COCO workflow requires LSDMap input file when using Gromacs

[TensorDuck]

I get this error when I try running COCO using Gromacs as the simulator.

ExTASY version :  0.1-20-g347657f
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/coco.json
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/namd.json
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/sleep.json
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/amber.json
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/test.json
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/lsdmap.json
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/mmpbsa.json
Loading kernel configurations from /home/extasy/ExTASY/ExTASY-tools/lib/python2.7/site-packages/radical/ensemblemd/mdkernels/configs/gromacs.json
Session UID: rp.session.jchen-Vostro-260.extasy.016699.0002 
Pilot UID       : pilot.0000 
Preprocessing stage ....
An error occurred: 'module' object has no attribute 'lsdm_config_file'
Closing session, exiting now ...

My .wcfg is:

#-------------------------Applications----------------------
simulator                = 'Gromacs'          # Simulator to be loaded
analyzer                 = 'CoCo'           # Analyzer to be loaded

#-------------------------General---------------------------
num_iterations          = 1                 # Number of iterations of Simulation-Analysis
start_iter              = 0                 # Iteration number with which to start
num_CUs                 = 16                # Number of tasks or Compute Units
nsave                   = 1                 # Iterations after which output is transfered to local machine
checkfiles              = 5                 # Iterations after which to test if the expected files are present on remote/ does not download to local

#-------------------------Simulation-----------------------
num_cores_per_sim_cu    = 2                 # Number of cores per Simulation Compute Units
mdp_file           = './grompp-verlet.mdp'    # Entire path to MD Input file - Do not use $HOME or the likes
md_input_file        = './helix.gro'     # Entire path to Coordinates file - Do not use $HOME or the likes
top_file                = './topol.top'     # Entire path to Topology file - Do not use $HOME or the likes
logfile                 = 'coco.log'        # Name of the log file created by pyCoCo
atom_selection          = None              # Select entire residue or protein

#-------------------------Analysis--------------------------
grid                    = '5'               # Number of points along each dimension of the CoCo histogram
dims                    = '3'               # The number of projections to consider from the input pcz file

COCO doesn't through the error when using Amber. I was wondering if this was intended or not? In principle, the lsdm_config_file is not needed for COCO and shouldn't be a required field when using Gromacs.

[vivek-bala]

Hey, Justin. Extasy 0.1 is bound to gromacs-lsdmap and amber-coco. Patterns with gromacs-coco can be implemented with 0.2. (it might be possible to have that in 0.1, but I think the idea was to use 0.2 for such new combinations).

[TensorDuck]

That makes sense. I was having trouble installing 0.2 as well. Is it currently in a state to be released and installed?

[vivek-bala]

Yes. Please be sure to use the devel branch (as in the documentation)

Docs link: http://extasy.readthedocs.org/en/extasy_0.2/

Please let me know about any installation issues.

On Mon, Sep 21, 2015 at 6:05 PM, Justin Chen notifications@github.com wrote:

That makes sense. I was having trouble installing 0.2 as well. Is it currently in a state to be released and installed?

— Reply to this email directly or view it on GitHub https://github.com/radical-cybertools/ExTASY/issues/191#issuecomment-142123510 .

[vivek-bala]

@TensorDuck I'm closing this ticket, if you encounter an error with 0.2 installation please open a new ticket.