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radical-cybertools / ExTASY

MDEnsemble
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failure of rp 0.3.14 gromacs/lsdmap on archer #234

Closed ebreitmo closed 8 years ago

ebreitmo commented 8 years ago

virtualenv-1.11.6/scripts/virtualenv 14Jan source 14Jan/bin/activate pip install radical.ensemblemd ensemblemd-version 0.3.14 mkdir $HOME/extasy-tutorial/ cd $HOME/extasy-tutorial/

(Following instructions from http://extasy.readthedocs.org/en/latest/pages/grlsd.html )

curl -k -O https://raw.githubusercontent.com/radical-cybertools/ExTASY/extasy_data/tarballs/grlsd-on-archer.tar.gz tar xvfz grlsd-on-archer.tar.gz cd grlsd-on-archer emacs -nw archer.rcfg (changing username to ‘ebreitmo’)

python extasy_gromacs_lsdmap.py --RPconfig archer.rcfg --Kconfig gromacslsdmap.wcfg

EnsembleMD (0.3.14)

Starting Allocation ok Verifying pattern ok

Starting pattern execution ok

Executing simulation-analysis loop with 1 iterations on 24 allocated core(s) on 'epsrc.archer'

Job waiting on queue... Job is now running ! pre_loop() not defined. Skipping.2016-01-14 16:53:41,117: radical.enmd.SingleClusterEnvironment: MainProcess : MainThread : ERROR : Fatal error during execution: global name 'grompp_options' is not defined. Fatal error during execution: global name 'grompp_options' is not defined. Starting Deallocation2016-01-14 16:53:41,117: radical.enmd.SingleClusterEnvironment: MainProcess : MainThread : ERROR : Fatal error during execution: global name 'grompp_options' is not defined. Fatal error: global name 'grompp_options' is not defined. File "/Users/elenabreitmoser/14Jan/lib/python2.7/site-packages/radical/ensemblemd/single_cluster_environment.py", line 244, in run plugin.execute_pattern(pattern, self) File "/Users/elenabreitmoser/14Jan/lib/python2.7/site-packages/radical/ensemblemd/exec_plugins/simulation_analysis_loop/static.py", line 250, in execute_pattern if isinstance(pattern.simulation_step(iteration=iteration, instance=1),list): File "extasy_gromacs_lsdmap.py", line 93, in simulation_step if grompp_options is not None:

    done
vivek-bala commented 8 years ago

This should be resolved in master and extasy_data. I tested on stampede. Please try again.

vivek-bala commented 8 years ago

similar to #232

ibethune commented 8 years ago

OK, so this problem is indeed fixed if you install from master.

ibethune commented 8 years ago

Elena, if the default grlsd workflow is working for you, please close this. Having said that, I'm hitting #226