Using SCOOP for distributed parallel processing - #111

Closed

rwest wants to merge 45 commits into

ReactionMechanismGenerator:masterfrom

rwest:scoop

Commits on Apr 3, 2013

Commits on Apr 5, 2013

Added an rmgpy.utilities module with path_checksum() function.
rwest
committed
7fca647
Cache the RMG Database in a pickle and a hash, to speed up reloading it.
rwest
committed
6800963
Use scoop.shared module to share database cache location and hash.
rwest
committed
6c12a79

Commits on Aug 14, 2013

Merged master into scoop, and resolved the conflict.
keceli
committed
211231c

Commits on Aug 28, 2013

First attempt to add QM capability with scoop.
keceli
committed
507a875

Commits on Aug 29, 2013

Some explanation on how to install and use scoop mainly on Pharos
keceli
committed
997e8d8

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
56ca670

Commits on Oct 11, 2013

Commits on Oct 12, 2013

attempt to run RMG without thermolibrary
keceli
committed
384db4e

Commits on Oct 22, 2013

Parallelizing thermoEstimator.py.
keceli
committed
79e6713

Commits on Oct 31, 2013

PM6 and PM7 options are added for MOPAC. Usage software=MOPACPM6, etc.
keceli
committed
13af2d9

Commits on Nov 1, 2013

Commits on Nov 5, 2013

resolving conflicts to merge with master
keceli
committed
9566913
Reverting a mistake I did during the merge with master
keceli
committed
f3e0bdf

Commits on Nov 8, 2013

Thermoestimator generates output even if the job does not finish
keceli
committed
f87faf9
Added profiling for thermoEstimator
keceli
committed
458c5e7

Commits on Nov 9, 2013

Added makeProfileGraph as a script to be able to modify profile graphics with different thresholds
keceli
committed
6ec8ae7

Commits on Nov 12, 2013

Moved generateQMData to higher QMMolecule class along with minor modifications
keceli
committed
5dd2c17

Commits on Nov 13, 2013

scoop jobs can now be run through SGE
keceli
committed
1901b8a

Commits on Nov 14, 2013

Added examples for SCOOP and some minor improvements
keceli
committed
d3a2926

Commits on Nov 15, 2013

Revert "attempt to run RMG without thermolibrary"
keceli
committed
e08ce78
Fixed a comment and revert an unnecessary change.
keceli
committed
f716b5b

Commits on Nov 16, 2013

Fixing some problems with makeProfileGraph
keceli
committed
dad02b4

Commits on Nov 22, 2013

Improved argument parsing and increased chunk size
keceli
committed
4fadd44

Commits on Nov 24, 2013

Load only thermo libraries
keceli
committed
fcb5c20

Commits on Nov 25, 2013

Commits on Dec 2, 2013

Improved argument parsing in thermoEstimator
keceli
committed
fa87afe

Commits on Dec 18, 2013

Fixed the problem with linear molecules
keceli
committed
210ea35
Pulled master
keceli
committed
08f210f

Commits on Dec 21, 2013

Limit lone pair drawing to Nitrogen atoms only.

connie
authored and
keceli
committed
0c31eb0
Draw lone electron pairs only for nitrogen containing species

bbuesser
authored and
keceli
committed
67d1cf6
Make transport writing compatible with Python 2.6

rwest
authored and
keceli
committed
5048034
Do not load salvation groups by default.
keceli
committed
b2f809f
Merge pull request #1 from keceli/scoop
rwest
committed
af7214f