Porting biodynamo to other linux platforms and others

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 +542,7 @@ _source_thisbdm()
   # OpenMP
   export OMP_PROC_BIND=true
 
+
   ###### Platform-specific Configuration
   # Apple specific
   if [ "$(uname)" = 'Darwin' ]; then
@@ -553,21 +554,89 @@ _source_thisbdm()
     os_id=$(grep -oP '(?<=^ID=).+' /etc/os-release | tr -d '"') || return 1
     if [ "$os_id" = 'centos' ]; then
         export MESA_GL_VERSION_OVERRIDE=3.3
-        if [ -z "${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 "$PROCVERSION" | grep -Eiq 'Red Hat' ; then
+     	. scl_source enable gcc-toolset-10 > /dev/null 2> /dev/null  || true
+  	. scl_source enable devtoolset-10  > /dev/null 2> /dev/null  || true
+  	. scl_source enable gcc-toolset-11 > /dev/null 2> /dev/null  || true
+  	. scl_source enable devtoolset-11  > /dev/null 2> /dev/null  || true
+        . /etc/profile.d/modules.sh || return 1
+     	module load mpi || return 1
+     fi
+  fi
+
+  #Select (export) the correct compiler version
+  GCC_VER=$(gcc --version | grep gcc)
+  if [ -n "${GCC_VER}" ]; then
+  	read -ra tokens <<< $GCC_VER
+  	result=()
+  	current_token=""
+	for token in "${tokens[@]}"; do
+	    if [[ -n $current_token ]]; then 
+			current_token+=" $token"
+		if [[ $current_token == *')' ]]; then
+			result+=("$current_token")
+			current_token=""
+		fi
+	    else
+		if [[ $token == '('* && $token != *')' ]]; then
+			current_token="$token"
+                else
+			result+=("$token")
+		fi
+	   fi
+	done 
+        if [[ -n $current_token ]]; then
+		result+=("$current_token")
+	fi 
+        GCC_VER=${result[2]}
+        GCC_VER=$( echo $GCC_VER | cut -d '.' -f 1-2)
+  fi
+
+  if [ -z "${GCC_VER}" ] || [ `echo "$GCC_VER >= 12" | bc -q` -ne 0 ]  ||  [ `echo "$GCC_VER < 9" | bc -q` -ne 0 ]; 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
+      export QMAKE_CC=gcc-11
+      export QMAKE_CXX=g++-11
+      export LINK=g++-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=$BDMSYS/third_party/gcc/bin/gfortran
+      export QMAKE_CC=$BDM_PROJECT_DIR_2/third_party/gcc/bin/gcc
+      export QMAKE_CXX=$BDM_PROJECT_DIR_2/third_party/gcc/bin/g++
+      export LINK=$BDM_PROJECT_DIR_2/third_party/gcc/bin/g++
+
+    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 +694,9 @@ _source_thisbdm()
     esac
   fi
 
+
+
+
   return 0
 }