mirror of
https://github.com/mindthemath/fenics.git
synced 2025-05-11 19:34:37 -06:00
working compilations
This commit is contained in:
Michael Pilosov
commit
9d8e9e6ab1
72
Dockerfile
Normal file
72
Dockerfile
Normal file
@ -0,0 +1,72 @@
|
||||
FROM docker.io/python:3.9.7-bullseye
|
||||
|
||||
ARG DEBIAN_FRONTEND=noninteractive
|
||||
# dolfin
|
||||
RUN apt-get update -yqq && \
|
||||
apt-get install -yqq \
|
||||
build-essential \
|
||||
cmake \
|
||||
gfortran \
|
||||
liblapack3 liblapack-dev \
|
||||
libblas3 libblas-dev \
|
||||
libeigen3-dev \
|
||||
libboost-all-dev \
|
||||
petsc-dev \
|
||||
slepc-dev \
|
||||
&& \
|
||||
apt-get -qq purge && \
|
||||
apt-get -qq clean && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
RUN pip install numpy scipy
|
||||
# fenics
|
||||
RUN pip install -U fenics-ffc
|
||||
ENV FENICS_VERSION=2019.1.0.post0
|
||||
RUN mkdir -p /tmp/src/
|
||||
|
||||
RUN git config --global user.email mm@clfx.cc
|
||||
RUN git config --global user.name mm
|
||||
|
||||
#RUN apt-get update -yqq && apt-get install libopenmpi-dev
|
||||
RUN cd /tmp/src/ && \
|
||||
git clone --branch=$FENICS_VERSION https://bitbucket.org/fenics-project/dolfin
|
||||
COPY *.patch /tmp/src/dolfin/
|
||||
RUN cd /tmp/src/dolfin && \
|
||||
git am algorithm.patch && \
|
||||
git am boost.patch && \
|
||||
cd .. && \
|
||||
mkdir dolfin/build && cd dolfin/build && \
|
||||
cmake .. && make install
|
||||
|
||||
ENV PYBIND11_VERSION=2.2.3
|
||||
|
||||
RUN cd /tmp/src/ && \
|
||||
wget -nc --quiet https://github.com/pybind/pybind11/archive/v${PYBIND11_VERSION}.tar.gz && \
|
||||
tar -xf v${PYBIND11_VERSION}.tar.gz && \
|
||||
cd pybind11-${PYBIND11_VERSION} && \
|
||||
mkdir build && cd build && \
|
||||
cmake -DPYBIND11_TEST=off .. && make install && \
|
||||
rm -rf v${PYBIND11_VERSION}.tar.gz
|
||||
|
||||
RUN cd /tmp/src/dolfin/python && \
|
||||
pip3 install .
|
||||
|
||||
# mshr
|
||||
RUN apt-get update -yqq && \
|
||||
apt-get install -yqq \
|
||||
libgmp-dev \
|
||||
libmpfr-dev \
|
||||
&& \
|
||||
apt-get -qq purge && \
|
||||
apt-get -qq clean && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
RUN cd /tmp/src/ && \
|
||||
git clone --branch=2019.1.0 https://bitbucket.org/fenics-project/mshr && \
|
||||
mkdir mshr/build && cd mshr/build && \
|
||||
cmake .. && make install
|
||||
|
||||
RUN cd /tmp/src/mshr/python && \
|
||||
pip3 install .
