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
============================================================
