Merge pull request #46 from leobago/devel

Release candidate for version 0.9.6

.travis.yml

@@ -0,0 +1,39 @@
+sudo: required
+dist: trusty
+
+language: c
+
+env:
+  global:
+    - BUILD_DIR="$TRAVIS_BUILD_DIR/build"
+    - secure: "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"
+
+addons:
+  coverity_scan:
+    project:
+      name: sclaomir/fti
+      description: Fault Tolerance Interface
+    notification_email: [email protected]
+    build_command_prepend: cmake ..
+    build_command: make
+    branch_pattern: devel
+
+os:
+  - linux
+
+compiler:
+  - gcc
+
+cache:
+  apt: true
+
+before_install:
+  - sudo apt-get update -qq
+  - sudo apt-get install -y cmake gcc gfortran openmpi-bin libopenmpi-dev
+
+before_script:
+  - mkdir $BUILD_DIR
+  - cd $BUILD_DIR
+  - cmake ..
+
+script: make

AUTHORS

@@ -5,6 +5,7 @@ Author:
 Collaborators:
 
     Julien BIGOT
+    Slawomir Zdanowski
     Adele VILLIERMET
     Sheng DI
     Faysal BOUI

CMakeLists.txt

@@ -1,70 +1,85 @@
-cmake_minimum_required(VERSION 2.8)
-list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/CMakeScripts")
+cmake_minimum_required(VERSION 2.8.8 FATAL_ERROR)
 
-if ( "${CMAKE_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_SOURCE_DIR}" )
+if("${CMAKE_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_SOURCE_DIR}")
 	project(FTI C Fortran)
 endif()
 
+option(ENABLE_FORTRAN "Enables the generation of the Fortran wrapper for FTI" ON)
+option(ENABLE_EXAMPLES "Enables the generation of examples" ON)
+
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/CMakeScripts")
 include(AppendProperty)
 include(BPP)
 include(FortranCInterface)
+
 find_package(MPI REQUIRED)
 
-option(ENABLE_FORTRAN "Enables the generation of the Fortran wrapper for FTI" ON)
+add_subdirectory(deps)
 
-include_directories("${CMAKE_CURRENT_BINARY_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/src" "${CMAKE_CURRENT_SOURCE_DIR}/include" ${MPI_Fortran_INCLUDE_PATH} ${MPI_C_INCLUDE_PATH})
+include_directories("${CMAKE_CURRENT_BINARY_DIR}"
+	"${CMAKE_CURRENT_SOURCE_DIR}/src" "${CMAKE_CURRENT_SOURCE_DIR}/include"
+	${MPI_Fortran_INCLUDE_PATH} ${MPI_C_INCLUDE_PATH})
 
-set (LIBRARY_OUTPUT_PATH ${CMAKE_CURRENT_BINARY_DIR}/lib)
-set (CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/include)
+set(LIBRARY_OUTPUT_PATH ${CMAKE_CURRENT_BINARY_DIR}/lib)
+set(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/include)
 
 set(SRC_FTI
-	src/galois.c
-	src/jerasure.c
-	src/dictionary.c
-	src/iniparser.c
-	src/checkpoint.c
-	src/postckpt.c
-	src/recover.c
-	src/postreco.c
-	src/topo.c
-	src/conf.c
-	src/meta.c
-	src/tools.c
-	src/api.c
-)
-append_property(SOURCE ${SRC_FTI} PROPERTY COMPILE_FLAGS " ${MPI_C_COMPILE_FLAGS} ")
-
-add_library(fti.static STATIC ${SRC_FTI})
+	src/api.c src/checkpoint.c src/conf.c src/meta.c
+	src/postckpt.c src/postreco.c src/recover.c
+	src/tools.c src/topo.c)
+
+append_property(SOURCE ${SRC_FTI}
+	PROPERTY COMPILE_FLAGS "${MPI_C_COMPILE_FLAGS}")
+
+add_library(fti.static STATIC ${SRC_FTI}
+    $<TARGET_OBJECTS:iniparser> $<TARGET_OBJECTS:jerasure>)
+add_library(fti.shared SHARED ${SRC_FTI}
+    $<TARGET_OBJECTS:iniparser> $<TARGET_OBJECTS:jerasure>)
+
+append_property(TARGET fti.static fti.shared
+	PROPERTY LINK_FLAGS "${MPI_C_LINK_FLAGS}")
+set_property(TARGET fti.static fti.shared
+	PROPERTY OUTPUT_NAME fti)
+
 target_link_libraries(fti.static ${MPI_C_LIBRARIES})
-add_library(fti.shared SHARED ${SRC_FTI})
 target_link_libraries(fti.shared ${MPI_C_LIBRARIES})
-append_property(TARGET fti.static fti.shared PROPERTY LINK_FLAGS " ${MPI_C_LINK_FLAGS} ")
-set_property(TARGET fti.static fti.shared PROPERTY OUTPUT_NAME fti)
 
