Merge pull request #266 from mfem/mfem_48_dev

MFEM 4.8 support

Author: sshiraiwa

.github/workflows/build-and-test-callable.yml

@@ -49,7 +49,7 @@ on:
       phases:
         description: 'When true, run each build step individually (mfem, swig, pymfem)'
         type: boolean
-        default: true
+        default: false
 
 jobs:
   build-and-test:
@@ -67,11 +67,11 @@ jobs:
       CUDA_HOME: '/usr/local/cuda'
       # These are all passed to setup.py as one concatenated string
       build-flags: >-
-        ${{ inputs.parallel && '--with-parallel' || '' }}
-        ${{ inputs.cuda && '--with-cuda' || '' }}
-        ${{ inputs.libceed && '--with-libceed' || '' }}
-        ${{ inputs.gslib && '--with-gslib' || '' }}
-        ${{ (!(inputs.mfem-branch == 'default') && format('--mfem-branch=''{0}''', inputs.mfem-branch)) || '' }}
+        ${{ inputs.parallel && '-C"with-parallel=Yes"' || '' }}
+        ${{ inputs.cuda && '-C"with-cuda=Yes"' || '' }}
+        ${{ inputs.libceed && '-C"with-libceed=Yes"' || '' }}
+        ${{ inputs.gslib && '-C"with-gslib=Yes"' || '' }}
+        ${{ (!(inputs.mfem-branch == 'default') && format('-C"mfem-branch={0}"', inputs.mfem-branch)) || '' }}
 
     # -------------------------------------------------------------------------------------------------
     # Begin workflow
@@ -89,14 +89,25 @@ jobs:
     # Download/install dependencies
     # -------------------------------------------------------------------------------------------------
     - name: Install core dependencies via requirements.txt
-      run: pip install -r requirements.txt --verbose
+      run: |
+        pip install -U setuptools>=79.0.1
+        pip install -U numpy>=2.0.0
+        pip install -U cmake>=4.0.0
+        pip install -U swig>=4.3
+
+    #- name: Install chrpath on ubuntu
+    #  if: inputs.os == 'ubuntu-latest'
+    #  run: |
+    #    sudo apt-get install chrpath
 
     - name: Install MPI
       if: inputs.parallel
       run: |
-        sudo apt-get install mpich libmpich-dev
+        sudo apt-get install openmpi-bin libopenmpi-dev
+        export OMPI_MCA_rmaps_base_oversubscribe=1
+        # (broken?) sudo apt-get install mpich libmpich-dev
         pip install mpi4py
-
+        mpirun -np 2 python -c "from  mpi4py import MPI;print(MPI.COMM_WORLD.rank)"
 
     - name: Purge PIP chach
       run: pip cache purge
@@ -133,21 +144,26 @@ jobs:
     # -------------------------------------------------------------------------------------------------
     # Build MFEM + SWIG Bindings + PyMFEM
     # -------------------------------------------------------------------------------------------------
-    - name: Build MFEM (step 1)
-      if: inputs.phases
-      run: python setup.py install --ext-only --vv ${{ env.build-flags }}
+    # - name: Build MFEM (step 1)
+    #   if: inputs.phases
+    #   run: pip install -e . -C"--build-option=--ext-only" -C"--build-option=--vv" ${{ env.build-flags }}
+    #   run: python setup.py install --ext-only --vv ${{ env.build-flags }}
+
+    # - name: Build SWIG wrappers (step 2)
+    #   if: inputs.phases
+    #   run: python setup.py install --swig --vv ${{ env.build-flags }}
 
-    - name: Build SWIG wrappers (step 2)
-      if: inputs.phases
-      run: python setup.py install --swig --vv ${{ env.build-flags }}
+    # - name: Build PyMFEM (step 3)
+    #   if: inputs.phases
+    #   run: python setup.py install --skip-ext --skip-swig --vv ${{ env.build-flags }}
 
-    - name: Build PyMFEM (step 3)
-      if: inputs.phases
-      run: python setup.py install --skip-ext --skip-swig --vv ${{ env.build-flags }}
+    #- name: Build all (steps 1-3)
+    #  if: inputs.phases == false
+    #  run: pip install -e . -C"--build-option=--vv" ${{ env.build-flags }}
 
     - name: Build all (steps 1-3)
       if: inputs.phases == false
-      run: python setup.py install --vv ${{ env.build-flags }}
+      run: pip install . ${{ env.build-flags }} --verbose
 
