bash scripts for runing Dales on JUWELS and yamo

rundales/runDALES_bind4proc_local.sh

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+#!/bin/bash
+#
+# on which CPU to run
+export ICPU="2,3,4,5"   # as tested by Niklas
+#----------------------------------------------------------------------
+# Script for running DALES#
+#----------------------------------------------------------------------
+#
+# - requires following variables:
+#     $USERN    ::  username
+#     $DAYC      ::  current day of model of code adjustment/compilation
+#  
+# ----------------------------------------
+#  based on tcshell scritps from prof Roel Neggers
+#  scripted and checked by Jan Chylik, August 2016 
+#  inquiries and error reports: [email protected]
+#  
+# last update: 21 September 2016, 11 January 2017
+
+# === setting  ================================================
+# if the script is run from dales_prepare.sh, the setting does not require any changes
+
+# ---- directory setting ---------------------------------
+#  directroy in which to run 
+    export rundir=./
+    # # export rundir=/work/${USERN}/dales/dales4/experiments/Juelich/juelich20130605_imicro2_16x16
+# busy file 
+    export busyfile="runDALES_busy.txt"
+# runlog
+    export RUNLOG="runlog.txt"
+# setting 
+    export N_MPI=4 
+    # 1
+    export DALES="dales4"
+# === script ==============================================
+
+#------------- important directories ----------------------
+
+
+
+# -------- run  itself ------------------------------------
+
+if [ ! -e $busyfile ]; then
+
+  #--- create file indicating that job is ongoing ---
+  echo "runDALES job is busy ... don't interfere!" > $busyfile
+
+  cd ${rundir}
+
+  #echo "test" > test.txt
+
+  # running dales
+  echo "Starting dales run, you can view the run log  ${rundir}$RUNLOG "
+  echo "You can view it in other terminal."
+  echo "Do not close this terminal until the job is finished."
+  #./dales_roel4_20140423
+  # mpirun -np $N_MPI ./${DALES_VERSION}_${USERN}_${DAYC}_${MACHINE_TYPE}>$RUNLOG
+  mpirun -np $N_MPI --report-bindings --cpu-list ${ICPU} ${DALES}>$RUNLOG
+  # mpirun -np $N_MPI  ${DALES}>$RUNLOG
+  # note: it keeps the name of the original executable so we can have more different dales executables possibly used alongside each other if needed
+
+  #--- cleanup --- 
+  rm $busyfile
+
+  echo " "
+  echo "Dales run has ended."
+  exit 0
+
+else
+
+  echo " "
+  echo "A runDALES job is already in progress ... aborting"
+  echo "Exitting with exit status 3"
+  exit 3
+
+fi
+
+
+
+# ===========================================================
+
+

rundales/runDALES_bind4proc_yamo.sh

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+#!/bin/bash
+#
+# on which CPU to run
+export ICPU="17,18,19,20"   # as tested by Niklas
+#----------------------------------------------------------------------
+# Script for running DALES#
+#----------------------------------------------------------------------
+#
+# - requires following variables:
+#     $USERN    ::  username
+#     $DAYC      ::  current day of model of code adjustment/compilation
+#  
+# ----------------------------------------
+#  based on tcshell scritps from prof Roel Neggers
+#  scripted and checked by Jan Chylik, August 2016 
+#  inquiries and error reports: [email protected]
+#  
+# last update: 21 September 2016, 11 January 2017
+
+# === setting  ================================================
+# if the script is run from dales_prepare.sh, the setting does not require any changes
+
+# ---- directory setting ---------------------------------
+#  directroy in which to run 
+    export rundir=./
+    # # export rundir=/work/${USERN}/dales/dales4/experiments/Juelich/juelich20130605_imicro2_16x16
+# busy file 
+    export busyfile="runDALES_busy.txt"
+# runlog
+    export RUNLOG="runlog.txt"
+# setting 
+    export N_MPI=4 
+    # 1
+    export DALES="dales4"
+# === script ==============================================
+
+#------------- important directories ----------------------
+
+
+
+# -------- run  itself ------------------------------------
+
+if [ ! -e $busyfile ]; then
+
+  #--- create file indicating that job is ongoing ---
+  echo "runDALES job is busy ... don't interfere!" > $busyfile
+
+  cd ${rundir}
+
+  #echo "test" > test.txt
+
+  # running dales
+  echo "Starting dales run, you can view the run log  ${rundir}$RUNLOG "
+  echo "You can view it in other terminal."
+  echo "Do not close this terminal until the job is finished."
+  #./dales_roel4_20140423
+  # mpirun -np $N_MPI ./${DALES_VERSION}_${USERN}_${DAYC}_${MACHINE_TYPE}>$RUNLOG
+  mpirun -np $N_MPI --report-bindings --cpu-list ${ICPU} --bind-to cpu-list:ordered  ${DALES}>$RUNLOG
+  # mpirun -np $N_MPI  ${DALES}>$RUNLOG
+  # note: it keeps the name of the original executable so we can have more different dales executables possibly used alongside each other if needed
+
+  #--- cleanup --- 
+  rm $busyfile
+
+  echo " "
+  echo "Dales run has ended."
+  exit 0
+
+else
+
+  echo " "
+  echo "A runDALES job is already in progress ... aborting"
+  echo "Exitting with exit status 3"
+  exit 3
+
+fi
+
+
+
+# ===========================================================
+
+