|
||||
|
||||
RUN echo "source /usr/local/share/dolfin/dolfin.conf" >> /root/.profile
|
||||
73
Dockerfile-2019.1.0
Normal file
73
Dockerfile-2019.1.0
Normal file
@ -0,0 +1,73 @@
|
||||
FROM docker.io/python:3.9.7-buster
|
||||
|
||||
ARG DEBIAN_FRONTEND=noninteractive
|
||||
# dolfin
|
||||
RUN apt-get update -yqq && \
|
||||
apt-get install -yqq \
|
||||
build-essential \
|
||||
cmake \
|
||||
gfortran \
|
||||
liblapack3 liblapack-dev \
|
||||
libblas3 libblas-dev \
|
||||
libeigen3-dev \
|
||||
libboost-all-dev \
|
||||
petsc-dev \
|
||||
slepc-dev \
|
||||
&& \
|
||||
apt-get -qq purge && \
|
||||
apt-get -qq clean && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
RUN pip install numpy scipy
|
||||
# fenics
|
||||
RUN pip install -U fenics-ffc
|
||||
ENV FENICS_VERSION=2019.1.0
|
||||
RUN mkdir -p /tmp/src/
|
||||
|
||||
RUN git config --global user.email mm@clfx.cc
|
||||
RUN git config --global user.name mm
|
||||
|
||||
#RUN apt-get update -yqq && apt-get install libopenmpi-dev
|
||||
RUN cd /tmp/src/ && \
|
||||
git clone --branch=$FENICS_VERSION https://bitbucket.org/fenics-project/dolfin
|
||||
COPY *.patch /tmp/src/dolfin/
|
||||
RUN cd /tmp/src/dolfin && \
|
||||
git revert 8e92f6ee1bb004ab95d9f0788eab25a2b7c45010 && \
|
||||
git am algorithm.patch && \
|
||||
git am boost.patch && \
|
||||
cd .. && \
|
||||
mkdir dolfin/build && cd dolfin/build && \
|
||||
cmake .. && make install
|
||||
|
||||
ENV PYBIND11_VERSION=2.2.3
|
||||
|
||||
RUN cd /tmp/src/ && \
|
||||
wget -nc --quiet https://github.com/pybind/pybind11/archive/v${PYBIND11_VERSION}.tar.gz && \
|
||||
tar -xf v${PYBIND11_VERSION}.tar.gz && \
|
||||
cd pybind11-${PYBIND11_VERSION} && \
|
||||
mkdir build && cd build && \
|
||||
cmake -DPYBIND11_TEST=off .. && make install && \
|
||||
rm -rf v${PYBIND11_VERSION}.tar.gz
|
||||
|
||||
RUN cd /tmp/src/dolfin/python && \
|
||||
pip3 install .
|
||||
|
||||
# mshr
|
||||
RUN apt-get update -yqq && \
|
||||
apt-get install -yqq \
|
||||
libgmp-dev \
|
||||
libmpfr-dev \
|
||||
&& \
|
||||
apt-get -qq purge && \
|
||||
apt-get -qq clean && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
RUN cd /tmp/src/ && \
|
||||
git clone --branch=$FENICS_VERSION https://bitbucket.org/fenics-project/mshr && \
|
||||
mkdir mshr/build && cd mshr/build && \
|
||||
cmake .. && make install
|
||||
|
||||
RUN cd /tmp/src/mshr/python && \
|
||||
pip3 install .
|
||||
|
||||
RUN echo "source /usr/local/share/dolfin/dolfin.conf" >> /root/.profile
|
||||
72
Dockerfile-2019.1.0.post0
Normal file
72
Dockerfile-2019.1.0.post0
Normal file
@ -0,0 +1,72 @@
|
||||
FROM docker.io/python:3.9.7-bullseye
|
||||
|
||||
ARG DEBIAN_FRONTEND=noninteractive
|
||||
# dolfin
|
||||
RUN apt-get update -yqq && \
|
||||
apt-get install -yqq \
|
||||
build-essential \
|
||||
cmake \
|
||||
gfortran \
|
||||
liblapack3 liblapack-dev \
|
||||
libblas3 libblas-dev \
|
||||
libeigen3-dev \
|
||||
libboost-all-dev \
|
||||
petsc-dev \
|
||||
slepc-dev \
|
||||
&& \
|
||||
apt-get -qq purge && \
|
||||
apt-get -qq clean && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
RUN pip install numpy scipy
|
||||
# fenics
|
||||
RUN pip install -U fenics-ffc
|
||||
ENV FENICS_VERSION=2019.1.0.post0
|
||||
RUN mkdir -p /tmp/src/
|
||||
|
||||
RUN git config --global user.email mm@clfx.cc
|
||||
RUN git config --global user.name mm
|
||||
|
||||
#RUN apt-get update -yqq && apt-get install libopenmpi-dev
|
||||
RUN cd /tmp/src/ && \
|
||||
git clone --branch=$FENICS_VERSION https://bitbucket.org/fenics-project/dolfin
|
||||
COPY *.patch /tmp/src/dolfin/
|
||||
RUN cd /tmp/src/dolfin && \
|
||||
git am algorithm.patch && \
|
||||
git am boost.patch && \
|
||||
cd .. && \
|
||||
mkdir dolfin/build && cd dolfin/build && \
|
||||
cmake .. && make install
|
||||
|
||||
ENV PYBIND11_VERSION=2.2.3
|
||||
|
||||
RUN cd /tmp/src/ && \
|
||||
wget -nc --quiet https://github.com/pybind/pybind11/archive/v${PYBIND11_VERSION}.tar.gz && \
|
||||
tar -xf v${PYBIND11_VERSION}.tar.gz && \
|
||||
cd pybind11-${PYBIND11_VERSION} && \
|
||||
mkdir build && cd build && \
|
||||
cmake -DPYBIND11_TEST=off .. && make install && \
|
||||
rm -rf v${PYBIND11_VERSION}.tar.gz
|
||||
|
||||
RUN cd /tmp/src/dolfin/python && \
|
||||
pip3 install .
