Merge branch 'fix_examples' into 'master'

Fix examples

See merge request !5


Former-commit-id: c60ad5a329706e7393f3ee39e9e3e75e1ac5f518

examples/runs.sh

@@ -3,6 +3,30 @@
 # Set some global stuff
 export OMP_WAIT_POLICY=PASSIVE
 
+# Generate the initial conditions if they are not present.
+if [ ! -e SodShock/sodShock.hdf5 ]
+then
+    echo "Generating initial conditions for the SodShock example..."
+    cd SodShock
+    python makeIC.py
+    cd ..
+fi
+if [ ! -e SedovBlast/sedov.hdf5 ]
+then
+    echo "Generating initial conditions for the SedovBlast example..."
+    cd SedovBlast/
+    python makeIC_fcc.py
+    cd ..
+fi
+if [ ! -e CosmoVolume/cosmoVolume.hdf5 ]
+then
+    echo "Downloading initial conditions for the CosmoVolume example..."
+    cd CosmoVolume
+    ./getIC.sh
+    cd ..
+fi
+
+
 # Loop over number of cores
 for cpu in {1..32}
 do
@@ -10,11 +34,11 @@ do
     # Sod-Shock runs
     if [ ! -e SodShock_mindt_${cpu}.dump ]
     then
-        ./test_mindt -c 1.0 -t $cpu -f SodShock/sodShock.hdf5 -m 0.1 -w 5000 -d 1.0 > SodShock_${cpu}.dump
+        ./test_mindt -c 1.0 -t $cpu -f SodShock/sodShock.hdf5 -m 0.01 -w 5000 -d 1.0 > SodShock_${cpu}.dump
     fi
     if [ ! -e SodShock_fixed_${cpu}.dump ]
     then
-        ./test_fixdt -r 1000 -t $cpu -f SodShock/sodShock.hdf5 -m 0.0075 -w 5000 -d 1e-4 > SodShock_fixed_${cpu}.dump
+        ./test_fixdt -r 1000 -t $cpu -f SodShock/sodShock.hdf5 -m 0.01 -w 5000 -d 1e-4 > SodShock_fixed_${cpu}.dump
     fi
     
