remove duplicated flags

CMakeLists.txt

@@ -1,18 +1,6 @@
 ########################################################################################
 # CMAKE for build the Material subroutine for BVP solution
 ########################################################################################
-# OPTIONS = standard (alternative): meaning
-#-------------------------------------------------------------
-# F90            = ifort (gfortran): compiler type, choose Intel or GNU
-# COMPILERNAME   = name of the compiler executable (if not the same as the ype), e.g. using mpich-g90 instead of ifort
-# PORTABLE       = TRUE (FALSE): decision, if executable is optimized for the machine on which it was built.
-# OPTIMIZATION   = DEFENSIVE (OFF,AGGRESSIVE,ULTRA): Optimization mode: O2, O0, O3 + further options for most files, O3 + further options for all files
-# OPENMP         = TRUE (FALSE): OpenMP multiprocessor support
-# PREFIX         = arbitrary prefix (before compilername)
-# OPTION         = arbitrary option (just before file to compile)
-# SUFFIX         = arbitrary suffix (after file to compile)
-# STANDARD_CHECK = checking for Fortran 2008, compiler dependend
-########################################################################################
 cmake_minimum_required (VERSION 3.1.0 FATAL_ERROR)
 project (DAMASK Fortran)
 
@@ -28,7 +16,7 @@ if (NOT DEFINED HDF5_DIR)
     message (FATAL_ERROR "HDF5_DIR is not found!" )
 endif (NOT DEFINED HDF5_DIR)
 
-# OUTPUT TYPE
+# DAMASK DRIVER SELECTION
 set (SPECTRAL OFF)
 set (FEM      OFF)
 if (DAMASK_DRIVER STREQUAL "SPECTRAL")
@@ -36,7 +24,7 @@ if (DAMASK_DRIVER STREQUAL "SPECTRAL")
 elseif (DAMASK_DRIVER STREQUAL "FEM")
     set (FEM      ON )
 else (DAMASK_DRIVER STREQUAL "SPECTRAL")
-    message (FATAL_ERROR "Unknown output, check build script!")
+    message (FATAL_ERROR "Unknown driver detected, check build script!")
 endif (DAMASK_DRIVER STREQUAL "SPECTRAL")
 
 # COMPILE VARIABLES
@@ -51,7 +39,7 @@ if (FEM)
     add_definitions(-DFEM)
 endif(FEM)
 
-# brutal force to find the variables defined in PETSC
+# BRUTAL FORCE TO FIND THE VARIABLES DEFINED IN PETSC
 # ref:
 # https://github.com/jedbrown/cmake-modules/blob/master/FindPETSc.cmake
 set(petsc_conf_variables "${PETSC_DIR}/lib/petsc/conf/variables")
@@ -59,7 +47,7 @@ set(petsc_conf_rules     "${PETSC_DIR}/lib/petsc/conf/rules"    )
 # A temporary makefile to probe the PETSc configuration
 set (petsc_config_makefile "${PROJECT_BINARY_DIR}/Makefile.petsc")
 file (WRITE "${petsc_config_makefile}"
-"## This file was autogenerated by FindPETSc.cmake
+"## This file was auto generated by CMake
 # PETSC_DIR  = ${PETSC_DIR}
 # PETSC_ARCH = ${PETSC_ARCH}
 SHELL = /bin/sh
@@ -86,11 +74,11 @@ linker:
 find_program (MAKE_EXECUTABLE NAMES make gmake)
 execute_process(COMMAND ${MAKE_EXECUTABLE} -f ${petsc_config_makefile} "includes"
                 RESULT_VARIABLE PETSC_INCLUDES_RETURN
-                OUTPUT_VARIABLE PETSC_INCLUDES
+                OUTPUT_VARIABLE petsc_includes
                 OUTPUT_STRIP_TRAILING_WHITESPACE)
 execute_process(COMMAND ${MAKE_EXECUTABLE} -f ${petsc_config_makefile} "extlibs"
                 RESULT_VARIABLE PETSC_EXTERNAL_LIB_RETURN
-                OUTPUT_VARIABLE PETSC_EXTERNAL_LIB
+                OUTPUT_VARIABLE petsc_external_lib
                 OUTPUT_STRIP_TRAILING_WHITESPACE)
 execute_process(COMMAND ${MAKE_EXECUTABLE} -f ${petsc_config_makefile} "linker"
                 RESULT_VARIABLE PETSC_LINK_LIB_RETURN
@@ -102,14 +90,27 @@ execute_process(COMMAND ${MAKE_EXECUTABLE} -f ${petsc_config_makefile} "compiler
                 OUTPUT_STRIP_TRAILING_WHITESPACE)
 file (REMOVE ${petsc_config_makefile})
 
+# remove duplicate flags for compiler and linking
+string( REGEX MATCHALL "-I([^\" ]+)" TMP_LIST "${petsc_includes}")
+list(REMOVE_DUPLICATES TMP_LIST)
+foreach (dir ${TMP_LIST})
+    set(PETSC_INCLUDES "${PETSC_INCLUDES} ${dir}")
+endforeach(dir)
+string( REGEX MATCHALL "-[lLW]([^\" ]+)" TMP_LIST "${petsc_external_lib}")
+list(REMOVE_DUPLICATES TMP_LIST)
+foreach (exlib ${TMP_LIST})
+    set(PETSC_EXTERNAL_LIB "${PETSC_EXTERNAL_LIB} ${exlib}")
+endforeach(exlib)
+
+
 message("***Found PETSC_DIR:\n${PETSC_DIR}\n")
 message("***Set PETSC_INCLUDES to:\n${PETSC_INCLUDES}\n")
 message("***Set PETSC_EXTERNAL_LIB to:\n${PETSC_EXTERNAL_LIB}\n")
 message("***Set PETSC_LINK_LIB to:\n${PETSC_LINK_LIB}\n")
-message("***Use PETSC wrapped compiler @: ${MPIEXEC}\n")
+message("***Use PETSC wrapped compiler:\n${MPIEXEC}\n")
 
 # set system include directories
-set (DAMASK_INCLUDE_FLAGS "${DAMASK_INCLUDE_FLAGS} ${PETSC_INCLUDES} -I${PROJECT_SOURCE_DIR}/lib -I${HDF5_DIR}/include")
+set (DAMASK_INCLUDE_FLAGS "${PETSC_INCLUDES} -I${PROJECT_SOURCE_DIR}/lib -I${HDF5_DIR}/include -lm")
 set (DAMASK_LINK_FLAGS    "${PETSC_LINK_LIB} ${PETSC_EXTERNAL_LIB} -L${HDF5_DIR}/lib")
 
 ##
@@ -186,7 +187,6 @@ set (COMPILE_OPTIONS_ifort   "${COMPILE_OPTIONS_ifort} -warn ignore_loc"
 set (COMPILE_OPTIONS_ifort   "${COMPILE_OPTIONS_ifort} -warn alignments"            )
 set (COMPILE_OPTIONS_ifort   "${COMPILE_OPTIONS_ifort} -warn unused"                )
 set (COMPILE_OPTIONS_ifort   "${COMPILE_OPTIONS_ifort} -diag-remark 7410"           )
-set (COMPILE_OPTIONS_ifort   "${COMPILE_OPTIONS_ifort} -stand none"                 )
 set (COMPILE_OPTIONS_ifort   "${COMPILE_OPTIONS_ifort} -warn nostderrors"           )
 ###################################################################################################
 # COMPILE SWITCHES FOR RUNTIME DEBUGGING