ExTASY

The goal of this package is to execute Adaptive sampling on HPCs in a scalable, efficient way.

New release v2

Now with python3 and asynchronous execution supported.

Setup and installation on Local system, not necessary for Summit

Make a new conda python (python2 or python3) installation:

conda install -c conda-forge rabbitmq-server tmux pip git python
pip install radical.entk

Check radical-stack to make sure radical packages are installed.

Setup and installation on remote system

For Summit

Load publicly accessible python environment:

export RADICAL_LOG_LVL="DEBUG"
export RADICAL_LOG_TGT="radical.log"
export RMQ_HOSTNAME=two.radical-project.org
export RMQ_PORT=33239
module load cuda/9.1.85
module load cmake
module load gcc/7.4.0
module load python/3.6.6-anaconda3-5.3.0
conda activate extasy
cd $MEMBERWORK/bipxxx

Download this repository

git clone https://github.com/ClementiGroup/extasy.git
cd extasy

Executing the example

The settings file for the example is settings/settings_extasy_chignolin_example.wcfg. It will run cmicro adaptive strategy for Chignolin protein with 5 replicas for couple iterations. Change the remote_output_directory in the settings file, so that the directory is empty and accessible to you. ExTASY will append to the previous results in the directory. For longer simulations run inside tmux on a machine which can run undisturbed for long times. Execution command for example:

python extasy.py --Kconfig settings/settings_extasy_chignolin_example.wcfg

The expected run time is 10 minutes in addition to the queue time.

Results

• The output directory as specified in settings files will have some output for each iteration.
• The subdirectories md_logs, results, restart and alltrajs will have additional information.
• To debug look into the re.session.xxx directory as specified in the output of the execution. Additional files to debug are in radical.pilot.sandbox

Adapt to a protein of your choice

• Copy the directory files-chignolin, replace the pdb structures and the xml files with files of your protein.
• Copy settings/settings_extasy_example_chignolin.wcfg and change md_dir, md_input_file, md_reference.
• If necessary change in the settings file the walltime, NODESIZE and num_replicas.

Change molecular dynamics engine to your choice

• Copy extasy_tica.py and change sim_task parameters, the sim_task.arguments has to call your script with required files and paths.
• copy helper_scrips/run-openmm7.py and change the script to your MD engine.
• Change in settings file parameter md_run_file from run-openmm7.py to your md script.
• change in extasy.py the molecular dynamics tasks parameters, the sim_task.arguments has to call your script with required files and paths.

Adapt analysis step to your choice

• Copy helper_scrips/run-vamp3.py and change the analysis steps as desired.
• Change in settings file parameter script_ana from run-vamp3.py to your analysis script.
• change in extasy.py the analysis tasks parameters, the ana_task.arguments has to call your script with required files and paths.

Notes

The extasy.py script contains information about the application execution workflow and the associated data movement. The directory helper_scripts contains script performing molecular dynamics and analysis.