diff --git a/.github/workflows/test_macos.yml b/.github/workflows/test_macos.yml index 677be326..76ef3380 100644 --- a/.github/workflows/test_macos.yml +++ b/.github/workflows/test_macos.yml @@ -43,5 +43,5 @@ jobs: conda run -n svfsiplus pytest -rPv --durations=0 - name: Run unit tests run: | - cd build/svFSI-build/Source/svFSI + cd build/svFSIplus-build/Source/svFSI ctest --verbose diff --git a/.github/workflows/test_ubuntu.yml b/.github/workflows/test_ubuntu.yml index 54765d05..6470bad5 100644 --- a/.github/workflows/test_ubuntu.yml +++ b/.github/workflows/test_ubuntu.yml @@ -56,17 +56,17 @@ jobs: conda run -n svfsiplus pytest -rPv --durations=0 - name: Run unit tests run: | - cd build/svFSI-build/Source/svFSI + cd build/svFSIplus-build/Source/svFSI ctest --verbose - name: Generate code coverage run: | - cd build/svFSI-build + cd build/svFSIplus-build make coverage - name: Save coverage report uses: actions/upload-artifact@v3 with: name: coverage_report - path: build/svFSI-build/coverage + path: build/svFSIplus-build/coverage - name: Upload coverage reports to Codecov uses: codecov/codecov-action@v3 env: diff --git a/CMakeLists.txt b/CMakeLists.txt index 20105156..d5443c65 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -54,6 +54,7 @@ endif() #----------------------------------------------------------------------------- Project(SV_TOP) +message(STATUS "SV_TOP: ${SV_TOP}") #----------------------------------------------------------------------------- #----------------------------------------------------------------------------- @@ -124,9 +125,9 @@ set(SV_EXTERNALS_TOPLEVEL_DIR "${CMAKE_BINARY_DIR}/Externals-build/sv_externals" # svFSIplus solver. set(SV_ADDITIONAL_CMAKE_ARGS "" CACHE STRING "If more options want to be provided to the sv_externals build, they can be with this string") set(SV_APPLE_CMAKE_ARGS) -ExternalProject_Add(svFSI +ExternalProject_Add(svFSIplus SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/Code - BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/svFSI-build + BINARY_DIR ${CMAKE_CURRENT_BINARY_DIR}/svFSIplus-build DEPENDS Externals DOWNLOAD_COMMAND "" UPDATE_COMMAND "" diff --git a/Code/CMake/SimVascularDependentOptions.cmake b/Code/CMake/SimVascularDependentOptions.cmake index 798836dc..9fb258f9 100644 --- a/Code/CMake/SimVascularDependentOptions.cmake +++ b/Code/CMake/SimVascularDependentOptions.cmake @@ -82,9 +82,16 @@ endif() #----------------------------------------------------------------------------- # Shared Libs #----------------------------------------------------------------------------- -set(SV_INSTALL_HEADERS ON) -set(SV_INSTALL_EXTERNALS ON) -set(SV_INSTALL_LIBS ON) + +set(SV_INSTALL_HEADERS OFF) +#set(SV_INSTALL_HEADERS ON) + +set(SV_INSTALL_EXTERNALS OFF) +#set(SV_INSTALL_EXTERNALS ON) + +set(SV_INSTALL_LIBS OFF) +#set(SV_INSTALL_LIBS ON) + if(BUILD_SHARED_LIBS) set(SV_LIBRARY_TYPE "SHARED" CACHE STRING "Shared cache" FORCE) set(SV_STATIC_BUILD "0") diff --git a/Code/CMakeLists.txt b/Code/CMakeLists.txt index c541d1de..4f10255c 100644 --- a/Code/CMakeLists.txt +++ b/Code/CMakeLists.txt @@ -90,14 +90,14 @@ include(SimVascularDependentOptions) include(SimVascularInstallSetup) #set(SV_USE_TRILINOS {SV_USE_TRILINOS} PARENT_SCOPE) -#set(SV_USE_TRILINOS OFF CACHE INTERNAL BOOL "Use Trilinos Library with svFSI") +#set(SV_USE_TRILINOS OFF CACHE INTERNAL BOOL "Use Trilinos Library with svFSIplus") #set(SV_USE_TRILINOS OFF CACHE BOOL INTERNAL) #----------------------------------------------------------------------------- #----------------------------------------------------------------------------- # Set EXE names for the executables -set(SV_SVFSI_EXE "svFSI") +set(SV_SVFSI_EXE "svfsiplus") #----------------------------------------------------------------------------- #----------------------------------------------------------------------------- @@ -159,8 +159,3 @@ if(SV_ENABLE_DISTRIBUTION) endif() #----------------------------------------------------------------------------- -#----------------------------------------------------------------------------- -# Configure Exe Scripts, this should be the last subdirectory -include(SimVascularInstallLibs) -add_subdirectory(Scripts) -#----------------------------------------------------------------------------- diff --git a/Code/Scripts/CMakeLists.txt b/Code/Scripts/CMakeLists.txt deleted file mode 100644 index 2efa2501..00000000 --- a/Code/Scripts/CMakeLists.txt +++ /dev/null @@ -1,116 +0,0 @@ -include(${CMAKE_CURRENT_SOURCE_DIR}/SimVascularScriptMacros.cmake) -file(MAKE_DIRECTORY ${TEMP_DIR}/developer ${TEMP_DIR}/install) - -set(core_str) -if(UNIX) - file(READ ${SV_SOURCE_DIR}/Scripts/home-locate-linux.sh locate_script) - set(core_str "${locate_script}\n") - set_env_string_concat(SV_HOME "$DIR" core_str) -endif() -if(WIN32 AND NOT UNIX) - set(core_str "@echo off\r\n") - set_env_string_concat(SV_HOME "%~dp0" core_str) -endif() - -set(core_vars SV_OS SOFTWARE_PLATFORM COMPILER_VERSION - SV_VERSION OPEN_SOFTWARE_BINARIES_TOPLEVEL - LICENSED_SOFTWARE_TOPLEVEL SV_STATIC_BUILD) - - -foreach(var ${core_vars}) - set_env_string_concat(${var} "\@${var}\@" core_str) - string(CONFIGURE "${core_str}" core_str @ONLY) -endforeach() - - -set(SCRIPT_FILES ${HOME_FILE_STRING}) -if(UNIX) - set(WIN_PATH ) - set(WIN_EXE ) - set(WIN_BAT ) - set(OSTYPE linux) -endif() - -#Generate output scripts -if(WIN32 AND NOT CYGWIN) - set(WIN_EXE ".exe") - set(WIN_BAT ".bat") - set(OSTYPE windows) -endif() - -set(developer_script_string) -set(install_script_string) -set(FRAGMENT_INJECTION_STRING) -#--- -# Write extra FILES -env_variable_to_value_variable(ENV_SV_HOME SV_HOME) - -#configure_file(${SV_SOURCE_DIR}/../Distribution/windows/registry-patch-notargets.xml.in "${TEMP_DIR}/patch.xml" @ONLY) -set(PREAMBLE_DEVELOPER_FILE "${TEMP_DIR}/developer-preample") -set(PREAMBLE_INSTALL_FILE "${TEMP_DIR}/install-preample") -set(EXE_FILE_STRING "") - -#---------------------------------------------------------------------------- -# add runtime and lib paths -if(WIN32) - set(developer_script_string "${developer_script_string}\nREM svSolver runtime and library locations\n") - set(install_script_string "${install_script_string}\nREM svSolver runtime and library locations\n") -else() - set(developer_script_string "${developer_script_string}\n# svSolver runtime and library locations\n") - set(install_script_string "${install_script_string}\n# svSolver runtime and library locations\n") -endif() -append_env_string_concat(${ENV_LIBRARY_PATH_VARIABLE} "${ENV_SV_HOME}/${SV_INSTALL_LIBRARY_DIR}" install_script_string) -append_env_string_concat(${ENV_LIBRARY_PATH_VARIABLE} "${ENV_SV_HOME}/${SV_INSTALL_HOME_DIR}" install_script_string) -append_env_string_concat(${ENV_LIBRARY_PATH_VARIABLE} "${ENV_SV_HOME}/${SV_INSTALL_RUNTIME_DIR}" install_script_string) - -append_env_string_concat(${ENV_LIBRARY_PATH_VARIABLE} "${CMAKE_BINARY_DIR}/bin" developer_script_string) -append_env_string_concat(${ENV_LIBRARY_PATH_VARIABLE} "${CMAKE_BINARY_DIR}/lib" developer_script_string) -append_env_string_concat(${ENV_LIBRARY_PATH_VARIABLE} "${CMAKE_BINARY_DIR}/bin/RelWithDebInfo" developer_script_string) -#---------------------------------------------------------------------------- - - -file(WRITE ${PREAMBLE_DEVELOPER_FILE} "${core_str}\n") -file(APPEND ${PREAMBLE_DEVELOPER_FILE} "${developer_script_string}\n") - -file(WRITE ${PREAMBLE_INSTALL_FILE} "${core_str}\n") -file(APPEND ${PREAMBLE_INSTALL_FILE} "${install_script_string}\n") - -set(SCRIPT_FILES "${TEMP_DIR}/\@mode\@-preample") - -# CHANGE FOR EXECUTABLE RENAME REMOVE -set(SCRIPT_FILES ${SCRIPT_FILES} "${SV_SOURCE_DIR}/Scripts/executable/\@mode\@/\@tar\@-\@OSTYPE\@.in") - -unset(GDB) -unset(GDB_FLAGS) -set(INSTALL_SYMLINK_FILE "${TEMP_DIR}/setup-symlinks.sh") -file(WRITE ${INSTALL_SYMLINK_FILE} "${locate_script}\n\necho $DIR\n\n") -dev_message("SV_SCRIPT_TARGETS: ${SV_SCRIPT_TARGETS}") -foreach(tar ${SV_SCRIPT_TARGETS}) - simvascular_configure_script( - TARGET "${tar}" - FILES ${SCRIPT_FILES} - INSTALL - ) - if(WIN32 AND NOT CYGWIN) - message("${tar}") - ADD_CUSTOM_TARGET(${tar}-copy ALL - DEPENDS ${tar} - COMMAND ${CMAKE_COMMAND} -E remove ${OUTBIN_DIR}/$ - COMMAND ${CMAKE_COMMAND} -E copy $ ${OUTBIN_DIR} - COMMENT "Copying ${tar} to ${OUTBIN_DIR}" - ) - endif() - if(UNIX) - file(APPEND ${INSTALL_SYMLINK_FILE} "rm -f /usr/local/bin/${${tar}_INSTALL_SCRIPT_NAME}${WIN_BAT}\n") - file(APPEND ${INSTALL_SYMLINK_FILE} "ln -s $DIR/${${tar}_INSTALL_SCRIPT_NAME}${WIN_BAT} /usr/local/bin/${${tar}_INSTALL_SCRIPT_NAME}${WIN_BAT}\n") - #file(APPEND ${INSTALL_SYMLINK_FILE} "chmod a+x /usr/local/bin/${${tar}_INSTALL_SCRIPT_NAME}${WIN_BAT}\n") - endif() -endforeach() -if(UNIX) - install(PROGRAMS ${INSTALL_SYMLINK_FILE} DESTINATION ${SV_INSTALL_SCRIPT_DIR}) - install(FILES "README-install" DESTINATION ${SV_INSTALL_SCRIPT_DIR}) - #install(CODE "execute_process(COMMAND \"${INSTALL_SYMLINK_FILE}\"")") -endif() -if(BUILD_TESTING) - configure_file(executable_names.tcl.in ${SV_TEST_DIR}/common/executable_names.tcl) -endif() diff --git a/Code/Scripts/README-install b/Code/Scripts/README-install deleted file mode 100644 index 360a4c50..00000000 --- a/Code/Scripts/README-install +++ /dev/null @@ -1,26 +0,0 @@ -You may need to install libxss, mpich2, or libgfortran. -If you're on linux these may work: - -sudo apt-get install libxss -sudo apt-get install mpich2 -sudo apt-get install gfortran - --------- - -To use Meshim on linux copy your license file into the simvascular directory and rename it meshsim-license.dat - --------- - -To add SimVascular to your path (this is very helpful with using svsolver), you will need to run the post-install script: - -sudo bash setup-symlinks.sh - -This script places symbolic links in /usr/local/bin to the simvascular executable scripts. -You may wish to edit the symbolic links. - -Note that the solver can be run with mpiexec. -For example to run on two processors: -cd /folder/with/input -mpiexec -np 2 svsolver - --- \ No newline at end of file diff --git a/Code/Scripts/README-postinstall b/Code/Scripts/README-postinstall deleted file mode 100644 index 5c288542..00000000 --- a/Code/Scripts/README-postinstall +++ /dev/null @@ -1,3 +0,0 @@ - -To add SimVascular to your path, you will need to run the post-install script. -This script places symbolic links in /usr/local/bin to the simvascular executables. \ No newline at end of file diff --git a/Code/Scripts/SimVascularScriptMacros.cmake b/Code/Scripts/SimVascularScriptMacros.cmake deleted file mode 100644 index 0d7b5727..00000000 --- a/Code/Scripts/SimVascularScriptMacros.cmake +++ /dev/null @@ -1,151 +0,0 @@ -# Copyright (c) 2014-2015 The Regents of the University of California. -# All Rights Reserved. -# -# Permission is hereby granted, free of charge, to any person obtaining -# a copy of this software and associated documentation files (the -# "Software"), to deal in the Software without restriction, including -# without limitation the rights to use, copy, modify, merge, publish, -# distribute, sublicense, and/or sell copies of the Software, and to -# permit persons to whom the Software is furnished to do so, subject -# to the following conditions: -# -# The above copyright notice and this permission notice shall be included -# in all copies or substantial portions of the Software. