[GE users] qrsh problem

reuti reuti at staff.uni-marburg.de
Mon Aug 30 18:28:23 BST 2010


Am 30.08.2010 um 18:59 schrieb deadline:

>> Am 30.08.2010 um 15:09 schrieb deadline:
>>
>>>> Am 28.08.2010 um 20:07 schrieb deadline:
>>>>
>>>>>>> <snip>
>>>>>>> See below. The only thing I can think of it is talking
>>>>>>> to the wrong daemon or starting the wrong daemon?
>>>>>>
>>>>>> then the next step could be to fall back to the -builtin-
>>>>>> communication
>>>>>> method (as I see "sshd" below). Is this also not working?
>>>>>
>>>>> I assume you mean rsh? That was my thought as well.
>>>>
>>>> No. SGE has also a -builtin- startup method. Just put a plain
> "builtin" w/o the quotes in all 6 entries for *_command and *_daemon
> (`man sge_conf`). Unless you need X11 forwarding, there is no need for
> using SSH. It's also possible to use for the rlogin_* and qlogin_*
> SSH, while a
>>>> startup between nodes uses the "builtin" method.
>>>>
>>>> If you want to fall back to true `rsh`, it's not in the man page but
> here:
>>>>
>>>> http://gridengine.sunsource.net/issues/show_bug.cgi?id=2757
>>>
>>> I switched to built-in and the behavior is the same.
>>> Several things I noticed. First, the file "addgrpid"
>>> is not written to the active_jobs sub folder.
>>
>> Is there anything in the messages file of the qmster or node i.e.
> $SGE_ROOT/default/spool/qmaster/messages
>
> I submit the job:
>
> qrsh  -l h=norbert  hostname
>
> qstat shows:
>
> 584 0.50000 hostname   deadline     r     08/30/2010 12:45:53
> cluster at norbert
>
> Then I qdel it:
>
> qmaster messages:
>
> 08/30/2010 12:46:55|worker|norbert|W|job 584.1 failed on host norbert
> assumedly after job because: job 584.1 died through signal HUP (1)
>
> execd messages on norbert:
>
>> 08/30/2010 12:46:55|  main|norbert|W|reaping job "584" ptf complains:
> Job does not exist
> 08/30/2010 12:46:55|  main|norbert|E|can't open file
> active_jobs/584.1/error: No such file or directory

As other jobs are working, that spool directory doesn't seem to be full or write protected.

Can you qrsh "local" - from the headnode to itself?

