diff --git a/ThirdParty/AllClean.stage2 b/ThirdParty/AllClean.stage2 index c0836c575..b365a998b 100755 --- a/ThirdParty/AllClean.stage2 +++ b/ThirdParty/AllClean.stage2 @@ -57,6 +57,7 @@ uninstallPackage openmpi-1.5 $1 uninstallPackage openmpi-1.6.5 $1 uninstallPackage openmpi-1.8.4 $1 uninstallPackage openmpi-3.1.0 $1 +uninstallPackage openmpi-4.0.0 $1 echo echo ======================================== diff --git a/ThirdParty/AllMake.stage2 b/ThirdParty/AllMake.stage2 index 93519fa98..37c556d26 100755 --- a/ThirdParty/AllMake.stage2 +++ b/ThirdParty/AllMake.stage2 @@ -113,6 +113,14 @@ then -f --define '_configureAdditionalArgs "$WM_THIRD_PARTY_USE_OPENMPI_311_ConfigureAdditionalArgs"') } + # openmpi 4.0.0 + # + [ ! -z "$WM_THIRD_PARTY_USE_OPENMPI_400" ] && { + echo "Building openmpi 4.0.0" + ( rpm_make -p openmpi-4.0.0 -s openmpi-4.0.0.spec -u https://www.open-mpi.org/software/ompi/v4.0/downloads/openmpi-4.0.0.tar.gz \ + -f --define '_configureAdditionalArgs "$WM_THIRD_PARTY_USE_OPENMPI_400_ConfigureAdditionalArgs"') + } + # mvipich2-2.2 # [ ! -z "$WM_THIRD_PARTY_USE_MVAPICH2_22" ] && { diff --git a/ThirdParty/rpmBuild/SOURCES/openmpi-3.1.1.patch b/ThirdParty/rpmBuild/SOURCES/openmpi-3.1.1.patch new file mode 100644 index 000000000..f8124ca05 --- /dev/null +++ b/ThirdParty/rpmBuild/SOURCES/openmpi-3.1.1.patch @@ -0,0 +1,28 @@ +--- openmpi-3.1.1_orig/ompi/include/mpi.h.in 2018-06-29 20:38:13.000000000 +0430 ++++ openmpi-3.1.1/ompi/include/mpi.h.in 2019-01-30 22:03:31.021316632 +0330 +@@ -307,7 +307,11 @@ + * when building OMPI). + */ + #if !OMPI_BUILDING ++#if defined(c_plusplus) || defined(__cplusplus) ++#define OMPI_PREDEFINED_GLOBAL(type, global) (static_cast (static_cast (&(global)))) ++#else + #define OMPI_PREDEFINED_GLOBAL(type, global) ((type) ((void *) &(global))) ++#endif + #else + #define OMPI_PREDEFINED_GLOBAL(type, global) ((type) &(global)) + #endif +@@ -753,8 +757,13 @@ + */ + #define MPI_INFO_ENV OMPI_PREDEFINED_GLOBAL(MPI_Info, ompi_mpi_info_env) + ++#if defined(c_plusplus) || defined(__cplusplus) ++#define MPI_STATUS_IGNORE (static_cast (0)) ++#define MPI_STATUSES_IGNORE (static_cast (0)) ++#else + #define MPI_STATUS_IGNORE ((MPI_Status *) 0) + #define MPI_STATUSES_IGNORE ((MPI_Status *) 0) ++#endif + + /* + * Special MPI_T handles diff --git a/ThirdParty/rpmBuild/SOURCES/openmpi-4.0.0.patch b/ThirdParty/rpmBuild/SOURCES/openmpi-4.0.0.patch new file mode 100644 index 000000000..30beee336 --- /dev/null +++ b/ThirdParty/rpmBuild/SOURCES/openmpi-4.0.0.patch @@ -0,0 +1,28 @@ +--- openmpi-4.0.0_orig/ompi/include/mpi.h.in 2018-11-12 23:50:53.000000000 +0330 ++++ openmpi-4.0.0/ompi/include/mpi.h.in 2019-01-30 22:04:14.433503290 +0330 +@@ -325,7 +325,11 @@ + * when building OMPI). + */ + #if !OMPI_BUILDING ++#if defined(c_plusplus) || defined(__cplusplus) ++#define OMPI_PREDEFINED_GLOBAL(type, global) (static_cast (static_cast (&(global)))) ++#else + #define OMPI_PREDEFINED_GLOBAL(type, global) ((type) ((void *) &(global))) ++#endif + #else + #define OMPI_PREDEFINED_GLOBAL(type, global) ((type) &(global)) + #endif +@@ -765,8 +769,13 @@ + */ + #define MPI_INFO_ENV OMPI_PREDEFINED_GLOBAL(MPI_Info, ompi_mpi_info_env) + ++#if defined(c_plusplus) || defined(__cplusplus) ++#define MPI_STATUS_IGNORE (static_cast (0)) ++#define MPI_STATUSES_IGNORE (static_cast (0)) ++#else + #define MPI_STATUS_IGNORE ((MPI_Status *) 0) + #define MPI_STATUSES_IGNORE ((MPI_Status *) 0) ++#endif + + /* + * Special MPI_T handles diff --git a/ThirdParty/rpmBuild/SPECS/openmpi-3.1.1.spec b/ThirdParty/rpmBuild/SPECS/openmpi-3.1.1.spec index 2c882b529..19ad48569 100644 --- a/ThirdParty/rpmBuild/SPECS/openmpi-3.1.1.spec +++ b/ThirdParty/rpmBuild/SPECS/openmpi-3.1.1.spec @@ -72,10 +72,11 @@ License: Unkown Name: %{name} Version: %{version} Release: %{release} -URL: