Modified structure of Codes directory, now code is divided into SAM and MaM....

Modified structure of Codes directory, now code is divided into SAM and MaM. Exec files must be updated to consider changes in configuration

Codes/Main/Main.c → Codes/SAM/Main/Main.c

@@ -8,8 +8,8 @@
 #include "Main_datatypes.h"
 #include "configuration.h"
 #include "../IOcodes/results.h"
-#include "../malleability/distribution_methods/Distributed_CommDist.h"
-#include "../malleability/MAM.h"
+#include "../MaM/distribution_methods/Distributed_CommDist.h"
+#include "../MaM/MAM.h"
 
 #define DR_MAX_SIZE 1000000000
 

Codes/SAM/Makefile

+CC = gcc
+MCC = mpicc
+#C_FLAGS_ALL = -Wconversion -Wpedantic
+C_FLAGS = -Wall -Wextra -Wshadow -Wfatal-errors
+LD_FLAGS = -lm -pthread -lmam
+
+MAM_HOME = ../MaM
+MAM_FLAGS = -I$(MAM_HOME) -L$(MAM_HOME)/build
+
+# Final binary
+BIN = a.out
+# Put all auto generated stuff to this build dir.
+BUILD_DIR = ./build
+
+# List of all directories where source files are located
+SRCDIRS = IOcodes Main
+
+# List of all .c source files.
+C_FILES = $(foreach dire, $(SRCDIRS), $(wildcard $(dire)/*.c))
+
+# All .o files go to build dir.
+OBJ = $(C_FILES:%.c=$(BUILD_DIR)/%.o)
+# Gcc will create these .d files containing dependencies.
+DEP = $(OBJ:%.o=%.d)
+
+# BASIC RULES
+.PHONY : clean clear install
+
+all: install
+
+clean:
+	-rm $(BUILD_DIR)/$(BIN) $(BUILD_DIR)/$(CONFIG) $(OBJ) $(DEP)
+clear:
+	-rm -rf $(BUILD_DIR)
+
+install: $(BIN) $(CONFIG)
+	echo "Done"
+
+# SPECIFIC RULES
+# Default target named after the binary.
+$(BIN) : $(BUILD_DIR)/$(BIN)
+
+# Actual target of the binary - depends on all .o files.
+$(BUILD_DIR)/$(BIN) : $(OBJ)
+	$(MCC) $(C_FLAGS) $(MAM_FLAGS) $^ -o $@ $(LD_FLAGS)
+
+# Include all .d files
+# .d files are used for knowing the dependencies of each source file
+-include $(DEP)
+
+# Build target for every single object file.
+# The potential dependency on header files is covered
+# by calling `-include $(DEP)`.
+# The -MMD flags additionaly creates a .d file with
+# the same name as the .o file.
+$(BUILD_DIR)/%.o : %.c
+	@mkdir -p $(@D)
+	$(MCC) $(C_FLAGS) $(MAM_FLAGS) $(DEF) -MMD -c $< -o $@

Codes/runBase.sh

@@ -6,9 +6,7 @@
 partition='P1'
 
 source build/config.txt
-codeDir="/Codes"
-execDir="/Exec"
-cores=$(bash $dir$execDir/BashScripts/getCores.sh $partition)
+cores=$(bash $PROTEO_HOME$execDir/BashScripts/getCores.sh $partition)
 
 nodelist=$SLURM_JOB_NODELIST
 nodes=$SLURM_JOB_NUM_NODES
@@ -22,11 +20,11 @@ fi
 
 echo "MPICH provider=$FI_PROVIDER"
 mpirun --version
-numP=$(bash $dir$execDir/BashScripts/getNumPNeeded.sh $configFile 0)
-initial_nodelist=$(bash $dir$execDir/BashScripts/createInitialNodelist.sh $numP $cores $nodelist)
+numP=$(bash $PROTEO_HOME$execDir/BashScripts/getNumPNeeded.sh $configFile 0)
+initial_nodelist=$(bash $PROTEO_HOME$execDir/BashScripts/createInitialNodelist.sh $numP $cores $nodelist)
 echo $initial_nodelist
 echo "Test PreRUN $numP $nodelist"
-mpirun -hosts $initial_nodelist -np $numP $dir$codeDir/build/a.out $configFile $outIndex 
+mpirun -hosts $initial_nodelist -np $numP $PROTEO_BIN $configFile $outIndex 
 
 echo "END RUN"
 sed -i 's/application called MPI_Abort(MPI_COMM_WORLD, -100) - process/shrink cleaning/g' slurm-$SLURM_JOB_ID.out

