requesting pull of bug fixes and performance improvements that should be merged into amaya-library

CMakeLists.txt

@@ -1,5 +1,9 @@
-cmake_minimum_required(VERSION 2.8.8)
-
+cmake_minimum_required(VERSION 2.8.8) 
+# compiler set in ../cmake/cmake_template.cmake.XeonPhi
+#message ("for Xeon Phi:")
+#message ("cmake .. -DCMAKE_TOOLCHAIN_FILE=../cmake/cmake_template.cmake.XeonPhi")
+#message ("for Xeon:")
+#message ("cmake .. -DCMAKE_TOOLCHAIN_FILE=../cmake/cmake_template.cmake.Xeon")
 #
 # Project declaration
 #
@@ -13,17 +17,53 @@ project(iPic3D)
 set(EXECUTABLE_OUTPUT_PATH exec/${CMAKE_BUILD_TYPE})
 set(LIBRARY_OUTPUT_PATH lib)
 
+#
+# Set compiler flags per system
+#
+if (${CMAKE_SYSTEM_PROCESSOR} STREQUAL "k1om") ## Xeon Phi
+   option(IPIC_XEONPHI "ipic xeon phi standard compile flags" on)
+   if(IPIC_XEONPHI) 
+     set(CMAKE_CXX_FLAGS "-O3 -openmp -fno-exceptions -vec-report -mmic")
+   else()
+     set(CMAKE_CXX_FLAGS "-mmic")
+   endif()
+   #set(CMAKE_CXX_FLAGS "$(CMAKE_CXX_FLAGS) -mmic")
+   #set(CMAKE_CXX_FLAGS "-O3 -openmp -fno-exceptions -vec-report -mmic")
+   #set(CMAKE_CXX_FLAGS "-openmp -g -mmic") # set flags for Xeon Phi, totalview
+elseif (${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64") ## Xeon
+   option(IPIC_XEON "icpc with optimization" on)
+   if(IPIC_XEON) 
+     # reporting: -g -vec-report
+     # optimization: -O3 -xHost -fno-exceptions
+     set(CMAKE_CXX_FLAGS "-openmp -fno-exceptions -O3 -xHost -vec-report")
+     set(CMAKE_CXX_COMPILER "icpc")  
+   endif()
+   #set(CMAKE_CXX_FLAGS "-O3 -openmp -g -xHost -fno-exceptions -vec-report")
+else()
+   #set(CMAKE_CXX_FLAGS "-O3")
+endif()
+
 #
 # Find third class libraries
 #
+if (${CMAKE_SYSTEM_PROCESSOR} STREQUAL "k1om") ## Xeon Phi
+   set(CMAKE_PREFIX_PATH /opt/hdf5/1.8.10-patch1-mic)			
+   set(VARIOUS_LIB /opt/intel/lib/mic)
+   set (EXTRA_LIBS ${VARIOUS_LIB}/libimf.so ${VARIOUS_LIB}/libsvml.so ${VARIOUS_LIB}/libirng.so ${VARIOUS_LIB}/libintlc.so ${MPELIB})
+else()
+   find_package(MPI REQUIRED)
+   set(EXTRA_LIBS "")   
+endif()
 
 find_package(HDF5 COMPONENTS HL C REQUIRED)
-find_package(MPI REQUIRED)
+message("HDF5_INCLUDE_DIRS is ${HDF5_INCLUDE_DIRS}")
+
 
 #
 # include and lib directories
 #
 
+# include_directories: files there are accessible to the project
 include_directories(
         include
         ${HDF5_INCLUDE_DIRS}
@@ -33,6 +73,7 @@ include_directories(
 link_directories(
         ${HDF5_LIBRARY_DIRS}
         ${MPI_LIBRARY_DIRS}
+	${EXTRA_LIBS}
 )
 
 #
@@ -58,7 +99,6 @@ file(
         communication/*.cpp
         fields/*.cpp
         grids/*.cpp
-        iPIC3D.cpp/*.cpp
         inputoutput/*.cpp
         mathlib/*.cpp
         mpidata/*.cpp
@@ -67,52 +107,38 @@ file(
         processtopology/*.cpp
         solvers/*.cpp
         utility/*.cpp
-        main/iPic3Dlib.cpp
+        main/*.cpp
 )
 
 #
-# Compilation options
+# Macro definitions
 #
 
-set(IPIC_TESTS_DIR "${CMAKE_BINARY_DIR}/tests" CACHE STRING "Location of the source files for iPic3D")
-
-option(IPIC_PARALLEL_HDF5 "Output is done using the parallel HDF5 library" OFF)
-if(IPIC_PARALLEL_HDF5)
-  add_definitions(-DPHDF5)
-endif()
-
-option(IPIC_BATSRUS "Compile library with coupling code for BATS-R-US" OFF)
-if(IPIC_BATSRUS)
+set(TEST_B $ENV{BATSRUS})
+if(DEFINED TEST_B)
   add_definitions( -DBATSRUS )
-endif()
-
-option(IPIC_XEONPHI "Compile options for Xeon Phi" OFF)
-if(IPIC_XEONPHI)
-  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS}")
-endif()
-
-option(IPIC_TESTS "Set up the code tests" OFF)
-
-option(IPIC_BUILD_SHARED "Compile shared library" OFF)
-if(IPIC_BUILD_SHARED)
-  set(IPIC_BUILD_TYPE SHARED)
-else()
-  set(IPIC_BUILD_TYPE STATIC)
-endif()
+  message(" WARNING: BATSRUS flag is active.")
+else(DEFINED TEST_B)
+  message(" INFO: BATSRUS is not active.")
+endif(DEFINED TEST_B)
 
