[ccp4bb] Stack trace terminated abnormally. cns solve on macosx leopard

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Blake and Phillips 1962
From: Elspeth Garman elspeth {- at -} BIOP {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-05-21

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Subject: Re: Stack trace terminated abnormally. cns solve on macosx leopard
From: Axel Brunger brunger {- at -} STANFORD {- dot -} EDU
Date: 2008-05-21

Subject: Stack trace terminated abnormally. cns solve on macosx leopard
From: xiaoyazi2008 xiaoyazi2008 {- at -} HOTMAIL {- dot -} COM
Date: 2008-05-21

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

Zhihong@Sinapore

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
> ============================================================

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Blake and Phillips 1962
From: Elspeth Garman elspeth {- at -} BIOP {- dot -} OX {- dot -} AC {- dot -} UK
Date: 2008-05-21

Next message:
Subject: Re: Stack trace terminated abnormally. cns solve on macosx leopard
From: Axel Brunger brunger {- at -} STANFORD {- dot -} EDU
Date: 2008-05-21