README_bridges_install.md

Conda Environment Setup on XSEDE Bridges

Python2 remote RCT installation on Bridges

module load anaconda2
source /opt/packages/anaconda/anaconda2-5.2.0/etc/profile.d/conda.sh
conda create -n entk python=2.7.15
conda activate entk
pip install radical.entk

Python3 remote installation on Bridges

module load cuda/10.1
module load anaconda3
source /opt/packages/anaconda/anaconda3-5.2.0/etc/profile.d/conda.sh
conda create -n vampextasy
conda activate vampextasy
conda install -y -c omnia openmm
conda install -y -c omnia mdtraj
conda install -y -c conda-forge pyemma
conda install -y -c anaconda scikit-learn
conda install -y -c pip
pip install tensorflow-gpu

check installation of Python2 on Bridges

module load anaconda2
source /opt/packages/anaconda/anaconda2-5.2.0/etc/profile.d/conda.sh
conda create -n entk python=2.7.15
conda activate entk
conda install numpy
radical-stack

check installation of Python3 on Bridges

interactive on GPU node

module load cuda/10.1
module load anaconda3
source /opt/packages/anaconda/anaconda3-5.2.0/etc/profile.d/conda.sh
conda activate vampextasy
python -c 'import tensorflow as tf; print(tf.__version__)'
python -m simtk.testInstallation

Configuration - RabbitMQ, MongoDB

export RMQ_HOSTNAME=two.radical-project.org
export RMQ_PORT=33239
(optional) export RADICAL_PILOT_DBURL='mongodb://'

Run

module load anaconda2
source /opt/packages/anaconda/anaconda2-5.2.0/etc/profile.d/conda.sh
conda activate entk
python extasy_tica_bridges.py --Kconfig settings_extasy_tica3_chignolin_long_bridges.wcfg 2>&1 | tee log_extasy_tica_chignolin_long_bridges.log

Other instructions are omitted as described in the README.md

Run on Bridges login node (Client Inside)

Extasy can be located in Bridges which will be one of login nodes e.g. [user@login018 ~]. This will require ssh to connect to Bridges using PSC credentials similar to gsissh from outside. This needs to exercise the ssh key registration at PSC described below.

• Setting up a PSC password if not done before, this is not XSEDE password. (https://apr.psc.edu/autopwdreset/autopwdreset.html)
• If your PSC account is not active or not created, contact to [email protected].
• Create a ssh key pair or use existing one to submit a key (public key, i.e. .pub file extension) to PSC (https://grants.psc.edu/cgi-bin/ssh/listKeys.pl)
  • Note that the key has to be passwordless
• Administrator reviews/authorizes a key registration in 1-2 days

Once a key registration is complete, setup conda or virtualenv on Bridges login nodes: go back to the installation

• place the private key (passphraseless) in ~/.ssh/ with a name id_rsa
  • use a vim/nano/emacs editor for a quick copy and paste of key strings
• change the permission to read/write for owner only by
  • chmod 600 ~/.ssh/id_rsa
• Verify ssh passwordless connection by
  • ssh bridges

Last step is to specify ssh as a protocol instead of gsissh as we run Extasy inside of Bridges.

• Change the script i.e. extasy_tica_bridges.py
• access_schema has to be ssh in the res_dict e.g. line 270 and 283 in the script, gsissh only works with myproxy credentials