|
||||
|
||||
# mshr
|
||||
RUN apt-get update -yqq && \
|
||||
apt-get install -yqq \
|
||||
libgmp-dev \
|
||||
libmpfr-dev \
|
||||
&& \
|
||||
apt-get -qq purge && \
|
||||
apt-get -qq clean && \
|
||||
rm -rf /var/lib/apt/lists/*
|
||||
|
||||
RUN cd /tmp/src/ && \
|
||||
git clone --branch=2019.1.0 https://bitbucket.org/fenics-project/mshr && \
|
||||
mkdir mshr/build && cd mshr/build && \
|
||||
cmake .. && make install
|
||||
|
||||
RUN cd /tmp/src/mshr/python && \
|
||||
pip3 install .
|
||||
|
||||
RUN echo "source /usr/local/share/dolfin/dolfin.conf" >> /root/.profile
|
||||
7
Makefile
Normal file
7
Makefile
Normal file
@ -0,0 +1,7 @@
|
||||
build: 2019.1.0
|
||||
|
||||
2019.1.0:
|
||||
docker build -t fenics -t fenics-2019.1.0 -f Dockerfile-2019.1.0
|
||||
|
||||
2019.1.0.post0:
|
||||
docker build -t fenics -t fenics-2019.1.0.post0 -f Dockerfile-2019.1.0.post0
|
||||
29
README.md
Normal file
29
README.md
Normal file
@ -0,0 +1,29 @@
|
||||
# fenics installation
|
||||
|
||||
Comes with `dolfin` / `fenics` / `mshr`.
|
||||
Batteries: `petsc`, `slepc`, `boost`, `blas`, `lapack`, `fortran`, `eigen3`
|
||||
Also includes: `numpy` and `scipy`
|
||||
|
||||
Primarily for use as a base image (reflecting the desired python version)
|
||||
|
||||
```sh
|
||||
make
|
||||
```
|
||||
|
||||
```sh
|
||||
docker run --rm -ti fenics bash
|
||||
```
|
||||
|
||||
There is also the option to build the latest release
|
||||
|
||||
```sh
|
||||
make 2019.1.0.post0
|
||||
```
|
||||
|
||||
|
||||
## patches
|
||||
Some patches needed to be applied to successfully compile.
|
||||
|
||||
On `bullseye`, `petsc` causes problems which are fixed by using `2019.1.0.post0`.
|
||||
There is an unused patch for `petsc` and `slepsc` which is included "just in case" it becomes useful at a future date.
|
||||
|
||||
39
algorithm.patch
Normal file
39
algorithm.patch
Normal file
@ -0,0 +1,39 @@
|
||||
From 569bbc7f0d218432e76e68137b3f647b4b8faa6f Mon Sep 17 00:00:00 2001
|
||||
From: =?UTF-8?q?Stefan=20Br=C3=BCns?= <stefan.bruens@rwth-aachen.de>
|
||||
Date: Thu, 15 Oct 2020 16:09:19 +0200
|
||||
Subject: [PATCH] Add missing algorithm include for std::min_element/count
|
||||
|
||||
algorithm is no longer pulled in implicitly by current boost versions,
|
||||
do it explicitly.
