[GE users] qrsh problem

deadline deadline at basement-supercomputing.com
Mon Aug 30 17:59:01 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

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

> 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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>>>>>>>>>> [users-unsubscribe at gridengine.sunsource.net].
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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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--
Doug



--
Doug

--
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