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Re: [ccp4bb] phaser:- set a breakpoint in malloc error break to debug
 

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CCP4bb <-- 2008 <-- May 2008 <-- 01 May 2008
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Subject: Re: phaser:- set a breakpoint in malloc error break to debug
From: hari jayaram harijay {- at -} GMAIL {- dot -} COM
Date: 2008-05-01
Hello Ethan Meritt,
Thanks for your reply,

I have only recently started using the 8 core Mac pro , and in the last
three days have faced many such issues with swapsize and running out of
memory (the machine has 4GB total).
Just Yesterday I had a problem on a different dataset with a cns simulated
annealing run which stopped because of swapsize issues. I know that phenix
on this machine has a setting in the com file which uses ulimit (csh tcsh)
to unlimit everything . On a related note, I think Apple also changed its
csh such that unlimit requires an argument such as unlimit stacksize
etc..and not just unlimit

Since I am an OSX leopard newbie, Should I ( or could I ) use ulimit or
unlimit as a systemwide shell setting and should I put this into the
ccp4.setup.sh and ccp4.setup or in /etc/bashrc or /etc/cshrc so that I dont
run into such problems. From the seetings it seems like I have a very small
swapsize of 8192 kbytes

At the present moment the limit command on this machine when run in csh
returns

cputime unlimited
filesize unlimited
datasize 6144 kbytes
stacksize 8192 kbytes
coredumpsize 0 kbytes
memoryuse unlimited
descriptors 256
memorylocked unlimited
maxproc 266

I am wondering why I havent had to mess with similar settings on linux
while this multi-core machine with a massive disk and reasonable amount of
memory , seems a little touchy with its swap size and other settings.

Thank you for your help,

Hari


On Thu, May 1, 2008 at 2:49 PM, Ethan Merritt
wrote:

> On Thursday 01 May 2008 11:37, hari jayaram wrote:
> > Hi
> > I was running phaser on an 8 core Mac pro using the fink 10.5 (intel)
> ccp4
> > binaries provided by W.G Scott .
> > Today I saw a very strange error and phaser FAILED.
> >
> > #CCP4I TERMINATION STATUS 0 "phaser(88098) malloc: ***
> mmap(size=1185792000)
> > failed (error code=12) *** error: can't allocate region *** set a
> breakpoint
> > in malloc_error_break to debug"
>
> This is telling you that you ran out of memory.
> Perhaps you had more jobs running than usual, and not enough swap space.
> Perhaps something in the Phaser run caused it to calculate a map with
> finer grid spacing than your other runs. Perhaps something else entirely.
> I would start by checking the swap space.
>
> Ethan Merritt
>
> --
> Ethan A Merritt Courier Deliveries: 1959 NE Pacific
> Dept of Biochemistry Regular Mail: Mailstop 357742
> Health Sciences Building
> University of Washington - Seattle WA 98195-7742
>
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