|
||||
---
|
||||
dolfin/geometry/IntersectionConstruction.cpp | 1 +
|
||||
dolfin/mesh/MeshFunction.h | 1 +
|
||||
2 files changed, 2 insertions(+)
|
||||
|
||||
diff --git a/dolfin/geometry/IntersectionConstruction.cpp b/dolfin/geometry/IntersectionConstruction.cpp
|
||||
index 765dbb6..7ba99a8 100644
|
||||
--- a/dolfin/geometry/IntersectionConstruction.cpp
|
||||
+++ b/dolfin/geometry/IntersectionConstruction.cpp
|
||||
@@ -18,6 +18,7 @@
|
||||
// First added: 2014-02-03
|
||||
// Last changed: 2017-12-12
|
||||
|
||||
+#include <algorithm>
|
||||
#include <iomanip>
|
||||
#include <dolfin/mesh/MeshEntity.h>
|
||||
#include "predicates.h"
|
||||
diff --git a/dolfin/mesh/MeshFunction.h b/dolfin/mesh/MeshFunction.h
|
||||
index 08cbc82..4e68324 100644
|
||||
--- a/dolfin/mesh/MeshFunction.h
|
||||
+++ b/dolfin/mesh/MeshFunction.h
|
||||
@@ -27,6 +27,7 @@
|
||||
#include <map>
|
||||
#include <vector>
|
||||
|
||||
+#include <algorithm>
|
||||
#include <memory>
|
||||
#include <unordered_set>
|
||||
#include <dolfin/common/Hierarchical.h>
|
||||
--
|
||||
2.28.0
|
||||
|
||||
50
boost.patch
Normal file
50
boost.patch
Normal file
@ -0,0 +1,50 @@
|
||||
From 50d619e29f7664825a87fa526d3d933b521fabf0 Mon Sep 17 00:00:00 2001
|
||||
From: =?UTF-8?q?Stefan=20Br=C3=BCns?= <stefan.bruens@rwth-aachen.de>
|
||||
Date: Thu, 15 Oct 2020 16:44:30 +0200
|
||||
Subject: [PATCH] Use __BYTE_ORDER__ instead of removed Boost endian.hpp
|
||||
|
||||
endian.hpp has been removed with Boost 1.73.
|
||||
---
|
||||
dolfin/io/VTKFile.cpp | 5 ++---
|
||||
dolfin/io/VTKWriter.cpp | 1 -
|
||||
2 files changed, 2 insertions(+), 4 deletions(-)
|
||||
|
||||
diff --git a/dolfin/io/VTKFile.cpp b/dolfin/io/VTKFile.cpp
|
||||
index 2fee53b..4dba84d 100644
|
||||
--- a/dolfin/io/VTKFile.cpp
|
||||
+++ b/dolfin/io/VTKFile.cpp
|
||||
@@ -20,7 +20,6 @@
|
||||
#include <vector>
|
||||
#include <iomanip>
|
||||
#include <boost/cstdint.hpp>
|
||||
-#include <boost/detail/endian.hpp>
|
||||
|
||||
#include "pugixml.hpp"
|
||||
|
||||
@@ -614,9 +613,9 @@ void VTKFile::vtk_header_open(std::size_t num_vertices, std::size_t num_cells,
|
||||
std::string endianness = "";
|
||||
if (encode_string == "binary")
|
||||
{
|
||||
- #if defined BOOST_LITTLE_ENDIAN
|
||||
+ #if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
|
||||
endianness = "byte_order=\"LittleEndian\"";
|
||||
- #elif defined BOOST_BIG_ENDIAN
|
||||
+ #elif __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__
|
||||
endianness = "byte_order=\"BigEndian\"";;
|
||||
#else
|
||||
dolfin_error("VTKFile.cpp",
|
||||
diff --git a/dolfin/io/VTKWriter.cpp b/dolfin/io/VTKWriter.cpp
|
||||
index eff6934..b57a665 100644
|
||||
--- 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>
|
||||
--
|
||||
2.28.0
|
||||
|
||||
73
petsc-slepc.patch
Normal file
73
petsc-slepc.patch
Normal file
@ -0,0 +1,73 @@
|
||||
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.
|
||||
|
||||
PETSC: https://gitlab.com/petsc/petsc/-/merge_requests/2754
|
||||
|
||||
commit 6fe8eb356ce6cf9027a2b889b1835f808039fe5e
|
||||
Merge: fd0ee0fbd7 2eefe1c6f1
|
||||
Author: Satish Balay <balay@mcs.anl.gov>
|
||||
Date: Tue Jun 9 01:08:49 2020 +0000
|
||||
|
||||
Merge branch 'MR--config-lowercase-pkgname' into 'master'
|
||||
|
||||
config: pkg-config: default to lowercase file.pc
|
||||
|
||||
See merge request petsc/petsc!2754
|
||||
|
||||
SLEPc: https://gitlab.com/slepc/slepc/-/merge_requests/68
|
||||
|
||||
commit 1632350b0a681e0c4fd08c171912be6e17f3c3f7
|
||||
Merge: 3c38a3419 b2fcc7199
|
||||
Author: Jose E. Roman <jroman@dsic.upv.es>
|
||||
Date: Sun Jun 14 16:19:22 2020 +0000
|
||||
|
||||
Merge branch 'jose/pkg-config' into 'master'
|
||||
|
||||
pkg-config: default to lowercase file.pc
|
||||
|
||||
See merge request slepc/slepc!68
|
||||
|
||||
Signed-off-by: Alexei Colin <acolin@isi.edu>
|
||||
---
|
||||
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
|
||||
|
||||
Loading…
Reference in New Issue
Block a user