This commit includes several changes:

1) Porting biodynamo to other linux platforms like all red hat and debian based distros with the option of compiling requirements like root qt abnd paraview (changes included on the cmakelists file, the corresponding root, qt and paraview cmake files as well as scripts included on the /util/build-third-party directory as well as changes in the util.sh file that performs the detection of the new operating systems with the DetectOs2 function) as well as requirements scripts and files that cover a wide range of redhat based and debian based distros
2) Because gcc versions older than 8 and newer than 11 can cause installation and project running problems (especially with the case of omp.h) we also provide gcc 11.5.0
3) The option of installing nest with biodynamo (provided via a cmake option (-Dnest) and build via build-nest_new.sh located on the util/build-third-party directory)
4) Fixing sbml support on mac os by compiling libroadrunner via a script located in util/build-third-party directory
5) Also experimental suse linux support (root does not compile due to a bug)

Possible bugs:
Sometimes after the compilation of paraview, biodynamo fails to compile.
In this case just rerun the installation.

*Note* In order to prevent the recompilation of any requirement due to a failure that may occur later on the installation reuirements are installed in the biodynamo(src)/third-party directory and then copied into the appriopriate build and installation directory

Author: johnpapad24

CMakeLists.txt

@@ -13,7 +13,6 @@
 # -----------------------------------------------------------------------------
 
 cmake_minimum_required(VERSION 3.19.3 FATAL_ERROR)
-
 set(policy_new CMP0072 CMP0077)
 foreach(policy ${policy_new})
   if(POLICY ${policy})
@@ -98,6 +97,7 @@ set(CMAKE_INSTALL_DATADIR       "${CMAKE_INSTALL_ROOT}/share")
 set(CMAKE_INSTALL_CMAKEDATADIR  "${CMAKE_INSTALL_DATADIR}/cmake")
 set(CMAKE_INSTALL_THIRDPARTY    "${CMAKE_INSTALL_ROOT}")
 
+
 # It is used by format/style checks. It needs to be defined here such
 # to enable relocation of the scripts.
 set(BUILD_SUPPORT_DIR "${CMAKE_SOURCE_DIR}/util/housekeeping")
@@ -137,8 +137,14 @@ option(jemalloc  "Use jemalloc for memory allocations." OFF)
 option(website   "Enable website generation (make website<-live>)." OFF)
 option(valgrind  "Enable valgrind tests and make build compatible with valgrind tool." ON)
 option(rpath     "Link libraries with built-in RPATH (run-time search path)." OFF)
+option(nest	 "Install The Neural Simulation Tool (NEST) for spiking neural network models." ON) 
 option(real_t    "Define data type for real numbers. Currently supported: float, double" double)
 
+if(EXISTS "${CMAKE_SOURCE_DIR}/third_party/gcc")
+    	file(COPY "${CMAKE_SOURCE_DIR}/third_party/gcc" DESTINATION "${CMAKE_SOURCE_DIR}/build/third_party")
+endif()
+
+
 if(APPLE)
   # ParaView on Apple devices
   set(CMAKE_BDM_PVVERSION "5.10")
@@ -416,7 +422,15 @@ endif()
 
 if(sbml)
   if(APPLE)
-    message(FATAL_ERROR "Currently SBML is not supported on MacOS (see https://trello.com/c/vKPbh4iG).")
+  	SET(LLRR_BLD_SCRIPT_LOCATION "${CMAKE_SOURCE_DIR}/util/build-third-party")
+    	if(EXISTS "${CMAKE_SOURCE_DIR}/third_party/install_roadrunner")
+		file(COPY "${CMAKE_SOURCE_DIR}/third_party/install_roadrunner" DESTINATION "${CMAKE_SOURCE_DIR}/build/third_party")
+	else()
+		execute_process(COMMAND bash ${LLRR_BLD_SCRIPT_LOCATION}/build-roadrunner_new.sh ${CMAKE_SOURCE_DIR} RESULT_VARIABLE LLRR_DOWNLOAD_OR_BUILD)
+		file(COPY "${CMAKE_SOURCE_DIR}/third_party/install_roadrunner" DESTINATION "${CMAKE_SOURCE_DIR}/build/third_party")
+	endif()
+	find_package(Libroadrunner)
+        #message(FATAL_ERROR "Currently SBML is not supported on MacOS (see https://trello.com/c/vKPbh4iG).")
   endif()
   find_package(Libroadrunner)
   if(NOT Libroadrunner_FOUND)
@@ -425,6 +439,16 @@ if(sbml)
   endif()
 endif()
 
