#HTSOHM-dev

Master Branch Status:

This is a package which can be used to map the structure-property space
spanned by hypothetical, porous pseudo materials. This package contains
modules that manage randomly-generating libraries of pseudo-materials,
distributing many simulations across a computing cluster, and selectively
mutating rare materials--in an iterative process.

Getting started

This package was built to be run locally, or on a computing cluster. To run on
a cluster, the following must be installed:

• Torque/PBS (qsub)
• Python 3.5.1
  In any case, following Python packages are required:
• pyyaml
• psycopg2
• numpy
• SQLAlchemy
• RASPA2 (git+https://github.com/WilmerLab/raspa2)

First time setup

# If using environment modules    
module purge   
module load python/3.5.1/environment/module    

# Clone HTSOHM repo    
git clone https://github.com/WilmerLab/HTSOHM-dev.git    

# Create virual environment for Python packages    
mkdir -p ~/venv    
pyvenv ~/venv/htsohm    
source ~/venv/htsohm/bin/activate    

# Install Python packages   
cd path/to/htsohm/repo    
pip install -r requirements.txt    

You will need a database.yaml file for HTSOHM to use to store results. You
can use the database.sample.yaml file (just copy it to database.yaml) if you
just want to use a local SQLite database. Otherwise, enter in your
connection_string into the database.yaml file per the format of the example
file.

You will also need configuration file to specify the run-parameters. You can
use the htsohm.sample.yaml file (just copy it and change the values specified
within).

Running HTSOHM

Activating the htsohm virtual environment:

module purge
module load python/3.5.1/environment/module
source ~/venv/htsohm/bin/activate
cd path/to/htsohm/repo

Starting a run:

./hts.py start path/to/config      

Launching a worker locally:

./hts.py launch_worker run_id    

Launching workers on a cluster:

qsub -v='run_id' launch_workers_qsub.sh   

When running on a cluster, we recommend using GNU screen or Tmux; one screen
running the htsohm virtual environment, and one to be used to access cluster
resources such as PBS/Torque.

Install to virtual environment:

cd /path/to/htsohm/repo
~/venv/htsohm/bin/python setup.py install

Please send questions/comments/concerns to [email protected].

License

HTSOHM-dev and related modules released under the MIT License 2016.

Development environment

3.5.1 |Anaconda 2.4.1 (64-bit)| (default, Dec  7 2015, 11:16:01)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)]
Bash 4.1.2(1)-release
RHEL 6.6	2.6.32-358
psql (PostgreSQL) 8.4.20