Codes/runTrace.sh

@@ -6,9 +6,7 @@
 
 scriptDir="$(dirname "$0")"
 source $scriptDir/build/config.txt
-codeDir="/Codes/build"
 resultsDir="/Results"
-execDir="/Exec"
 
 nodelist=$SLURM_JOB_NODELIST
 nodes=$SLURM_JOB_NUM_NODES
@@ -17,13 +15,13 @@ outIndex=$2
 
 echo "MPICH"
 
-numP=$(bash $dir$execDir/BashScripts/getNumPNeeded.sh $configFile 0)
+numP=$(bash $PROTEO_HOME$execDir/BashScripts/getNumPNeeded.sh $configFile 0)
 
 name_res="Extrae_"$nodes"_Test_"$numP
-dir_name_res=$dir$resultsDir"/"$name_res
+dir_name_res=$PROTEO_HOME$resultsDir"/"$name_res
 
-#mpirun -np $numP $dir$codeDir/a.out $configFile $outIndex $nodelist $nodes
-srun -n$numP --mpi=pmi2 ./trace.sh $dir$codeDir/a.out $configFile $outIndex $nodelist $nodes
+#mpirun -np $numP $PROTEO_BIN $configFile $outIndex $nodelist $nodes
+srun -n$numP --mpi=pmi2 ./trace.sh $PROTEO_BIN $configFile $outIndex $nodelist $nodes
 
 echo "END RUN"
 sed -i 's/application called MPI_Abort(MPI_COMM_WORLD, -100) - process/shrink cleaning/g' slurm-$SLURM_JOB_ID.out

Codes/runValgrind.sh

@@ -5,20 +5,7 @@
 #SBATCH --exclude=c01,c00,c02
 
 source build/config.txt
-codeDir="/Codes"
-execDir="/Exec"
-cores=$(bash $dir$execDir/BashScripts/getCores.sh $partition)
-
-#configFile=$1
-#outIndex=$2
-
-#echo "MPICH"
-#module load mpich-3.4.1-noucx
-#export HYDRA_DEBUG=1
-
-#mpirun --version
-#numP=$(bash $dir$execDir/BashScripts/getNumPNeeded.sh $configFile 0)
-#mpirun -np $numP valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes --trace-children=yes --log-file=nc.vg.%p $dir$codeDir/build/a.out $configFile $outIndex
+cores=$(bash $PROTEO_HOME$execDir/BashScripts/getCores.sh $partition)
 
 nodelist=$SLURM_JOB_NODELIST
 nodes=$SLURM_JOB_NUM_NODES
@@ -32,11 +19,11 @@ fi
 
 echo "MPICH provider=$FI_PROVIDER"
 mpirun --version
-numP=$(bash $dir$execDir/BashScripts/getNumPNeeded.sh $configFile 0)
-initial_nodelist=$(bash $dir$execDir/BashScripts/createInitialNodelist.sh $numP $cores $nodelist)
+numP=$(bash $PROTEO_HOME$execDir/BashScripts/getNumPNeeded.sh $configFile 0)
+initial_nodelist=$(bash $PROTEO_HOME$execDir/BashScripts/createInitialNodelist.sh $numP $cores $nodelist)
 echo $initial_nodelist
 echo "Test PreRUN $numP $nodelist"
-mpirun -hosts $initial_nodelist -np $numP valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes --trace-children=yes --log-file=vg.sp.%p.$SLURM_JOB_ID $dir$codeDir/build/a.out $configFile $outIndex 
+mpirun -hosts $initial_nodelist -np $numP valgrind --leak-check=full --show-leak-kinds=all --track-origins=yes --trace-children=yes --log-file=vg.sp.%p.$SLURM_JOB_ID $PROTEO_BIN $configFile $outIndex 
 
 echo "END RUN"
 sed -i 's/application called MPI_Abort(MPI_COMM_WORLD, -100) - process/shrink cleaning/g' slurm-$SLURM_JOB_ID.out