http://www.open-mpi.org/software/ompi/v1.8/downloads +URL: http://www.open-mpi.org/software/ompi/v3.0/downloads Source: %url/%{name}-%{version}.tar.gz Prefix: %{_prefix} Group: Development/Tools +Patch0: openmpi-3.1.1.patch %define _installPrefix %{_prefix}/packages/%{name}-%{version}/platforms/%{_WM_OPTIONS} @@ -95,6 +96,8 @@ Group: Development/Tools %prep %setup -q +%patch0 -p1 + %build # export WM settings in a form that GNU configure recognizes diff --git a/ThirdParty/rpmBuild/SPECS/openmpi-4.0.0.spec b/ThirdParty/rpmBuild/SPECS/openmpi-4.0.0.spec new file mode 100644 index 000000000..7333e3fa6 --- /dev/null +++ b/ThirdParty/rpmBuild/SPECS/openmpi-4.0.0.spec @@ -0,0 +1,267 @@ +#------------------------------------------------------------------------------ +# ========= | +# \\ / F ield | foam-extend: Open Source CFD +# \\ / O peration | +# \\ / A nd | For copyright notice see file Copyright +# \\/ M anipulation | +#------------------------------------------------------------------------------ +# License +# This file is part of foam-extend. +# +# foam-extend is free software: you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the +# Free Software Foundation, either version 3 of the License, or (at your +# option) any later version. +# +# foam-extend is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with foam-extend. If not, see . +# +# Script +# RPM spec file for openmpi-4.0.0 +# +# Description +# RPM spec file for creating a relocatable RPM +# +# Author: +# Martin Beaudoin, (2018) +# +#------------------------------------------------------------------------------ + +# We grab the value of WM_THIRD_PARTY and WM_OPTIONS from the environment variable +%{expand:%%define _WM_THIRD_PARTY_DIR %(echo $WM_THIRD_PARTY_DIR)} +%{expand:%%define _WM_OPTIONS %(echo $WM_OPTIONS)} + +# Disable the generation of debuginfo packages +%define debug_package %{nil} + +# The topdir needs to point to the $WM_THIRD_PARTY/rpmbuild directory +%define _topdir %{_WM_THIRD_PARTY_DIR}/rpmBuild +%define _tmppath %{_topdir}/tmp + +# Will install the package directly $WM_THIRD_PARTY_DIR +# Some comments about package relocation: +# By using this prefix for the Prefix: parameter in this file, you will make this +# package relocatable. +# +# This is fine, as long as your software is itself relocatable. +# +# Simply take note that libraries built with libtool are not relocatable because the +# prefix we specify will be hard-coded in the library .la files. +# Ref: http://sourceware.org/autobook/autobook/autobook_80.html +# +# In that case, if you ever change the value of the $WM_THIRD_PARTY_DIR, you will +# not be able to reutilize this RPM, even though it is relocatable. You will need to +# regenerate the RPM. +# +%define _prefix %{_WM_THIRD_PARTY_DIR} + +%define name openmpi +%define release %{_WM_OPTIONS} +%define version 4.0.0 + +%define buildroot %{_topdir}/BUILD/%{name}-%{version}-root + +BuildRoot: %{buildroot} +Summary: openmpi +License: Unkown +Name: %{name} +Version: %{version} +Release: %{release} +URL: http://www.open-mpi.org/software/ompi/v4.0/downloads +Source: %url/%{name}-%{version}.tar.gz +Prefix: %{_prefix} +Group: Development/Tools +Patch0: openmpi-4.0.0.patch + + +%define _installPrefix %{_prefix}/packages/%{name}-%{version}/platforms/%{_WM_OPTIONS} + +#-------------------------------------------------------------------------- +# +# Here, we define default compiling options for openmpi +# +# One can override the option on the commande line : --define='MACRO EXPR' +# +%{!?