     # -------------------------------------------------------------------------------------------------
     # Run tests

.github/workflows/build-and-test-dispatch.yml

@@ -30,7 +30,7 @@ jobs:
       fail-fast: false
       matrix:
         mfem-branch: [master, default] # 'default' uses a specific commit hash defined in setup.py:repos_sha
-        python-version: ['3.8', '3.9', '3.10', '3.11'] # 3.12 is not supported by scipy
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
         parallel: [false]
     name: test-linux | ${{ matrix.mfem-branch }} | ${{ matrix.python-version }} | ${{ matrix.parallel && 'parallel' || 'serial' }}
     uses: ./.github/workflows/build-and-test-callable.yml
@@ -46,7 +46,7 @@ jobs:
       fail-fast: false
       matrix:
         mfem-branch: [master, default] # 'default' uses a specific commit hash defined in setup.py:repos_sha
-        python-version: ['3.9', '3.10', '3.11'] # 3.12 is not supported by scipy
+        python-version: ['3.9', '3.10', '3.11', '3.12', '3.13']
         parallel: [true]
     name: test-linux | ${{ matrix.mfem-branch }} | ${{ matrix.python-version }} | ${{ matrix.parallel && 'parallel' || 'serial' }}
     uses: ./.github/workflows/build-and-test-callable.yml

.github/workflows/release_binary.yml

@@ -22,8 +22,9 @@ jobs:
           echo "!!!!!: "$REF
           git checkout $REF
           #
-          export PATH=/opt/python/cp37-cp37m/bin:$PATH
+          export PATH=/opt/python/cp38-cp38/bin:$PATH
 
+          pip install -U packaging
           pip3 install wheel six auditwheel twine
           pip3 install urllib3==1.26.6    # use older version to avoid OpenSSL vesion issue
           pip3 install numpy==1.21.6
@@ -36,11 +37,11 @@ jobs:
           ls -l dist/
           #python3 -m twine upload --repository-url https://test.pypi.org/legacy/ --password ${{ secrets.TEST_PYPI_TOKEN }} --username __token__ --verbose dist/*
           python3 -m twine upload --password ${{ secrets.PYPI_TOKEN }} --username __token__ --verbose dist/*
-  make_binary_3_8_9_10_11:
+  make_binary_3_8_9_10_11_12:
     needs: make_sdist
     strategy:
       matrix:
-        pythonpath: ["cp38-cp38", "cp39-cp39", "cp310-cp310", "cp311-cp311"]
+        pythonpath: ["cp38-cp38", "cp39-cp39", "cp310-cp310", "cp311-cp311", "cp312-cp312"]
 
     runs-on: ubuntu-latest
     container: quay.io/pypa/manylinux2014_x86_64
@@ -59,14 +60,17 @@ jobs:
           #
           ls -l /opt/python/
           export PATH=/opt/python/${{ matrix.pythonpath }}/bin:$PATH
+
+          pip install setuptools
+          pip install -U packaging
           pip3 install auditwheel twine
           pip3 install urllib3==1.26.6    # use older version to avoid OpenSSL vesion issue
 
           pip3 install -r requirements.txt
 
           CWD=$PWD
           yum install -y zlib-devel
-          yum install -y chrpath
+          #yum install -y chrpath
 
           mkdir dist
 

.github/workflows/testrelease_binary.yml

@@ -22,8 +22,9 @@ jobs:
           echo "!!!!!: "$REF
           git checkout $REF
           #
-          export PATH=/opt/python/cp37-cp37m/bin:$PATH
+          export PATH=/opt/python/cp38-cp38/bin:$PATH
 
+          pip install -U packaging
           pip3 install wheel six auditwheel twine
           pip3 install urllib3==1.26.6    # use older version to avoid OpenSSL vesion issue
           pip3 install numpy==1.21.6
@@ -35,12 +36,11 @@ jobs:
           python3 setup.py sdist
           ls -l dist/
           python3 -m twine upload --repository-url https://test.pypi.org/legacy/ --password ${{ secrets.TEST_PYPI_TOKEN }} --username __token__ --verbose dist/*
-          #python3 -m twine upload --password ${{ secrets.PYPI_TOKEN }} --username __token__ --verbose dist/*
-  make_binary_3_8_9_10_11:
+  make_binary_3_8_9_10_11_12:
     needs: make_sdist
     strategy:
       matrix:
-        pythonpath: ["cp38-cp38", "cp39-cp39", "cp310-cp310", "cp311-cp311"]
+        pythonpath: ["cp38-cp38", "cp39-cp39", "cp310-cp310", "cp311-cp311", "cp312-cp312"]
 
