Hi Haoran, that error is the hallmark of a corrupted volume file. Do you mind sending the log, or at least the end of it? It’d be helpful to see when this error is actually occurring.

 

thanks

Andrew

 

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Haoran Xu <haoran.x@gmail.com>
Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Date: Thursday, December 20, 2018 at 1:05 PM
To: FS Help <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] surfreg cannot allocate memory

 

        External Email - Use Caution        

Thanks for the suggestion! But it seems the max memory size was unlimited already. Any more thoughts about this?

Best,

Haroan

 

 

$ ulimit -a

core file size          (blocks, -c) 0

data seg size           (kbytes, -d) unlimited

scheduling priority             (-e) 0

file size               (blocks, -f) unlimited

pending signals                 (-i) 96121

max locked memory       (kbytes, -l) 64

max memory size         (kbytes, -m) unlimited

open files                      (-n) 1024

pipe size            (512 bytes, -p) 8

POSIX message queues     (bytes, -q) 819200

real-time priority              (-r) 0

stack size              (kbytes, -s) 8192

cpu time               (seconds, -t) unlimited

max user processes              (-u) 96121

virtual memory          (kbytes, -v) unlimited

file locks                      (-x) unlimited

 

 

On Wed, Dec 19, 2018 at 7:14 PM fsbuild <fsbuild@contbay.com> wrote:

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Hello Haoran,

 

You could try looking at your shell limits and see if the memory size is listed as something other than “unlimited”.  

 

In bash shell,

 

$ bash
$ ulimit -a
core file size          (blocks, -c) 0
data seg size           (kbytes, -d) unlimited
scheduling priority             (-e) 0
file size               (blocks, -f) unlimited
pending signals                 (-i) 256605
max locked memory       (kbytes, -l) 64
max memory size         (kbytes, -m) unlimited
open files                      (-n) 65535
pipe size            (512 bytes, -p) 8
POSIX message queues     (bytes, -q) 819200
real-time priority              (-r) 0
stack size              (kbytes, -s) unlimited
cpu time               (seconds, -t) unlimited
max user processes              (-u) 256605
virtual memory          (kbytes, -v) unlimited
file locks                      (-x) unlimited

If memory does not read as unlimited then,

 

$ ulimit -m unlimited

 

- R.

 

On Dec 19, 2018, at 18:30, Haoran Xu <haoran.x@gmail.com> wrote:

 

        External Email - Use Caution        

 

Hello FreeSurfer Developers,

I am using surfreg to map one of my subject "subj001" to "fsaverage_sym" by these commands:

 

surfreg --s subj001 --t fsaverage_sym --lh
surfreg --s subj001 --t fsaverage_sym --lh --xhemi

 

The first command worked well, however the second did not. It showed error:

 

"znzTAGskip: tag=1952870258, failed to calloc 1768846336 bytes!
Cannot allocate memory"

 

Searched the archive but without good luck. Any suggestions? Appreciated!

 

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. 

2) Platform: UBUNTU 16.04 LTS with 23.5GB memory and 1.4TB available space. (With this, 1.7G should be fine.)

3) uname -a: Linux haoranPC 4.15.0-43-generic #46~16.04.1-Ubuntu SMP Fri Dec 7 13:31:08 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

 

Regards,

Haoran Xu

 

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