Nova inputs and Misc

Exec/science/nova/analysis/polaris.submit

@@ -0,0 +1,74 @@
+#!/bin/sh
+#PBS -l select=12:system=polaris
+#PBS -l filesystems=home:eagle:grand
+#PBS -l place=scatter
+#PBS -l walltime=02:00:00
+#PBS -q prod
+#PBS -A AstroExplosions
+
+EXEC=./Castro2d.gnu.MPI.CUDA.ex
+INPUTS=inputs_nova_t7
+
+# Enable GPU-MPI (if supported by application)
+##export MPICH_GPU_SUPPORT_ENABLED=1
+
+module swap PrgEnv-nvhpc PrgEnv-gnu
+module load nvhpc-mixed
+
+# Change to working directory
+cd ${PBS_O_WORKDIR}
+
+# MPI and OpenMP settings
+NNODES=`wc -l < $PBS_NODEFILE`
+NRANKS_PER_NODE=$(nvidia-smi -L | wc -l)
+NDEPTH=8
+NTHREADS=1
+
+NTOTRANKS=$(( NNODES * NRANKS_PER_NODE ))
+
+function find_chk_file {
+    # find_chk_file takes a single argument -- the wildcard pattern
+    # for checkpoint files to look through
+    chk=$1
+
+    # find the latest 2 restart files.  This way if the latest didn't
+    # complete we fall back to the previous one.
+    temp_files=$(find . -maxdepth 1 -name "${chk}" -print | sort | tail -2)
+    restartFile=""
+    for f in ${temp_files}
+    do
+        # the Header is the last thing written -- check if it's there, otherwise,
+        # fall back to the second-to-last check file written
+        if [ ! -f ${f}/Header ]; then
+            restartFile=""
+        else
+            restartFile="${f}"
+        fi
+    done
+
+}
+
+# look for 7-digit chk files
+find_chk_file "*chk???????"
+
+if [ "${restartFile}" = "" ]; then
+    # look for 6-digit chk files
+    find_chk_file "*chk??????"
+fi
+
+if [ "${restartFile}" = "" ]; then
+    # look for 5-digit chk files
+    find_chk_file "*chk?????"
+fi
+
+# restartString will be empty if no chk files are found -- i.e. new run
+if [ "${restartFile}" = "" ]; then
+    restartString=""
+else
+    restartString="amr.restart=${restartFile}"
+fi
+
+
+# For applications that need mpiexec to bind MPI ranks to GPUs
+mpiexec -n ${NTOTRANKS} --ppn ${NRANKS_PER_NODE} --depth=${NDEPTH} --cpu-bind depth --env OMP_NUM_THREADS=${NTHREADS} -env OMP_PLACES=threads ./set_affinity_gpu_polaris.sh ${EXEC} ${INPUTS} ${restartString}
+

Exec/science/nova/analysis/profile.submit

@@ -0,0 +1,36 @@
+#!/bin/sh
+#PBS -l select=1:ncpus=32:system=polaris
+#PBS -l filesystems=home:eagle:grand 
+#PBS -l place=scatter
+#PBS -l walltime=00:30:00
+#PBS -q debug
+#PBS -A AstroExplosions
+shopt -s nullglob
+
+#Loading Modules
+module load gnu-parallel
+module load conda
+conda activate projectA
+
+# Change to working directory
+cd $PBS_O_WORKDIR
+outdir="./stats"
+mkdir -p $outdir
+
+script=./HorizontalAvg2d.cray.x86-rome.ex
+
+# GNU Parallel options
+declare -a plts
+for plotfile in ./*plt* ./stats/*plt*; do
+    [[ ! -d "$plotfile" ]] && continue
+    [[ "$plotfile" == *plt*.old.* ]] && continue
+    [[ -e "$(basename $plotfile)_profile.dat" ]] && continue
+    plts+=($plotfile)
+done
+
+NTASK=$((PBS_NNODES * 32))
+
+parallel="parallel -j $NTASK --delay .2 -X"
+$parallel "$script {}" ::: "${plts[@]}"
+
+

Exec/science/nova/analysis/series_variable.py

@@ -0,0 +1,16 @@
+import numpy as np
+import matplotlib.pyplot as plt
+
+file = np.loadtxt('grid_diag.out', skiprows=2)
+
+time = file[: ,1] 
+temperature = file[:, 20] 
+
+fig = plt.figure(figsize=(8,6))
+ax = fig.add_subplot(111)
+ax.plot(time, temperature)
+ax.set_ylim([3.0e5, 2.0e8])
+ax.set_xlabel(r"$time\quad[s]$")
+ax.set_ylabel(r"$T\quad[K]$")
+
+fig.savefig("temp_t.png")