     runs-on: ubuntu-latest
     container: quay.io/pypa/manylinux2014_x86_64
@@ -60,14 +60,16 @@ jobs:
           ls -l /opt/python/
           export PATH=/opt/python/${{ matrix.pythonpath }}/bin:$PATH
 
+          pip install setuptools
+          pip install -U packaging
           pip3 install auditwheel twine
           pip3 install urllib3==1.26.6    # use older version to avoid OpenSSL vesion issue
 
           pip3 install -r requirements.txt
 
           CWD=$PWD
           yum install -y zlib-devel
-          yum install -y chrpath
+          #yum install -y chrpath
 
           mkdir dist
 

INSTALL.md

@@ -1,14 +1,24 @@
 # Installation Guide
 
-## Basic install
+## Basic serial install
 
-Most users will be fine using the binary bundled in the default `pip` install:
+Most users (on Linux and Mac) will be fine using the binary bundled in the default `pip` install:
 
 ```shell
 pip install mfem
 ```
 The above installation will download and install a *serial* version of `MFEM`.
 
+##  Environmental variables
+Build script checks the following environmental variables
+- CC : c compiler for parallel build
+- CXX : c++ compiler for serial build
+- MPICC : c compiler for parallel build
+- MPICXX : c++ compiler for parallel build
+- CXX11FLAG : C++11 flag for C++ compiler
+- MPIINC : the location of MPI.h (if this variable is set, the parallle PyMFEM is build with CXX, not MPICXX)
+
+
 ##  Building from source
 PyMFEM has many options for installation, when building from source, including:
  - Serial and parallel (MPI) wrappers
@@ -19,15 +29,28 @@ PyMFEM has many options for installation, when building from source, including:
    - `libceed`
    - `metis`
 
-Most of the options for PyMFEM can be used directly when installing via `python setup.py install`, e.g.
+Most of the options for PyMFEM can be used directly when installing via `pip install . or python setup.py install`, e.g.
 ```shell
 git clone git@github:mfem/PyMFEM.git
 cd PyMFEM
+pip install . --user
+
+or
+
 python setup.py install --user
 ```
-For example, parallel (MPI) support is built with  the `--with-parallel` flag:
+
+Note that `python setup.py install` is deprecated and will be removed soon in favor of `pip`.
+When installing via `pip`, options are specified using the `-C` flag using the syntax `-C"name=value"`; e.g. the `--with-parallel` option is now specified as `-C"with-parallel=Yes`.
+The name and value of each option should be written explicitly with a dedicated -C flag.
+
+For example, parallel (MPI) support and GSlib support is built with  `--with-parallel`
+and `--with-gslib' flags as follows.
+
 ```shell
-python setup.py install --with-parallel
+python setup.py install --with-parallel --with-gslib
+or
+pip install . -C"with-parallel=Yes" -C"with-gslib=Yes"
 ```
 
 Note: this option turns on building `metis` and `Hypre`
@@ -105,7 +128,7 @@ option.
 
 (example)
 ```shell
-python setup.py install --mfem-branch=master
+pip install . -C"mfem-branch=master"
 ```
 
 ### Using MFEM build externally.
@@ -136,43 +159,38 @@ and `--mfem-prefix`
 | `--ext-only` | build exteranl libraries and exit.|
 
 During the development, often we update depenencies (such as MFEM) and edit `*.i` file.
+These options allows for building PyMFEM in a step-by-step manner, without rebuilding
+the entire wrapper everytime.
 