-- Reuti


>
>> To avoid a mismatch of programs: did you check `qconf -sconfl` that
> there is no custom definition for the headnode?
>>
>
> yes, "no config defined"
>
>> A `qsub`ed job works fine on the headnode?
>
> yes
>
> --
> Doug
>
>
>>
>> -- Reuti
>>
>>
>>> Second, examining the shepherd trace, I see that both
>>> the threads are created without an error, but fail at
>>>
>>> 888    *exit_status = wait_my_child(job_pid, ...
>>>
>>> in sge_shepherd_ijs.c.  Here is the trace
>>>
>>> 08/29/2010 19:46:47 [0:19972]: parent: creating pty_to_commlib thread
> 08/29/2010 19:46:47 [0:19972]: parent: creating commlib_to_pty thread
> 08/29/2010 19:46:47 [0:19972]: parent: created both worker threads, now
> waiting for jobs end
>>> 08/29/2010 19:46:59 [0:19972]: wait3 returned -1
>>>
>>> It is odd because the threads seem to start fine (no errors), but then
> go away. As I said it works fine if I run it on the host
>>> it only happened when I qrsh to the host from a worker node.
>>> When I think about it, it must be some configuration
>>> issue on the host (Scientific Linux 5.4), but I am not sure
>>> where to look. Firewall is off.
>>>
>>> --
>>> Doug
>>>
>>>
>>>>>>>>>>> "norbert" is head node running sge_qmaster and sge_execd worker
> nodes are "n0" an "n2"
>>>>>>>>>>>
>>>>>>>>>>> From norbert I can "qrsh -l n=X hostname" where X is any node.
> I can
>>>>>>> do the same from any worker node to any worker node.
>>>>>>>>>>> But, I cannot run jobs like "qrsh -l n=norbert hostname" from a
>>>>>>> worker node (it does work on norbert-> norbert, however)
>>>>>>>>>>>
>>>>>>>>>>> Firewall is off, I checked permissions, all nodes
>>>>>>>>>>> are exec and submit hosts, norbert is admin host.
>>>>>>>>>>> ssh is used for remote login.
>>>>>>>>>>> I spent time going through debug traces and logs
>>>>>>>>>>> and cannot find anything obvious.
>>>>>>>>>>>
>>>>>>>>>>> Does anyone have any ideas on what to check next?
>>>>>>>>>>> I am wondering if the host node has some security
>>>>>>>>>>> feature preventing qrsh from working, but I cannot
>>>>>>>>>>> think of anything.
>>>>>>>>>>>
>>>>>>>>>>> Here are some data:
>>>>>>>>>>>
>>>>>>>>>>> CASE 1: From worker node to head node (UNSUCCESSFUL)
>>>>>>>>>>> ====================================================
>>>>>>>>>>>
>>>>>>>>>>> "qrsh  -l h=norbert  hostname"
>>>>>>>>>>>
>>>>>>>>>>> Example ps output on head node (norbert)
>>>>>>>>>>> ----------------------------------------
>>>>>>>>>>> 14231 ?        Sl     0:00
>>>>>>>>>>> /opt/gridengine/bin/lx26-amd64/sge_execd
>>>>>>> 14257
>>>>>>>>>>> ?        S      0:00  \_ sge_shepherd-490 -bg
>>>>>>>>>>> 14258 ?        Ss     0:00      \_ sge_shepherd-490 -bg
>>>>>>>>>>>
>>>>>>>>>>> Trace from qrsh on node (dl=3)
>>>>>>>>>>> ==============================
>>>>>>>>>>> 18   6647         main     R E A D I N G    J O B ! ! ! ! ! ! ! !
>>>>>>>>>>> !
>>>>>>>>>>> !
>>>>>>>>>>> ! 19   6647         main
>>>>>>>>>>> ============================================ 20   6647
>>>>>>>>>>> main
>>>>>>> random polling set to 3
>>>>>>>>>>> 21   6647         main     ---- got NO valid socket! ---- 22
> 6647         main     sge_set_auth_info: username(uid) =
> deadline(500), groupname = deadline(500)
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> Relevant parts of execd trace file for job
>>>>>>>>>>> ------------------------------------------
>>>>>>>>>>> 08/26/2010 08:31:32 [0:14441]: now running with uid=0, euid=0
>>>>>>> 08/26/2010 08:31:32 [0:14441]: start qlogin
>>>>>>>>>>> 08/26/2010 08:31:32 [0:14441]: calling
>>>>>>>>>>> qlogin_starter(/opt/gridengine/default/spool/sge_execd/norbert/active_jobs/493.1,
>>>>>>> /usr/sbin/sshd -i);
>>>>>>>>>>> 08/26/2010 08:31:32 [0:14441]: uid = 0, euid = 0, gid = 0, egid =
>>>>>>>>>>> 0
>>>>>>> 08/26/2010 08:31:32 [0:14441]: using sfd 0
>>>>>>>>>>> 08/26/2010 08:31:32 [0:14441]: bound to port 39897
>>>>>>>>>>> 08/26/2010 08:31:32 [0:14441]: write_to_qrsh - data =
>>>>>>>>>>> 0:39897:/opt/gridengine/utilbin/lx26-amd64:/opt/gridengine/default/spool/sge_execd/norbert/active_jobs/493.1:norbert
>>>>>>> 08/26/2010 08:31:32 [0:14441]: write_to_qrsh - address =
>>>>>>>>>>> n2.cluster:56747
>>>>>>>>>>> 08/26/2010 08:31:32 [0:14441]: write_to_qrsh - host =