+if(nest)
+  if(EXISTS "${CMAKE_SOURCE_DIR}/third_party/nest")
+    	file(COPY "${CMAKE_SOURCE_DIR}/third_party/nest" DESTINATION "${CMAKE_SOURCE_DIR}/build/third_party")
+  else()
+        SET(NEST_BLD_SCRIPT_LOCATION "${CMAKE_SOURCE_DIR}/util/build-third-party")
+        execute_process(COMMAND bash ${NEST_BLD_SCRIPT_LOCATION}/build-nest_new.sh ${CMAKE_SOURCE_DIR} RESULT_VARIABLE NEST_DOWNLOAD_OR_BUILD) 
+        file(COPY "${CMAKE_SOURCE_DIR}/third_party/nest" DESTINATION "${CMAKE_SOURCE_DIR}/build/third_party")
+  endif()
+endif()
+
 # Load libgit2 if it is enabled
 if (libgit2)
     include(external/Libgit2)

cmake/FindROOT.cmake

@@ -16,9 +16,16 @@
 # Updated by K. Smith (ksmith37@nd.edu) to properly handle
 #  dependencies in ROOT_GENERATE_DICTIONARY
 
+if(NOT DEFINED ENV{ROOTSYS})
+SET(ENV{ROOTSYS} "${CMAKE_SOURCE_DIR}/third_party/root")
+elseif("$ENV{ROOTSYS}" STREQUAL "")
+SET(ENV{ROOTSYS} "${CMAKE_SOURCE_DIR}/third_party/root")
+endif()
+
 find_program(ROOT_CONFIG_EXECUTABLE NAMES root-config
   HINTS "$ENV{ROOTSYS}/bin" "$ENV{BDM_ROOT_DIR}/bin" "${CMAKE_THIRD_PARTY_DIR}/root/bin")
-
+  
+  
 execute_process(
     COMMAND ${ROOT_CONFIG_EXECUTABLE} --prefix
     OUTPUT_VARIABLE ROOTSYS

cmake/env/thisbdm.fish

@@ -101,7 +101,7 @@ function source_thisbdm
 
     set -l curr_filename (status --current-filename)
     set -gx BDMSYS (fish -c "cd (dirname $curr_filename)/..; and pwd"); or return 1
-    
+
     if test -n "$old_bdmsys"; and test "$old_bdmsys" != "$BDMSYS"
         _bdm_warn "[WARN] You've already sourced another 'thisbdm' in your current shell session."
         _bdm_warn "       -> prev. installation='$old_bdmsys'"
@@ -252,7 +252,7 @@ function source_thisbdm
         end
 
         pyenv init --path $PYENV_NO_REHASH | source; or return 1
-        pyenv init - $PYENV_NO_REHASH | source; or return 1        
+        pyenv init - $PYENV_NO_REHASH | source; or return 1
         pyenv shell @pythonvers@; or return 1
 
         # Location of jupyter executable (installed with `pip install` command)
@@ -269,7 +269,7 @@ function source_thisbdm
     end
     ########
 
-    #### ROOT Specific Configurations ####    
+    #### ROOT Specific Configurations ####
     if test -z "$BDM_CUSTOM_ROOT"
         if test -z "$ROOTSYS"
             set -gx BDM_CUSTOM_ROOT false
@@ -278,7 +278,7 @@ function source_thisbdm
         end
     end
 
