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FSL  October 2007

FSL October 2007

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Subject:

Re: FSL on XGrid w/ XServe (now SGE)

From:

Steve Smith <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Thu, 11 Oct 2007 11:32:39 +0100

Content-Type:

text/plain

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Parts/Attachments

text/plain (337 lines)

Hi,

Most of this has now been answered by others:


On 9 Oct 2007, at 20:17, Jeremy Bronson wrote:

> Hi,
>
> I tried to get FSL working with XGrid during the summer, but wasn't
>  quite successful, and was recommended to use SGE in its place by  
> Steve and
>  others.  I'm giving it another go, but I've run into a few questions
>  while setting up SGE. Hopefully they're easy enough to answer...
>
> -The SGE manual says that each host must have the same user account
>  names and passwords, which is the alternate to XGrid's nobody:nobody
>  permissions, but seems equally impractical.  If SGE is really  
> designed to be
>  implemented in large grids, I'm not sure how it could scale beyond a
>  handful of managed machines.   My question is whether this is how the
>  lab is configured at Oxford or any other site, or alternately are all
>  jobs submitted under a single username?
>
> -All scan data resides on an XServe, automounted via NFS. What kind of
>  permissions are necessary on this share?
>
> -Is anyone using the multiple queues available in SGE, or only using
>  one for large jobs?

We use multiple queues - but that's just a matter of choice, and  
either option is easy to setup.  fsl_sub just needs customising to  
reflect whatever you setup.

Cheers.