-install(TARGETS fti.static fti.shared DESTINATION lib)
-install(FILES "include/fti.h" "include/dictionary.h" "include/galois.h" "include/iniparser.h" "include/jerasure.h" DESTINATION include)
+install(TARGETS fti.static fti.shared
+	DESTINATION lib)
+install(FILES "include/fti.h"
+	DESTINATION include)
 
-if ( ENABLE_FORTRAN )
+if(ENABLE_FORTRAN)
 	bpp_preprocess(BPP_FTI_F90
-		src/interface.F90.bpp
-	)
-	set(SRC_FTI_F90
-		${BPP_FTI_F90}
-		src/ftif.c
-	)
-	append_property(SOURCE ${SRC_FTI_F90} PROPERTY COMPILE_FLAGS " ${MPI_Fortran_COMPILE_FLAGS} ")
+		src/fortran/interface.F90.bpp)
+	set(SRC_FTI_F90 ${BPP_FTI_F90}
+		src/fortran/ftif.c)
+	append_property(SOURCE ${SRC_FTI_F90}
+		PROPERTY COMPILE_FLAGS "${MPI_Fortran_COMPILE_FLAGS}")
 
 	add_library(fti_f90.static STATIC ${SRC_FTI_F90})
-	target_link_libraries(fti_f90.static fti.static ${MPI_Fortran_LIBRARIES} ${MPI_C_LIBRARIES})
+	target_link_libraries(fti_f90.static
+		fti.static ${MPI_Fortran_LIBRARIES} ${MPI_C_LIBRARIES})
+
 	add_library(fti_f90.shared SHARED ${SRC_FTI_F90})
-	target_link_libraries(fti_f90.shared fti.shared ${MPI_Fortran_LIBRARIES} ${MPI_C_LIBRARIES})
-	append_property(TARGET fti_f90.static fti_f90.shared PROPERTY LINK_FLAGS " ${MPI_Fortran_LINK_FLAGS} ${MPI_C_LINK_FLAGS} ")
-	set_property(TARGET fti_f90.static fti_f90.shared PROPERTY OUTPUT_NAME fti_f90)
+	target_link_libraries(fti_f90.shared
+		fti.shared ${MPI_Fortran_LIBRARIES} ${MPI_C_LIBRARIES})
 
-	install(TARGETS fti_f90.static fti_f90.shared DESTINATION lib)
-        install(FILES ${CMAKE_Fortran_MODULE_DIRECTORY}/fti.mod DESTINATION include)
+	append_property(TARGET fti_f90.static fti_f90.shared
+		PROPERTY LINK_FLAGS "${MPI_Fortran_LINK_FLAGS} ${MPI_C_LINK_FLAGS}")
+	set_property(TARGET fti_f90.static fti_f90.shared
+		PROPERTY OUTPUT_NAME fti_f90)
+
+	install(TARGETS fti_f90.static fti_f90.shared
+		DESTINATION lib)
+	install(FILES ${CMAKE_Fortran_MODULE_DIRECTORY}/fti.mod
+		DESTINATION include)
 endif()
 
-if ( NOT "${CMAKE_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_SOURCE_DIR}" )
+if(NOT "${CMAKE_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_SOURCE_DIR}")
 	set(FTI_INCLUDE_PATH "${CMAKE_CURRENT_BINARY_DIR}" "${CMAKE_CURRENT_SOURCE_DIR}/include" PARENT_SCOPE)
 endif()
+
+if(ENABLE_EXAMPLES)
+	add_subdirectory(examples)
+endif()

deps/CMakeLists.txt

@@ -0,0 +1,2 @@
+add_subdirectory(iniparser)
+add_subdirectory(jerasure)

deps/iniparser/CMakeLists.txt

@@ -0,0 +1,8 @@
+set(SRC_iniparser
+    dictionary.h dictionary.c
+    iniparser.h iniparser.c)
+
+append_property(SOURCE ${SRC_iniparser}
+    PROPERTY COMPILE_FLAGS "-fPIC")
+
+add_library(iniparser OBJECT ${SRC_iniparser})

