AMBER Archive (2007)

Subject: AMBER: pmemd segmentation fault

From: Vlad Cojocaru (Vlad.Cojocaru_at_eml-r.villa-bosch.de)
Date: Mon Mar 26 2007 - 03:14:50 CST

Deat Amber users,

I am trying to set up some Amber runs on a large cluster. So, I switched
from sander (AMEBR 8) to pmemd (AMBER 9) and I ran it on 512 processors.
The job runs for 400 (out of 1.000.000) steps and then it is interrupted
with the error below. In the output I get the follwoing warning:
"WARNING: Stack usage limited by a hard resource limit of 4294967295
bytes! If segment violations occur, get your sysadmin to increase the
limit.". Could anyone advise me how to deal with this?. I should also
tell you that the same job runs fine using sander (AMBER 8) on 32
processors or 4 CPUs.

And a second question ... when I tried sander (AMBER 8) on 256 CPUs, the
job exits with an error "The number of processors must be a power of 2
and no greater than 128 , but is 256". Is 128 CPUs the upper limit for
sander iun AMBER 8? Does sander in AMBER 9 has the same limit ?

Thanks in advance

Best wishes
Vlad
 

forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
pmemd 4000000000067010 Unknown Unknown Unknown
pmemd 400000000002D8C0 Unknown Unknown Unknown
pmemd 4000000000052F10 Unknown Unknown Unknown
pmemd 40000000000775B0 Unknown Unknown Unknown
pmemd 40000000000B8730 Unknown Unknown Unknown
pmemd 40000000000049D0 Unknown Unknown Unknown
Unknown 20000000005913F0 Unknown Unknown Unknown
pmemd 4000000000004400 Unknown Unknown Unknown

Stack trace terminated abnormally.
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
pmemd 40000000000625A0 Unknown Unknown Unknown
pmemd 400000000002DA60 Unknown Unknown Unknown
pmemd 4000000000052F10 Unknown Unknown Unknown
pmemd 40000000000775B0 Unknown Unknown Unknown
pmemd 40000000000B8730 Unknown Unknown Unknown
pmemd 40000000000049D0 Unknown Unknown Unknown
Unknown 20000000005913F0 Unknown Unknown Unknown
pmemd 4000000000004400 Unknown Unknown Unknown

Stack trace terminated abnormally. 

-- 
----------------------------------------------------------------------------
Dr. Vlad Cojocaru

EML Research gGmbH
Schloss-Wolfsbrunnenweg 33
69118 Heidelberg

Tel: ++49-6221-533266
Fax: ++49-6221-533298

e-mail:Vlad.Cojocaru[at]eml-r.villa-bosch.de

http://projects.villa-bosch.de/mcm/people/cojocaru/

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