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 :::
|