-    if  begin; 
+    if  begin;
             test -z "$BDM_ROOT_DIR"; and test -z "$ROOTSYS";
         end; or test "$BDM_CUSTOM_ROOT" = false
         set -gx BDM_ROOT_DIR "$BDMSYS/third_party/root"
@@ -322,13 +322,13 @@ function source_thisbdm
                 set -gx BDM_CUSTOM_PV true
             end
         end
-    
+
         if test "$BDM_CUSTOM_PV" = false; or test -z "$ParaView_DIR"
             set -gx ParaView_DIR "$BDMSYS/third_party/paraview"
         else
             _bdm_info "[INFO] Custom ParaView 'ParaView_DIR=$ParaView_DIR'"
         end
-     
+
         if not test -d "$ParaView_DIR"
             _bdm_err "[ERR] We are unable to find ParaView! Please make sure it is installed"
             _bdm_err "      on your system! You can manually specify its location by executing"
@@ -377,7 +377,7 @@ function source_thisbdm
                 set -gx BDM_CUSTOM_QT true
             end
         end
-        
+
         if test "$BDM_CUSTOM_QT" = false; or test -z "$Qt5_DIR"
             set -gx Qt5_DIR "$BDMSYS/third_party/qt"
         else
@@ -415,6 +415,26 @@ function source_thisbdm
     # OpenMP
     set -gx OMP_PROC_BIND true
 
+
+    #Select (export) the correct compiler version
+    if test (echo "$GCC_VER >= 12" | bc -q) -eq 1 || test (echo "$GCC_VER < 8" | bc -q) -eq 1
+      if command -q gcc-11 && command -q g++-11 && command -q gfortran-11
+          set -gx CC gcc-11
+          set -gx CXX g++-11
+          set -gx FC gfortran-11
+          set -gx OMPI_CC gcc-11
+          set -gx OMPI_CXX g++-11
+          set -gx OMPI_FC gfortran-11
+      else if test -d "$BDMSYS/third_party/gcc"
+          set -gx CC "$BDMSYS/third_party/gcc/bin/gcc"
+          set -gx CXX "$BDMSYS/third_party/gcc/bin/g++"
+          set -gx FC "$BDMSYS/third_party/gcc/bin/gfortran"
+          set -gx OMPI_CC "$BDMSYS/third_party/gcc/bin/gcc"
+          set -gx OMPI_CXX "$BDMSYS/third_party/gcc/bin/g++"
+          set -gx OMPI_FC "$BDMSYS/third_party/gcc/bin/gfortran"
+      end
+    end
+
     ###### Platform-specific Configuration
     # Apple specific
     if test (uname) = 'Darwin'
@@ -429,15 +449,21 @@ function source_thisbdm
                 . scl_source enable devtoolset-10; or return 1
             end
 
-            . /etc/profile.d/modules.sh; or return 1
-            module load mpi; or return 1
-
             # load llvm 6 required for libroadrunner
             if test -d "$BDMSYS"/third_party/libroadrunner
                 . scl_source enable llvm-toolset-7; or return 1
             end
         end
     end
+
+    #LOAD MPI SUPPORT MODULE FOR ALL RHEL DISTROS
+    if test (uname) = "Linux"
+    	set PROCVERSION (cat /proc/version)
+    	if string match -iq '*Red Hat*' -- $PROCVERSION
+        	source /etc/profile.d/modules.sh; or return 1
+        	module load mpi; or return 1
+    	end
+    end
     #######
 
     ### Enable commands in child shells (like in bash) ###

cmake/env/thisbdm.sh

@@ -109,7 +109,7 @@ _source_thisbdm()
     # silent->quiet
     export BDM_THISBDM_LOGLEVEL=0 # disable everything
   fi
-  
+
   if [ "$BDM_THISBDM_LOGLEVEL" -le 2 ]; then
     export BDM_THISBDM_NOPROMPT=true
   else
@@ -135,7 +135,7 @@ _source_thisbdm()
     return 1
   fi
   ########
-  
+
   local old_bdmsys
   if [ -n "${BDMSYS}" ]; then
      old_bdmsys=${BDMSYS}
@@ -232,7 +232,7 @@ _source_thisbdm()
         LD_LIBRARY_PATH=$_newpath
       fi
     fi
-  fi    
+  fi
 