> My basic goal is to allow users to login, start multiple large jobs on
>  the grid, then log out and retrieve the results later.  The FEAT
>  first-level analyses tend to tie up all the machines for a time,  
> so I'd love
>  to speed them up by running the jobs in parallel and in the  
> background.
>
>
> Thanks in advance!
>
> Jeremy
>
>
>
>
>
>
> On Tue, 14 Aug 2007 06:24:00 +0100, Steve Smith <[log in to unmask]>
>  wrote:
>> Hi Jeremy,
>>
>> I agree with Andrew, most people seem much happier with SGE than with
>
>> XGrid, so if it's not too late I would consider that.
>>
>> Anyway - yes, hopefully FSL 4.0 should be fairly easy to setup with
>> either (though much easier with SGE as that's what we have so should
>
>> need much less customising).
>>
>> First, see the brief intro at:
>> http://www.fmrib.ox.ac.uk/fsl/fsl/downloading.html#sge
>> So if the user runs any of these programs on a machine which can
>> submit to the cluster then that should happen automatically, after
>> the sysadmin has:
>>
>> Setup the central cluster-controlling script
>> $FSLDIR/bin/fsl_sub
>>
>> This is a heavily commented shell script and hopefully should be
>> reasonably easy to follow and customise.....
>>
>>
>> So hopefully the user can just run FSL programs on their normal
>> working machine, and if it's setup to be a cluster submission host,
>> then whenever a "big" job is run that will automatically get sent to
>
>> the queue.
>>
>> Cheers, Steve.
>>
>>
>>
>>
>>
>> On 14 Aug 2007, at 05:59, Jeremy Bronson wrote:
>>
>>> Hi All,
>>>
>>> I'm the new administrator of a neuroimaging research lab, and I'm
>>> working on getting FSL and other MRI-analysis tools running on
>>> XGrid.  I'm not yet intimately familiar with how FSL works, so I'm
>
>>> hoping there are others out there who have already figured out how
>
>>> to run it on a cluster, so I don't have to reinvent the wheel.
>>> I've heard of several existing clusters that run FSL, albeit a
>>> modified version.  I'm hoping it can be done with the off-the-shelf
>
>>> version, perhaps it's now possible with the just-released 4.0?  If
>
>>> anybody could point me in the direction of some specifics, I'd be
>>> most grateful.
>>>
>>> We've got an XServe with RAID that houses all the data, and FSL is
>
>>> installed and configured on all host (agent) machines.  Most users
>
>>> use the GUI, and manually point the tools to the appropriate data,
>
>>> so I assume they'll need to familiarize themselves with the
>  command-
>>> line tools and specifying data directories on the CLI (or via
>>> GridStuffer).  I'm thinking that each machine will need the data
>>> volume to be auto-mounted (NFS?) at startup with appropriate
>>> directories having read/write access for the 'nobody' user. Does
>>> this sound correct?
>>>
>>> Additionally, each tool that's part of the FSL package seems to
>>> launch a number of other UNIX commands during analysis, to copy,
>>> move and otherwise manipulate the result data.  Will this confuse
>>> XGrid, or will the job and all sub-commands run until the original
>
>>> command completes? (e.g. A complete FEAT analysis)
>>>
>>> Hopefully this isn't too difficult, and afterwards I'd like to take
>
>>> the time to post a HOWTO on macresearch.org or the like, so others
>
>>> might take advantage of the info.  Thanks in advance to anyone who
>
>>> might be able to help.
>>>
>>>
>>> Jeremy Bronson
>>> Systems Administrator
>>> Frey Research Lab
>>> University of Oregon
>>
>>
>>
>   
> ---------------------------------------------------------------------- 
> --
>> ---
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director,  Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
>> +44 (0) 1865 222726  (fax 222717)
>> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
>>
>   
> ---------------------------------------------------------------------- 
> --
>> ---
>>
>
>
>
>
>
> Hi,
>
> I tried to get FSL working with XGrid during the summer, but wasn't
>  quite successful, and was recommended to use SGE in its place by  
> Steve and
>  others.  I'm giving it another go, but I've run into a few questions
>  while setting up SGE. Hopefully they're easy enough to answer...
>
> -The SGE manual says that each host must have the same user account
>  names and passwords, which is the alternate to XGrid's nobody:nobody
>  permissions, but seems equally impractical.  If SGE is really  
> designed to be
>  implemented in large grids, I'm not sure how it could scale beyond a
>  handful of managed machines.   My question is whether this is how the
>  lab is configured at Oxford or any other site, or alternately are all
>  jobs submitted under a single username?
>
> -All scan data resides on an XServe, automounted via NFS. What kind of
>  permissions are necessary on this share?
>
> -Is anyone using the multiple queues available in SGE, or only using
>  one for large jobs?
>
> My basic goal is to allow users to login, start multiple large jobs on
>  the grid, then log out and retrieve the results later.  The FEAT
>  first-level analyses tend to tie up all the machines for a time,  
> so I'd love
>  to speed them up by running the jobs in parallel and in the  
> background.
>
>
> Thanks in advance!
>
> Jeremy
>
>
>
>
>
>
> On Tue, 14 Aug 2007 06:24:00 +0100, Steve Smith <[log in to unmask]>
>  wrote:
>> Hi Jeremy,
>>
>> I agree with Andrew, most people seem much happier with SGE than with
>
>> XGrid, so if it's not too late I would consider that.
>>
>> Anyway - yes, hopefully FSL 4.0 should be fairly easy to setup with
>> either (though much easier with SGE as that's what we have so should
>
>> need much less customising).
>>
>> First, see the brief intro at:
>> http://www.fmrib.ox.ac.uk/fsl/fsl/downloading.html#sge
>> So if the user runs any of these programs on a machine which can
>> submit to the cluster then that should happen automatically, after
>> the sysadmin has:
>>
>> Setup the central cluster-controlling script
>> $FSLDIR/bin/fsl_sub
>>
>> This is a heavily commented shell script and hopefully should be
>> reasonably easy to follow and customise.....
>>
>>
>> So hopefully the user can just run FSL programs on their normal
>> working machine, and if it's setup to be a cluster submission host,
>> then whenever a "big" job is run that will automatically get sent to
>
>> the queue.
>>
>> Cheers, Steve.
>>
>>
>>
>>
>>
>> On 14 Aug 2007, at 05:59, Jeremy Bronson wrote:
>>
>>> Hi All,
>>>
>>> I'm the new administrator of a neuroimaging research lab, and I'm
>>> working on getting FSL and other MRI-analysis tools running on
>>> XGrid.  I'm not yet intimately familiar with how FSL works, so I'm
>
>>> hoping there are others out there who have already figured out how
>
>>> to run it on a cluster, so I don't have to reinvent the wheel.
>>> I've heard of several existing clusters that run FSL, albeit a
>>> modified version.  I'm hoping it can be done with the off-the-shelf
>
>>> version, perhaps it's now possible with the just-released 4.0?  If
>
>>> anybody could point me in the direction of some specifics, I'd be
>>> most grateful.
>>>
>>> We've got an XServe with RAID that houses all the data, and FSL is
>
>>> installed and configured on all host (agent) machines.  Most users
>
>>> use the GUI, and manually point the tools to the appropriate data,
>
>>> so I assume they'll need to familiarize themselves with the
>  command-
>>> line tools and specifying data directories on the CLI (or via
>>> GridStuffer).  I'm thinking that each machine will need the data
>>> volume to be auto-mounted (NFS?) at startup with appropriate
>>> directories having read/write access for the 'nobody' user. Does
>>> this sound correct?
>>>
>>> Additionally, each tool that's part of the FSL package seems to
>>> launch a number of other UNIX commands during analysis, to copy,
>>> move and otherwise manipulate the result data.  Will this confuse
>>> XGrid, or will the job and all sub-commands run until the original
>
>>> command completes? (e.g. A complete FEAT analysis)
>>>
>>> Hopefully this isn't too difficult, and afterwards I'd like to take
>
>>> the time to post a HOWTO on macresearch.org or the like, so others
>
>>> might take advantage of the info.  Thanks in advance to anyone who
>
>>> might be able to help.
>>>
>>>
>>> Jeremy Bronson
>>> Systems Administrator
>>> Frey Research Lab
>>> University of Oregon
>>
>>
>>
>   
> ---------------------------------------------------------------------- 
> --
>> ---
>> Stephen M. Smith, Professor of Biomedical Engineering
>> Associate Director,  Oxford University FMRIB Centre
>>
>> FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
>> +44 (0) 1865 222726  (fax 222717)
>> [log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
>>
>   
> ---------------------------------------------------------------------- 
> --
>> ---
>>
>
>
>
>
>
>


------------------------------------------------------------------------ 
---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director,  Oxford University FMRIB Centre

FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
+44 (0) 1865 222726  (fax 222717)
[log in to unmask]    http://www.fmrib.ox.ac.uk/~steve
------------------------------------------------------------------------ 
---

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