gnu: fenics-dolfin: Fix build.
* gnu/packages/patches/fenics-dolfin-algorithm.patch, gnu/packages/patches/fenics-dolfin-boost.patch, gnu/packages/patches/fenics-dolfin-config-slepc.patch, gnu/packages/patches/fenics-dolfin-demo-init.patch: New patches. * gnu/local.mk (dist_patch_DATA): Register them. * gnu/packages/simulation.scm (fenics-dolfin)[source]: Use them.
This commit is contained in:
Eric Bavier
parent
dd823172d8
commit
41b11c459b
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@ -1053,6 +1053,10 @@ dist_patch_DATA = \
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%D%/packages/patches/fasthenry-spSolve.patch \
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%D%/packages/patches/fasthenry-spFactor.patch \
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%D%/packages/patches/fbreader-curl-7.62.patch \
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%D%/packages/patches/fenics-dolfin-algorithm.patch \
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%D%/packages/patches/fenics-dolfin-demo-init.patch \
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%D%/packages/patches/fenics-dolfin-boost.patch \
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%D%/packages/patches/fenics-dolfin-config-slepc.patch \
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%D%/packages/patches/fifengine-boost-compat.patch \
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%D%/packages/patches/fifengine-swig-compat.patch \
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%D%/packages/patches/fifo-map-fix-flags-for-gcc.patch \
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37
gnu/packages/patches/fenics-dolfin-algorithm.patch
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37
gnu/packages/patches/fenics-dolfin-algorithm.patch
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@ -0,0 +1,37 @@
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Fix compilation errors:
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dolfin/geometry/IntersectionConstruction.cpp: In static member function ‘static std::vector<dolfin::Point> dolfin::IntersectionConstruction::intersection_segment_segment_2d(const dolfin::Point&, const dolfin::Point&, const dolfin::Point&, const dolfin::Point&)’:
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dolfin/geometry/IntersectionConstruction.cpp:442:24: error: ‘min_element’ is not a member of ‘std’; did you mean ‘tuple_element’?
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442 | const auto it = std::min_element(oo.begin(), oo.end());
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| ^~~~~~~~~~~
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| tuple_element
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dolfin/mesh/MeshFunction.h: In member function ‘std::vector<long unsigned int> dolfin::MeshFunction<T>::where_equal(T)’:
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dolfin/mesh/MeshFunction.h:652:26: error: ‘count’ is not a member of ‘std’; did you mean ‘cout’?
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652 | std::size_t n = std::count(_values.get(), _values.get() + _size, value);
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| ^~~~~
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| cout
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Submitted upstream at https://bitbucket.org/fenics-project/dolfin/issues/1128
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--- a/dolfin/geometry/IntersectionConstruction.cpp
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+++ b/dolfin/geometry/IntersectionConstruction.cpp
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@@ -18,7 +18,8 @@
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// First added: 2014-02-03
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// Last changed: 2017-12-12
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+#include <algorithm>
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#include <iomanip>
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#include <dolfin/mesh/MeshEntity.h>
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#include "predicates.h"
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--- a/dolfin/mesh/MeshFunction.h
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+++ b/dolfin/mesh/MeshFunction.h
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@@ -24,6 +24,7 @@
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#ifndef __MESH_FUNCTION_H
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#define __MESH_FUNCTION_H
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+#include <algorithm>
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#include <map>
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#include <vector>
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45
gnu/packages/patches/fenics-dolfin-boost.patch
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45
gnu/packages/patches/fenics-dolfin-boost.patch
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@ -0,0 +1,45 @@
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The `BOOST_LITTLE_ENDIAN` and `BOOST_BIG_ENDIAN` macros, along with the
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"boost/detail/endian.hpp" header, were deprecated in boost 1.69.0 and finally
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removed in boost 1.73.0. They are superseded by the BOOST_ENDIAN_LITTLE_BYTE
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and BOOST_ENDIAN_BIG_BYTE macros and "boost/predef/other/endian.h" header.
