Yes, 8GB with a quad core should be enough for 4 probtrackx processes. I
don't do a lot of TBSS, but a single machine with that setup would be fine
for that purpose. If you want to do things even faster, you might get
multiple machines and link them together using the clustering software SGE.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Lindgren, Kristen, Ann
Sent: Friday, January 16, 2009 2:01 PM
To: [log in to unmask]
Subject: Re: [FSL] Error running multiple probtrackx windows
Thanks, Matt. That's what I figured. I also have a Mac that I'm
running things on (2.5GHz Quad processor, PowerPC G5). It currently has
2.5GB but I'm looking into upgrading that. So if I upped that
computer's RAM to 8GB, I should be able to run 4 probtrackx windows,
right?
Also, since I'm figuring out our lab's processing capabilities, how much
RAM do TBSS analyses typically require?
Thanks!
Kristen
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
Behalf Of Matt Glasser
Sent: Thursday, January 15, 2009 11:32 AM
To: [log in to unmask]
Subject: Re: [FSL] Error running multiple probtrackx windows
Probtrackx can use up to 2GB PER THREAD on a typical 2x2x2 60 direction
human dataset. To run 4 probtrackx threads I have 8GB of RAM and
typically
this is enough for both the probtrackx and any system use without
swapping
to disk. Having to swap to disk will significantly increase the time it
takes to run a probtrackx, as your CPU will not always be fully
utilized.
You might also gain additional speed improvements by running probtrackx
natively (in Linux or Mac). If you added 2GB to the VM + allowed for
atleast 2GB of swap space, you should be able to run two probtrackx
without
error. Keep in mind that if you are also running things like FSLView,
this
can use significant amounts of RAM.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
Behalf
Of Lindgren, Kristen, Ann
Sent: Thursday, January 15, 2009 10:09 AM
To: [log in to unmask]
Subject: [FSL] Error running multiple probtrackx windows
Hello again. So I'm running FSL on a PC with a Linux Virtual Machine.
I have been able to run 4 simultaneous bedpostx terminals without any
problem. I tried running two terminals with probtrackx (two different
subjects) and got an error on the first one I ran (the second one ran
all the way through). Basically probtrackx conked out and gave an error
(I think the pop up dialogue said "child killed"). I was able to rerun
it by itself with no errors so it's probably not the data.
Is this just a RAM issue? The computer itself has 3GB of RAM but I
believe only 1GB is allocated to the virtual machine. I looked at the
swap space by typing top in the terminal and it looked like it had the
recommended 2GB. Although, the amount of hard drive originally
allocated for the virtual machine wasn't very much so it basically has
just about 2GB of hard drive space extra right now (trying to see what I
can delete) and I'm working on having additional hard drive space
allocated and formatted for it.
Do you think this could be fixed by having extra hard drive space free
or allocating more RAM to the virtual machine? Any ideas or am I stuck
only running one subject at a time? Thanks!
Kristen
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