There is an operating system bug in mac osx 10.5.x that may cause
this problem if you
are running the program with input redirection, but without output
redirection, i.e.,
cns < test.inp
and the input file contains one ore more blank lines.
try:
cns < test.inp > test.out
Axel Brunger
On May 21, 2008, at 8:37 PM, xiaoyazi2008 wrote:
Hi,
Recently I've installed the CNS 1.2 on Mac Pro successfully. But
when I run cns_solve to do annealing refinement, the following error
information appear:
_____________________________________________________________
FFT3C: Using FFTPACK4.1
CNSsolve>{+ file: anneal.inp +}
CNSsolve>{+ directory: xtal_refine +}
CNSsolve>{+ description: Crystallographic simulated annealing
refinement +}
CNSsolve>{+ authors: Axel T. Brunger, Luke M. Rice and Paul D.
Adams +}
CNSsolve>{+ copyright: Yale University +}
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
cns_solve 003548DF Unknown Unknown Unknown
cns_solve 00339FBB Unknown Unknown Unknown
cns_solve 000F62EC Unknown Unknown Unknown
Stack trace terminated abnormally.
------------------------------------------------
Can anybody help me to fix that problem? Thanks a lot
[EMAIL PROTECTED]
On May 1, 2008, at 3:33 AM, hari jayaram wrote:
Hi
Since I am not on the cnsbb yet I am posting this here.
I downloaded the cns 1.2.2 intel build and was trying to run a
simulated annealing refinement on my macbook pro ( Intel) running
10.5.2
However the annealing job crashes roughly 40 minutes into the
refinement with the following message
"There is not enough memory available to the program.
This may be because of too little physical memory (RAM)
or too little swap space on the machine. It could also be
the result of user or system limits. On most Unix systems
the "limit" command can be used to check the current user
limits. Please check that the datasize, memoryuse and
vmemoryuse limits are set at a large enough value."
Unfortunately on Leopard it seems that unlimit and limit are not
available under bash
Further when I use csh , I get the following values for the limits
[mango:~/aps_04_21_2008/p10_2] hari% limit
cputime unlimited
filesize unlimited
datasize 6144 kbytes
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
descriptors 256
memorylocked unlimited
maxproc 266
In the same csh shell unlimit returns
[mango:~/aps_04_21_2008/p10_2] hari% unlimit
unlimit: descriptors: Can't remove limit (Invalid argument)
How can I setup cns to have free reign and use up unlimited
datasize and stacksize for all cns jobs?
Thanks for your help in advance
Hari Jayaram
The detailed error is posted below
ASSFIL: file /Users/hari/cns/cns_solve_1.2/libraries/toppar/
torsionmdmods opened.
MESSage=NORM
EVALUATE: symbol $MESSAGE_OLD_TMOD set to "NORM" (string)
ECHO=FALSe {OFF}
EVALUATE: symbol $ECHO_OLD_TMOD set to FALSE (logical)
NEXTCD: condition evaluated as false
Program version= 1.2 File version= 1.2
SELRPN: 0 atoms have been selected out of 2380
cns_solve(93676) malloc: *** mmap(size=3000000512) failed (error
code=12)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug
ALLHP: request for -1294967296 bytes
---------------------------------------------------------
There is not enough memory available to the program.
This may be because of too little physical memory (RAM)
or too little swap space on the machine. It could also be
the result of user or system limits. On most Unix systems
the "limit" command can be used to check the current user
limits. Please check that the datasize, memoryuse and
vmemoryuse limits are set at a large enough value.
---------------------------------------------------------
%ALLHP error encountered: not enough memory available
(CNS is in mode: SET ABORT=NORMal END)
*****************************************************
ABORT mode will terminate program execution.
*****************************************************
Program will stop immediately.
============================================================
Maximum dynamic memory allocation: 139649464 bytes
Maximum dynamic memory overhead: 944 bytes
Program started at: 14:51:17 on 30-Apr-2008
Program stopped at: 15:09:16 on 30-Apr-2008
CPU time used: 1077.7678 seconds
============================================================
Axel T. Brunger
Investigator, Howard Hughes Medical Institute
Professor of Molecular and Cellular Physiology
Stanford University
Web: http://atbweb.stanford.edu
Email: [EMAIL PROTECTED]
Phone: +1 650-736-1031
Fax: +1 650-745-1463