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Deprecated: https://github.com/boostorg/predef/commit/32d4581c1689370444f2e565cfbb8421d5071807
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Removed: https://github.com/boostorg/predef/commit/aa6e232bf170ad8b856aff9e7c70334f77441c7f
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Adaptation of patch from https://bitbucket.org/fenics-project/dolfin/issues/1116
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--- a/dolfin/io/VTKFile.cpp
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+++ b/dolfin/io/VTKFile.cpp
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@@ -20,7 +20,7 @@
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#include <vector>
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#include <iomanip>
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#include <boost/cstdint.hpp>
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-#include <boost/detail/endian.hpp>
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+#include <boost/predef/other/endian.h>
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#include "pugixml.hpp"
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@@ -614,9 +614,9 @@
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std::string endianness = "";
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if (encode_string == "binary")
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{
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- #if defined BOOST_LITTLE_ENDIAN
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+ #if defined BOOST_ENDIAN_LITTLE_BYTE
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endianness = "byte_order=\"LittleEndian\"";
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- #elif defined BOOST_BIG_ENDIAN
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+ #elif defined BOOST_ENDIAN_BIG_BYTE
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endianness = "byte_order=\"BigEndian\"";;
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#else
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dolfin_error("VTKFile.cpp",
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--- a/dolfin/io/VTKWriter.cpp
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+++ b/dolfin/io/VTKWriter.cpp
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@@ -24,7 +24,6 @@
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#include <sstream>
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#include <vector>
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#include <iomanip>
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-#include <boost/detail/endian.hpp>
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#include <dolfin/fem/GenericDofMap.h>
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#include <dolfin/fem/FiniteElement.h>
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48
gnu/packages/patches/fenics-dolfin-config-slepc.patch
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48
gnu/packages/patches/fenics-dolfin-config-slepc.patch
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@ -0,0 +1,48 @@
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From https://bitbucket.org/fenics-project/dolfin/issues/1120
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From f627a442350560e50dbbb11f7828b6d807369533 Mon Sep 17 00:00:00 2001
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From: Alexei Colin <acolin@isi.edu>
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Date: Sun, 11 Apr 2021 20:40:00 -0400
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Subject: [PATCH] cmake: PETSc,SLEPc: match lowercase .pc pkg-config files
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Upstream has moved to lowercase. PETSc has kept the mixed-case file for
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compatibility, but SLEPc hasn't.
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pkg_search_module takes multiple patterns and succeeds on first match,
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so this commit is backward-compatible with older installations of PETSc,
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SLEPc.
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---
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cmake/modules/FindPETSc.cmake | 2 +-
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cmake/modules/FindSLEPc.cmake | 2 +-
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2 files changed, 2 insertions(+), 2 deletions(-)
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diff --git a/cmake/modules/FindPETSc.cmake b/cmake/modules/FindPETSc.cmake
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index 80faffdad..728a6ec30 100644
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--- a/cmake/modules/FindPETSc.cmake
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+++ b/cmake/modules/FindPETSc.cmake
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@@ -51,7 +51,7 @@ find_package(PkgConfig REQUIRED)
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# Find PETSc pkg-config file. Note: craypetsc_real is on Cray systems
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set(ENV{PKG_CONFIG_PATH} "$ENV{CRAY_PETSC_PREFIX_DIR}/lib/pkgconfig:$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig:$ENV{PETSC_DIR}/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}")
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-pkg_search_module(PETSC craypetsc_real PETSc)
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+pkg_search_module(PETSC craypetsc_real petsc PETSc)
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# Extract major, minor, etc from version string
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if (PETSC_VERSION)
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diff --git a/cmake/modules/FindSLEPc.cmake b/cmake/modules/FindSLEPc.cmake
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index 327cffc23..dec26fcc4 100644
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--- a/cmake/modules/FindSLEPc.cmake
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+++ b/cmake/modules/FindSLEPc.cmake
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@@ -48,7 +48,7 @@ find_package(PkgConfig REQUIRED)
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set(ENV{PKG_CONFIG_PATH} "$ENV{SLEPC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig:$ENV{SLEPC_DIR}/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}")
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set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig:$ENV{PETSC_DIR}/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}")
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set(ENV{PKG_CONFIG_PATH} "$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}:$ENV{PETSC_DIR}:$ENV{PKG_CONFIG_PATH}")
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-pkg_search_module(SLEPC crayslepc_real SLEPc)
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+pkg_search_module(SLEPC crayslepc_real slepc SLEPc)
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# Extract major, minor, etc from version string
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if (SLEPC_VERSION)
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--
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2.30.0
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39
gnu/packages/patches/fenics-dolfin-demo-init.patch
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39
gnu/packages/patches/fenics-dolfin-demo-init.patch
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@ -0,0 +1,39 @@
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Ensure MPI is initialized before getting rank, which may be called early by
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Logger::write() via dolfin::info().
