[GE users] [OT] Running R under SGE and OpenMPI

Sean Davis sdavis2 at mail.nih.gov
Thu Oct 9 18:06:49 BST 2008


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On Thu, Oct 9, 2008 at 12:42 PM, Reuti <reuti at staff.uni-marburg.de> wrote:
> Sean,
>
> Am 09.10.2008 um 17:47 schrieb Sean Davis:
>
>> On Thu, Oct 9, 2008 at 11:31 AM, Rayson Ho <rayrayson at gmail.com> wrote:
>>>
>>> On 10/9/08, Sean Davis <sdavis2 at mail.nih.gov> wrote:
>>>>
>>>> I can confirm that there is no --with-sge in the configure --help
>>>> output, even in 1.2.7.
>>>
>>> Yes, that's only in 1.3.
>>>
>>> BTW, how is your PE defined?? The error message tells you that the
>>> remote execd is not starting the remote tasks:
>>>
>>>  error: got no connection within 60 seconds
>>>  [octopus:21290] ERROR: A daemon on node shakespeare.nci.nih.gov failed
>>>  to start as expected.
>
> is there any firewall installed on the machines?

No.  And shakespeare is the qmaster of an otherwise working cluster.

Sean

>> Thanks, Rayson.
>>
>>> qconf -sp orte
>>
>> pe_name            orte
>> slots              999
>> user_lists         NONE
>> xuser_lists        NONE
>> start_proc_args    /bin/true
>> stop_proc_args     /bin/true
>> allocation_rule    $round_robin
>> control_slaves     TRUE
>> job_is_first_task  FALSE
>> urgency_slots      min
>> accounting_summary FALSE
>>
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>
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