Porting to rhel platforms

cmake/env/thisbdm.fish

@@ -423,11 +423,10 @@ function source_thisbdm
     else # GNU/Linux
         # CentOS specifics (no longer officially supported)
         set -l os_id (grep -oP '(?<=^ID=).+' /etc/os-release | tr -d '"'); or return 1
+        set -l os_proc_id (cat /proc/version); or return 1
         if test "$os_id" = 'centos'
             set -gx MESA_GL_VERSION_OVERRIDE "3.3"
-            if test -z "$CXX"; and test -z "$CC"
-                . scl_source enable devtoolset-10; or return 1
-            end
+
 
             . /etc/profile.d/modules.sh; or return 1
             module load mpi; or return 1
@@ -436,7 +435,18 @@ function source_thisbdm
             if test -d "$BDMSYS"/third_party/libroadrunner
                 . scl_source enable llvm-toolset-7; or return 1
             end
+
         end
+        if string match -iq '*Red Hat*' -- $os_proc_id
+            . scl_source enable gcc-toolset-10 ^ /dev/null ^& /dev/null or true
+            . scl_source enable devtoolset-10 ^ /dev/null ^& /dev/null or true
+            . scl_source enable gcc-toolset-11 ^ /dev/null ^& /dev/null or true
+            . scl_source enable devtoolset-11 ^ /dev/null ^& /dev/null or true
+
+            . /etc/profile.d/modules.sh or return 1
+            module load mpi or return 1
+        end
+
     end
     #######
 

cmake/env/thisbdm.sh

@@ -551,19 +551,26 @@ _source_thisbdm()
     # CentOS specifics (no longer officially supported)
     local os_id
     os_id=$(grep -oP '(?<=^ID=).+' /etc/os-release | tr -d '"') || return 1
+    os_proc_id=$(cat /proc/version) || 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
+    if echo "$os_proc_id" | 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
   #######
 

cmake/utils.cmake

@@ -31,16 +31,32 @@ function(detect_os)
         set(DETECTED_OS_VERS "${BDM_OS}-${MACOS_VERSION}-${MACOS_ARCH}" PARENT_SCOPE)
     else()
         set(GET_OS_ID "echo $(grep -oP '(?<=^ID=).+' /etc/os-release | tr -d '\"')")
+        set(GET_OS_ID_PROC "echo $(cat /proc/version)")
         set(GET_OS_VERSION "echo $(grep -oP '(?<=^VERSION_ID=).+' /etc/os-release | tr -d '\"')")
+
         execute_process(COMMAND bash -c "${GET_OS_ID}"
                         OUTPUT_VARIABLE DISTRO_NAME
                         OUTPUT_STRIP_TRAILING_WHITESPACE)
+        execute_process(COMMAND bash -c "${GET_OS_ID_PROC}"
+                        OUTPUT_VARIABLE DISTRO_NAME_PROC
+                        OUTPUT_STRIP_TRAILING_WHITESPACE)
         execute_process(COMMAND bash -c "${GET_OS_VERSION}"
                         OUTPUT_VARIABLE DISTRO_VERSION
                         OUTPUT_STRIP_TRAILING_WHITESPACE)
         execute_process(COMMAND arch
                         OUTPUT_VARIABLE DISTRO_ARCH OUTPUT_STRIP_TRAILING_WHITESPACE)
         set(BDM_OS "${DISTRO_NAME}-${DISTRO_VERSION}")
+	      if(BDM_OS MATCHES "debian|mint|eepin")
+		       set(BDM_OS "ubuntu-24.04")
+        elseif (BDM_OS MATCHES "buntu")
+       	   set(BDM_OS "ubuntu-${DISTRO_VERSION}")
+           if (BDM_OS MATCHES "buntu-24|buntu-25|buntu-26")
+       	     set(BDM_OS "ubuntu-24.04")
+           endif()
+        endif()
+        if(DISTRO_NAME_PROC MATCHES "Red Hat")
+          set(BDM_OS "centos-7")
+        endif()
         set(DETECTED_OS "${BDM_OS}" PARENT_SCOPE)
         set(DETECTED_ARCH "${DISTRO_ARCH}" PARENT_SCOPE)
         if("${DISTRO_ARCH}" STREQUAL "aarch64")

install.sh

@@ -44,5 +44,11 @@ if [ $? != 0 ]; then
    exit 1
 fi
 
+# Activate mpi on centos/rhel
+if echo "$BDM_DETECTED_OS" | grep -Eiq 'centos|rhel'; then
+  . /etc/profile.d/modules.sh
+  module load mpi/openmpi-x86_64
+fi
+
 # call install script for the detected OS
 $BDM_PROJECT_DIR/util/installation/common/install.sh ${BDM_DETECTED_OS}

src/core/exporter.h

@@ -17,6 +17,7 @@
 
 #include <memory>
 #include <string>
+#include <cstdint>
 
 namespace bdm {
 

third_party/cxxopts-v2.2.1/cxxopts.h

@@ -37,6 +37,7 @@ THE SOFTWARE.
 #include <string>
 #include <unordered_map>
 #include <unordered_set>
+#include <cstdint>
 #include <vector>
 
