Hi,
Let me explain it again. On a 3 TByte disk I've made a partition of 20 GB to run OSX10.7. When I run recon-all all input and output data are on the large partition which has about 1.5 TByte free space. This means that all temporary and intermediate files that are created by recon-all (e.g. in /tmp) are residing on the 20 GB partition which has a free space of 11 GB initially. And all this free space is consumed (I assume by all these temporary/ intermediate files) by mri-topo-fixer.
Cheers, Ed
On 10 Mar 2016, at 18:00, <freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
Hi Ed,
I am a bit confused by your two emails.
In one you state that you have a MacPro OSX10.7 installed on a partition of 20 GB with FreeSurfer v6 beta
Then in the next post you state that the disk you have is 1.5TB (is that the disk or partition?)
I'm also confused, because you stated that at the time you ran into trouble the disk had 11GB. You then said you ran out of disk (I assume that means you had 0GB left). Then you said when you rebooted you had 11GB (no files were created at all?).
This is a dangerous way in general to run a machine. If a program core dumps you have less disk space then your RAM. General advice is to keep at least 5% of disk space free (or a bare minimum of > RAM size). It may be worth doing this after a fresh reboot and checking your RAM to make sure you don't have apps that autostart sucking up RAM, causing you to swap. If you try to swap, without enough free space that can easily crash your machine.
First, What is the full disk partition setup?
Next, run df (on the relevant partition) and show the output before running FreeSurfer.
Then run recon-all and if possible show the df output at the crash
Then run df on reboot.
hth d
PS it may be worth pointing out that beta 6 was withdrawn for more development.
On 3/10/16 5:09 AM, Gronenschild Ed (NP) wrote: Hi,
I'm using a MacPro with 32 GByte RAM. The output of FreeSurfer is written to a disk with 1.5 TByte free space.
At the time I ran into trouble the free disk space was about 11 GByte. When I wanted to inspect the progress after a few hours I noticed that the disk has ran out of space. I couldn't do anything but restarting the MacPro. Then the disk space was again about 11 GByte. So I reran the subject with recon-all -autorecon2 -autorecon3 and it happened again. Inspecting the log files I noticed that both times the problem occurred at exactly the same stage in the pipeline: mris-topo-fixer.
Cheers, Ed
On 10 Mar 2016, at 10:41, <freesurfer-request@nmr.mgh.harvard.edumailto:freesurfer-request@nmr.mgh.harvard.edu mailto:freesurfer-request@nmr.mgh.harvard.edu> wrote:
20 GB is not a lot for a full macos install + data, how much room was free before you ran recon-all? What is the hardware? CPU, RAM etc.
hth d
On Wed, Mar 9, 2016 at 12:09 PM, Gronenschild Ed (NP) <ed.gronenschild@maastrichtuniversity.nlmailto:ed.gronenschild@maastrichtuniversity.nl mailto:ed.gronenschild@maastrichtuniversity.nl> wrote: Hi developers,
Could you please help me out on this problem. Should I upload the data?
Cheers, Ed
Begin forwarded message:
From: Ed Gronenschild <ed.gronenschild@maastrichtuniversity.nlmailto:ed.gronenschild@maastrichtuniversity.nl mailto:ed.gronenschild@maastrichtuniversity.nl> Subject: System crash by extremely much generated output v6 beta Date: 7 March 2016 12:57:57 CET To: <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu>
Hi developers,
My environment: MacPro OSX10.7 installed on a partition of 20 GByte; FreeSurfer v6 beta
During processing recon-all on 4 subjects in parallel using 4 terminal windows, the 20 GByte partition got full. This happened twice and I managed to trace down the offending stage in the pipeline: topology fixing, in particular the tool mris_topo_fixer. Most probably it went into an endless iteration loop generating so much output the disk got full.
Cheers, Ed