Re: [AMBER] PTRAJ (clustering)-Segmentation fault

From: Thomas Cheatham <>
Date: Tue, 15 Oct 2019 20:11:10 +0000

Let's see, AMBER 12 was from 2012 and it is 2019 and I personally (nor has anyone else I think) modified or tested the PTRAJ code since about that time (or potentially 2013), well it is tested maybe, but not developed so much.

I would look at CPPTRAJ either from AmberTools (the current version) or hit the GitHub page for CPPTRAJ at:

Otherwise, if you are trying to use a special feature of the ptraj clustering that is no longer supported that may require some time to figure out (and we would need all the inputs,etc to debug).

Oh wait/snap - I actually see the problem -- you are trying to allocate ~172 GB of RAM and are likely blowing memory on your machine noting if you are clustering that many frames with a pairwise comparison it will take a long time. Use the sieve options, like sieve 10 or sieve 25 and it should work...

From: Rui Chen <>
Sent: Tuesday, October 15, 2019 9:35:56 AM
To: AMBER Mailing List
Subject: [AMBER] PTRAJ (clustering)-Segmentation fault


I am using PTRAJ Version: "AMBER 12.0 integrated" (4/2012) to do
clustering. I got the following errors.

1. Error in file clusterLib.c line 5439 when calling SafeMalloc() to alloc
of 1800180004 bytes.
2. /cm/local/apps/slurm/var/spool/job244628/slurm_script: line 16: 23253
Segmentation fault
Details please find the attached file.

Could you please help solve the problem? Thank you.

Best regards,

AMBER mailing list
Received on Tue Oct 15 2019 - 13:30:02 PDT
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