Hi All,
some more details to the segfault. The critical program is mris_fix_topology, which allocates around 3.7GB of memory and hogs the CPU for at least an hour, then while holding around 3.6GB goes into D state (as seen by top) and then after some time segfaults with the error code 4. Error code 4 most likely means (on Linux x86_64) user_mode page_not_found on read. If I can help debug this I would be happy to.
Ahoi Sebastian
Hi Sebastian,
take a look at your surfaces. If it's using that much memory something is probably dramatically wrong. Most likely either the cerebellum is attached or the skull.
cheers, Bruce On Tue, 28 Feb 2006, Sebastian Moeller wrote:
Hi All,
some more details to the segfault. The critical program is mris_fix_topology, which allocates around 3.7GB of memory and hogs the CPU for at least an hour, then while holding around 3.6GB goes into D state (as seen by top) and then after some time segfaults with the error code 4. Error code 4 most likely means (on Linux x86_64) user_mode page_not_found on read. If I can help debug this I would be happy to.
Ahoi Sebastian
Hi Bruce,
On 28. Feb 2006, at 15:20 Uhr, Bruce Fischl wrote:
Hi Sebastian,
take a look at your surfaces. If it's using that much memory something is probably dramatically wrong. Most likely either the cerebellum is attached or the skull.
Will do that. A question though, the machine has 4GB Ram and 4GB swap space and addressable space somewhere in the low TB, why is it that it breaks, even if it allocates too_much_memoryTM?
Ahoi Sebastian
cheers, Bruce On Tue, 28 Feb 2006, Sebastian Moeller wrote:
Hi All,
some more details to the segfault. The critical program is mris_fix_topology, which allocates around 3.7GB of memory and hogs the CPU for at least an hour, then while holding around 3.6GB goes into D state (as seen by top) and then after some time segfaults with the error code 4. Error code 4 most likely means (on Linux x86_64) user_mode page_not_found on read. If I can help debug this I would be happy to.
Ahoi Sebastian
Hi Bruce,
On 28. Feb 2006, at 16:04 Uhr, Sebastian Moeller wrote:
Hi Bruce,
On 28. Feb 2006, at 15:20 Uhr, Bruce Fischl wrote:
Hi Sebastian,
take a look at your surfaces. If it's using that much memory something is probably dramatically wrong. Most likely either the cerebellum is attached or the skull.
Aargh, yeah I have some skull and all of the cerebellum attached to lh.orig. Well I am trying my best in skullstripping now (hard, as I only have highly inhomogenous surface coil for send and receive scans). I am using the monkey skullstripping guide posted recently by Florent (thanks). About the cerebellum I will try my cutting skills at the wm.mgz...
Ahoi Sebastian
Will do that. A question though, the machine has 4GB Ram and 4GB swap space and addressable space somewhere in the low TB, why is it that it breaks, even if it allocates too_much_memoryTM?
Ahoi Sebastian
cheers, Bruce On Tue, 28 Feb 2006, Sebastian Moeller wrote:
Hi All,
some more details to the segfault. The critical program is mris_fix_topology, which allocates around 3.7GB of memory and hogs the CPU for at least an hour, then while holding around 3.6GB goes into D state (as seen by top) and then after some time segfaults with the error code 4. Error code 4 most likely means (on Linux x86_64) user_mode page_not_found on read. If I can help debug this I would be happy to.
Ahoi Sebastian
-- Sebastian Moeller
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