[GE users] qrsh problem

deadline deadline at basement-supercomputing.com
Mon Aug 30 14:09:31 BST 2010


> 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.

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

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