[ase-users] NEB parallel with Abinit parallel

[Kondov, Ivan (SCC)]

Dear all,

 

I think that the ASE/NEB and the Calculator can run both in parallel only if the Calculator is GPAW. This is because the NEB and the process spawned by the Calculator have to share an MPI communicator (I am not sure about any existing tricks with application/machinefiles and mpirun options). Thus parallel NEB will work with VASP or Abinit in serial mode only. Also serial NEB will work with the parallel versions of VASP, Abinit etc.

 

In order to run a parallel NEB with parallel VASP, the NEB implementation in the VTST package can be used (http://theory.cm.utexas.edu/vasp/) and VASP has to be patched. For Abinit I do not know such a solution.

 

A generic solution with ASE could be to split the calculations of the images in each BFGS iteration into several jobs and distribute them on the cluster. After all jobs are ready then their outputs are collected and passed to BFGS and the next image geometries are computed, distributed and so on until BFGS converges. Unfortunately I do not have an implementation yet but I would prefer (and recommend) to use a workflow system such as FireWorks for this.

 

Best regards,

Ivan

 

 

From: ase-users-bounces at listserv.fysik.dtu.dk [mailto:ase-users-bounces at listserv.fysik.dtu.dk] On Behalf Of Offermans Willem via ase-users
Sent: Thursday, November 15, 2018 2:39 PM
To: Kondov, Ivan (SCC) via ase-users
Subject: [ase-users] NEB parallel with Abinit parallel

 

Dear ASE friends,

 

I like to do a NEB calculation with 3 images in parallel.

 

The calculator is abinit, which can run in parallel as well.

 

How do I specify this in the python script.

 

I have used the following example as basis:

 

https://wiki.fysik.dtu.dk/gpaw/tutorials/neb/neb.html#neb-calculations-parallelized-over-images

 

I like to replace the calc definition from the python script:

 

<snip>

…

        calc = GPAW(h=0.3,
                    kpts=(2, 2, 1),
                    txt='neb%d.txt' % j,
                    communicator=ranks)

…

</snip>

 

with corresponding settings for abinit.

 

Is this possible?

 

Can you provide an example for abinit?

 

 

I expect something like:

 

<snip>

….

       

execAbinit = 'mpirun -np ' + torqueTasks + ' -machinefile machinefile.' + pbsJobID + ' ~/bin/abinit < PREFIX.files > pd.log’

...

 calc = Abinit(command=execAbinit,

                autoparal=1,

                communicator=ranks,

                ecut=intEcut * Ha,

                ixc=11,

                kpts=[intKpoints, intKpoints, 1],

                label='pd',

                nstep=400,

                occopt=7,

                pawecutdg=intPawEcut * Ha,

                pawovlp=6,

                pps='pawxml',

                toldfe=1.0e-6,

                tsmear=0.02*eV,

                txt='neb%d.txt' % j,

                xc='PBE')

 

 

Can you comment on the Abinit specification?

 

 

 

Met vriendelijke groeten,

Mit freundlichen Grüßen,

 

 

Willem Offermans

Researcher Electrocatalysis SCT

VITO NV | Boeretang 200 | 2400 Mol

Phone:+32(0)14335263 Mobile:+32(0)492182073 

 

Willem.Offermans at Vito.be


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