Using SCOOP for distributed parallel processing#111

Closed

rwest wants to merge 45 commits intoReactionMechanismGenerator:masterfrom

rwest:scoop

Commits on Apr 5, 2013

Added an rmgpy.utilities module with path_checksum() function.
rwest
committed
Cache the RMG Database in a pickle and a hash, to speed up reloading it.
rwest
committed
Use scoop.shared module to share database cache location and hash.
rwest
committed

Commits on Aug 14, 2013

Merged master into scoop, and resolved the conflict.
keceli
committed

Commits on Aug 28, 2013

First attempt to add QM capability with scoop.
keceli
committed

Commits on Aug 29, 2013

Some explanation on how to install and use scoop mainly on Pharos
keceli
committed

Commits on Oct 4, 2013

rmgpy/qm/mopac.py: Wait for 1 sec for the buffer to write to disc. Temporary solution to avoid attribute errors from cclib during parsing.
keceli
committed

Commits on Oct 12, 2013

attempt to run RMG without thermolibrary
keceli
committed

Commits on Oct 22, 2013

Parallelizing thermoEstimator.py.
keceli
committed

Commits on Oct 31, 2013

PM6 and PM7 options are added for MOPAC. Usage software=MOPACPM6, etc.
keceli
committed

Commits on Nov 1, 2013

Commits on Nov 5, 2013

Commits on Nov 8, 2013

Commits on Nov 9, 2013

Added makeProfileGraph as a script to be able to modify profile graphics with different thresholds
keceli
committed

Commits on Nov 12, 2013

Moved generateQMData to higher QMMolecule class along with minor modifications
keceli
committed

Commits on Nov 13, 2013

scoop jobs can now be run through SGE
keceli
committed

Commits on Nov 14, 2013

Added examples for SCOOP and some minor improvements
keceli
committed

Commits on Nov 15, 2013

Commits on Nov 16, 2013

Fixing some problems with makeProfileGraph
keceli
committed

Commits on Nov 22, 2013

Improved argument parsing and increased chunk size
keceli
committed

Commits on Nov 24, 2013

Load only thermo libraries
keceli
committed

Commits on Dec 2, 2013

Improved argument parsing in thermoEstimator
keceli
committed

Commits on Dec 18, 2013

Commits on Dec 21, 2013