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS -# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED -# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A -# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER -# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -include (CMakeParseArguments) - -if(WIN32) - set(ENV_SET_COMMAND "set") - set(ENV_PATH_VARIABLE "PATH") - set(ENV_LIBRARY_PATH_VARIABLE "PATH") - set(ENV_SEPERATOR ";") - set(DIR_SEPERATOR "\\") - set(COMMENT_CHAR "rem") -endif() - -if(UNIX) - set(ENV_SET_COMMAND "export") - set(ENV_PATH_VARIABLE "PATH") - set(ENV_SEPERATOR ":") - set(DIR_SEPERATOR "/") - set(COMMENT_CHAR "#") - if(APPLE) - set(ENV_LIBRARY_PATH_VARIABLE "DYLD_LIBRARY_PATH") - set(DYLD "DYLD") - endif() - if(UNIX AND NOT APPLE) - set(ENV_LIBRARY_PATH_VARIABLE "LD_LIBRARY_PATH") - set(DYLD "LD") - endif() -endif() - -#----- -# Script Macros -# -macro(simvascular_configure_script) - set(options INSTALL) - set(oneValueArgs TARGET OUTPUT_NAME DESTINATION) - set(multiValueArgs FILES) - - CMAKE_PARSE_ARGUMENTS("" - "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN} ) - message(STATUS "Generating ${_TARGET} scripts. Dev name: ${${_TARGET}_DEVELOPER_SCRIPT_NAME}, install name: ${${_TARGET}_INSTALL_SCRIPT_NAME}") - foreach(MODE DEVELOPER INSTALL) - - string(TOLOWER ${MODE} mode) - dev_message("mode: ${MODE} ${mode}") - if(MODE MATCHES "^INSTALL$") - set(RELEASE_MODE 1) - else() - set(RELEASE_MODE 0) - endif() - - set(sc ";") - set(ACCUM_SCRIPT_STRING) - set(TEMP_SCRIPT) - string(CONFIGURE "${SCRIPT_FILES}" ${MODE}_FILES @ONLY) - dev_message("${SCRIPT_FILES} \n ${${MODE}_FILES}") - foreach(file ${${MODE}_FILES}) - dev_message(" Processing file: ${file}") - file(READ ${file} TEMP_SCRIPT) - STRING(REGEX REPLACE ";" "\@sc\@" TEMP_SCRIPT "${TEMP_SCRIPT}") - set(ACCUM_SCRIPT_STRING "${ACCUM_SCRIPT_STRING}${TEMP_SCRIPT}\n") - endforeach() - string(CONFIGURE ${ACCUM_SCRIPT_STRING} SCRIPT_STRING @ONLY) - - FILE(WRITE "${TEMP_DIR}/${mode}/${${_TARGET}_${MODE}_SCRIPT_NAME}${WIN_BAT}" - "${SCRIPT_STRING}") - - endforeach() - - file(REMOVE "${SV_DEVELOPER_SCRIPT_DIR}/${${_TARGET}_DEVELOPER_SCRIPT_NAME}${WIN_BAT}") - file(COPY "${TEMP_DIR}/developer/${${_TARGET}_DEVELOPER_SCRIPT_NAME}${WIN_BAT}" - DESTINATION ${SV_DEVELOPER_SCRIPT_DIR} - FILE_PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ - GROUP_EXECUTE WORLD_READ WORLD_EXECUTE) - - #add_custom_target(CopyScriptDev-${_TARGET} ALL - # COMMAND ${CMAKE_COMMAND} -E rename - # ${SV_DEVELOPER_SCRIPT_DIR}/${${_TARGET}_DEVELOPER_SCRIPT_NAME}${WIN_BAT}-config ${SV_DEVELOPER_SCRIPT_DIR}/${${_TARGET}_DEVELOPER_SCRIPT_NAME}${WIN_BAT}) - - #add_custom_target(CopyScriptInstall-${_TARGET} ALL - # COMMAND ${CMAKE_COMMAND} -E rename - # ${TEMP_DIR}/install/${${_TARGET}_INSTALL_SCRIPT_NAME}${WIN_BAT}-config ${TEMP_DIR}/install/${${_TARGET}_INSTALL_SCRIPT_NAME}${WIN_BAT}) - - if(_INSTALL) - install(FILES ${TEMP_DIR}/install/${${_TARGET}_INSTALL_SCRIPT_NAME}${WIN_BAT} - DESTINATION ${SV_INSTALL_SCRIPT_DIR} - PERMISSIONS - OWNER_READ OWNER_WRITE OWNER_EXECUTE - GROUP_READ GROUP_EXECUTE - WORLD_READ WORLD_EXECUTE - COMPONENT ExecutableScripts - ) - endif() - -endmacro() - - -macro(env_variable_to_value_variable value_variable variable) - if(WIN32 AND NOT UNIX) - set(${value_variable} "%${variable}%") - endif() - if(UNIX) - set(${value_variable} "$${variable}") - endif() -endmacro() - -function(append_env_string