>>>>>>>>>>> n2.cluster,
>>>>>>>>>>> port =
>>>>>>>>>>> 56747
>>>>>>>>>>> 08/26/2010 08:31:32 [0:14440]: parent: forked "job" with pid 14441
>>>>>>> 08/26/2010 08:31:32 [0:14440]: parent: job-pid: 14441
>>>>>>>>>>> 08/26/2010 08:32:17 [0:14440]: wait3 returned -1
>>>>>>>>>>>
>>>>>>>>>>> CASE 2: From worker node to worker node (SUCCESSFUL)
>>>>>>>>>>> ====================================================
>>>>>>>>>>>
>>>>>>>>>>> "qrsh  -l h=n0  hostname"
>>>>>>>>>>>
>>>>>>>>>>> Example ps output on worker node (n0)
>>>>>>>>>>> -----------------------------
>>>>>>>>>>> 3875 ?        Sl     0:11
>>>>>>>>>>> /opt/gridengine/bin/lx26-amd64/sge_execd
>>>>>>> 4083 ?        S      0:00  \_ sge_shepherd-483 -bg
>>>>>>>>>>> 4084 ?        Ss     0:00      \_ sshd: deadline [priv] 4086 ?
>      S      0:00          \_ sshd: deadline at notty 4087 ?
> Ss     0:00              \_
>>>>>>>>>>> /opt/gridengine/utilbin/lx26-amd64/qrsh_starter /op
>>>>>>>>>>> t/gridengine/default/spool/sge_execd/n0/active_jobs/483.1 4100
> ?        S      0:00                  \_ sleep 500
>>>>>>>>>>>
>>>>>>>>>>> Trace from qrsh on node (dl=3)
>>>>>>>>>>> ==============================
>>>>>>>>>>> 18   6640         main     R E A D I N G    J O B ! ! ! ! ! ! ! !
>>>>>>>>>>> !
>>>>>>>>>>> !
>>>>>>>>>>> ! 19   6640         main
>>>>>>>>>>> ============================================ 20   6640
>>>>>>>>>>> main
>>>>>>> random polling set to 3
>>>>>>>>>>> 21   6640         main     accepted client connection, fd = 3 22
>>>>>>> 6640         main     qlogin_starter sent:
>>>>>>>>>>> 0:58576:/opt/gridengine/utilbin/lx26-amd64:/opt/gridengine/default/spool/sge_execd/n0/active_jobs/509.1:n0
> 23   6640         main     accepted client connection, fd = 3
> 24
>>>>>>> 6640         main     exit_status = 0
>>>>>>>>>>> l
>>>>>>>>>>> Relevant parts of execd trace file for job on worker node
> ---------------------------------------------------------
> 08/26/2010 08:39:57 [0:4355]: now running with uid=0, euid=0
> 08/26/2010 08:39:57 [0:4355]: start qlogin
>>>>>>>>>>> 08/26/2010 08:39:57 [0:4355]: calling
>>>>>>>>>>> qlogin_starter(/opt/gridengine/default/spool/sge_execd/n0/active_jobs/499.1,
>>>>>>> /usr/sbin/sshd -i);
>>>>>>>>>>> 08/26/2010 08:39:57 [0:4355]: uid = 0, euid = 0, gid = 0, egid = 0
>>>>>>> 08/26/2010 08:39:57 [0:4355]: using sfd 0
>>>>>>>>>>> 08/26/2010 08:39:57 [0:4355]: bound to port 48105
>>>>>>>>>>> 08/26/2010 08:39:57 [0:4355]: write_to_qrsh - data =
>>>>>>>>>>> 0:48105:/opt/gridengine/utilbin/lx26-amd64:/opt/gridengine/default/spool/sge_execd/n0/active_jobs/499.1:n0
>>>>>>> 08/26/2010 08:39:57 [0:4355]: write_to_qrsh - address =
>>>>>>>>>>> n2.cluster:54407
>>>>>>>>>>> 08/26/2010 08:39:57 [0:4355]: write_to_qrsh - host =
> n2.cluster, port =
>>>>>>>>>>> 54407 08/26/2010 08:39:57 [0:4355]: waiting for connection.
> 08/26/2010 08:39:57 [0:4355]: accepted connection on fd 1
> 08/26/2010 08:39:57 [0:4355]: daemon to start: |/usr/sbin/sshd
> -i|
>>>>>>> 08/26/2010 08:39:57 [0:4354]: wait3 returned 4355 (status: 0;
> WIFSIGNALED:
>>>>>>>>>>> 0,  WIFEXITED: 1, WEXITSTATUS: 0)
>>>>>>>>>>> 08/26/2010 08:39:57 [0:4354]: job exited with exit status 0
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> Doug
>>>>>>>>>>>
>>>>>>>>>>> ------------------------------------------------------
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>>>>>>>>>>>
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>>>>>>>>>>
>>>>>>>>>> --
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>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Doug
>>>>>>>>>
>>>>>>>>> --
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>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Doug
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Doug
>>>>>>>
>>>>>>> --
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>>>>>> --
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>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Doug
>>>>>
>>>>> --
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>>>
>>>
>>> --
>>> Doug
>>>
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>>
>
>
> --
> Doug
>
>
>
> --
> Doug
>
> --
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