Executable version of odld using the MPI work-manager.

odld_exe_MPI-WM/env.sh

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+#!/bin/bash
+
+# Set up environment for dynamics
+module purge
+module load gcc/8.2.0
+module load openmpi/4.0.3
+
+# Set WESTPA-related variables
+export WEST_SIM_ROOT="$PWD"
+export SIM_NAME=$(basename $WEST_SIM_ROOT)
+

odld_exe_MPI-WM/init.sh

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+#!/bin/bash
+
+# Set up simulation environment
+source env.sh
+
+# Clean up from previous/ failed runs
+rm -rf traj_segs seg_logs istates west.h5
+mkdir   seg_logs traj_segs istates
+
+# Set bstate
+BSTATES="--bstate initial,1.0"
+
+# Run w_init
+w_init $BSTATES --work-manager=serial "$@"

odld_exe_MPI-WM/odld.py

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+#!/usr/bin/env python
+
+import numpy as np
+from numpy.random import normal as random_normal
+
+SEG_STATUS_COMPLETE = 2
+
+PI = np.pi
+
+coord_len = 21
+coord_dtype = np.float32
+
+A = 2
+B = 10
+C = 0.5
+x0 = 1
+
+# Implement a reflecting boundary at this x value
+# (or None, for no reflection)
+reflect_at = 10.0
+
+coords = np.empty(coord_len, dtype=coord_dtype)
+
+f = open('odld.crd', 'r')
+coords[0] = f.readline()
+f.close
+
+twopi_by_A = 2 * PI / A
+half_B = B / 2
+sigma = 0.001 ** (0.5)
+gradfactor = sigma * sigma / 2
+all_displacements = np.zeros(coord_len, dtype=coord_dtype)
+
+for istep in range(1, coord_len):
+    x = coords[istep - 1]
+
+    xarg = twopi_by_A * (x - x0)
+
+    eCx = np.exp(C * x)
+    eCx_less_one = eCx - 1.0
+
+    all_displacements[istep] = displacements = random_normal(scale=sigma, size=(1,))
+    grad = half_B / (eCx_less_one * eCx_less_one) * (twopi_by_A * eCx_less_one * np.sin(xarg) + C * eCx * np.cos(xarg))
+
+    newx = x - gradfactor * grad + displacements
+
+    if reflect_at is not None:
+        # Anything that has moved beyond reflect_at must move back that much
+
+        # boolean array of what to reflect
+        to_reflect = newx > reflect_at
+
+        # how far the things to reflect are beyond our boundary
+        reflect_by = newx[to_reflect] - reflect_at
+
+        # subtract twice how far they exceed the boundary by
+        # puts them the same distance from the boundary, on the other side
+        newx[to_reflect] -= 2 * reflect_by
+
+    coords[istep] = newx
+
+f = open('odld.rst', 'w')
+f.write('{:12.8f}'.format(coords[coord_len-1])+'\n')
+f.close
+
+f = open('pcoords.dat', 'w')
+for element in coords.flat:
+    f.write('{:12.8f}'.format(element)+'\n')
+f.close
+
+f = open('displacements.dat', 'w')
+for element in all_displacements.flat:
+    f.write('{:12.8f}'.format(element)+'\n')
+f.close
+

odld_exe_MPI-WM/run.sh

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+#!/bin/bash
+#SBATCH --job-name=odld
+#SBATCH --nodes=2
+#SBATCH --ntasks-per-node=28
+#SBATCH --cluster=mpi
+#SBATCH --partition=opa
+#SBATCH --time=1:00:00
+
+# Make sure environment is set
+source env.sh
+
+# These variable are specific to Pitt CRC HPC cluster
+export OMPI_MCA_pml=ob1
+export OMPI_MCA_btl="self,tcp"
+export OMPI_MCA_opal_warn_on_missing_libcuda=0
+
+which mpirun
+echo $SLURM_NTASKS
+
+# Clean up
+rm -f west.log
+
+mpirun -n $SLURM_NTASKS \
+          w_run --work-manager=mpi "$@"  &> west.log

