Re: [ccp4bb] Memory allocation error in phaser - Mac os

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

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Subject: Memory allocation error in phaser - Mac os
From: Narayanan Ramasubbu ramasun1 {- at -} UMDNJ {- dot -} EDU
Date: 2009-12-04

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Subject: Re: Memory allocation error in phaser - Mac os
From: Vellieux Frederic Frederic {- dot -} Vellieux {- at -} IBS {- dot -} FR
Date: 2009-12-04

Hi Subbu,

Vaguely rings a bell. From years ago.

Try the command "limit" in tcsh or csh (I think it's ulimit in bash,
don't use bash myself).
[Mac OS X is a Unix system (BSD) so it should be similar if not identical].

I get here on a Linux box:

limit (followed by carriage return)
cputime unlimited
filesize unlimited
datasize unlimited
stacksize unlimited
coredumpsize 0 kbytes
memoryuse unlimited
vmemoryuse unlimited
descriptors 1024
memorylocked 32 kbytes
maxproc 32736

and make sure that memoryuse is unlimited

You add a line in your .cshrc or .tcshrc file:

limit memoryuse unlimited

Of course this will apply if the problem is due to your system not allocating enough
memory for the process.
If it's something else, I wouldn't know.

HTH,

Fred.

Narayanan Ramasubbu wrote:
> Dear All:
> How to increase the memory size (?) to avoid the following error?
>
> ***************************************************************************
>
> * Information from CCP4Interface script
> ***************************************************************************
>
> The program run with command: /sw/share/xtal/ccp4-6.1.1/bin/phaser
> has failed with error message
> phaser(1393) malloc: *** vm_allocate(size=402313216) failed (error
> code=3)
> phaser(1393) malloc: *** error: can't allocate region
> phaser(1393) malloc: *** set a breakpoint in szone_error to debug
> phaser(1393) malloc: *** vm_allocate(size=402313216) failed (error
> code=3)
> phaser(1393) malloc: *** error: can't allocate region
> phaser(1393) malloc: *** set a breakpoint in szone_error to debug
> ***************************************************************************
>
>
> Thanks
> Subbu
>
>

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

Previous message:
Subject: Memory allocation error in phaser - Mac os
From: Narayanan Ramasubbu ramasun1 {- at -} UMDNJ {- dot -} EDU
Date: 2009-12-04

Next message:
Subject: Re: How to reduce free-R factor
From: Lionel Mourey lionel {- dot -} mourey {- at -} IPBS {- dot -} FR
Date: 2009-12-04