1. Installation of Firedake#
To install firedrake, the computer should have access to the Internet. Otherwise, please refer to Installation without Network.
1.1. Ubuntu#
1.1.1. Install with default options#
The easiest way to intall firedrake is to download the installation script firedrake-install and run it using Python.
This method will intall the real number version by defaults.
Download the installation script
curl -O https://raw.githubusercontent.com/firedrakeproject/firedrake/master/scripts/firedrake-install
Install by running the script
python3 firedrake-installIf you need to know more installation options, please refer to the help documentation.
python3 firedrake-install -h
Note
Sometimes there may be issues with accessing the pip source during installation, and error messages similar to the following may appear:
Starting new HTTPS connection (6): pypi.org:443
Could not fetch URL https://pypi.org/simple/pulp/: connection error: HTTPSConnectionPool(host='pypi.org', port=443): Max retries exceeded with url: /simple/pulp/ (Caused by NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x7f43dce52bc0>: Failed to establish a new connection: [Errno 101] Network is unreachable')) - skipping
Skipping link: not a file: https://pypi.org/simple/pulp/
Given no hashes to check 0 links for project 'pulp': discarding no candidates
ERROR: Could not find a version that satisfies the requirement PuLP (from versions: none)
ERROR: No matching distribution found for PuLP
This can be fixed by setting the source of pip, such as changing it to the source of USTC:
mkdir -p $HOME/.pip && \
cat > $HOME/.pip/pip.conf <<EOF
[global]
index-url = https://pypi.mirrors.ustc.edu.cn/simple
[install]
trusted-host=pypi.mirrors.ustc.edu.cn
EOF
Note
After the installation, we can install some useful python packages:
pip install gmsh, meshio
1.1.2. Test and run examples#
1.1.2.1. Test firedrake#
source <path-to-firedrake-env>/bin/activate
cd $VIRTUAL_ENV/src/firedrake
pytest tests/regression/ -k "poisson_strong or stokes_mini or dg_advection"
1.1.2.2. Run examples#
Create a python file example.py with the following content:
from firedrake import *
N = 8
mesh = RectangleMesh(nx=N, ny=N, Lx=1, Ly=1)
x, y = SpatialCoordinate(mesh)
f = sin(pi*x)*sin(pi*y)
g = Constant(0)
V = FunctionSpace(mesh, 'CG', degree=1)
u, v = TrialFunction(V), TestFunction(V)
a = inner(grad(u), grad(v))*dx
L = inner(f, v)*dx
bc = DirichletBC(V, g=g, sub_domain='on_boundary')
u_h = Function(V, name='u_h')
solve(a == L, u_h, bcs=bc)
Run in serial:
python example.py
Run in parallel:
mpiexec -n 4 python example.py
1.1.3. Install with custom options#
1.1.3.1. Install real-int32 and/or real-int32-debug#
Download the installation script
curl -O https://raw.githubusercontent.com/firedrakeproject/firedrake/master/scripts/firedrake-install
Enable PETSc’s debug option (optional)
This option is turned off in firedrake by default. If you need to turn it on, you can use the following command to enable it.
DEBUG='-debug' sed -i.bak -e 's/\(--with-debugging=\)0/\11/g' firedrake-install
Install
PETSC_CONFIGURE_OPTIONS=" \ --download-fftw --download-mmg --download-p4est --download-parmmg \ --download-triangle --download-tetgen --download-ctetgen \ --download-hpddm --download-libpng \ --download-pragmatic --download-eigen" \ python3 firedrake-install --disable-ssh \ --documentation-dependencies \ --netgen --slepc \ --venv-name $HOME/opt/firedrake/firedrake-real-int32$DEBUG
Note
If you would like to install int64 version, please use
--petsc-int-type int64instead.pragmaticcannot be used withint64
1.1.3.2. Install complex-int32, and/or complex-int32-debug#
Download the installation script
curl -O https://raw.githubusercontent.com/firedrakeproject/firedrake/master/scripts/firedrake-install
Enable PETSc’s debug option (optional)
DEBUG='-debug' sed -i.bak -e 's/\(--with-debugging=\)0/\11/g' firedrake-install
Install
PETSC_CONFIGURE_OPTIONS=" \ --download-fftw --download-mmg --download-p4est --download-parmmg \ --download-triangle --download-tetgen --download-ctetgen \ --download-hpddm --download-libpng" \ python3 firedrake-install --disable-ssh \ --documentation-dependencies \ --netgen --slepc \ --petsc-int-type int32 --complex \ --venv-name $HOME/opt/firedrake/firedrake-complex-int32$DEBUG
1.1.3.3. Install with MKL#
If you want to use solvers provided by MKL, you can follow the following steps to install firedrake with MKL
Warning
The following steps are not tested for the recent version of firedrake.