odld_exe_MPI-WM/system.py

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+import numpy as np
+from westpa.core.binning import RectilinearBinMapper
+from westpa.core.propagators import WESTPropagator
+from westpa.core.systems import WESTSystem
+
+import logging
+log = logging.getLogger(__name__)
+log.debug('loading module %r' % __name__)
+
+class System(WESTSystem):
+    """
+    Over-damped Langevin dynamics
+    """
+
+    def initialize(self):
+        self.pcoord_ndim = 1
+        self.pcoord_len = 21
+        self.pcoord_dtype = np.float32
+
+        self.bin_mapper = RectilinearBinMapper([ list(np.arange(0.0, 10.1, 0.1)) ])
+        self.bin_target_counts = np.empty((self.bin_mapper.nbins,), np.int_)
+        self.bin_target_counts[...] = 10
+
+def displacement_loader(fieldname, coord_filename, segment, single_point=False):
+    """
+    Loads and stores coordinates
+
+    **Arguments:**
+        :*fieldname*:      Key at which to store dataset
+        :*coord_filename*: Temporary file from which to load coordinates
+        :*segment*:        WEST segment
+        :*single_point*:   Data to be stored for a single frame
+                           (should always be false)
+    """
+
+    # Load coordinates
+    n_frames = 21
+    coord    = np.loadtxt(coord_filename, dtype = np.float32)
+    coord    = np.reshape(coord, (n_frames))
+
+    # Save to hdf5
+    segment.data[fieldname] = coord
+
+def seg_status_loader(fieldname, log_filename, segment, single_point=False):
+    """
+    Loads and stores log
+
+    **Arguments:**
+        :*fieldname*:    Key at which to store dataset
+        :*log_filename*: Temporary file from which to load log
+        :*segment*:      WEST segment
+        :*single_point*: Data to be stored for a single frame
+                         (should always be false)
+    """
+
+    # Load log
+#   with open(log_filename, 'r') as log_file:
+#       raw_text = [line.strip() for line in log_file.readlines()]
+
+    # Save to hdf5
+
+    f = open(log_filename, 'r')
+    seg_status = f.read()
+    f.close 
+
+    with open(log_filename, 'r') as log_file:
+        for line in log_file:
+            segment.status = int(line)
+

odld_exe_MPI-WM/west.cfg

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+# The master WEST configuration file for a simulation.
+# vi: set filetype=yaml :
+---
+west: 
+  system:
+    driver: system.System
+    module_path: $WEST_SIM_ROOT
+  propagation:
+    max_total_iterations: 50
+    max_run_wallclock: 24:00:00
+    propagator: executable
+    gen_istates: true
+    block_size: 10000
+  data:
+    west_data_file: west.h5
+    aux_compression_threshold: 16384 # data sets bigger than this are compressed
+                                     # unless overridden by an entry in ``datasets`` below
+    datasets:
+      - name: pcoord
+        scaleoffset: 4
+      - name: displacement
+        dtype: float32
+        scaleoffset: 4
+
+    data_refs: # how to convert segments and states to paths, etc
+      segment:       $WEST_SIM_ROOT/traj_segs/{segment.n_iter:06d}/{segment.seg_id:06d}
+      basis_state:   $WEST_SIM_ROOT/bstates/{basis_state.auxref}
+      initial_state: $WEST_SIM_ROOT/istates/{initial_state.iter_created}/{initial_state.state_id}.crd
+  plugins:
+  executable:
+    environ:
+      PROPAGATION_DEBUG: 1
+    datasets:
+      - name:    displacement
+        loader:  system.displacement_loader
+        enabled: true
+      - name:    seg_status
+        loader:  system.seg_status_loader
+        enabled: true
+    propagator:
+      executable: $WEST_SIM_ROOT/westpa_scripts/runseg.sh
+      stdout:     $WEST_SIM_ROOT/seg_logs/{segment.n_iter:06d}-{segment.seg_id:06d}.log
+      stderr:     stdout
+      stdin:      null
+      cwd:        null
+      environ:
+        SEG_DEBUG: 1
+    get_pcoord:
+      executable: $WEST_SIM_ROOT/westpa_scripts/get_pcoord.sh
+      stdout:     /dev/null
+      stderr:     stdout
+    gen_istate:
+      executable: $WEST_SIM_ROOT/westpa_scripts/gen_istate.sh
+      stdout:     /dev/null
+      stderr:     stdout
+    post_iteration:
+      enabled:    true
+      executable: $WEST_SIM_ROOT/westpa_scripts/post_iter.sh
+      stderr:     stdout
+    pre_iteration:
+      enabled:    false
+      executable: $WEST_SIM_ROOT/westpa_scripts/pre_iter.sh
+      stderr:     stdout
+  analysis:
+     # Settings for w_ipa, an interactive analysis program that can also automate analysis.
+     directory: ANALYSIS                # specify the directory all analysis files should exist in.
+     postanalysis: True                 # should the routines for w_reweight be run?
+     kinetics:                          # general options for both kinetics routines.
+       # Command line arguments with values should be specified as key: value (see below)
+       # Command line arguments that are flags without values should be included as a list value
+       # in the extra key (extra: [ 'disable-correl', 'disable-bootstrap' ])
+       # These are global options for each scheme; individual schemes can have different values,
+       # set in their respective section.
+       step_iter: 10
+       evolution: cumulative
+       extra: [ 'disable-correl' ]
+     analysis_schemes:                  # Analysis schemes.  Required: name (TEST), states, and bins
+       TEST:
+         enabled: True
+         states:
+           - label: unbound
+             coords: [[8.0]]
+           - label: bound
+             coords: [[3.99]]
+         bins:
+           - type: RectilinearBinMapper
+             boundaries: [[0.0,4.0,8.00,100000]]

