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

History of AFNI updates  

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October 07, 2021 12:43PM
Hi AFNI team,

I'm running 3dDeconvolve on my dataset and it often got killed. The dataset is quite large. It has 32 runs of 10 min scanning, each run is ~400MB.

I run it on different computers and it seems not solely depend on the size of memory whether the process will be killed.

Here are my questions:

1) why is it that some computers have enough memory and hard drive but still got killed? For example, I ran this on two computers, both have 64GB memory and >500GB hard drive. One always ran successfully and another always got killed. What could be the reason, the age of computers?

2) Is there anything I can do to reduce the memory it uses so I can run it on computers with smaller memory?

3) Currently the process takes whole 5 days and I'm running a deadline, is there any way to speed it up?

4) Could 3) and 2) be solved using the parallel job option in the 3dDeconvolve? My computers usually have 4 cores, so I should use -jobs 4. But will this require each of the core have a large memory?

Thank you so much!

--Lingyan
Subject Author Posted

3dDeconvolve "killed" because out of memory

swallowwly October 07, 2021 12:43PM

Re: 3dDeconvolve "killed" because out of memory

rick reynolds October 07, 2021 01:16PM

Re: 3dDeconvolve "killed" because out of memory

swallowwly October 07, 2021 01:40PM

Re: 3dDeconvolve "killed" because out of memory

swallowwly October 08, 2021 11:01AM

Re: 3dDeconvolve "killed" because out of memory

rick reynolds October 08, 2021 11:33AM

Re: 3dDeconvolve "killed" because out of memory

swallowwly October 08, 2021 12:19PM

Re: 3dDeconvolve "killed" because out of memory

rick reynolds October 08, 2021 03:39PM

Re: 3dDeconvolve "killed" because out of memory

swallowwly October 11, 2021 12:05AM

Re: 3dDeconvolve "killed" because out of memory

Daniel Glen October 08, 2021 12:57PM

Re: 3dDeconvolve "killed" because out of memory

swallowwly October 08, 2021 01:48PM