   # If we run on macOS, we add the following exports for libomp support
   if [ "$(uname)" = "Darwin" ]; then
@@ -542,6 +542,33 @@ _source_thisbdm()
   # OpenMP
   export OMP_PROC_BIND=true
 
+  #Select (export) the correct compiler version
+  GCC_VER=$(gcc --version | grep gcc | awk '{print $NF}' | cut -d '.' -f 1-2)
+
+  if (echo "$GCC_VER >= 12" | bc -q > /dev/null)  ||  (echo "$GCC_VER < 8" | bc -q > /dev/null); then
+
+
+    if  $(command -v gcc-11 > /dev/null)  &&  $(command -v g++-11 > /dev/null)  &&  $(command -v gfortran-11 > /dev/null); then
+
+      export CC=gcc-11
+      export CXX=g++-11
+      export FC=gfortran-11
+      export OMPI_CC=gcc-11
+      export OMPI_CXX=g++-11
+      export OMPI_FC=gfortran-11
+
+    elif [ -d $BDMSYS/third_party/gcc ]; then
+
+      export CC=$BDMSYS/third_party/gcc/bin/gcc
+      export CXX=$BDMSYS/third_party/gcc/bin/g++
+      export FC=$BDMSYS/third_party/gcc/bin/gfortran
+      export OMPI_CC=$BDMSYS/third_party/gcc/bin/gcc
+      export OMPI_CXX=$BDMSYS/third_party/gcc/bin/g++
+      export OMPI_FC=$BDMSYS/third_party/gcc/bin/gfortran
+
+    fi
+  fi
+
   ###### Platform-specific Configuration
   # Apple specific
   if [ "$(uname)" = 'Darwin' ]; then
@@ -556,18 +583,27 @@ _source_thisbdm()
         if [ -z "${CXX}" ] && [ -z "${CC}" ] ; then
             . scl_source enable devtoolset-10 || return 1
         fi
-        . /etc/profile.d/modules.sh || return 1
-        module load mpi || return 1
 
         # load llvm 6 required for libroadrunner
         if [ -d "${BDMSYS}"/third_party/libroadrunner ]; then
           . scl_source enable llvm-toolset-7 || return 1
         fi
     fi
   fi
+
+  #LOAD MPI SUPPORT MODULE FOR ALL RHEL DISTROS
+  if [ "$(uname)" = "Linux" ]; then
+     # linux
+     PROCVERSION=$(cat /proc/version)
+     if echo "$PROCVERSION" | grep -Eiq 'Red Hat' ; then
+        . /etc/profile.d/modules.sh || return 1
+     	module load mpi || return 1
+     fi
+  fi
+
   #######
 
-  # completions for bash: really primitive (but useful nonetheless) 
+  # completions for bash: really primitive (but useful nonetheless)
   if [ -n "$BASH_VERSION" ]; then
     complete -W "new build clean run demo" biodynamo
   fi
@@ -625,6 +661,9 @@ _source_thisbdm()
     esac
   fi
 
+
+
+
   return 0
 }
 

cmake/external/ParaView.cmake

@@ -1,26 +1,48 @@
 include(utils)
 
 SET(PARAVIEW_SOURCE_DIR "${CMAKE_THIRD_PARTY_DIR}/paraview")
+SET(PARAVIEW_BLD_SCRIPT_LOCATION "${CMAKE_SOURCE_DIR}/util/build-third-party")
 
-if(APPLE AND "${DETECTED_ARCH}" STREQUAL "i386")
-  # The release of cmake 3.23.0 broke our build of ParaView on MacOSX. 
-  # The build was fixed with a reupload and carries the additional tag cm233.
-  SET(PARAVIEW_TAR_FILE paraview_v5.10.0_cm323_${DETECTED_OS_VERS}_default.tar.gz)
-elseif(APPLE AND "${DETECTED_ARCH}" STREQUAL "arm64")
-  SET(PARAVIEW_TAR_FILE paraview_v5.10.0_${DETECTED_OS_VERS}_default.tar.gz)
-else()
-  SET(PARAVIEW_TAR_FILE paraview_v5.9.0_${DETECTED_OS_VERS}_default.tar.gz)
+if(NOT EXISTS "${CMAKE_SOURCE_DIR}/build/third_party")
+		file(MAKE_DIRECTORY "${CMAKE_SOURCE_DIR}/build/third_party")
 endif()
-set(PARAVIEW_SHA_KEY ${DETECTED_OS_VERS}-ParaView)
-set(PARAVIEW_SHA ${${PARAVIEW_SHA_KEY}})
 
