RE: AMBER: error in safe

From: Ross Walker <>
Date: Mon, 24 Oct 2005 07:25:38 -0700

Dear Claire,
Your job is asking for a single block of memory of over 1.3GB. Such large
allocations can often pose problems, especially on 32 bit machines. You
could try rebooting the machine and bringing it up with the minimal
services. E.g. no X Windows, no NFS, no samba, sendmail etc. Ideally single
user mode with no networking would be your best bet. This will free the most
amount of system resources and may allow the allocation to work. Note the
program actually needs more memory than just this single allocation, this is
just the one that failed. So you'll probably need around 3 to 4GB of ram
(with high memory access turned on in the kernel) to get things to run well.
Failing this I would try to find a large memory 64 bit machine or
alternatively see if you can make your system smaller in some way, say by
doing it in pieces... Memory is often an issue in calculations that deal
with frequencies since you have to store the Hessian matrix which requires a
lot of space.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
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From: [] On Behalf Of
Claire Zerafa
Sent: Monday, October 24, 2005 06:19
Subject: AMBER: error in safe

Hi amber users
i am doing pca in ptraj and i get this error message:
error in safe_malloc Error in alloc of 1432894120 bytes
Is it correct to assume that this is because I have too many jobs running
simultaneously and RAM and virtual memory cant cope?

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Received on Mon Oct 24 2005 - 15:53:00 PDT
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