env.sh

#!/bin/bash


source ~/.bash_profile
module purge
module load shared
module load gpu/0.15.4
module load slurm
module load openmpi/4.0.4
module load cuda/11.0.2
#module load amber/20-patch15
#module load conda
conda activate westpa-2.0


export PATH=$PATH:$HOME/bin
export PYTHONPATH=/home/ssonti/miniconda3/envs/westpa-2.0/bin/python
export LD_LIBRARY_PATH=/expanse/lustre/scratch/ssonti/temp_project/amber_learn/chignolin_tutorial/westpa_tutorials/tutorial7.3-chignolin/plumed/lib:$LD_LIBRARY_PATH

# Explicitly name our simulation root directory
if [[ -z "$WEST_SIM_ROOT" ]]; then
    export WEST_SIM_ROOT="$PWD"
fi

export SIM_NAME=$(basename $WEST_SIM_ROOT)
echo "simulation $SIM_NAME root is $WEST_SIM_ROOT"


# Set up environment for dynamics
#source $AMBERHOME/amber.sh




# Set runtime commands (this is said to be easier on the filesystem)
export NODELOC=/expanse/lustre/scratch/ssonti/temp_project/amber_learn/chignolin_tutorial/westpa_tutorials/tutorial7.3-chignolin/ParGaMD
export USE_LOCAL_SCRATCH=1

export WM_ZMQ_MASTER_HEARTBEAT=100
export WM_ZMQ_WORKER_HEARTBEAT=100
export WM_ZMQ_TIMEOUT_FACTOR=300
export BASH=$SWROOT/bin/bash
export PERL=$SWROOT/usr/bin/perl
export ZSH=$SWROOT/bin/zsh
export GPUMD_PATH=/expanse/lustre/scratch/ssonti/temp_project/amber_learn/chignolin_tutorial/westpa_tutorials/tutorial7.3-chignolin/GPUMD-3.9.4/src/gpumd
export PLUMED_KERNEL=/expanse/lustre/scratch/ssonti/temp_project/amber_learn/chignolin_tutorial/westpa_tutorials/tutorial7.3-chignolin/plumed/lib/libplumedKernel.so
export IFCONFIG=$SWROOT/bin/ifconfig
export CUT=$SWROOT/usr/bin/cut
export TR=$SWROOT/usr/bin/tr
export LN=$SWROOT/bin/ln
export CP=$SWROOT/bin/cp
export RM=$SWROOT/bin/rm
export SED=$SWROOT/bin/sed
export CAT=$SWROOT/bin/cat
export HEAD=$SWROOT/bin/head
export TAR=$SWROOT/bin/tar
export AWK=$SWROOT/usr/bin/awk
export PASTE=$SWROOT/usr/bin/paste
export GREP=$SWROOT/bin/grep
export SORT=$SWROOT/usr/bin/sort
export UNIQ=$SWROOT/usr/bin/uniq
export HEAD=$SWROOT/usr/bin/head
export MKDIR=$SWROOT/bin/mkdir
export ECHO=$SWROOT/bin/echo
export DATE=$SWROOT/bin/date
#export SANDER=$AMBERHOME/bin/sander
#export PMEMD=$AMBERHOME/bin/pmemd.cuda
#export CPPTRAJ=$AMBERHOME/bin/cpptraj