Install mkl
Add repo of mkl
wget -O- https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB \ | gpg --dearmor | sudo tee /usr/share/keyrings/oneapi-archive-keyring.gpg > /dev/null echo "deb [signed-by=/usr/share/keyrings/oneapi-archive-keyring.gpg] \ https://apt.repos.intel.com/oneapi all main" \ | sudo tee /etc/apt/sources.list.d/oneAPI.list sudo apt update
Install libs and headers of MKL
# sudo apt install intel-basekit sudo apt install intel-oneapi-mkl sudo apt install intel-oneapi-mkl-devel
Download the installation script and enable the debug option if necessary
Download the script as before
curl -O \ https://raw.githubusercontent.com/firedrakeproject/firedrake/master/scripts/firedrake-install
Enable the debug option and patch the script for
mklandhpddmsed -i.bak -e 's/\(--with-debugging=\)0/\11/g' -e 's/\({0}\/lib\)/\1\/intel64/g' \ -e 's/\(.*\)\(--C\)\(FLAGS=-I{}\/include\)\(.*\)/\1\2\3\4\n\1\2XX\3\4/' \ firedrake-install
's/\(--with-debugging=\)0/\11/g'for petsc debug's/\({0}\/lib\)/\1\/intel64/g'formkllib's/\(.*\)\(--C\)\(FLAGS=-I{}\/include\)\(.*\)/\1\2\3\4\n\1\2XX\3\4/'forhpddmwithmkl
Install Firedrake
real-int32time PETSC_CONFIGURE_OPTIONS="--download-fftw --download-mmg \ --download-p4est --download-parmmg --download-triangle \ --download-tetgen --download-ctetgen --download-hpddm --download-libpng \ --download-slepc --download-pragmatic --download-eigen \ --with-mkl_pardiso-dir=/opt/intel/oneapi/mkl/latest \ --with-mkl_cpardiso-dir=/opt/intel/oneapi/mkl/latest" \ python3 firedrake-install --disable-ssh --documentation-dependencies \ --with-blas=/opt/intel/oneapi/mkl/latest \ --venv-name $HOME/opt/firedrake/firedrake-real-int32-mkl-debug
Fix the error on
mkl_cpardisoIf you run the following test, there will be an error:
$ cd $(dirname `which python`)/../src/petsc/src/binding/petsc4py/demo/kspsolve $ python test_mat_ksp.py -pc_type lu -pc_factor_mat_solver_type mkl_cpardiso -ksp_view Intel MKL FATAL ERROR: Cannot load symbol MKLMPI_Get_wrappers.
Patch
petsc4pyPatch
petsc4pyby the following file$ git diff diff --git a/src/binding/petsc4py/conf/confpetsc.py b/src/binding/petsc4py/conf/confpetsc.py index 5801b146ff..b00fab2d32 100644 --- a/src/binding/petsc4py/conf/confpetsc.py +++ b/src/binding/petsc4py/conf/confpetsc.py @@ -319,6 +319,11 @@ class PetscConfig: self._configure_ext(extension, petsc_inc, preppend=True) self._configure_ext(extension, petsc_lib) + blas_lib = flaglist(self['BLASLAPACK_LIB']) + blas_inc = flaglist(self['BLASLAPACK_INCLUDE']) + self._configure_ext(extension, blas_inc, preppend=True) + self._configure_ext(extension, blas_lib) + def configure_compiler(self, compiler): if compiler.compiler_type != 'unix': return getenv = os.environ.get
Note
The value of BLASLAPACK_LIB is
LASLAPACK_LIB="-Wl,-rpath,/opt/intel/oneapi/mkl/latest/lib/intel64 \ -L/opt/intel/oneapi/mkl/latest/lib/intel64 \ -lmkl_intel_lp64 -lmkl_core -lmkl_gnu_thread \ -lmkl_blacs_intelmpi_lp64 -lgomp -ldl -lpthread"
The other way to fix this is modifing the file
firedrake-installby adding the following content toblas["LDFLAGS"]blas["LDFLAGS"] = "-Wl,-rpath,/opt/intel/oneapi/mkl/latest/lib/intel64 \ -L/opt/intel/oneapi/mkl/latest/lib/intel64 \ -lmkl_intel_lp64 -lmkl_core -lmkl_gnu_thread \ -lmkl_blacs_intelmpi_lp64 -lgomp -ldl -lpthread"
Recompile and install petsc4py (in the activated Firedrake environment)
export PETSC_DIR=$(readlink -f $(dirname `which python`)/../src/petsc) export PETSC_ARCH=default cd $PETSC_DIR/src/binding/petsc4py make clean python -m pip install --no-build-isolation --no-binary mpi4py,randomgen,islpy,numpy \ --no-deps -vvv --ignore-installed .
