > Is there already something running on this port - any older version of the execd?
> >
> >
> > > 11/13/2012 13:44:44|  main|node0|E|commlib error: can't bind socket (no additional information available)
> > > 11/13/2012 13:45:12|  main|node0|C|abort qmaster registration due to communication errors
> > > 11/13/2012 13:45:14|  main|node0|W|daemonize error: child exited before sending daemonize state
> > >
> > > but then i killed the proces and restarted the gridengine-execd but then i get the following:
> > >
> > > /etc/init.d/gridengine-exec restart
> > > * Restarting Sun Grid Engine Execution Daemon sge_execd                                                    error: can't resolve host name
> > > error: can't get configuration from qmaster -- backgrounding
> > >
> > > What can i do to fix this?
> >
> > Any firewall on the machines? Ports 6444 and 6445 need to be excluded.
> >
> > -- Reuti
> >
> > > _______________________________________________
> > > users mailing list
> > > users at gridengine.org
> > > https://gridengine.org/mailman/listinfo/users
> >
> >
> 
> 
> 




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