Probably I'll switch back to one queue - four slots. Helios has four
physical cores. Thanks for the tip with the logfile - I've been
looking for that one frantically.
Best regards
Cornelius
On Thu, Jul 29, 2010 at 8:22 PM, Matt Glasser <[log in to unmask]> wrote:
> Do you only want a single slot in each queue? How many cores exist on
> Helios? Also, have a look at /var/spool/gridengine/qmaster/messages for the
> cause of the errors.
>
> Peace,
>
> Matt.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
> Of Cornelius Werner
> Sent: Thursday, July 29, 2010 1:16 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Co-installable FSL Debian packages
>
> Hi Matt, sorry for the delay in answering.
>
> qstat -f gives me the following:
>
> queuename qtype resv/used/tot. load_avg arch
> states
> ----------------------------------------------------------------------------
> -----
> long.q@Helios BIP 0/0/1 0.92 lx26-amd64
> ----------------------------------------------------------------------------
> -----
> short.q@Helios BIP 0/0/1 0.92 lx26-amd64
> ----------------------------------------------------------------------------
> -----
> verylong.q@Helios BIP 0/0/1 0.92 lx26-amd64
> ----------------------------------------------------------------------------
> -----
> veryshort.q@Helios BIP 0/0/1 0.92 lx26-amd64
>
> That is, without issuing any qsubs. Thanks for the help!
>
> Best regards,
> Cornelius
>
> On Tue, Jul 27, 2010 at 12:17 AM, Matt Glasser <[log in to unmask]> wrote:
>> What is the output of qstat -f in your terminal?
>>
>> Peace,
>>
>> Matt.
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
>> Of Cornelius Werner
>> Sent: Monday, July 26, 2010 2:13 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] Co-installable FSL Debian packages
>>
>> Hi,
>>
>> yeah, I followed those instructions, and some other tutorials, too
>> (such as http://test.ubuntuforums.org/showthread.php?t=1097594).
>> Additionally, I added four queues as proposed by the FSL wiki
>> (https://www.fmrib.ox.ac.uk/phpwiki/index.php/FslSge). Strangely,
>> everything seems to work until I start submitting jobs. They all get
>> stuck in "pending" mode with an "E" (error) flag. I cannot figure out
>> the error, though. Did it work with you by just keeping the main.q?
>> Sorry for posting on the FSL list, by the way.
>>
>> Cheers,
>> Cornelius
>>
>>
>> On Mon, Jul 26, 2010 at 2:17 PM, Michael Hanke <[log in to unmask]>
>> wrote:
>>> On Mon, Jul 26, 2010 at 01:35:20PM +0200, Cornelius Werner wrote:
>>>> Hi,
>>>>
>>>> I just wanted to say thanks! Having FSL available as a *.deb is simply
>>>> beautiful. The only thing that doesn't seem to work is installing SGE
>>>> and FSL via apt-get, and having both work together without further
>>>> intervention (on a single quad-core machine). Well, speaking of
>>>> further interventions, even those didn't seem to work in my case, but
>>>> that's another story :-))
>>>
>>> Once you have configured SGE to work properly there should be no need
>>> for further configuration to make FSL play with it.
>>>
>>> Have you read /usr/share/doc/gridengine-common/README.Debian ? I found
>>> it quite helpful to get things started quickly.
>>>
>>> Thanks for thanks ;-)
>>>
>>> Michael
>>>
>>> --
>>> GPG key: 1024D/3144BE0F Michael Hanke
>>> http://mih.voxindeserto.de
>>>
>>
>>
>>
>> --
>> Dr. med. Cornelius J. Werner
>>
>> Department of Neurology
>> RWTH Aachen University
>> Pauwelsstr. 30
>> 52074 Aachen
>> Germany
>>
>> Institute of Neuroscience and Medicine
>> MR Physics - INM4
>> Research Centre Juelich
>> 52425 Juelich
>> Germany
>>
>> ::: Please encrypt confidential data :::
>>
>
>
>
> --
> Dr. med. Cornelius J. Werner
>
> Department of Neurology
> RWTH Aachen University
> Pauwelsstr. 30
> 52074 Aachen
> Germany
>
> Institute of Neuroscience and Medicine
> MR Physics - INM4
> Research Centre Juelich
> 52425 Juelich
> Germany
>
> ::: Please encrypt confidential data :::
>
--
Dr. med. Cornelius J. Werner
Department of Neurology
RWTH Aachen University
Pauwelsstr. 30
52074 Aachen
Germany
Institute of Neuroscience and Medicine
MR Physics - INM4
Research Centre Juelich
52425 Juelich
Germany
::: Please encrypt confidential data :::
|