[Mne_analysis] question for Martinos MNE-python users

[Help Desk -- Sam Mehl]

The 'gpfs problem' is resolved by rebooting, as we mentioned on batch-users.

I have instructed Kestas to reboot his computer.

-- Sam Mehl (http://help.nmr.mgh.harvard.edu)



On Fri, 28 Feb 2014 1:46pm, Martin Luessi wrote:

> Hi Kestas,
>
> It is definitely due to the gpfs problems as Dan mentioned. The problem
> is that when starting python many small files are accessed, which can be
> slow. I assume you are using EPD? It is a bit faster if you use
> anaconda, i.e., add this to your path:
>
> /usr/pubsw/packages/python/anaconda/bin
>
> and get an academic license from here:
>
> https://store.continuum.io/cshop/academicanaconda
>
> anaconda is faster to start than EPD because many files are included as
> zip files, which reduces the number of file system operations when
> starting python.
>
> Hope this helps,
>
> Martin
>
>
>
> On 02/28/14 13:32, Kestas Kveraga wrote:
>> Thanks, Dan, I will now.
>>
>> On 02/28/2014 01:29 PM, dgw wrote:
>>> Hi Kestas,
>>>
>>> It is likely related to the gpfs server problems mentioned on the
>>> batch-users mailing list. Have you tried contacting help@?
>>>
>>> D
>>>
>>> On Fri, Feb 28, 2014 at 1:27 PM, Kestas Kveraga
>>> <kestas at nmr.mgh.harvard.edu> wrote:
>>>> Hello,
>>>> I've used the Martinos network version of ipython before with no
>>>> problems to run some stuff in MNE-python.
>>>>
>>>> Now when I try to start it up by typing 'ipython' after setting the path
>>>> exactly as per 'Getting Started" instructions, it does not start for
>>>> many minutes (20+) and when it finally starts, it is extremely slow
>>>> (compared to previous usage or running a local version on a Mac laptop).
>>>>
>>>> The problem is not with the machine, which has gobs of free RAM (8GB+)
>>>> and 4 CPUs that are mostly idle. Last time I quit ipython, it was using
>>>>  >5GB of RAM, which seems excessive.
>>>>
>>>> What am I missing here? Should I install a local version, e.g., Canopy?
>>>>
>>>> Thanks,
>>>> Kestas
>>>>
>>>>
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>>
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>
>
> -- 
> Martin Luessi, Ph.D.
>
> Research Fellow
>
> Department of Radiology
> Athinoula A. Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
> Harvard Medical School
> 149 13th Street
> Charlestown, MA 02129
>
> Fax: +1 617 726-7422
>
>
>