odld_exe_MPI-WM/westpa_scripts/gen_istate.sh

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+#!/bin/bash
+
+if [ -n "$SEG_DEBUG" ] ; then
+    set -x
+    env | sort
+fi
+
+cd $WEST_SIM_ROOT
+
+mkdir -p $(dirname $WEST_ISTATE_DATA_REF)
+echo 8.0 > $WEST_ISTATE_DATA_REF

odld_exe_MPI-WM/westpa_scripts/get_pcoord.sh

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+#!/bin/bash
+
+if [ -n "$SEG_DEBUG" ] ; then
+    set -x
+    env | sort
+fi
+
+cd $WEST_SIM_ROOT
+
+# Get progress coordinate
+echo 8.0 > $WEST_PCOORD_RETURN
+
+if [ -n "$SEG_DEBUG" ] ; then
+    head -v $WEST_PCOORD_RETURN
+fi

odld_exe_MPI-WM/westpa_scripts/post_iter.sh

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+#!/bin/bash
+
+if [ -n "$SEG_DEBUG" ] ; then
+    set -x
+    env | sort
+fi
+
+cd $WEST_SIM_ROOT || exit 1
+
+ITER=$(printf "%06d" $WEST_CURRENT_ITER)
+tar -cf seg_logs/$ITER.tar seg_logs/$ITER-*.log
+rm  -f  seg_logs/$ITER-*.log

odld_exe_MPI-WM/westpa_scripts/runseg.sh

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+#!/bin/bash
+
+if [ -n "$SEG_DEBUG" ] ; then
+    set -x
+    env | sort
+fi
+
+cd $WEST_SIM_ROOT
+
+# Set up the run
+mkdir -pv $WEST_CURRENT_SEG_DATA_REF
+cd $WEST_CURRENT_SEG_DATA_REF
+
+case $WEST_CURRENT_SEG_INITPOINT_TYPE in
+    SEG_INITPOINT_CONTINUES)
+        # A continuation from a prior segment
+        # $WEST_PARENT_DATA_REF contains the reference to the
+        #   parent segment
+        ln -sv $WEST_PARENT_DATA_REF/odld.log ./parent.log
+        ln -sv $WEST_PARENT_DATA_REF/odld.rst ./odld.crd
+    ;;
+
+    SEG_INITPOINT_NEWTRAJ)
+        # Initiation of a new trajectory
+        # $WEST_PARENT_DATA_REF contains the reference to the
+        #   appropriate basis or initial state
+        ln -sv $WEST_PARENT_DATA_REF ./odld.crd
+    ;;
+
+    *)
+        echo "unknown init point type $WEST_CURRENT_SEG_INITPOINT_TYPE"
+        exit 2
+    ;;
+esac
+
+# Propagate segment
+python $WEST_SIM_ROOT/odld.py >& odld.log
+
+# Calculate progress coordinate
+cat pcoords.dat > $WEST_PCOORD_RETURN
+
+cat displacements.dat > $WEST_DISPLACEMENT_RETURN
+

odld_exe_MPI-WM/westpa_scripts/tar_segs.sh

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+#!/bin/bash
+
+[ -z "$WEST_SIM_ROOT" ] &&
+    exit 1
+[ ! -d $WEST_SIM_ROOT/traj_segs ] &&
+    exit 1
+
+cd $WEST_SIM_ROOT/traj_segs
+
+ITERS=($(ls | grep '^[0-9][0-9][0-9][0-9][0-9][0-9]$'))
+ITERS=("${ITERS[@]:0:${#ITERS[@]}-1}")
+for ITER in ${ITERS[@]}; do
+    [ ! -f $ITER.tar ] &&
+        tar -cvf $ITER.tar $ITER
+done
+