Install
slepc4pyexport SLEPC_DIR="$(find $PETSC_DIR/$PETSC_ARCH/externalpackages \ -maxdepth 1 -name '*slepc*')" python -m pip install --no-build-isolation --no-binary mpi4py,randomgen,islpy,numpy \ --no-deps -vvv --ignore-installed $SLEPC_DIR/src/binding/slepc4py
The complex version complex-int32 with debug can be installed using the following command.
PETSC_CONFIGURE_OPTIONS=" \
--download-fftw --download-mmg --download-pragmatic --download-eigen \
--download-p4est --download-parmmg --download-triangle \
--download-tetgen --download-ctetgen --download-hpddm --download-libpng \
--download-slepc --download-scalapack --download-mumps \
--with-mkl_pardiso-dir=/opt/intel/oneapi/mkl/latest \
--with-mkl_cpardiso-dir=/opt/intel/oneapi/mkl/latest" \
python3 firedrake-install --disable-ssh \
--documentation-dependencies \
--with-blas=/opt/intel/oneapi/mkl/latest --complex \
--venv-name firedrake/complex-int32-mkl-debug
If you encounter the same error of solver mkl_cpardiso, you can fix it by using the same method as before.
1.1.3.4. Install with petsc packages pre-downloaded into a directory#
Sometimes, some of the packages that petsc depends on cannot be downloaded automatically. We can add the option
--with-packages-download-dir=<path/to/petsc/packages>
to command configure of petsc to obtain the list of required packages.
Then download these packages manually and put them into the path.
Afterwards, configure it again with the above option.
The python script download_petsc_pkgs.py can be used to download the packages.
Save the output of petsc configure to a file, for example pkgs_info.txt.
Then run the following command to download packages:
python3 download_petsc_pkgs.py -d <path/to/petsc/packages> pkgs_info.txt
Here is an example illustrating how to install firedrake with the above option.
Create directory to install firedrake
yang@606d6cb4b0c4:~$ mkdir -p $HOME/opt/firedrake yang@606d6cb4b0c4:~$ cd $HOME/opt/firedrake
Download the install script
yang@606d6cb4b0c4:~/opt/firedrake$ curl -O https://raw.githubusercontent.com/firedrakeproject/firedrake/master/scripts/firedrake-install % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 94330 100 94330 0 0 142k 0 --:--:-- --:--:-- --:--:-- 142k
Create a shell scipt
install.shwith install commandyang@606d6cb4b0c4:~/opt/firedrake$ cat install.sh PETSC_CONFIGURE_OPTIONS=" \ --with-packages-download-dir=$HOME/opt/firedrake/pkgs --download-fftw --download-mmg --download-p4est --download-parmmg \ --download-triangle --download-tetgen --download-ctetgen \ --download-hpddm --download-libpng \ --download-pragmatic --download-eigen" \ python3 firedrake-install --disable-ssh \ --documentation-dependencies \ --netgen --slepc \ --venv-name $HOME/opt/firedrake/firedrake-real-int32
Create the dir to store pkgs for petsc
yang@606d6cb4b0c4:~/opt/firedrake$ mkdir $HOME/opt/firedrake/pkgs
Run the install script first time
This process may take 1-2 minutes before raising exception as expected. Some output is omit as its too long.
