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01/02: gnu: fenics-dolfin: Fix build.
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From: |
guix-commits |
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Subject: |
01/02: gnu: fenics-dolfin: Fix build. |
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Date: |
Sat, 5 Feb 2022 01:33:26 -0500 (EST) |
bavier pushed a commit to branch master
in repository guix.
commit 41b11c459bda26b0a7c20ef39486eef917416860
Author: Eric Bavier <bavier@posteo.net>
AuthorDate: Fri Feb 4 23:13:57 2022 -0600
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.
---
gnu/local.mk | 4 ++
gnu/packages/patches/fenics-dolfin-algorithm.patch | 37 +++++++++++++++++
gnu/packages/patches/fenics-dolfin-boost.patch | 45 ++++++++++++++++++++
.../patches/fenics-dolfin-config-slepc.patch | 48 ++++++++++++++++++++++
gnu/packages/patches/fenics-dolfin-demo-init.patch | 39 ++++++++++++++++++
gnu/packages/simulation.scm | 14 +++----
6 files changed, 180 insertions(+), 7 deletions(-)
diff --git a/gnu/local.mk b/gnu/local.mk
index b906d234fc..3ae66803f2 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -1053,6 +1053,10 @@ dist_patch_DATA =
\
%D%/packages/patches/fasthenry-spSolve.patch \
%D%/packages/patches/fasthenry-spFactor.patch \
%D%/packages/patches/fbreader-curl-7.62.patch \
+ %D%/packages/patches/fenics-dolfin-algorithm.patch \
+ %D%/packages/patches/fenics-dolfin-demo-init.patch \
+ %D%/packages/patches/fenics-dolfin-boost.patch \
+ %D%/packages/patches/fenics-dolfin-config-slepc.patch \
%D%/packages/patches/fifengine-boost-compat.patch \
%D%/packages/patches/fifengine-swig-compat.patch \
%D%/packages/patches/fifo-map-fix-flags-for-gcc.patch \
diff --git a/gnu/packages/patches/fenics-dolfin-algorithm.patch
b/gnu/packages/patches/fenics-dolfin-algorithm.patch
new file mode 100644
index 0000000000..e2a3148a64
--- /dev/null
+++ b/gnu/packages/patches/fenics-dolfin-algorithm.patch
@@ -0,0 +1,37 @@
+Fix compilation errors:
+
+ 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&)’:
+ dolfin/geometry/IntersectionConstruction.cpp:442:24: error: ‘min_element’ is
not a member of ‘std’; did you mean ‘tuple_element’?
+ 442 | const auto it = std::min_element(oo.begin(), oo.end());
+ | ^~~~~~~~~~~
+ | tuple_element
+
+ dolfin/mesh/MeshFunction.h: In member function ‘std::vector<long unsigned
int> dolfin::MeshFunction<T>::where_equal(T)’:
+ dolfin/mesh/MeshFunction.h:652:26: error: ‘count’ is not a member of ‘std’;
did you mean ‘cout’?
+ 652 | std::size_t n = std::count(_values.get(), _values.get() + _size,
value);
+ | ^~~~~
+ | cout
+
+Submitted upstream at https://bitbucket.org/fenics-project/dolfin/issues/1128
+
+--- a/dolfin/geometry/IntersectionConstruction.cpp
++++ b/dolfin/geometry/IntersectionConstruction.cpp
+@@ -18,7 +18,8 @@
+ // First added: 2014-02-03
+ // Last changed: 2017-12-12
+
++#include <algorithm>
+ #include <iomanip>
+ #include <dolfin/mesh/MeshEntity.h>
+ #include "predicates.h"
+
+--- a/dolfin/mesh/MeshFunction.h
++++ b/dolfin/mesh/MeshFunction.h
+@@ -24,6 +24,7 @@
+ #ifndef __MESH_FUNCTION_H
+ #define __MESH_FUNCTION_H
+
++#include <algorithm>
+ #include <map>
+ #include <vector>
+
diff --git a/gnu/packages/patches/fenics-dolfin-boost.patch
b/gnu/packages/patches/fenics-dolfin-boost.patch
new file mode 100644
index 0000000000..de56ebb9b3
--- /dev/null
+++ b/gnu/packages/patches/fenics-dolfin-boost.patch
@@ -0,0 +1,45 @@
+The `BOOST_LITTLE_ENDIAN` and `BOOST_BIG_ENDIAN` macros, along with the
+"boost/detail/endian.hpp" header, were deprecated in boost 1.69.0 and finally
+removed in boost 1.73.0. They are superseded by the BOOST_ENDIAN_LITTLE_BYTE
+and BOOST_ENDIAN_BIG_BYTE macros and "boost/predef/other/endian.h" header.