 #
 # Executable declaration
 #
 
+# Particle solver
 add_executable(
         iPic3D
         iPic3D.cpp
 )
 
+
+#build iPic as a library also
+#libiPic3Dlib.so in folder lib
 add_library(
-        iPic3Dlib
-        ${IPIC_BUILD_TYPE}
-        ${inc_files}
+        iPic3Dlib  #name of the library
+        SHARED	   #type of the library
+        ${inc_files}    # stuff to build the library
         ${src_files}
 )
 
@@ -125,33 +151,24 @@ target_link_libraries(
          ${HDF5_LIBRARIES}
          ${HDF5_HL_LIBRARIES}
          ${MPI_LIBRARIES}
+	 ${EXTRA_LIBS}
 )
 
 target_link_libraries(
          iPic3D
          iPic3Dlib
 )
 
-#
-# Code testing
-#
+## to save the executable in the folder where the CMakeLists.txt file is, i.e. CMAKE_CURRENT_SOURCE_DIR
+#set_target_properties(iPic3D PROPERTIES RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
 
-if(IPIC_TESTS)
-  enable_testing()
+## debug releases have a _d appended to the executable
+set_target_properties(iPic3D PROPERTIES DEBUG_POSTFIX "_d")
 
-  add_test(NAME GEM-test
-           COMMAND ${CMAKE_COMMAND}
-           -DIPIC_TESTS_DIR=${IPIC_TESTS_DIR}
-           -DIPIC_SOURCE_DIR=${CMAKE_SOURCE_DIR}
-           -DIPICEXEC=$<TARGET_FILE:iPic3D>
-           -DMPIEXEC=${MPIEXEC}
-           -DMPIEXEC_NUMPROC_FLAG=${MPIEXEC_NUMPROC_FLAG}
-           -DMPIEXEC_POSTFLAGS=${MPIEXEC_POSTFLAGS}
-           -DIPIC_TESTS_DIR=${IPIC_TESTS_DIR}
-           -P ${CMAKE_SOURCE_DIR}/testfiles/CMakeRunTest-GEM.txt)
 
-  add_test(NAME uname-test
-           COMMAND ${CMAKE_COMMAND}
-           -P ${CMAKE_SOURCE_DIR}/testfiles/CMakeRunTest-uname.txt)
+message("Which system am I compiling for:")
+message("CMAKE_SYSTEM_PROCESSOR is ${CMAKE_SYSTEM_PROCESSOR}")
 
-endif(IPIC_TESTS)
+message("Compiler & compiler flags:")
+message("CMAKE_CXX_COMPILER is ${CMAKE_CXX_COMPILER}")
+message("CMAKE_CXX_FLAGS is ${CMAKE_CXX_FLAGS}")

ConfigFile/src/ConfigFile.cpp

@@ -1,6 +1,8 @@
 // ConfigFile.cpp
 
 #include "ConfigFile.h"
+#include "errors.h"
+#include "debug.h"
 
 using std::string;
 
@@ -11,7 +13,8 @@ ConfigFile::ConfigFile(string filename, string delimiter, string comment, string
   std::ifstream in(filename.c_str());
 
   if (!in)
-    throw file_not_found(filename);
+    eprintf("file not found: %s", filename.c_str());
+    //throw file_not_found(filename);
 
   in >> (*this);
 }

ConfigFile/src/ConfigFile.h

@@ -48,6 +48,7 @@
 #include <iostream>
 #include <fstream>
 #include <sstream>
+#include "errors.h" // for eprintf
 
 using std::string;
 
@@ -165,7 +166,6 @@ template <> inline bool ConfigFile::string_as_T < bool > (const string & s) {
     *p = toupper(*p);           // make string all caps
   if (sup == string("FALSE") || sup == string("F") || sup == string("NO") || sup == string("N") || sup == string("0") || sup == string("NONE")) {
     b = false;
-    cout << "siamo qua " << endl;
   }
   return b;
 }
@@ -175,7 +175,8 @@ template < class T > T ConfigFile::read(const string & key) const {
   // Read the value corresponding to key
   mapci p = myContents.find(key);
   if (p == myContents.end())
-    throw key_not_found(key);
+    eprintf("key not found: %s", key.c_str());
+    //throw key_not_found(key);
   return string_as_T < T > (p->second);
 }