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

From: David A Case <>
Date: Mon, 6 May 2019 10:52:18 -0400

On Mon, May 06, 2019, Charo del Genio wrote:

>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.

It's worth noting that Amber is not currently compatible with the
default OpenMPI4.x. It will compile if you add the
"--enable-mpi1-compatibility" flag, but there may still be problems

>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

No, I don't think so. You could hand-edit your config.h file, remove
references to libmpi_cxx and try to just re-compile sander. But I'm
thinking that only cpptraj.MPI needs this library.

Note that you don't have to rely on your sysadmin: you should be able to
run AMBERHOME/AmberTools/src/configure_openmpi, to get whatever kind of
MPI installation you want (no need for root access, and you won't
interfere with any other users MPI codes.) Might also be worth trying
configure_mpich instead, just to see if it is somehow related to which
MPI stack you are using.

>- Could a memory leak be caused by its absence?

No idea....

>- 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.

There certainly could be a bug in sander, leading to a memory leak.
It's probably going to be tough to debug remotely, since it seems to
happen only on your cluster.

>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

Finding memory leaks in parallel codes is above my pay grade.... :-(


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Received on Mon May 06 2019 - 08:00:04 PDT
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