AMBER Archive (2004)

Subject: Re: AMBER: ptraj hbond memory allocation on opteron

From: Fabian Boes (
Date: Tue Dec 14 2004 - 08:33:42 CST

Dear Amber users,

i solved the problem by modifying the safe_malloc routine in

- safe_malloc(int size)

+ safe_malloc(size_t size)

Right now ptraj is running using 11 gb of ram.



> Hi,
>> ERROR in safe_malloc: Error in alloc of -2144460096 bytes
> ...You/ptraj seem to have requested more than 2GB of mem at once.
> Since safe_malloc takes an int (size) as argument and passes (size_t)
> size to the usual malloc, this fails. If you're running x86_64 linux,
> there might by routines that allow allocating more at once, but I don't
> know.
> good luck
> Andreas


Fabian Bös

Institute of Technical Biochemistry University of Stuttgart / Germany

Phone: +49-711-6857481 Fax: +49-711-6853196 Email:

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