[GE users] qrsh problem

reuti reuti at staff.uni-marburg.de
Mon Aug 30 15:58:46 BST 2010


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

To avoid a mismatch of programs: did you check `qconf -sconfl` that there is no custom definition for the headnode?

A `qsub`ed job works fine on the headnode?

-- 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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>>>>>>>
>>>>>>> --
>>>>>>> Doug
>>>>>>>
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>>>>>
>>>>>
>>>>> --
>>>>> Doug
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Doug
>>>>>
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>>>
>>>
>>> --
>>> Doug
>>>
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>
> --
> Doug
>
> --
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