+
+Deprecated:
https://github.com/boostorg/predef/commit/32d4581c1689370444f2e565cfbb8421d5071807
+Removed:
https://github.com/boostorg/predef/commit/aa6e232bf170ad8b856aff9e7c70334f77441c7f
+
+Adaptation of patch from
https://bitbucket.org/fenics-project/dolfin/issues/1116
+
+--- a/dolfin/io/VTKFile.cpp
++++ b/dolfin/io/VTKFile.cpp
+@@ -20,7 +20,7 @@
+ #include <vector>
+ #include <iomanip>
+ #include <boost/cstdint.hpp>
+-#include <boost/detail/endian.hpp>
++#include <boost/predef/other/endian.h>
+
+ #include "pugixml.hpp"
+
+@@ -614,9 +614,9 @@
+ std::string endianness = "";
+ if (encode_string == "binary")
+ {
+- #if defined BOOST_LITTLE_ENDIAN
++ #if defined BOOST_ENDIAN_LITTLE_BYTE
+ endianness = "byte_order=\"LittleEndian\"";
+- #elif defined BOOST_BIG_ENDIAN
++ #elif defined BOOST_ENDIAN_BIG_BYTE
+ endianness = "byte_order=\"BigEndian\"";;
+ #else
+ dolfin_error("VTKFile.cpp",
+
+--- a/dolfin/io/VTKWriter.cpp
++++ b/dolfin/io/VTKWriter.cpp
+@@ -24,7 +24,6 @@
+ #include <sstream>
+ #include <vector>
+ #include <iomanip>
+-#include <boost/detail/endian.hpp>
+
+ #include <dolfin/fem/GenericDofMap.h>
+ #include <dolfin/fem/FiniteElement.h>
+
\ No newline at end of file
diff --git a/gnu/packages/patches/fenics-dolfin-config-slepc.patch
b/gnu/packages/patches/fenics-dolfin-config-slepc.patch
new file mode 100644
index 0000000000..fa06179285
--- /dev/null
+++ b/gnu/packages/patches/fenics-dolfin-config-slepc.patch
@@ -0,0 +1,48 @@
+From https://bitbucket.org/fenics-project/dolfin/issues/1120
+
+From f627a442350560e50dbbb11f7828b6d807369533 Mon Sep 17 00:00:00 2001
+From: Alexei Colin <acolin@isi.edu>
+Date: Sun, 11 Apr 2021 20:40:00 -0400
+Subject: [PATCH] cmake: PETSc,SLEPc: match lowercase .pc pkg-config files
+
+Upstream has moved to lowercase. PETSc has kept the mixed-case file for
+compatibility, but SLEPc hasn't.
+
+pkg_search_module takes multiple patterns and succeeds on first match,
+so this commit is backward-compatible with older installations of PETSc,
+SLEPc.
+
+---
+ cmake/modules/FindPETSc.cmake | 2 +-
+ cmake/modules/FindSLEPc.cmake | 2 +-
+ 2 files changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/cmake/modules/FindPETSc.cmake b/cmake/modules/FindPETSc.cmake
+index 80faffdad..728a6ec30 100644
+--- a/cmake/modules/FindPETSc.cmake
++++ b/cmake/modules/FindPETSc.cmake
+@@ -51,7 +51,7 @@ find_package(PkgConfig REQUIRED)
+
+ # Find PETSc pkg-config file. Note: craypetsc_real is on Cray systems
+ 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:$ENV{PKG_CONFIG_PATH}")
+-pkg_search_module(PETSC craypetsc_real PETSc)
++pkg_search_module(PETSC craypetsc_real petsc PETSc)
+
+ # Extract major, minor, etc from version string
+ if (PETSC_VERSION)
+diff --git a/cmake/modules/FindSLEPc.cmake b/cmake/modules/FindSLEPc.cmake
+index 327cffc23..dec26fcc4 100644
+--- a/cmake/modules/FindSLEPc.cmake
++++ b/cmake/modules/FindSLEPc.cmake
+@@ -48,7 +48,7 @@ find_package(PkgConfig REQUIRED)
+ set(ENV{PKG_CONFIG_PATH}
"$ENV{SLEPC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig:$ENV{SLEPC_DIR}/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}")
+ set(ENV{PKG_CONFIG_PATH}
"$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}/lib/pkgconfig:$ENV{PETSC_DIR}/lib/pkgconfig:$ENV{PKG_CONFIG_PATH}")
+ set(ENV{PKG_CONFIG_PATH}
"$ENV{PETSC_DIR}/$ENV{PETSC_ARCH}:$ENV{PETSC_DIR}:$ENV{PKG_CONFIG_PATH}")
+-pkg_search_module(SLEPC crayslepc_real SLEPc)
++pkg_search_module(SLEPC crayslepc_real slepc SLEPc)
+
+ # Extract major, minor, etc from version string
+ if (SLEPC_VERSION)
+--
+2.30.0
+
diff --git a/gnu/packages/patches/fenics-dolfin-demo-init.patch
b/gnu/packages/patches/fenics-dolfin-demo-init.patch
new file mode 100644
index 0000000000..5a01320147
--- /dev/null
+++ b/gnu/packages/patches/fenics-dolfin-demo-init.patch
@@ -0,0 +1,39 @@
+Ensure MPI is initialized before getting rank, which may be called early by
+Logger::write() via dolfin::info().