rundales/runDALES_cheops

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+runDALES_n8nod1_cheops2023_gcc_openmpi.sh

rundales/runDALES_debug_n8nod2_cheops2023_gcc_openmpi.sh

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+#!/bin/bash -l
+#SBATCH --partition=devel-rh7
+#SBATCH --ntasks=8
+#SBATCH --nodes=2
+#SBATCH --ntasks-per-node=4
+#SBATCH --mem=40gb     # --mem-per-cpu=20gb
+#SBATCH --time=1:00:00
+#SBATCH --account=UniKoeln
+
+# number of nodes in $SLURM_NNODES (default: 1)
+# number of tasks in $SLURM_NTASKS (default: 1)
+# number of tasks per node in $SLURM_NTASKS_PER_NODE (default: 1)
+# number of threads per task in $SLURM_CPUS_PER_TASK (default: 1)
+
+
+# load  modules
+  module load netcdf/4.9.0_gnu  gnu/7.4.0   # !! these versions agree  (2023)
+  module load openmpi
+  module load cmake
+
+
+echo "# of nodes, tasks:" $SLURM_NNODES $SLURM_NTASKS
+
+LD_LIBRARY_PATH="$LD_LIBRARY_PATH:/opt/rrzk/lib/netcdf/f_4.6.0_gnu_7.4.0/lib/"
+
+srun -n $SLURM_NTASKS dales4
+
+
+

rundales/runDALES_juwels

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+runDALES_n32nod2_juwels2023_gcc_parastation.sh

rundales/runDALES_levante

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+runDALES_n32nod2_levante2023_gcc_openmpi.sh

rundales/runDALES_local.sh

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+#!/bin/bash
+#----------------------------------------------------------------------
+# Script for running DALES#
+#----------------------------------------------------------------------
+#
+# - requires following variables:
+#     $USERN    ::  username
+#     $DAYC      ::  current day of model of code adjustment/compilation
+#  
+# ----------------------------------------
+#  based on tcshell scritps from prof Roel Neggers
+#  scripted and checked by Jan Chylik, August 2016 
+#  inquiries and error reports: [email protected]
+#  
+# last update: 21 September 2016, 11 January 2017
+
+# === setting  ================================================
+# if the script is run from dales_prepare.sh, the setting does not require any changes
+
+# ---- directory setting ---------------------------------
+#  directroy in which to run 
+    export rundir=./
+    # # export rundir=/work/${USERN}/dales/dales4/experiments/Juelich/juelich20130605_imicro2_16x16
+# busy file 
+    export busyfile="runDALES_busy.txt"
+# runlog
+    export RUNLOG="runlog.txt"
+# setting 
+    export N_MPI=1
+    export DALES="dales4"
+# === script ==============================================
+
+#------------- important directories ----------------------
+
+
+
+# -------- run  itself ------------------------------------
+
+if [ ! -e $busyfile ]; then
+
+  #--- create file indicating that job is ongoing ---
+  echo "runDALES job is busy ... don't interfere!" > $busyfile
+
+  cd ${rundir}
+
+  #echo "test" > test.txt
+
+  # running dales
+  echo "Starting dales run, you can view the run log  ${rundir}$RUNLOG "
+  echo "You can view it in other terminal."
+  echo "Do not close this terminal until the job is finished."
+  #./dales_roel4_20140423
+  # mpirun -np $N_MPI ./${DALES_VERSION}_${USERN}_${DAYC}_${MACHINE_TYPE}>$RUNLOG
+  mpirun -np $N_MPI ${DALES}>$RUNLOG
+  # note: it keeps the name of the original executable so we can have more different dales executables possibly used alongside each other if needed
+
+  #--- cleanup --- 
+  rm $busyfile
+
+  echo " "
+  echo "Dales run has ended."
+  exit 0
+
+else
+
+  echo " "
+  echo "A runDALES job is already in progress ... aborting"
+  echo "Exitting with exit status 3"
+  exit 3
+
+fi
+
+
+
+# ===========================================================
+
+

