[FieldTrip] ft_statistics_montecarlo runs slow under ubuntu 13.10

[berry van den berg]

I pinpointed the problem to being the access time of the second HDD mounted
as a ntfs filesystem. Not having this HDD in my searchpath solves my
problem.

Berry

---------- Forwarded message ----------
From: Gio Piantoni <gio at gpiantoni.com>
Date: 20 January 2014 14:01
Subject: Re: [FieldTrip] ft_statistics_montecarlo runs slow under ubuntu
13.10
To: berry van den berg <berryv.dberg at gmail.com>


sorry, I don't know much more than this, but it makes sense that Linux
needs some extra time to access a non-native filesystem. If I were
you, I'd just comment out the part in ft_statistics_montecarlo that
checks for the toolbox, once you know that the toolbox is installed,
you don't need to check it every time.
Good luck!

On Mon, Jan 20, 2014 at 12:56 PM, berry van den berg
<berryv.dberg at gmail.com> wrote:
> Yeah, you are right, having a folder on that harddisk added to the search
> path slowed those functions (which, exist) by A LOT! I copied fieldtrip to
> the main SSD and removed everything from the path in matlab on the ntfs
> drive, which is mounted through ntfs-3g. Even though I dont actually use
> those functions, it slows up the process by a lot: 1 second versus 6
seconds
> when fieldtrip is on the ssd with ext4....
>
> I wonder if it is due to the drive being ntfs, or something else... Any
> ideas?
>
>
> On 20 January 2014 12:00, Gio Piantoni <gio at gpiantoni.com> wrote:
>>
>> Hi Berry,
>>
>> interesting debugging. Not sure exactly what's going on, but I noticed
>> that Linux might become slower if you have samba/cifs disks mounted.
>> Is that the case for you maybe?
>>
>> HTH,
>> -g
>>
>> On Mon, Jan 20, 2014 at 11:45 AM, berry van den berg
>> <berryv.dberg at gmail.com> wrote:
>> > Ok, I dove a bit deeper into the problem, using the matlab profiler I
>> > was
>> > able to pinpoint the problem to ft_hastoolbox.m called by
findcluster.m,
>> > and
>> > specifically the functions fileparts and exist.... Copy pasting those
>> > two
>> > functions to ft_statistics_montecarlo solves the issue for me for now.
>> >
>> > The problem seems to be that matlab accessing my filesystem runs slow
>> > under
>> > linux compared to windows.. I have no idea why and how to solve it but
>> > it is
>> > not related to fieldtrip. If anyone has suggestions what this might be
I
>> > would be glad to hear them!
>> >
>> > Cheers,
>> >
>> >
>> >
>> >
>> > On 16 January 2014 17:11, berry van den berg <berryv.dberg at gmail.com>
>> > wrote:
>> >>
>> >> Dear Fieldtrip experts,
>> >>
>> >> This might be an odd question, but maybe someone has an idea where to
>> >> start.
>> >>
>> >> I just got a fancy new laptop (gigabyte p34g) and dual boot with
ubuntu
>> >> and windows. I usually work in Ubuntu for analysis, so I ran a time
>> >> freq
>> >> statistics analysis and noticed that ft_statistics_montecarlo runs
>> >> extremely
>> >> slow under Ubuntu.... In windows it runs at normal speed. The
>> >> difference is
>> >> huge, 97 seconds vs, 2 seconds for 100 iterations, 24 subjects.
>> >>
>> >> Speed also doesnt seem influenced by averaging over freq or/and time,
>> >> it
>> >> is just slow.
>> >>
>> >> It is not the cpu clock speed (ubuntu nicely utilizes turbo mode,
>> >> running
>> >> max 3ghz), the cpu is not fully utilized though (only 30 percent or
>> >> so)...
>> >>
>> >> I run matlab 2013b, fieldtrip 20140115
>> >>
>> >> Specs are
>> >> 8gb ram; only 4gb utilized.
>> >> 4700HQ cpu
>> >>
>> >> Any ideas, because I am clueless
>> >>
>> >> Cheers,
>> >>
>> >> --
>> >> Berry van den Berg
>> >> berryv.dberg at gmail.com
>> >
>> >
>> >
>> >
>> > --
>> > Berry van den Berg
>> > berryv.dberg at gmail.com
>> >
>> > _______________________________________________
>> > fieldtrip mailing list
>> > fieldtrip at donders.ru.nl
>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
>
> --
> Berry van den Berg
> berryv.dberg at gmail.com



-- 
Berry van den Berg
berryv.dberg at gmail.com


On 20 January 2014 11:45, berry van den berg <berryv.dberg at gmail.com> wrote:

> Ok, I dove a bit deeper into the problem, using the matlab profiler I was
> able to pinpoint the problem to ft_hastoolbox.m called by findcluster.m,
> and specifically the functions fileparts and exist.... Copy pasting those
> two functions to ft_statistics_montecarlo solves the issue for me for now.
>
> The problem seems to be that matlab accessing my filesystem runs slow
> under linux compared to windows.. I have no idea why and how to solve it
> but it is not related to fieldtrip. If anyone has suggestions what this
> might be I would be glad to hear them!
>
> Cheers,
>
>
>
>
> On 16 January 2014 17:11, berry van den berg <berryv.dberg at gmail.com>wrote:
>
>> Dear Fieldtrip experts,
>>
>> This might be an odd question, but maybe someone has an idea where to
>> start.
>>
>> I just got a fancy new laptop (gigabyte p34g) and dual boot with ubuntu
>> and windows. I usually work in Ubuntu for analysis, so I ran a time freq
>> statistics analysis and noticed that ft_statistics_montecarlo runs
>> extremely slow under Ubuntu.... In windows it runs at normal speed. The
>> difference is huge, 97 seconds vs, 2 seconds for 100 iterations, 24
>> subjects.
>>
>> Speed also doesnt seem influenced by averaging over freq or/and time, it
>> is just slow.
>>
>> It is not the cpu clock speed (ubuntu nicely utilizes turbo mode, running
>> max 3ghz), the cpu is not fully utilized though (only 30 percent or so)...
>>
>> I run matlab 2013b, fieldtrip 20140115
>>
>> Specs are
>> 8gb ram; only 4gb utilized.
>> 4700HQ cpu
>>
>> Any ideas, because I am clueless
>>
>> Cheers,
>>
>> --
>> Berry van den Berg
>> berryv.dberg at gmail.com
>>
>
>
>
> --
> Berry van den Berg
> berryv.dberg at gmail.com
>



-- 
Berry van den Berg
berryv.dberg at gmail.com
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