Merge branch 'develop' into docs/HPC_running

Author: shuds13

.github/workflows/basic.yml

@@ -129,4 +129,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.30.2
+        - uses: crate-ci/typos@v1.31.1

.github/workflows/extra.yml

@@ -180,4 +180,4 @@ jobs:
         runs-on: ubuntu-latest
         steps:
         - uses: actions/checkout@v4
-        - uses: crate-ci/typos@v1.30.2
+        - uses: crate-ci/typos@v1.31.1

examples/libE_submission_scripts/bebop_submit_pbs_central.sh

@@ -0,0 +1,14 @@
+#!/bin/bash -l
+#PBS -l select=4
+#PBS -l walltime=00:15:00
+#PBS -q bdwall
+#PBS -A [project]
+#PBS -N libE_example
+
+
+cd $PBS_O_WORKDIR
+# Choose MPI backend. Note that the built mpi4py in your environment should match.
+module load oneapi/mpi
+# module load openmpi
+
+python run_libe_example.py -n 16

examples/libE_submission_scripts/bebop_submit_pbs_distrib.sh

@@ -0,0 +1,89 @@
+#!/bin/bash
+#SBATCH -J libE_test
+#SBATCH -N 4
+#SBATCH -p [queue]
+#SBATCH -A <my_project>
+#SBATCH -o tlib.%j.%N.out
+#SBATCH -e tlib.%j.%N.error
+#SBATCH -t 01:00:00
+
+# Launch script that runs in distributed mode with mpi4py.
+#   Workers are evenly spread over nodes and manager added to the first node.
+#   Requires even distribution - either multiple workers per node or nodes per worker
+#   Option for manager to have a dedicated node.
+#   Use of MPI Executor will ensure workers co-locate tasks with workers
+#   If node_list file is kept, this informs libe of resources. Else, libe auto-detects.
+
+# User to edit these variables
+export EXE=libE_calling_script.py
+export NUM_WORKERS=4
+export MANAGER_NODE=false # true = Manager has a dedicated node (assign one extra)
+export USE_NODE_LIST=true # If false, allow libE to determine node_list from environment.
+
+# As libE shares nodes with user applications allow fallback if contexts overrun.
+unset I_MPI_FABRICS
+export I_MPI_FABRICS_LIST=tmi,tcp
+export I_MPI_FALLBACK=1
+
+# If using in calling script (After N mins manager kills workers and exits cleanly)
+export LIBE_WALLCLOCK=55
+
+#-----------------------------------------------------------------------------
+# Work out distribution
+if [[ $MANAGER_NODE = "true" ]]; then
+  WORKER_NODES=$(($SLURM_NNODES-1))
+else
+  WORKER_NODES=$SLURM_NNODES
+fi
+
+if [[ $NUM_WORKERS -ge $WORKER_NODES ]]; then
+  SUB_NODE_WORKERS=true
+  WORKERS_PER_NODE=$(($NUM_WORKERS/$WORKER_NODES))
+else
+  SUB_NODE_WORKERS=false
+  NODES_PER_WORKER=$(($WORKER_NODES/$NUM_WORKERS))
+fi;
+#-----------------------------------------------------------------------------
+
+# A little useful information
+echo -e "Manager process running on: $HOSTNAME"
+echo -e "Directory is:  $PWD"
+
+# Generate a node list with 1 node per line:
+srun hostname | sort -u > node_list
+
+# Add manager node to machinefile
+head -n 1 node_list > machinefile.$SLURM_JOBID
+
+# Add worker nodes to machinefile
+if [[ $SUB_NODE_WORKERS = "true" ]]; then
+  awk -v repeat=$WORKERS_PER_NODE '{for(i=0; i<repeat; i++)print}' node_list \
+  >>machinefile.$SLURM_JOBID
+else
+  awk -v patt="$NODES_PER_WORKER" 'NR % patt == 1' node_list \
+  >> machinefile.$SLURM_JOBID
+fi;
+
+if [[ $USE_NODE_LIST = "false" ]]; then
+  rm node_list
+  wait
+fi;
+
+# Put in a timestamp
+echo Starting execution at: `date`
+
+# To use srun
+export SLURM_HOSTFILE=machinefile.$SLURM_JOBID
+
+# The "arbitrary" flag should ensure SLURM_HOSTFILE is picked up
+# cmd="srun --ntasks $(($NUM_WORKERS+1)) -m arbitrary python $EXE"
+cmd="srun --ntasks $(($NUM_WORKERS+1)) -m arbitrary python $EXE $LIBE_WALLCLOCK"
+
+echo The command is: $cmd
+echo End PBS script information.
+echo All further output is from the process being run and not the script.\n\n $cmd
+
+$cmd
+
+# Print the date again -- when finished
+echo Finished at: `date`

examples/libE_submission_scripts/bebop_submit_slurm_central.sh

@@ -1,4 +1,4 @@
-flake8==7.1.2
+flake8==7.2.0
 coverage>=7.5
 pytest==8.3.5
 pytest-cov==6.0.0
@@ -8,4 +8,4 @@ python-dateutil==2.9.0.post0
 anyio==4.9.0
 matplotlib==3.10.1
 mpmath==1.3.0
-rich==13.9.4
+rich==14.0.0

examples/libE_submission_scripts/submit_distrib_mpi4py.sh

@@ -39,7 +39,7 @@ Issues = "https://github.com/Libensemble/libensemble/issues"
 
 [build-system]
 build-backend = "setuptools.build_meta"
-requires = ["setuptools", "wheel", "pip>=24.3.1,<26", "setuptools>=75.1.0,<77", ]
+requires = ["setuptools", "wheel", "pip>=24.3.1,<26", "setuptools>=75.1.0,<79", ]
 
 [tool.setuptools.packages.find]
 where = ["."]