src/iniparser.c → deps/iniparser/iniparser.c

@@ -74,13 +74,13 @@ static char * strlwc(const char * s)
 static char * strstrip(const char * s)
 {
     static char l[ASCIILINESZ+1];
-    char * last ;
+    char * last;
 
     if (s==NULL) return NULL ;
 
     while (isspace((int)*s) && *s) s++;
     memset(l, 0, ASCIILINESZ+1);
-    strcpy(l, s);
+    strncpy(l, s, ASCIILINESZ);
     last = l + strlen(l);
     while (last > l) {
         if (!isspace((int)*(last-1)))
@@ -562,7 +562,11 @@ static line_status iniparser_line(
     char        line[ASCIILINESZ+1];
     int         len ;
 
-    strcpy(line, strstrip(input_line));
+    memset(line, 0, ASCIILINESZ + 1);
+    len = (int)strlen(strstrip(input_line));
+    if (len > ASCIILINESZ)
+        len = ASCIILINESZ;
+    strncpy(line, strstrip(input_line), len);
     len = (int)strlen(line);
 
     sta = LINE_UNPROCESSED ;
@@ -608,6 +612,7 @@ static line_status iniparser_line(
     } else {
         /* Generate syntax error */
         sta = LINE_ERROR ;
+        printf("===== > %s   ===> %s\n", input_line, line);
     }
     return sta ;
 }

deps/jerasure/CMakeLists.txt

@@ -0,0 +1,8 @@
+set(SRC_jerasure
+    galois.h galois.c
+    jerasure.h jerasure.c)
+
+append_property(SOURCE ${SRC_jerasure}
+    PROPERTY COMPILE_FLAGS "-fPIC")
+
+add_library(jerasure OBJECT ${SRC_jerasure})

src/galois.c → deps/jerasure/galois.c

@@ -393,8 +393,9 @@ int galois_single_divide(int a, int b, int w)
     sum_j = galois_inverse(b, w);
     return galois_single_multiply(a, sum_j, w);
   }
-  fprintf(stderr, "Galois_single_divide - no implementation for w=%d\n", w);
-  exit(1);
+  // unreachable code
+  //fprintf(stderr, "Galois_single_divide - no implementation for w=%d\n", w);
+  //exit(1);
 }
 
 int galois_shift_divide(int a, int b, int w)

src/jerasure.c → deps/jerasure/jerasure.c

@@ -260,7 +260,10 @@ int *jerasure_matrix_to_bitmatrix(int k, int m, int w, int *matrix)
   int rowelts, rowindex, colindex, elt, i, j, l, x;
 
   bitmatrix = talloc(int, k*m*w*w);
-  if (matrix == NULL) { return NULL; }
+  if (matrix == NULL) {
+    free(bitmatrix);
+    return NULL;
+  }
 
   rowelts = k * w;
   rowindex = 0;
@@ -397,6 +400,8 @@ int jerasure_invert_matrix(int *mat, int *inv, int rows, int w)
     tmp = mat[row_start+i];
     if (tmp != 1) {
       inverse = galois_single_divide(1, tmp, w);
+      if (inverse < 0)
+        return -1;
       for (j = 0; j < cols; j++) {
         mat[row_start+j] = galois_single_multiply(mat[row_start+j], inverse, w);
         inv[row_start+j] = galois_single_multiply(inv[row_start+j], inverse, w);
@@ -825,7 +830,11 @@ static int **jerasure_generate_decoding_schedule(int k, int m, int w, int *bitma
   row_ids = talloc(int, k+m);
   ind_to_row = talloc(int, k+m);
 
-  if (set_up_ids_for_scheduled_decoding(k, m, erasures, row_ids, ind_to_row) < 0) return NULL;
+  if (set_up_ids_for_scheduled_decoding(k, m, erasures, row_ids, ind_to_row) < 0) {
+    free(row_ids);
+    free(ind_to_row);
+    return NULL;
+  }
 