-message(STATUS "Using  ParaView tarball    : ${PARAVIEW_TAR_FILE}")
-message(STATUS "Using  ParaView source dir : ${PARAVIEW_SOURCE_DIR}")
-message(STATUS "Using  ParaView SHA key    : ${PARAVIEW_SHA_KEY}")
-message(STATUS "Verify ParaView SHA        : ${PARAVIEW_SHA}")
+if(EXISTS "${CMAKE_SOURCE_DIR}/third_party/paraview")
+			file(COPY "${CMAKE_SOURCE_DIR}/third_party/paraview" DESTINATION "${CMAKE_SOURCE_DIR}/build/third_party")
+			#set(CMAKE_BDM_PVVERSION "5.11")
+
+else()
+	execute_process(COMMAND bash ${PARAVIEW_BLD_SCRIPT_LOCATION}/build-paraview_new.sh ${CMAKE_SOURCE_DIR} RESULT_VARIABLE PARAVIEW_DOWNLOAD_OR_BUILD)
+	if(${PARAVIEW_DOWNLOAD_OR_BUILD} EQUAL 1)
+		if(APPLE AND "${DETECTED_ARCH}" STREQUAL "i386")
+  		# The release of cmake 3.23.0 broke our build of ParaView on MacOSX. 
+  		# The build was fixed with a reupload and carries the additional tag cm233.
+  			SET(PARAVIEW_TAR_FILE paraview_v5.10.0_cm323_${DETECTED_OS_VERS}_default.tar.gz)
+		elseif(APPLE AND "${DETECTED_ARCH}" STREQUAL "arm64")
+  			SET(PARAVIEW_TAR_FILE paraview_v5.10.0_${DETECTED_OS_VERS}_default.tar.gz)
+		else()
+  			SET(PARAVIEW_TAR_FILE paraview_v5.9.0_${DETECTED_OS_VERS}_default.tar.gz)
+		endif()
+		set(PARAVIEW_SHA_KEY ${DETECTED_OS_VERS}-ParaView)
+		set(PARAVIEW_SHA ${${PARAVIEW_SHA_KEY}})
+
+		message(STATUS "Using  ParaView tarball    : ${PARAVIEW_TAR_FILE}")
+		message(STATUS "Using  ParaView source dir : ${PARAVIEW_SOURCE_DIR}")
+		message(STATUS "Using  ParaView SHA key    : ${PARAVIEW_SHA_KEY}")
+		message(STATUS "Verify ParaView SHA        : ${PARAVIEW_SHA}")
+
+		download_verify_extract(
+  		http://cern.ch/biodynamo-lfs/third-party/${PARAVIEW_TAR_FILE}
+  		${PARAVIEW_SOURCE_DIR}
+  		${PARAVIEW_SHA}
+		)
 
-download_verify_extract(
-  http://cern.ch/biodynamo-lfs/third-party/${PARAVIEW_TAR_FILE}
-  ${PARAVIEW_SOURCE_DIR}
-  ${PARAVIEW_SHA}
-)
+	if(${PARAVIEW_DOWNLOAD_OR_BUILD} EQUAL 0)
+		if(NOT EXISTS "${CMAKE_SOURCE_DIR}/build/third_party")
+			file(MAKE_DIRECTORY "${CMAKE_SOURCE_DIR}/build/third_party")
+		endif()
+			file(COPY "${CMAKE_SOURCE_DIR}/third_party/paraview" DESTINATION "${CMAKE_SOURCE_DIR}/build/third_party")
+			#set(CMAKE_BDM_PVVERSION "5.11")
+		
+	endif()
+endif()