Submitting Batch Jobs

jacapo-bsub myscript.py
jacapo-ver-bsub 9a myscript.py (select a specific version)

Jacapo Parallel NEB Example

You can find a Jacapo parallel NEB example here. This same script can be used for a restart (the interpolated traj files are only recreated if they don't exist).

Some important notes:

  • the number of processors selected for a parallel NEB must be an integer multiple of the NumberOfImages-2 (the images at the end points are "fixed").
  • Parallel NEB settings (e.g. number of cores) can be debugged running in the suncat-test queue with 1 processor per non-fixed image.
  • Later on in the NEB (discussed here) it is good to set climbing=True and switch to the FIRE method, shown here. As best I can tell, this page doesn't provide good instructions for when to turn those on.

Perturbing Jacapo Calculations

When taking an existing Jacapo calculation and making changes (e.g. adding an external field) it is important to not instantiate a new calculator (to work around some Jacapo bugs) but instead read in the previous atoms/calculator from the .nc file. Johannes Voss has kindly provided an example with some comments here.

Stripping Wavefunctions from Jacapo .nc Files

To strip wavefunctions from all subdirectories of the current directory (".", in the find command):

source /afs/slac/g/suncat/jacapo/setupenv
find . -name \*nc -exec /nfs/slac/g/suncatfs/sw/jacapov3/ase/ase/calculators/jacapo/tools/stripnetcdf {} \; -print

Versions

Version

Date

Comment

jacapov3

4/29/11

copy of v2, but ase from svn head to pick up Lars parallel neb code (and dacapo.run)

jacapov4

7/8/11

softlink to jacapov3, change setupenv/dacapo.run to use torque/maui aware openmpi

jacapov5

2/23/12

softlink to javapov3, change setupenv/dacapo.run to use lcls filesystem naming /reg/d/suncat

jacapov6

3/7/12

like v5, but use the TaskStarter/mympirun_wrapper script in dacapo.run so we can bstop/bresume jobs and fix accounting for non parneb jobs

jacapov7

4/12/12

like v6, but change dacapo.run script so that it can be used for normal jobs and parallel nebs

jacapov8

11/5/12

like v7, but change dacapo.run script to not use /afs version of mpirun. Appears to fix intermittent hang problem with parallel NEBs

jacapov9a

11/9/12

(suncat3 farm only) python packages rebuilt for RHEL6

jacapov10

2/21/13

like v8, but more recent version of ASE (3.6.1.2694)

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