   /* Now, we're going to create one decoding matrix which is going to
      decode everything with one call.  The hope is that the scheduler
@@ -1247,6 +1256,7 @@ int **jerasure_smart_bitmatrix_to_schedule(int k, int m, int w, int *bitmatrix)
   ptr = bitmatrix;
 
   bestdiff = k*w+1;
+  bestrow = -1;
   top = 0;
   for (i = 0; i < m*w; i++) {
     no = 0;
@@ -1312,7 +1322,8 @@ int **jerasure_smart_bitmatrix_to_schedule(int k, int m, int w, int *bitmatrix)
           operations[op][1] = j%w;
           operations[op][2] = k+row/w;
           operations[op][3] = row%w;
-          optodo = 1;
+          // unused value
+          //optodo = 1;
           op++;
         }
       }

examples/CMakeLists.txt

@@ -0,0 +1,42 @@
+link_directories(${CMAKE_BINARY_DIR}/lib)
+
+add_executable(hd.exe heatdis.c)
+target_link_libraries(hd.exe ${CMAKE_BINARY_DIR}/lib/libfti.a ${MPI_C_LIBRARIES} m)
+
+if(MPI_C_COMPILE_FLAGS)
+    set_target_properties(hd.exe PROPERTIES
+        COMPILE_FLAGS "${MPI_C_COMPILE_FLAGS}")
+endif()
+
+if(MPI_C_LINK_FLAGS)
+    set_target_properties(hd.exe PROPERTIES
+        LINK_FLAGS "${MPI_C_LINK_FLAGS}")
+endif()
+
+add_executable(hd2.exe heatd2.c)
+target_link_libraries(hd2.exe ${CMAKE_BINARY_DIR}/lib/libfti.a ${MPI_C_LIBRARIES} m)
+
+if(MPI_C_COMPILE_FLAGS)
+    set_target_properties(hd2.exe PROPERTIES
+        COMPILE_FLAGS "${MPI_C_COMPILE_FLAGS}")
+endif()
+
+if(MPI_C_LINK_FLAGS)
+    set_target_properties(hd2.exe PROPERTIES
+        LINK_FLAGS "${MPI_C_LINK_FLAGS}")
+endif()
+
+if(ENABLE_FORTRAN)
+    add_executable(hdf.exe fheatdis.f90)
+    target_link_libraries(hdf.exe fti_f90 ${CMAKE_BINARY_DIR}/lib/libfti.a ${MPI_Fortran_LIBRARIES} m)
+
+    if(MPI_Fortran_COMPILE_FLAGS)
+        set_target_properties(hdf.exe PROPERTIES
+            COMPILE_FLAGS "${MPI_Fortran_COMPILE_FLAGS}")
+    endif()
+
+    if(MPI_Fortran_LINK_FLAGS)
+        set_target_properties(hdf.exe PROPERTIES
+            LINK_FLAGS "${MPI_Fortran_LINK_FLAGS}")
+    endif()
+endif()

examples/Makefile

@@ -2,7 +2,7 @@
 ##   Makefile to test FTI library with the heat distribution program.
 
 ##   PLEASE SET THIS VARIABLE BEFORE COMPILING
-FTIPATH		= /path/to/fti/install/directory
+FTIPATH		= /path/to/fti/
 
 ##   COMPILERS
 MPICC 		?= mpicc
@@ -11,11 +11,11 @@ MPIRUN 		?= mpirun
 
 ##   FLAGS
 # Compiling using shared library
-FTIFLAG 	= -I$(FTIPATH)/include -L$(FTIPATH)/lib -lfti -lm
-FFTIFLAG 	= -I$(FTIPATH)/include -L$(FTIPATH)/lib -lfti_f90 -lfti -lm
+#FTIFLAG 	= -I$(FTIPATH)/include -L$(FTIPATH)/lib -lfti -lm
+#FFTIFLAG 	= -I$(FTIPATH)/include -L$(FTIPATH)/lib -lfti_f90 -lfti -lm
 # Compiling using static library
-#FTIFLAG 	= -I$(FTIPATH)/include $(FTIPATH)/lib/libfti.a
-#FFTIFLAG 	= -I$(FTIPATH)/include $(FTIPATH)/lib/libfti_f90.a $(FTIPATH)/lib/libfti.a
+FTIFLAG 	= -I$(FTIPATH)/include $(FTIPATH)/lib/libfti.a -lm
+FFTIFLAG 	= -I$(FTIPATH)/include $(FTIPATH)/lib/libfti_f90.a $(FTIPATH)/lib/libfti.a -lm
 
 ##   TARGETS
 all: 		hd hd2 hdf
@@ -30,7 +30,7 @@ hdf:		fheatdis.f90
 		$(MPIFC) -o hdf.exe fheatdis.f90 $(FFTIFLAG)
 
 hdt:
-		$(MPIRUN) -np 8 ./hd.exe 32 config.fti
+		$(MPIRUN) -np 8 ./hd.exe 4 config.fti
 
 hdv:
 		./plot.sh