Re: [AMBER] Random segfaults (invalid memory reference) in sander

From: Charo del Genio <>
Date: Mon, 6 May 2019 10:37:34 +0100

On 03/05/2019 13:29, Daniel Roe wrote:
> Hmm - I think both of you are using OpenMPI. Do you have another MPI
> library (mpich, mvapich, intel mpi) that you can test with?
> -Dan

So, I've tried running the simulations on two different workstations of mine, and I get no crashes there. The only difference with the cluster is that on the workstation I am using OpenMPI-2.0.2. So,
I asked the cluster admin to install this specific version of OpenMPI, and tried to run on the cluster again. The result is that I experience no segfault when running with OpenMPI-2.0.2.

However, a new problem happens, which looks very much like a memory leak, as the memory used slowly but continuously increases, until the node dies for running out of memory. Interestingly, this does
NOT happen on the two workstations. To see if there is any difference in libraries at all, I checked with ldd, and I found that the only difference between cluster and workstations is that OpenMPI on
the cluster is compiled without C++ support. In other words, on the cluster there is no I have already asked the admin to recompile OpenMPI including C++ support, to make sure
absolutely everything is identical, but in the meantime I'm pondering upon the following questions:

- Does sander actually need to link against
- Could a memory leak be caused by its absence?
- Alternatively, could the bug be actually in sander? On my workstations I am using gcc stack smashing protection by default, whereas on the cluster it is disabled.
- If not, could the problem be due to a difference in kernel? On my workstation I'm running kernel version 4.19.27, whereas on the cluster the kernel version is 2.6.32.

Personally, I'm leaning towards a bug in sander quietly taken care of by ssp. If this is the case, how do I/we go about finding precisely where it is?



Dr. Charo I. del Genio
Senior Lecturer in Statistical Physics
Applied Mathematics Research Centre (AMRC)
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Coventry University Technology Park
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Received on Mon May 06 2019 - 03:00:02 PDT
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