 #ifdef __cpp_lib_optional

util/installation/common/util.sh

@@ -48,7 +48,23 @@ function DetectOs {
     DISTRIBUTOR=$(grep -oP '(?<=^ID=).+' /etc/os-release | tr -d '"')
     RELEASE=$(grep -oP '(?<=^VERSION_ID=).+' /etc/os-release | tr -d '"')
     OS="${DISTRIBUTOR}-${RELEASE}"
-    echo $OS | awk '{print tolower($0)}'
+    PROCVERSION=$(cat /proc/version)
+	if echo "$OS" | grep -Eiq 'debian|mint|eepin' ; then
+		OS="ubuntu-24.04"
+    elif echo "$DISTRIBUTOR" | grep -Eiq 'buntu' ; then
+    		OS="ubuntu-${RELEASE}"
+        if echo "$OS" | grep -Eiq 'buntu-24|buntu-25|buntu-26' ; then
+          OS="ubuntu-24.04"
+        fi
+  elif echo "$PROCVERSION" | grep -Eiq 'Red Hat' ; then
+    if echo "$OS" | grep -Eiq 'centos-7'; then
+      OS="centos-7"
+    else
+      OS="rhel"
+    fi
+  fi
+  echo $OS | awk '{print tolower($0)}'
+
   elif [ `uname` = "Darwin" ]; then
     # macOS
     echo osx

util/installation/rhel/Dockerfile

@@ -0,0 +1,52 @@
+# -----------------------------------------------------------------------------
+#
+# Copyright (C) 2021 CERN & University of Surrey for the benefit of the
+# BioDynaMo collaboration. All Rights Reserved.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+#
+# See the LICENSE file distributed with this work for details.
+# See the NOTICE file distributed with this work for additional information
+# regarding copyright ownership.
+#
+# -----------------------------------------------------------------------------
+
+FROM centos:7
+
+# workaround for https://github.com/containers/buildah/issues/1046
+RUN echo "" >> /etc/hosts && cat /etc/hosts && yum -y install setup
+
+# man required by ROOT
+# mesa-dri-drivers: OpenGl driver (software renderer)
+RUN yum update -y && yum install -y \
+  git \
+  sudo \
+  man \
+  wget \
+  xorg-x11-server-Xvfb \
+  mesa-dri-drivers
+
+RUN git config --system user.name "Test User" && \
+    git config --system user.email user@test.com
+
+# update user id and group id such that mapped volumes can be accessed with the
+# same rights as on the host. Files created by the container can also be
+# accessed on the host without chowning.
+ARG HOST_UID
+ARG HOST_GID
+
+RUN groupadd -g $HOST_GID testuser && \
+    useradd -u $HOST_UID -g $HOST_GID -m -c "Testuser" testuser && \
+    passwd --delete testuser && \
+    echo "testuser ALL=(ALL) NOPASSWD: ALL" >> /etc/sudoers
+
+USER testuser
+
+# preserve the environment variable BDM_LOCAL_LFS when calling scripts with
+# sudo
+RUN echo "Defaults env_keep += \"BDM_LOCAL_LFS\"" | sudo tee -a /etc/sudoers
+
+# the OpenGL capabilities can be incorrectly detected -> override version
+# https://python.develop-bugs.com/article/10118323/paraview+needs+higher+OpenGL+in+Mesa
+ENV MESA_GL_VERSION_OVERRIDE=3.3

util/installation/rhel/package_list_extra

@@ -0,0 +1,25 @@
+doxygen
+graphviz
+libxml2-devel
+fontconfig-devel
+fontconfig
+freetype
+freetype-devel
+llvm-toolset-7
+llvm-toolset-7-clang-tools-extra
+llvm-toolset-7-llvm-devel
+llvm-toolset-7-llvm-static
+valgrind
+gsl-devel
+openssl-devel
+pcre-devel
+mesa-libGL-devel
+mesa-libGLU-devel
+cfitsio-devel
+libldap-dev
+python-devel
+libXt-devel 
+freeglut3-devel
+ncurses-devel
+
+

util/installation/rhel/package_list_required

@@ -0,0 +1,78 @@
+gcc
+g++
+gcc-gfortran
+bzip2-devel
+freeglut-devel
+git
+patch
+libXext-devel
+libXt-devel
+numactl-devel
+openmpi-devel
+wget
+zlib-devel
+python3-tkinter
+tk-devel
+
+@development
+gmp-devel
+mpfr-devel
+libmpc-devel
+bzip2
+readline-devel
+sqlite
+doxygen
+sqlite-devel
+openssl-devel
+xz
+xz-devel
+libffi-devel
+findutils
+lapack-devel
+blas-devel
+llvm-toolset
+openmpi
+libX11-devel
+libXpm-devel
+libXft-devel
+valgrind
+gsl-devel
+atlas-devel
+pcre-devel
+mesa-libGL-devel
+mesa-libGLU-devel
+glew-devel
+ftgl-devel
+mysql-devel
+fftw-devel
+cfitsio-devel
+graphviz-devel
+avahi-compat-libdns_sd-devel
+libldap-devel
+python-devel
+libxml2-devel
+gsl-static
+libXt-devel 
+freeglut3-devel
+ncurses-devel
+openldap-devel
+zlib
+libuuid-devel
+ffmpeg-free-devel
+libxkbcommon-devel
+libxkbcommon-x11-devel
+xcb-util-devel
+xcb-util-image-devel
+xcb-util-keysyms-devel
+xcb-util-xrm-devel
+xcb-util-cursor-devel
+xcb-util-renderutil-devel
+xcb-util-wm-devel
+libXi-devel
+xcb-proto
+tslib
+tslib-devel
+ncurses-compat-libs
+devtoolset-10-gcc*
+devtoolset-11-gcc*
+gcc-toolset-11*