AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Stephen J Fromm
February 02, 2009 10:59AM
A user I work with ran out of memory running 3dDeconvolve, getting these messages:
----------------------------
** FATAL ERROR: Total shared memory needed = 2355888128 >= 2147483648 (2 GB)
** SUGGESTION 1: Use 3dAutobox to automatically eliminate non-brain
areas from the 3d+time input dataset and reduce memory
requirements, e.g.
3dAutobox -prefix Subj1AllRuns_Smaller -input Subj1AllRuns
Then run 3dDeconvolve again with the smaller 3d+time input dataset

** SUGGESTION 2: Use 3dZcutup to slice dataset into smaller pieces
** and then 3dZcat to glue results back together.

** SUGGESTION 3: Run on a 64-bit computer system, instead of 32-bit.
holla!
----------------------------

I assume the suggestion of using a 64-bit OS means that it's not enough to have > 2 GB memory available, but rather that it needs to be one contiguous address space or something? The error msg was generated on a 32-bit SunOs 5.9 system with much more than 2 GB virtual memory.

If the answer is that this cannot be done on a 32-bit OS, what kind of swap space is OK on my 64-bit Linux box? If I create swap space with mkswap, do I have to make a single chunk with as much space as he needs? Or does it not matter how it's divided up?

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Subject Author Posted

"SUGGESTION 3: Run on a 64-bit computer system..."

Stephen J Fromm February 02, 2009 10:59AM

Re: "SUGGESTION 3: Run on a 64-bit computer system..."

rick reynolds February 02, 2009 11:20AM

Re: "SUGGESTION 3: Run on a 64-bit computer system..."

Stephen J Fromm February 02, 2009 11:31AM