[ase-users] CP2K calculator hangs

[Glen Jenness]

Eric,
That is good to know.  Once I get some free time I'll play with it.

Glen
On Mar 18, 2016 10:16 AM, "Eric Hermes" <ehermes at chem.wisc.edu> wrote:

> Hello,
>
>
>
> For what it's worth, I seem to have found the issue, and it is unrelated
> to ASE. CP2K seem to be very particular about the MPI toolset that it is
> compiled with and the MPI environment that it's run in. I had previously
> been compiling CP2K with mvapich2 and running it with slurm's "srun"
> command, but I found that it is necessary to compile CP2K with OpenMPI and
> run it with OpenMPI's "mpirun" to prevent random hangs.
>
>
>
> Glen, the CP2K interface for ASE is actually quite a bit nicer than VASP's
> in a way, in that rather than constantly starting and stopping the
> executable which requires lengthy initialization for each call, the CP2K
> calculator maintains a constant connection to CP2K's shell interface. This
> means that CP2K only has to initialize once per calculator instance, and
> therefore using CP2K with ASE incurs extremely little overhead. In
> principle, the VASP calculator could be made to do this too, as VASP has a
> hidden (undocumented) INCAR parameter "INTERACTIVE" that enables VASP to
> take atomic positions from stdin and output energies/forces to stdout. This
> would make using VASP with ASE far more efficient.
>
>
>
> Eric
>
>
>
> *From:* Glen Jenness [mailto:glenjenness at gmail.com]
> *Sent:* Wednesday, March 16, 2016 11:25 AM
> *To:* Eric Hermes <ehermes at chem.wisc.edu>
> *Cc:* ase-users at listserv.fysik.dtu.dk
> *Subject:* Re: [ase-users] CP2K calculator hangs
>
>
>
> Eric,
>
> I found with VASP that the python is being executed while the VASP
> executable is still cleaning up, resulting in oddities such as partial
> inputs, "node is busy" messages from the queue, etc.  In these cases, a
> pause of a few seconds is all that is needed (I use 5s).
>
>
>
> Glen
>
>
>
> On Wed, Mar 16, 2016 at 10:27 AM, Eric Hermes <ehermes at chem.wisc.edu>
> wrote:
>
> Hello,
>
>
>
> I have been trying for some time to get CP2K to work on our campus cluster
> with ASE. While I have managed to finally produce a working executable that
> doesn't segfault or buffer overflow (pro tip: use the GNU compilers plus
> OpenMPI), I am running into a persistent issue where the CP2K calculator
> seems to hang after a period of time. Specifically, what is happening is
> that the calculator initializes and runs properly at first, but if I am
> performing a geometry relaxation (and presumably AIMD, though I haven't
> tried this), the calculation will randomly hang after some number of ionic
> steps. The cp2k_shell executable and the python script are both still
> running on the compute nodes, but the calculation does not proceed.
> Occasionally, but not always, the "inp" file produced by the ASE calculator
> will be incomplete, usually truncated in the middle of the atomic position
> declarations. I worry that this issue is being caused by something like a
> race condition in the communication between ASE and the cp2k_shell
> executable. Does anybody have any insight into this issue? I am going to
> continue debugging this by putting a sleep(0.1) statement at the end of the
> _send() function in the CP2K class, but since the hangs seem to happen at
> random after several hours of working just fine I'll have to wait and see
> whether this actually does anything.
>
>
>
> Eric
>
>
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>
>
>
>
>
> --
>
> Dr. Glen Jenness
>
> Catalysis Center for Energy Innovation (CCEI)
>
> University of Delaware
>
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