adicksonlab / westpa-wexplore Goto Github PK
View Code? Open in Web Editor NEWA plugin to run the WExplore algorithm in the WESTPA toolkit
License: GNU General Public License v3.0
A plugin to run the WExplore algorithm in the WESTPA toolkit
License: GNU General Public License v3.0
Trying to get this up and running. I can get past the init.sh
part but when I run run.sh
I get this in the log:
System is being built only off of the system driver
Traceback (most recent call last):
File "/home/salotz/anaconda3/envs/westpa-2017.10/westpa-2017.10/lib/cmds/w_run.py", line 58, in <module>
sim_manager.load_plugins()
File "/home/salotz/anaconda3/envs/westpa-2017.10/westpa-2017.10/src/west/sim_manager.py", line 146, in load_plugins
plugin = extloader.get_object(plugin_name)(self, plugin_config)
File "/home/salotz/anaconda3/envs/westpa-2017.10/westpa-2017.10/lib/west_tools/westpa/extloader.py", line 78, in get_object
module = load_module(modspec, path)
File "/home/salotz/anaconda3/envs/westpa-2017.10/westpa-2017.10/lib/west_tools/westpa/extloader.py", line 45, in load_module
(fp, pathname, desc) = imp.find_module(next_component, path)
ImportError: No module named wex_plugin
Hello,
I am running WExplore for the first time. I am having issues running the examples.
I am getting the following error when I am running the kcrown ether example.:
Traceback (most recent call last):
File "/home/sreyoshi/westpa_new/envs/westpa-2017.10/westpa-2017.10/lib/cmds/w_init.py", line 75, in
system = westpa.rc.get_system_driver()
File "/home/sreyoshi/westpa_new/envs/westpa-2017.10/westpa-2017.10/lib/west_tools/westpa/_rc.py", line 496, in get_system_driver
self._system = self.new_system_driver()
File "/home/sreyoshi/westpa_new/envs/westpa-2017.10/westpa-2017.10/lib/west_tools/westpa/rc.py", line 345, in new_system_driver
system.initialize()
File "/home/sreyoshi/WESTPA-WExplore/examples/kcrownether/system.py", line 42, in initialize
np.array([0,], np.int))
File "build/bdist.linux-x86_64/egg/westpa_wexplore/wexplore.py", line 355, in balance_replicas
TypeError: set_node_attributes() got multiple values for keyword argument 'name'
I just installed WExplore plugin. I have only edited the env.sh file.
Attached is the env.sh file. I am not sure what I am doing wrong.
env.sh
export SCRATCH=$SCRATCH
export WEST_ROOT='/home/sreyoshi/westpa_new/envs/westpa-2017.10/westpa-2017.10'
export GROMACS_ROOT='/home/sreyoshi/gromacs-2016.3_gpu/bin/bin'
export WEST_PYTHONPATH='/home/sreyoshi/westpa_new/envs/WESTPA-WExplore'
export WEST_PYTHON='~/westpa_new/envs/WESTPA-WExplore/bin/python'
##Above parts changed by Sreyoshi Sur 4/8/2019
export PATH="$WEST_PYTHONPATH:$PWD:$ANACONDA_ROOT/bin:$WEST_ROOT/bin/:$GROMACS_ROOT/bin/:$PATH"
export LD_LIBRARY_PATH="$ANACONDA_ROOT/lib:$GROMACS_ROOT/bin:$LD_LIBRARY_PATH"
export WM_ZMQ_MASTER_HEARTBEAT=100
export WM_ZMQ_WORKER_HEARTBEAT=100
export WM_ZMQ_TIMEOUT_FACTOR=100
export WEST_ZMQ_DIRECTORY=server_files
export WEST_LOG_DIRECTORY=job_logs
export GMX=gmx
export TOP=18-crown-6-K+.top
export NDX=18-crown-6-K+.ndx
export REF=bound_state.tpr
Please let me know if anyone has encountered this error before. When I do 'import wexplore' in the python terminal inside the conda environment it does not show any error. So I don't think there was any installation issue.
Regards,
Sreyoshi Sur
Grossfield Lab
University of Rochester
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