_configureAdditionalArgs: %define _configureAdditionalArgs Undefined} + + +%description +%{summary} + +%prep +%setup -q + +%patch0 -p1 + + +%build + # export WM settings in a form that GNU configure recognizes + [ -n "$WM_CC" ] && export CC="$WM_CC" + [ -n "$WM_CXX" ] && export CXX="$WM_CXX" + [ -n "$WM_CFLAGS" ] && export CFLAGS="$WM_CFLAGS" + [ -n "$WM_CXXFLAGS" ] && export CXXFLAGS="$WM_CXXFLAGS" + [ -n "$WM_LDFLAGS" ] && export LDFLAGS="$WM_LDFLAGS" + + set +x + echo "" + echo "Compilation options:" + echo " _configureAdditionalArgs : %{_configureAdditionalArgs}" + echo "" + set -x + + unset mpiWith + # Enable GridEngine if it appears to be in use + # If you don't want any integration with SGE, simply unset the SGE + # environment variable + if [ -n "$SGE_ROOT" ] + then + mpiWith="$mpiWith --with-sge" + else + mpiWith="$mpiWith --without-sge" + mpiWith="$mpiWith --enable-mca-no-build=ras-gridengine,pls-gridengine" + fi + + # Infiniband support + # Adjust according to your local paths + # if [ -d /usr/local/ofed -a -d /usr/local/ofed/lib64 ] + # then + # mpiWith="$mpiWith --with-openib=/usr/local/ofed" + # mpiWith="$mpiWith --with-openib-libdir=/usr/local/ofed/lib64" + # fi + + ./configure \ + --prefix=%{_installPrefix} \ + --exec_prefix=%{_installPrefix} \ + --enable-mpirun-prefix-by-default \ + --enable-orterun-prefix-by-default \ + --enable-shared \ + --enable-mpi-cxx \ + --disable-static \ + --disable-mpi-fortran \ + --without-slurm \ + `echo %{?_configureAdditionalArgs}` + + [ -z "$WM_NCOMPPROCS" ] && WM_NCOMPPROCS=1 + make -j $WM_NCOMPPROCS + +%install + make install DESTDIR=$RPM_BUILD_ROOT + + # Creation of foam-extend specific .csh and .sh files" + + echo "" + echo "Generating foam-extend specific .csh and .sh files for the package %{name}-%{version}" + echo "" + # + # Generate package specific .sh file for foam-extend + # +mkdir -p $RPM_BUILD_ROOT/%{_installPrefix}/etc +cat << DOT_SH_EOF > $RPM_BUILD_ROOT/%{_installPrefix}/etc/%{name}-%{version}.sh +# Load %{name}-%{version} libraries and binaries +# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +export OPENMPI_DIR=\$WM_THIRD_PARTY_DIR/packages/%{name}-%{version}/platforms/\$WM_OPTIONS +export OPENMPI_BIN_DIR=\$OPENMPI_DIR/bin +export OPENMPI_LIB_DIR=\$OPENMPI_DIR/lib + +# Enable access to the package runtime applications and libraries +[ -d \$OPENMPI_BIN_DIR ] && _foamAddPath \$OPENMPI_BIN_DIR +[ -d \$OPENMPI_LIB_DIR ] && _foamAddLib \$OPENMPI_LIB_DIR + +export MPI_HOME=\$OPENMPI_DIR +export MPI_ARCH_PATH=\$MPI_HOME +export OPAL_PREFIX=\$MPI_ARCH_PATH + +# We initialize the rest of the environment using mpicc --showme: +export OPENMPI_INCLUDE_DIR="\`mpicc --showme:incdirs\`" +export OPENMPI_COMPILE_FLAGS="\`mpicc --showme:compile\`" +export OPENMPI_LINK_FLAGS="\`mpicc --showme:link\`" + +# Set the foam-extend compilation flags +export PINC=\$OPENMPI_COMPILE_FLAGS +export PLIBS=\$OPENMPI_LINK_FLAGS + + +if [ "\$FOAM_VERBOSE" -a "\$PS1" ] +then + echo " Environment variables defined for OpenMPI:" + echo " OPENMPI_BIN_DIR : \$OPENMPI_BIN_DIR" + echo " OPENMPI_LIB_DIR : \$OPENMPI_LIB_DIR" + echo " OPENMPI_INCLUDE_DIR : \$OPENMPI_INCLUDE_DIR" + echo " OPENMPI_COMPILE_FLAGS : \$OPENMPI_COMPILE_FLAGS" + echo " OPENMPI_LINK_FLAGS : \$OPENMPI_LINK_FLAGS" + echo "" + echo " MPI_HOME : \$MPI_HOME" + echo " MPI_ARCH_PATH : \$MPI_ARCH_PATH" + echo " MPIRUN_OPTIONS : \$MPIRUN_OPTIONS" + echo " OPAL_PREFIX : \$OPAL_PREFIX" + echo " PINC : \$PINC" + echo " PLIBS : \$PLIBS" +fi +DOT_SH_EOF + + # + # Generate package specific .csh file for foam-extend + # +cat << DOT_CSH_EOF > $RPM_BUILD_ROOT/%{_installPrefix}/etc/%{name}-%{version}.csh +# Load %{name}-%{version} libraries and binaries +# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +setenv OPENMPI_DIR \$WM_THIRD_PARTY_DIR/packages/%{name}-%{version}/platforms/\$WM_OPTIONS +setenv OPENMPI_BIN_DIR \$OPENMPI_DIR/bin +setenv OPENMPI_LIB_DIR \$OPENMPI_DIR/lib + +# Enable access to the package runtime applications and libraries +if ( -e \$OPENMPI_BIN_DIR ) then + _foamAddPath \$OPENMPI_BIN_DIR +endif + +if ( -e \$OPENMPI_LIB_DIR ) then + _foamAddLib \$OPENMPI_LIB_DIR +endif + +setenv MPI_HOME \$OPENMPI_DIR +setenv MPI_ARCH_PATH \$MPI_HOME +setenv OPAL_PREFIX \$MPI_ARCH_PATH + +# We initialize the rest of the environment using mpicc --showme: +setenv OPENMPI_INCLUDE_DIR "\`mpicc --showme:incdirs\`" +setenv OPENMPI_COMPILE_FLAGS "\`mpicc --showme:compile\`" +setenv OPENMPI_LINK_FLAGS "\`mpicc --showme:link\`" + +# Set the foam-extend compilation flags +setenv PINC "\$OPENMPI_COMPILE_FLAGS" +setenv PLIBS "\$OPENMPI_LINK_FLAGS" + + +if (\$?FOAM_VERBOSE && \$?prompt) then + echo " Environment variables defined for OpenMPI:" + echo " OPENMPI_BIN_DIR : \$OPENMPI_BIN_DIR" + echo " OPENMPI_LIB_DIR : \$OPENMPI_LIB_DIR" + echo " OPENMPI_INCLUDE_DIR : \$OPENMPI_INCLUDE_DIR" + echo " OPENMPI_COMPILE_FLAGS : \$OPENMPI_COMPILE_FLAGS" + echo " OPENMPI_LINK_FLAGS : \$OPENMPI_LINK_FLAGS" + echo "" + echo " MPI_HOME : \$MPI_HOME" + echo " MPI_ARCH_PATH : \$MPI_ARCH_PATH" + echo " MPIRUN_OPTIONS : \$MPIRUN_OPTIONS" + echo " OPAL_PREFIX : \$OPAL_PREFIX" + echo " PINC : \$PINC" + echo " PLIBS : \$PLIBS" +endif +DOT_CSH_EOF + + #finally, generate a .tgz file for systems where using rpm for installing packages + # as a non-root user might be a problem. + (mkdir -p %{_topdir}/TGZS/%{_target_cpu}; cd $RPM_BUILD_ROOT/%{_prefix}; tar -zcvf %{_topdir}/TGZS/%{_target_cpu}/%{name}-%{version}.tgz packages/%{name}-%{version}) + + +%clean +rm -rf %{buildroot} + +%files +%defattr(-,root,root) +%{_installPrefix} diff --git a/applications/utilities/mesh/generation/cfMesh/FLMAToSurface/FLMAToSurface.C b/applications/utilities/mesh/generation/cfMesh/FLMAToSurface/FLMAToSurface.C index b462bc0ef..3f00becd2 100644 --- a/applications/utilities/mesh/generation/cfMesh/FLMAToSurface/FLMAToSurface.C +++ b/applications/utilities/mesh/generation/cfMesh/FLMAToSurface/FLMAToSurface.C @@ -1,22 +1,25 @@ /*---------------------------------------------------------------------------*\ ========= | \\ / F ield | foam-extend: Open Source CFD - \\ / O peration | Version: 3.2 + \\ / O peration | Version: 4.1 \\ / A nd | Web: http://www.foam-extend.org \\/ M anipulation | For copyright notice see file Copyright +------------------------------------------------------------------------------- + Author | F.Juretic (franjo.juretic@c-fields.com) + Copyright | Copyright (C) Creative Fields, Ltd. ------------------------------------------------------------------------------- License This file is part of foam-extend. - foam-extend is free software: you can redistribute it and/or modify it + foam-extend is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the - Free Software Foundation, either version 3 of the License, or (at your + Free Software Foundation; either version 3 of the License, or (at your option) any later version. - foam-extend is distributed in the hope that it will be useful, but - WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - General Public License for more details. + foam-extend is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License + for more details. You should have received a copy of the GNU General Public License along with foam-extend. If not, see . @@ -27,8 +30,6 @@ Description \*---------------------------------------------------------------------------*/ #include "argList.H" -#include "objectRegistry.H" -#include "foamTime.H" #include "triSurf.H" #include "triSurfModifier.H" #include "triFaceList.H" diff --git a/applications/utilities/mesh/generation/cfMesh/FMSToSurface/FMSToSurface.C b/applications/utilities/mesh/generation/cfMesh/FMSToSurface/FMSToSurface.C index a4a617c3e..da6eb60cc 100644 --- a/applications/utilities/mesh/generation/cfMesh/FMSToSurface/FMSToSurface.C +++ b/applications/utilities/mesh/generation/cfMesh/FMSToSurface/FMSToSurface.C @@ -1,22 +1,25 @@ /*---------------------------------------------------------------------------*\ ========= | \\ / F ield | foam-extend: Open Source CFD - \\ / O peration | Version: 3.2 + \\ / O peration | Version: 4.1 \\ / A nd | Web: http://www.foam-extend.org \\/ M anipulation | For copyright notice see file Copyright +------------------------------------------------------------------------------- + Author | F.Juretic (franjo.juretic@c-fields.com) + Copyright | Copyright (C) Creative Fields, Ltd. ------------------------------------------------------------------------------- License This file is part of foam-extend. - foam-extend is free software: you can redistribute it and/or modify it + foam-extend is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the - Free Software Foundation, either version 3 of the License, or (at your + Free Software Foundation; either version 3 of the License, or (at your option) any later version. - foam-extend is distributed in the hope that it will be useful, but - WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - General Public License for more details. + foam-extend is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License + for more details. You should have received a copy of the GNU General Public License along with foam-extend. If not, see . @@ -27,8 +30,6 @@ Description \*---------------------------------------------------------------------------*/ #include "argList.H" -#include "objectRegistry.H" -#include "foamTime.H" #include "triSurf.H" #include "triSurfaceCopyParts.H" #include "demandDrivenData.H" diff --git a/applications/utilities/mesh/generation/cfMesh/FMSToVTK/FMSToVTK.C b/applications/utilities/mesh/generation/cfMesh/FMSToVTK/FMSToVTK.C index 19a269bba..50e7de25b 100644 --- a/applications/utilities/mesh/generation/cfMesh/FMSToVTK/FMSToVTK.C +++ b/applications/utilities/mesh/generation/cfMesh/FMSToVTK/FMSToVTK.C @@ -1,28 +1,31 @@ /*---------------------------------------------------------------------------*\ ========= | \\ / F ield | foam-extend: Open Source CFD - \\ / O peration | Version: 3.2 + \\ / O peration | Version: 4.1 \\ / A nd | Web: http://www.foam-extend.org \\/ M anipulation | For copyright notice see file Copyright +------------------------------------------------------------------------------- + Author | F.Juretic (franjo.juretic@c-fields.com) + Copyright | Copyright (C) Creative Fields, Ltd. ------------------------------------------------------------------------------- License This file is part of foam-extend. - foam-extend is free software: you can redistribute it and/or modify it + foam-extend is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the - Free Software Foundation, either version 3 of the License, or (at your + Free Software Foundation; either version 3 of the License, or (at your option) any later version. - foam-extend is distributed in the hope that it will be useful, but - WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU - General Public License for more details. + foam-extend is distributed in the hope that it will be useful, but WITHOUT + ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or + FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License + for more details. You should have received a copy of the GNU General Public License along with foam-extend. If not, see . Description - cfMesh utility to convert a surface file to VTK multiblock dataset + foam-extend utility to convert a surface file to VTK multiblock dataset format, including the patches, feature edges and surface features. Author @@ -45,7 +48,7 @@ using namespace Foam; void writePointsToVTK ( const fileName& fn, - const string& title, + const string& /*title*/, const UList& points ) { @@ -78,7 +81,7 @@ void writePointsToVTK const fileName& fn, const string& title, const UList& points, - unallocLabelList& addr + UList