-
-First clean everything.
+First clone the repository or clean everything.
 
 ```shell
+git clone git@github.com:mfem/PyMFEM.git;cd PyMFEM
 python setup.py clean --all
 ```
 
-Then, build externals alone
+Then, build externals alone using the ext-only option
 ```shell
-python setup.py install --with-parallel --ext-only --mfem-branch=master
+pip install . -C"ext-only=Yes" --verbose
+pip install . -C"with-parallel=Yes" -C"ext-only=Yes" --verbose
 ```
 
-Then, genrate swig wrappers.
+Then, generate swig wrappers, using the swig option, together with skip-ext, so that
+external libraies are not rebuild.
 ```shell
-python setup.py install --with-parallel --swig --mfem-branch=master
+pip install . -C"skip-ext=Yes"  -C"swig=Yes" --verbose
+pip install . -C"with-parallel=Yes" -C"skip-ext=Yes"  -C"swig=Yes" --verbose
 ```
 
 If you are not happy with the wrapper (`*.cxx` and `*.py`), you edit `*.i` and redo
-the same. When you are happy, build the wrapper. `--swig` does not clean the
-existing wrapper. So, it will only update wrapper for updated `*.i`
-
-When building a wrapper, you can use `--skip-ext` option. By default, it will re-run
-swig to generate entire wrapper codes.
-```shell
-python setup.py install --with-parallel --skip-ext --mfem-branch=master
-```
+the same. When you are happy, build the wrapper with skip-swig and skip-ext.
 
-If you are sure, you could use `--skip-swig` option, so that it compiles the wrapper
-codes without re-generating it.
 ```shell
-python setup.py install --with-parallel --skip-ext --skip-swig --mfem-branch=master
+pip install . -C"skip-ext=Yes"  -C"skip-swig=Yes" --verbose
+pip install . -C"with-parallel=Yes" -C"skip-ext=Yes"  -C"skip-swig=Yes" --verbose
 ```
 
 ### Other options
 `--unverifiedSSL` :
    This addresses error relating SSL certificate. Typical error message is
    `<urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:xxx)>`
-
-

LICENSE

@@ -1,6 +1,6 @@
 BSD 3-Clause License
 
-Copyright (c) 2020, Princeton Plasma Physics Laboratory
+Copyright (c) 2020-2025, Princeton Plasma Physics Laboratory
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

README.md

@@ -10,47 +10,32 @@ By default, "pip install mfem" downloads and builds the serial version of MFEM a
 Additionally, the installer supports building MFEM with specific options together with other external libraries, including MPI version.
 
 ## Install
+### Using pip (Serial MFEM)
 ```shell
-pip install mfem                    # binary install is available only on linux platforms (Py36-310)
+pip install mfem            # binary install is available only on linux platforms (Py38-312)
 
 ```
 
-## Build with additional features (MPI, GPU, GPU-Hypre, GSLIB, SuiteSparse, libCEED, LAPACK)
-The setup script accept various options. TO use it, one can either use --install-option flag
-with pip, or download the package manually and run the script. For example, the one below downloads
-and build parallel version of MFEM library (linked with Metis and Hypre)
-and installs under <prefix>/mfem. See also, docs/install.txt
+### Build with additional features (MPI, GPU, GPU-Hypre, GSLIB, SuiteSparse, libCEED, LAPACK)
 
+The setup script accept various options. Download the package manually and run the script. Examples below downloads and build parallel version of MFEM library (linked with Metis and Hypre) and installs under <prefix>/mfem. See INSTALL.md for various other options
 
-### Build from local source file
 ```shell
 # Download source and build
-$ pip download mfem --no-binary mfem (expand tar.gz file and move to the downloaded directory)
-or clone this repository
 $ git clone https://github.com/mfem/PyMFEM.git
 
-# Then, build it from local source
-$ python -m pip install ./ --install-option="--with-parallel" --install-option="--mfem-branch=master"
-or
-$ python setup.py install --with-parallel # it download and build metis/hypre/mfem
+# Build it from local source with MPI
+$ pip install ./ -C"with-parallel=Yes" --verbose
 
-# Verbose output
-$ python setup.py install --verbose # SWIG output and CMAKE_VERBOSE_MAKEFILE is on
 
 # Cleaning
 $ python setup.py clean --all # clean external dependencies + wrapper code
 
-# Choosing compiler
-$ python setup.py install --with-parallel --CC=icc --CXX=icpc --MPICC=mpiicc --MPICXX=mpiicpc
-
 # Run test
 cd test
 python test_examples.py -serial
 
-# For other configurations, see docs/install.txt or help
-$ python setup.py install --help
-
-```
+# For other configurations, see INSTALL.md
 
 ## Usage
 This example (modified from `ex1.cpp`) solves the Poisson equation,

_build_system/__init__.py

@@ -0,0 +1 @@
+k