evn_var value output_variable) - env_variable_to_value_variable(ENV_VALUE ${evn_var}) - set(${output_variable} "${ENV_SET_COMMAND} ${evn_var}=${ENV_VALUE}${ENV_SEPERATOR}${value}" PARENT_SCOPE) -endfunction() - -function(set_env_string evn_var value output_variable) - set(${output_variable} "${ENV_SET_COMMAND} ${evn_var}=${value}\n" PARENT_SCOPE) -endfunction() - -macro(set_env_string_concat evn_var value output_variable) - set_env_string(${evn_var} ${value} _tmp) - set(${output_variable} "${${output_variable}}${_tmp}") -endmacro() - -macro(append_env_string_concat evn_var value output_variable) - append_env_string(${evn_var} ${value} _tmp) - set(${output_variable} "${${output_variable}}${_tmp}\n") -endmacro() - -macro(comment_concat msg output_variable) - set(${output_variable} "${${output_variable}}${COMMENT_CHAR} ${msg}\n") -endmacro() diff --git a/Code/Scripts/executable/developer/locate-linux-script.in b/Code/Scripts/executable/developer/locate-linux-script.in deleted file mode 100644 index 72cf5eb5..00000000 --- a/Code/Scripts/executable/developer/locate-linux-script.in +++ /dev/null @@ -1,12 +0,0 @@ -SOURCE="${BASH_SOURCE[0]}" -while [ -h "$SOURCE" ]; do # resolve $SOURCE until the file is no longer a symlink - TARGET="$(readlink "$SOURCE")" - if [[ $SOURCE == /* ]]; then - SOURCE="$TARGET" - else - DIR="$( dirname "$SOURCE" )" - SOURCE="$DIR/$TARGET" # if $SOURCE was a relative symlink, we need to resolve it relative to the path where the symlink file was located - fi -done -RDIR="$( dirname "$SOURCE" )" -DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" diff --git a/Code/Scripts/executable/developer/svFSI-linux.in b/Code/Scripts/executable/developer/svFSI-linux.in deleted file mode 100644 index 19258165..00000000 --- a/Code/Scripts/executable/developer/svFSI-linux.in +++ /dev/null @@ -1 +0,0 @@ -$SV_HOME/bin/@SV_SVFSI_EXE@ $* diff --git a/Code/Scripts/executable/developer/svpost-linux.in b/Code/Scripts/executable/developer/svpost-linux.in deleted file mode 100644 index 0cafc659..00000000 --- a/Code/Scripts/executable/developer/svpost-linux.in +++ /dev/null @@ -1,11 +0,0 @@ - -# run the executable -case "$*" in -"") -$SV_HOME/bin/@SV_POSTSOLVER_EXE@ -;; -*) -$SV_HOME/bin/@SV_POSTSOLVER_EXE@ $* -;; -esac - diff --git a/Code/Scripts/executable/developer/svpost-windows.in b/Code/Scripts/executable/developer/svpost-windows.in deleted file mode 100644 index 4bbb6743..00000000 --- a/Code/Scripts/executable/developer/svpost-windows.in +++ /dev/null @@ -1,2 +0,0 @@ - -"%SV_HOME%\Bin\@SV_POSTSOLVER_EXE@@WIN_EXE@$ * diff --git a/Code/Scripts/executable/developer/svpre-linux.in b/Code/Scripts/executable/developer/svpre-linux.in deleted file mode 100644 index 8ed2639e..00000000 --- a/Code/Scripts/executable/developer/svpre-linux.in +++ /dev/null @@ -1 +0,0 @@ -$SV_HOME/bin/@SV_PRESOLVER_EXE@ $* diff --git a/Code/Scripts/executable/developer/svpre-windows.in b/Code/Scripts/executable/developer/svpre-windows.in deleted file mode 100644 index 129ae6bb..00000000 --- a/Code/Scripts/executable/developer/svpre-windows.in +++ /dev/null @@ -1,3 +0,0 @@ - - -"%SV_HOME%\Bin\@SV_PRESOLVER_EXE@@WIN_EXE@$ * diff --git a/Code/Scripts/executable/developer/svsolver-linux.in b/Code/Scripts/executable/developer/svsolver-linux.in deleted file mode 100644 index 75c07b22..00000000 --- a/Code/Scripts/executable/developer/svsolver-linux.in +++ /dev/null @@ -1,3 +0,0 @@ -export LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ -export FLOWSOLVER_CONFIG=@ENV_SV_HOME@/bin/ -$SV_HOME/bin/@SV_FLOWSOLVER_EXE@ $* diff --git a/Code/Scripts/executable/developer/svsolver-nompi-linux.in b/Code/Scripts/executable/developer/svsolver-nompi-linux.in