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Fixes "MPI_Comm_rank called before MPI_INIT" error from
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`demo_stokes-iterative_serial` and `demo_waveguide_serial` tests.
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Submitted upstream at https://bitbucket.org/fenics-project/dolfin/issues/1127
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--- a/dolfin/common/MPI.cpp
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+++ b/dolfin/common/MPI.cpp
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@@ -143,6 +143,7 @@ MPI_Info& dolfin::MPIInfo::operator*()
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unsigned int dolfin::MPI::rank(const MPI_Comm comm)
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{
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#ifdef HAS_MPI
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+ SubSystemsManager::init_mpi();
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int rank;
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MPI_Comm_rank(comm, &rank);
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return rank;
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diff --git a/dolfin/common/MPI.h b/dolfin/common/MPI.h
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index b93f6df30..854114a3f 100644
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--- a/dolfin/common/MPI.h
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+++ b/dolfin/common/MPI.h
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@@ -102,12 +102,13 @@ namespace dolfin
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/// communicator
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void reset(MPI_Comm comm);
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- /// Return process rank for the communicator
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+ /// Return process rank for the communicator. This function will
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+ /// also initialize MPI if it hasn't already been initialised.
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unsigned int rank() const;
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/// Return size of the group (number of processes) associated
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- /// with the communicator. This function will also intialise MPI
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- /// if it hasn't already been intialised.
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+ /// with the communicator. This function will also initialise MPI
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+ /// if it hasn't already been initialised.
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unsigned int size() const;
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/// Set a barrier (synchronization point)
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@ -1,6 +1,7 @@
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;;; GNU Guix --- Functional package management for GNU
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;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick <pgarlick@tourbillion-technology.com>
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;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
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;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
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;;;
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;;; This file is part of GNU Guix.
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;;;
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@ -430,6 +431,10 @@ (define-public fenics-dolfin
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(sha256
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(base32
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"1m91hwcq5gfj4qqswp8l8kj58nia48f0n4kq13w0xqj4biq7rla0"))
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(patches (search-patches "fenics-dolfin-algorithm.patch"
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"fenics-dolfin-demo-init.patch"
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"fenics-dolfin-boost.patch"
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"fenics-dolfin-config-slepc.patch"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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@ -498,11 +503,8 @@ (define-public fenics-dolfin
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;; git-lfs, so only the links are downloaded. The tests that
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;; require the absent meshes cannot run and are skipped.
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;;
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;; Two other serial tests fail and are skipped.
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;; i) demo_stokes-iterative_serial,
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;; The MPI_Comm_rank() function was called before MPI_INIT was
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;; invoked
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;; ii) demo_multimesh-stokes_serial:
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;; One serial test fails and is skipped.
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;; i) demo_multimesh-stokes_serial:
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;; Warning: Found no facets matching domain for boundary
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;; condition.
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;;
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@ -544,8 +546,6 @@ (define-public fenics-dolfin
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"demo_mesh-quality_serial "
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"demo_mesh-quality_mpi "
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"demo_multimesh-stokes_serial "
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"demo_stokes-iterative_serial "
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"demo_stokes-iterative_mpi "
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")\n") port)))
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#t))
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(replace 'check
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