     # Sedov blast

examples/runs_mpi_cv.sh

+#!/bin/bash
+
+# Set the number of runs
+RUNS=100
+
+# Cores per node
+CPN=12
+
+# The queue on which to run
+QUEUE=cosma
+PROJECT=durham
+PREFIX=CosmoVolume
+INPUT=$PREFIX/CosmoVolume.hdf5
+
+# Make sure the OMP threads don't go wild
+export OMP_WAIT_POLICY=PASSIVE
+
+# Set the library path so that libmetis is found
+export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/cosma/home/nnrw56/lib
+
+# Single-node runs
+for cpu in $(seq 1 $CPN)
+do
+    if [ ! -e ${PREFIX}_${QUEUE}_1x${cpu}.dump ]
+    then
+        bsub -oo ${PREFIX}_${QUEUE}_1x${cpu}.dump -q ${QUEUE} -P ${PROJECT} -x -n 1 -R "span[ptile=1]" ./test_fixdt -r $RUNS -t $cpu -f ${INPUT} -m 0.705 -w 6000 -z 300 -d 1e-8
+    fi
+done
+
+# Multi-node runs
+if [ ! -e ${PREFIX}_${QUEUE}_2x${cpu}.dump ]
+then
+    bsub -oo ${PREFIX}_${QUEUE}_2x${CPN}.dump -q ${QUEUE} -P ${PROJECT} -x -W 02:00 -n 2 -R "span[ptile=1]" mpirun -np 2 ./test_fixdt_mpi -r $RUNS -t $CPN -g "2 1 1" -f ${INPUT} -m 0.705 -w 6000 -z 300 -d 1e-8
+fi
+
+if [ ! -e ${PREFIX}_${QUEUE}_4x${cpu}.dump ]
+then
+    bsub -oo ${PREFIX}_${QUEUE}_4x${CPN}.dump -q ${QUEUE} -P ${PROJECT} -x -W 02:00 -n 4 -R "span[ptile=1]" mpirun -np 4 ./test_fixdt_mpi -r $RUNS -t $CPN -g "2 2 1" -f ${INPUT} -m 0.705 -w 6000 -z 300 -d 1e-8
+fi
+
+if [ ! -e ${PREFIX}_${QUEUE}_8x${cpu}.dump ]
+then
+    bsub -oo ${PREFIX}_${QUEUE}_8x${CPN}.dump -q ${QUEUE} -P ${PROJECT} -x -W 02:00 -n 8 -R "span[ptile=1]" mpirun -np 8 ./test_fixdt_mpi -r $RUNS -t $CPN -g "2 2 2" -f ${INPUT} -m 0.705 -w 6000 -z 300 -d 1e-8
+fi
+
+if [ ! -e ${PREFIX}_${QUEUE}_16x${cpu}.dump ]
+then
+    bsub -oo ${PREFIX}_${QUEUE}_16x${CPN}.dump -q ${QUEUE} -P ${PROJECT} -x -W 02:00 -n 16 -R "span[ptile=1]" mpirun -np 16 ./test_fixdt_mpi -r $RUNS -t $CPN -g "4 2 2" -f ${INPUT} -m 0.705 -w 6000 -z 300 -d 1e-8
+fi
+
+if [ ! -e ${PREFIX}_${QUEUE}_32x${cpu}.dump ]
+then
+    bsub -oo ${PREFIX}_${QUEUE}_32x${CPN}.dump -q ${QUEUE} -P ${PROJECT} -x -W 02:00 -n 32 -R "span[ptile=1]" mpirun -np 32 ./test_fixdt_mpi -r $RUNS -t $CPN -g "4 4 2" -f ${INPUT} -m 0.705 -w 6000 -z 300 -d 1e-8
+fi
+
+if [ ! -e ${PREFIX}_${QUEUE}_64x${cpu}.dump ]
+then
+    bsub -oo ${PREFIX}_${QUEUE}_64x${CPN}.dump -q ${QUEUE} -P ${PROJECT} -x -W 02:00 -n 64 -R "span[ptile=1]" mpirun -np 64 ./test_fixdt_mpi -r $RUNS -t $CPN -g "4 4 4" -f ${INPUT} -m 0.705 -w 6000 -z 300 -d 1e-8
+fi
+
+if [ ! -e ${PREFIX}_${QUEUE}_128x${cpu}.dump ]
+then
+    bsub -oo ${PREFIX}_${QUEUE}_128x${CPN}.dump -q ${QUEUE} -P ${PROJECT} -x -W 02:00 -n 128 -R "span[ptile=1]" mpirun -np 128 ./test_fixdt_mpi -r $RUNS -t $CPN -g "8 4 4" -f ${INPUT} -m 0.705 -w 6000 -z 300 -d 1e-8
+fi
+

src/common_io.c

@@ -31,6 +31,9 @@
 #include <stddef.h>
 #include <hdf5.h>
 #include <math.h>
+#ifdef WITH_MPI
+#include <mpi.h>
+#endif
 
 #include "const.h"
 #include "cycle.h"

src/error.h

@@ -27,7 +27,7 @@
  */
 #ifdef WITH_MPI
     extern int engine_rank;
-    #define error(s, ...) { fprintf( stderr , "[%03i] %s:%s():%i: " s "\n" , engine_rank , __FILE__ , __FUNCTION__ , __LINE__ , ##__VA_ARGS__ ); abort(); }
+    #define error(s, ...) { fprintf( stderr , "[%03i] %s:%s():%i: " s "\n" , engine_rank , __FILE__ , __FUNCTION__ , __LINE__ , ##__VA_ARGS__ ); MPI_Abort(MPI_COMM_WORLD, -1); }
 #else
     #define error(s, ...) { fprintf( stderr , "%s:%s():%i: " s "\n" , __FILE__ , __FUNCTION__ , __LINE__ , ##__VA_ARGS__ ); abort(); }
 #endif

src/parallel_io.c

@@ -23,6 +23,9 @@
 
 #if defined(HAVE_HDF5) && defined(WITH_MPI)
 
+/* Tell hdf5 that we intend to use shared-memory parallel stuff. */
+#define H5_HAVE_PARALLEL
+
 
 /* Some standard headers. */
 #include <stdio.h>

src/units.c

@@ -27,6 +27,9 @@
 #include <string.h>
 #include <stddef.h>
 #include <math.h>
+#ifdef WITH_MPI
+#include <mpi.h>
+#endif
 
 #include "const.h"
 #include "cycle.h"