deleted file mode 100644 index fc928d67..00000000 --- a/Code/Scripts/executable/developer/svsolver-nompi-linux.in +++ /dev/null @@ -1,3 +0,0 @@ -export LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ -export FLOWSOLVER_CONFIG=@ENV_SV_HOME@/Bin/ -$SV_HOME/bin/@SV_FLOWSOLVER_EXE@-nompi $* diff --git a/Code/Scripts/executable/developer/svsolver-nompi-windows.in b/Code/Scripts/executable/developer/svsolver-nompi-windows.in deleted file mode 100644 index 6e2f599f..00000000 --- a/Code/Scripts/executable/developer/svsolver-nompi-windows.in +++ /dev/null @@ -1,4 +0,0 @@ -set LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ -set FLOWSOLVER_CONFIG=@ENV_SV_HOME@\Bin\ - -%SV_HOME%\Bin\@SV_FLOWSOLVER_EXE@-nompi@WIN_EXE@ diff --git a/Code/Scripts/executable/developer/svsolver-windows.in b/Code/Scripts/executable/developer/svsolver-windows.in deleted file mode 100644 index 9fc7ad4e..00000000 --- a/Code/Scripts/executable/developer/svsolver-windows.in +++ /dev/null @@ -1,4 +0,0 @@ -set LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ -set FLOWSOLVER_CONFIG=@ENV_SV_HOME@\Bin\ - -"@MPIEXEC@" -np %1 "%SV_HOME%\Bin\@SV_FLOWSOLVER_EXE@@WIN_EXE@" %2 %3 %4 diff --git a/Code/Scripts/executable/install/svFSI-linux.in b/Code/Scripts/executable/install/svFSI-linux.in deleted file mode 100644 index e2131f5a..00000000 --- a/Code/Scripts/executable/install/svFSI-linux.in +++ /dev/null @@ -1 +0,0 @@ -$SV_HOME/@SV_INSTALL_RUNTIME_DIR@/@SV_SVFSI_EXE@@CMAKE_EXECUTABLE_SUFFIX@ $* diff --git a/Code/Scripts/executable/install/svpost-linux.in b/Code/Scripts/executable/install/svpost-linux.in deleted file mode 100644 index ad33a995..00000000 --- a/Code/Scripts/executable/install/svpost-linux.in +++ /dev/null @@ -1,11 +0,0 @@ - -# run the executable -case "$*" in -"") -$SV_HOME/@SV_INSTALL_RUNTIME_DIR@/@SV_POSTSOLVER_EXE@@CMAKE_EXECUTABLE_SUFFIX@ -;; -*) -$SV_HOME/@SV_INSTALL_RUNTIME_DIR@/@SV_POSTSOLVER_EXE@@CMAKE_EXECUTABLE_SUFFIX@ $* -;; -esac - diff --git a/Code/Scripts/executable/install/svpost-windows.in b/Code/Scripts/executable/install/svpost-windows.in deleted file mode 100644 index 88f0da19..00000000 --- a/Code/Scripts/executable/install/svpost-windows.in +++ /dev/null @@ -1,2 +0,0 @@ - -"%SV_HOME%\@SV_INSTALL_RUNTIME_DIR@\@SV_POSTSOLVER_EXE@@CMAKE_EXECUTABLE_SUFFIX@ * diff --git a/Code/Scripts/executable/install/svpre-linux.in b/Code/Scripts/executable/install/svpre-linux.in deleted file mode 100644 index 31b23450..00000000 --- a/Code/Scripts/executable/install/svpre-linux.in +++ /dev/null @@ -1 +0,0 @@ -$SV_HOME/@SV_INSTALL_RUNTIME_DIR@/@SV_PRESOLVER_EXE@@CMAKE_EXECUTABLE_SUFFIX@ $* diff --git a/Code/Scripts/executable/install/svpre-windows.in b/Code/Scripts/executable/install/svpre-windows.in deleted file mode 100644 index ddb60500..00000000 --- a/Code/Scripts/executable/install/svpre-windows.in +++ /dev/null @@ -1,3 +0,0 @@ - - -"%SV_HOME%\@SV_INSTALL_RUNTIME_DIR@\@SV_PRESOLVER_EXE@@CMAKE_EXECUTABLE_SUFFIX@ $* diff --git a/Code/Scripts/executable/install/svsolver-linux.in b/Code/Scripts/executable/install/svsolver-linux.in deleted file mode 100644 index a21fb800..00000000 --- a/Code/Scripts/executable/install/svsolver-linux.in +++ /dev/null @@ -1,3 +0,0 @@ -export LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ -export FLOWSOLVER_CONFIG=@ENV_SV_HOME@/@SV_INSTALL_RUNTIME_DIR@/ -$SV_HOME/@SV_INSTALL_RUNTIME_DIR@/@SV_FLOWSOLVER_EXE@@CMAKE_EXECUTABLE_SUFFIX@ $* diff --git a/Code/Scripts/executable/install/svsolver-nompi-linux.in b/Code/Scripts/executable/install/svsolver-nompi-linux.in deleted file mode 100644 index 0f924d05..00000000 --- a/Code/Scripts/executable/install/svsolver-nompi-linux.in +++ /dev/null @@ -1,3 +0,0 @@ -export LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ -export FLOWSOLVER_CONFIG=@ENV_SV_HOME@/@SV_INSTALL_RUNTIME_DIR@/ -$SV_HOME/@SV_INSTALL_RUNTIME_DIR@/@SV_FLOWSOLVER_EXE@-nompi@CMAKE_EXECUTABLE_SUFFIX@ $* diff --git a/Code/Scripts/executable/install/svsolver-nompi-windows.in b/Code/Scripts/executable/install/svsolver-nompi-windows.in deleted file mode 100644 index 84c3c6d5..00000000 --- a/Code/Scripts/executable/install/svsolver-nompi-windows.in +++ /dev/null @@ -1,4 +0,0 @@ -set LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ -set FLOWSOLVER_CONFIG=@ENV_SV_HOME@\@SV_INSTALL_RUNTIME_DIR@\ - -%SV_HOME%\@SV_INSTALL_RUNTIME_DIR@\@SV_FLOWSOLVER_EXE@-nompi@CMAKE_EXECUTABLE_SUFFIX@" %2 %3 %4 diff --git a/Code/Scripts/executable/install/svsolver-windows.in b/Code/Scripts/executable/install/svsolver-windows.in deleted file mode 100644 index facc7be7..00000000 --- a/Code/Scripts/executable/install/svsolver-windows.in +++ /dev/null @@ -1,4 +0,0 @@ -set LES_LICENSE_SERVER=@LES_LICENSE_SERVER@ -set FLOWSOLVER_CONFIG=@ENV_SV_HOME@\@SV_INSTALL_RUNTIME_DIR@\ - -%SV_HOME%\mpiexec@CMAKE_EXECUTABLE_SUFFIX@ -np %1 "%SV_HOME%\@SV_INSTALL_RUNTIME_DIR@\@SV_FLOWSOLVER_EXE@@CMAKE_EXECUTABLE_SUFFIX@" %2 %3 %4 diff --git a/Code/Scripts/home-locate-linux.sh b/Code/Scripts/home-locate-linux.sh deleted file mode 100644 index c364dfb2..00000000 --- a/Code/Scripts/home-locate-linux.sh +++ /dev/null @@ -1,39 +0,0 @@ -#!/bin/bash -f -# Copyright (c) 2014-2015 The Regents of the University of California. -# All Rights Reserved. -# -# Permission is hereby granted, free of charge, to any person obtaining -# a copy of this software and associated documentation files (the -# "Software"), to deal in the Software without restriction, including -# without limitation the rights to use, copy, modify, merge, publish, -# distribute, sublicense, and/or sell copies of the Software, and to -# permit persons to whom the Software is furnished to do so, subject -# to the following conditions: -# -# The above copyright notice and this permission notice shall be included -# in all copies or substantial portions of the Software. -# -# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS -# IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED -# TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A -# PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER -# OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, -# EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, -# PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR -# PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF -# LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING -# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -SOURCE="${BASH_SOURCE[0]}" -while [ -h "$SOURCE" ]; do -TARGET="$(readlink "$SOURCE")" - if [[ $SOURCE == /* ]]; then - SOURCE="$TARGET" - else - DIR="$( dirname "$SOURCE" )" - SOURCE="$DIR/$TARGET" - fi -done -RDIR="$( dirname "$SOURCE" )" -DIR="$( cd -P "$( dirname "$SOURCE" )" && pwd )" \ No newline at end of file diff --git a/Code/Source/svFSI/VtkData.cpp b/Code/Source/svFSI/VtkData.cpp index 46acca7e..12075365 100644 --- a/Code/Source/svFSI/VtkData.cpp +++ b/Code/Source/svFSI/VtkData.cpp @@ -32,6 +32,7 @@ #include "Array.h" #include +#include "vtkCellArray.h" #include "vtkCellData.h" #include #include diff --git a/Distribution/CMakeLists.txt b/Distribution/CMakeLists.txt index 9d195aa2..da86ec99 100644 --- a/Distribution/CMakeLists.txt +++ b/Distribution/CMakeLists.txt @@ -19,7 +19,7 @@ endif() #----------------------------------------------------------------------------- # Platform independent options #----------------------------------------------------------------------------- -set(CPACK_PACKAGE_NAME "svFSI") +set(CPACK_PACKAGE_NAME "svFSIplus") set(CPACK_PACKAGE_VENDOR "SimVascular.org") set(CPACK_PACKAGE_CONTACT "SimVascular") set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "SimVascular Solvers") @@ -35,7 +35,7 @@ string(REPLACE "." "-" SV_INSTALL_VERSION_DIR ${SV_FULL_VERSION}) #----------------------------------------------------------------------------- if(WIN32) # Package name - set(CPACK_PACKAGE_FILE_NAME "svFSI-windows-win-x64-${SV_FULL_VERSION}${INSTALL_TYPE_STR}") + set(CPACK_PACKAGE_FILE_NAME "svFSIplus-windows-win-x64-${SV_FULL_VERSION}${INSTALL_TYPE_STR}") # MPI dlls find_path(INTEL_REDIST_DIR names fmpich2.dll PATHS $ENV{PATH}) @@ -65,10 +65,10 @@ if(WIN32) set(CPACK_WIX_PROGRAM_MENU_FOLDER "SimVascular") set(CPACK_WIX_PRODUCT_GUID "39068F8A-D4E9-405F-B22B-9B417849AEE6") set(CPACK_WIX_UPGRADE_GUID "2359EF69-C03F-401C-9BC3-C19B10297E3B") - set(PACKAGE_NAME "svFSI") + set(PACKAGE_NAME "svFSIplus") elseif(SV_RELEASE_TYPE MATCHES "Beta") set(CPACK_WIX_PROGRAM_MENU_FOLDER "SimVascular-Beta") - set(PACKAGE_NAME "svFSI-beta") + set(PACKAGE_NAME "svFSIplus-beta") set(CPACK_PACKAGE_INSTALL_DIRECTORY "SimVascular/${TIMESTAMP}") set(CPACK_WIX_PRODUCT_GUID "9453BB7E-CD7E-46ED-AA9E-5514B56FC901") set(CPACK_WIX_UPGRADE_GUID "39C845FF-68E1-4AA7-B329-3407B47B3361") @@ -85,11 +85,11 @@ endif() #----------------------------------------------------------------------------- if(LINUX) # Package name - set(CPACK_PACKAGE_FILE_NAME "svFSI-linux-x64-${SV_FULL_VERSION}${INSTALL_TYPE_STR}") + set(CPACK_PACKAGE_FILE_NAME "svFSIplus-linux-x64-${SV_FULL_VERSION}${INSTALL_TYPE_STR}") if(SV_INSTALLER_TYPE STREQUAL DEB) set(CPACK_GENERATOR "DEB") - set(CPACK_PACKAGING_INSTALL_PREFIX "/usr/local/sv/svFSI/${SV_INSTALL_VERSION_DIR}") + set(CPACK_PACKAGING_INSTALL_PREFIX "/usr/local/sv/svFSIplus/${SV_INSTALL_VERSION_DIR}") elseif(SV_INSTALLER_TYPE STREQUAL TGZ) set(CPACK_GENERATOR "TGZ") set(CPACK_INCLUDE_TOPLEVEL_DIRECTORY ON) @@ -101,12 +101,10 @@ endif() #----------------------------------------------------------------------------- if(APPLE) # Package name - set(CPACK_PACKAGE_FILE_NAME "svFSI-darwin-x64-${SV_FULL_VERSION}${INSTALL_TYPE_STR}") + set(CPACK_PACKAGE_FILE_NAME "svFSIplus-darwin-x64-${SV_FULL_VERSION}${INSTALL_TYPE_STR}") - # Components - set(CPACK_COMPONENTS_ALL CoreExecutables CoreLibraries CoreHeaders - ThirdPartyLibraries ThirdPartyHeaders MPIExecutables MPILibraries - ExecutableScripts) + # Components. Just install the svFSIplus executable. + set(CPACK_COMPONENTS_ALL CoreExecutables) # Cpack install help set(CPACK_GENERATOR "productbuild") @@ -114,7 +112,7 @@ if(APPLE) # ${CMAKE_CURRENT_BINARY_DIR}/OSX/Info.plist @ONLY) # Install location - set(CPACK_PACKAGING_INSTALL_PREFIX "/usr/local/sv/svFSI/${SV_INSTALL_VERSION_DIR}") + set(CPACK_PACKAGING_INSTALL_PREFIX "/usr/local/sv/svFSIplus/${SV_INSTALL_VERSION_DIR}") endif() if(CPACK_PACKAGE_FILENAME_TAG) diff --git a/tests/conftest.py b/tests/conftest.py index d99e5ee9..107a285e 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -11,8 +11,8 @@ if platform.system() == "Darwin": is_not_Darwin = False this_file_dir = os.path.abspath(os.path.dirname(__file__)) -cpp_exec = os.path.join(this_file_dir, "..", "build", "svFSI-build", "bin", "svFSI") -cpp_exec_p = os.path.join(this_file_dir, "..", "build-petsc", "svFSI-build", "bin", "svFSI") +cpp_exec = os.path.join(this_file_dir, "..", "build", "svFSIplus-build", "bin", "svfsiplus") +cpp_exec_p = os.path.join(this_file_dir, "..", "build-petsc", "svFSIplus-build", "bin", "svfsiplus") # Relative tolerances for each tested field RTOL = {