rundales/runDALES_local_mosaic.sh

@@ -0,0 +1,81 @@
+#!/bin/bash
+#----------------------------------------------------------------------
+# Script for running DALES#
+#----------------------------------------------------------------------
+#
+# - requires following variables:
+#     $USERN    ::  username
+#     $DAYC      ::  current day of model of code adjustment/compilation
+#  
+# ----------------------------------------
+#  based on tcshell scritps from prof Roel Neggers
+#  scripted and checked by Jan Chylik, August 2016 
+#  inquiries and error reports: [email protected]
+#  
+# last update: 21 September 2016, 11 January 2017
+
+# === setting  ================================================
+# if the script is run from dales_prepare.sh, the setting does not require any changes
+
+# ---- directory setting ---------------------------------
+#  directroy in which to run 
+    export rundir=./
+    # # export rundir=/work/${USERN}/dales/dales4/experiments/Juelich/juelich20130605_imicro2_16x16
+# busy file 
+    export busyfile='runDALES_busy.txt'
+# runlog
+    export RUNLOG='runlog.txt'
+# message file 
+    export MSGFILE='dales_mosaic_ayil.txt'
+# setting 
+    export N_MPI=1
+    export DALES='dales4'
+# === script ==============================================
+
+#------------- important directories ----------------------
+
+
+
+# -------- run  itself ------------------------------------
+
+if [ ! -e $busyfile ]; then
+
+  #--- create file indicating that job is ongoing ---
+  echo "runDALES job is busy ... don't interfere!" > $busyfile
+
+  cd ${rundir}
+
+  #echo "test" > test.txt
+
+  # running dales
+  echo "Starting dales run, you can view the run log  ${rundir}$RUNLOG "
+  echo "You can view it in other terminal."
+  echo "Do not close this terminal until the job is finished."
+  #./dales_roel4_20140423
+  # mpirun -np $N_MPI ./${DALES_VERSION}_${USERN}_${DAYC}_${MACHINE_TYPE}>$RUNLOG
+  mpirun -np $N_MPI ${DALES}>$RUNLOG
+  # note: it keeps the name of the original executable so we can have more different dales executables possibly used alongside each other if needed
+
+  echo "finished local job" > $MSGFILE
+
+  #--- cleanup --- 
+  rm $busyfile
+
+  echo " "
+  echo "Dales run has ended."
+  exit 0
+
+else
+
+  echo " "
+  echo "A runDALES job is already in progress ... aborting"
+  echo "Exitting with exit status 3"
+  exit 3
+
+fi
+
+
+
+# ===========================================================
+
+

rundales/runDALES_n128nod4bind_juwels2024_gcc_parastation.sh

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+#!/bin/bash -x
+#SBATCH --account=rcongm
+#SBATCH --nodes=4
+#SBATCH --ntasks=128
+#SBATCH --ntasks-per-node=32
+#SBATCH --cpus-per-task=1
+#SBATCH --threads-per-core=1
+#SBATCH --time=24:00:00
+#SBATCH --partition=batch
+#SBATCH --output=./slurm_dales-%j.out
+#SBATCH --error=./slurm_error-%j.out
+
+# *** start of job script ***
+# Note: The current working directory at this point is
+# the directory where sbatch was executed.
+
+ module load Stages/2024
+ module load GCC/12.3.0   ParaStationMPI/5.9.2-1
+ module load netCDF-Fortran/4.6.1
+ # module load CMake         # not needed in rundales
+ # module load HDF5/1.14.2   # implicitly loaded
+ # module load netCDF/4.9.2  # implicitly loaded
+
+
+
+export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
+
+srun --cpu-bind=map_cpu:0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39 ./dales4 > runlog.txt
+###srun ./dales4 > stdlog.txt
+###python3 ./change_nml.py