+
+Fixes "MPI_Comm_rank called before MPI_INIT" error from
+`demo_stokes-iterative_serial` and `demo_waveguide_serial` tests.
+
+Submitted upstream at https://bitbucket.org/fenics-project/dolfin/issues/1127
+
+--- a/dolfin/common/MPI.cpp
++++ b/dolfin/common/MPI.cpp
+@@ -143,6 +143,7 @@ MPI_Info& dolfin::MPIInfo::operator*()
+ unsigned int dolfin::MPI::rank(const MPI_Comm comm)
+ {
+ #ifdef HAS_MPI
++ SubSystemsManager::init_mpi();
+ int rank;
+ MPI_Comm_rank(comm, &rank);
+ return rank;
+diff --git a/dolfin/common/MPI.h b/dolfin/common/MPI.h
+index b93f6df30..854114a3f 100644
+--- a/dolfin/common/MPI.h
++++ b/dolfin/common/MPI.h
+@@ -102,12 +102,13 @@ namespace dolfin
+ /// communicator
+ void reset(MPI_Comm comm);
+
+- /// Return process rank for the communicator
++ /// Return process rank for the communicator. This function will
++ /// also initialize MPI if it hasn't already been initialised.
+ unsigned int rank() const;
+
+ /// Return size of the group (number of processes) associated
+- /// with the communicator. This function will also intialise MPI
+- /// if it hasn't already been intialised.
++ /// with the communicator. This function will also initialise MPI
++ /// if it hasn't already been initialised.
+ unsigned int size() const;
+
+ /// Set a barrier (synchronization point)
diff --git a/gnu/packages/simulation.scm b/gnu/packages/simulation.scm
index 240549be47..3f2d8e136d 100644
--- a/gnu/packages/simulation.scm
+++ b/gnu/packages/simulation.scm
@@ -1,6 +1,7 @@
;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2017, 2018, 2019, 2020, 2021 Paul Garlick
<pgarlick@tourbillion-technology.com>
;;; Copyright © 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com>
+;;; Copyright © 2022 Eric Bavier <bavier@posteo.net>
;;;
;;; This file is part of GNU Guix.
;;;
@@ -430,6 +431,10 @@ FFC is part of the FEniCS Project.")
(sha256
(base32
"1m91hwcq5gfj4qqswp8l8kj58nia48f0n4kq13w0xqj4biq7rla0"))
+ (patches (search-patches "fenics-dolfin-algorithm.patch"
+ "fenics-dolfin-demo-init.patch"
+ "fenics-dolfin-boost.patch"
+ "fenics-dolfin-config-slepc.patch"))
(modules '((guix build utils)))
(snippet
'(begin
@@ -498,11 +503,8 @@ FFC is part of the FEniCS Project.")
;; git-lfs, so only the links are downloaded. The tests that
;; require the absent meshes cannot run and are skipped.
;;
- ;; Two other serial tests fail and are skipped.
- ;; i) demo_stokes-iterative_serial,
- ;; The MPI_Comm_rank() function was called before MPI_INIT was
- ;; invoked
- ;; ii) demo_multimesh-stokes_serial:
+ ;; One serial test fails and is skipped.
+ ;; i) demo_multimesh-stokes_serial:
;; Warning: Found no facets matching domain for boundary
;; condition.
;;
@@ -544,8 +546,6 @@ FFC is part of the FEniCS Project.")
"demo_mesh-quality_serial "
"demo_mesh-quality_mpi "
"demo_multimesh-stokes_serial "
- "demo_stokes-iterative_serial "
- "demo_stokes-iterative_mpi "
")\n") port)))
#t))
(replace 'check