yang@606d6cb4b0c4:~/opt/firedrake$ bash install.sh Running firedrake-install --disable-ssh --documentation-dependencies --netgen --slepc --venv-name /home/yang/opt/firedrake/firedrake-real-int32 Checking for presence of package build-essential... installed. Checking for presence of package autoconf... installed. Checking for presence of package automake... installed. ... ... Successfully cloned repository loopy. Checking out branch main Successfully checked out branch main Updating submodules. Successfully updated submodules. Installing petsc/ Depending on your platform, PETSc may take an hour or more to build! Traceback (most recent call last): File "/home/yang/opt/firedrake/firedrake-install", line 1865, in <module> install("petsc/") File "/home/yang/opt/firedrake/firedrake-install", line 1055, in install build_and_install_petsc() File "/home/yang/opt/firedrake/firedrake-install", line 1167, in build_and_install_petsc check_call([python, "./configure", "PETSC_DIR={}".format(petsc_dir), "PETSC_ARCH={}".format(petsc_arch)] + petsc_options) File "/home/yang/opt/firedrake/firedrake-install", line 668, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/lib/python3.10/subprocess.py", line 421, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/lib/python3.10/subprocess.py", line 526, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/home/yang/opt/firedrake/firedrake-real-int32/bin/python', './configure', 'PETSC_DIR=/home/yang/opt/firedrake/firedrake-real-int32/src/petsc', 'PETSC_ARCH=default', '--download-pnetcdf', '--download-metis', '--download-tetgen', '--download-chaco', '--with-c2html=0', '--download-p4est', '--download-pragmatic', '--download-mmg', '--with-debugging=0', '--download-hdf5', '--with-fortran-bindings=0', '--download-scalapack', '--with-packages-download-dir=/home/yang/opt/firedrake/pkgs', '--download-hpddm', '--download-eigen', '--download-bison', '--with-shared-libraries=1', '--download-mumps', '--with-zlib', '--download-hwloc', '--download-libpng', '--download-triangle', '--download-ptscotch', '--download-mpich', '--download-superlu_dist', '--download-cmake', '--download-fftw', '--download-hypre', '--download-suitesparse', '--download-ctetgen', '--download-pastix', '--download-netcdf', '--download-parmmg']' returned non-zero exit status 10. Install log saved in /home/yang/opt/firedrake/firedrake-install.log
Obtain the packages to download from the log file
firedrake-install.logyang@606d6cb4b0c4:~/opt/firedrake$ sed -n '/Download the following/,/Then run/p' firedrake-install.log > pkgs_info.txt yang@606d6cb4b0c4:~/opt/firedrake$ cat pkgs_info.txt 2024-02-01 10:37:28,382 DEBUG Download the following packages to /home/yang/opt/firedrake/pkgs mpich ['https://github.com/pmodels/mpich/releases/download/v4.1.2/mpich-4.1.2.tar.gz', 'https://www.mpich.org/static/downloads/4.1.2/mpich-4.1.2.tar.gz', 'https://web.cels.anl.gov/projects/petsc/download/externalpackages/mpich-4.1.2.tar.gz'] hwloc ['https://download.open-mpi.org/release/hwloc/v2.10/hwloc-2.10.0.tar.gz', 'https://web.cels.anl.gov/projects/petsc/download/externalpackages/hwloc-2.10.0.tar.gz'] cmake ['https://github.com/Kitware/CMake/releases/download/v3.28.1/cmake-3.28.1.tar.gz', 'https://gitlab.kitware.com/cmake/cmake/-/archive/v3.28.1/cmake-v3.28.1.tar.gz'] hdf5 ['https://web.cels.anl.gov/projects/petsc/download/externalpackages/hdf5-1.14.3-p1.tar.bz2'] netcdf ['https://web.cels.anl.gov/projects/petsc/download/externalpackages/netcdf-c-4.9.2-p1.tar.gz'] pnetcdf ['git clone https://github.com/parallel-netcdf/pnetcdf', 'https://github.com/parallel-netcdf/pnetcdf/archive/checkpoint.1.12.3.tar.gz', 'https://parallel-netcdf.github.io/Release/pnetcdf-1.12.3.tar.gz', 'https://web.cels.anl.gov/projects/petsc/download/externalpackages/pnetcdf-1.12.3.tar.gz'] hypre ['git clone https://github.com/hypre-space/hypre', 'https://github.com/hypre-space/hypre/archive/v2.30.0.tar.gz'] chaco ['git clone https://bitbucket.org/petsc/pkg-chaco.git', 'https://bitbucket.org/petsc/pkg-chaco/get/v2.2-p4.tar.gz'] metis ['git clone https://bitbucket.org/petsc/pkg-metis.git', 'https://bitbucket.org/petsc/pkg-metis/get/v5.1.0-p11.tar.gz'] suitesparse ['git clone https://github.com/DrTimothyAldenDavis/SuiteSparse', 'https://github.com/DrTimothyAldenDavis/SuiteSparse/archive/v7.6.0.tar.gz'] eigen ['git clone https://gitlab.com/libeigen/eigen.git', 'https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz', 'https://web.cels.anl.gov/projects/petsc/download/externalpackages/eigen-3.4.0.tar.gz'] ptscotch ['git clone https://gitlab.inria.fr/scotch/scotch.git', 'https://gitlab.inria.fr/scotch/scotch/-/archive/v7.0.3/scotch-v7.0.3.tar.gz', 'https://web.cels.anl.gov/projects/petsc/download/externalpackages/scotch-v7.0.3.tar.gz'] bison ['https://ftp.gnu.org/gnu/bison/bison-3.8.2.tar.gz', 'http://mirrors.kernel.org/gnu/bison/bison-3.8.2.tar.gz'] mumps ['https://graal.ens-lyon.fr/MUMPS/MUMPS_5.6.2.tar.gz', 'https://web.cels.anl.gov/projects/petsc/download/externalpackages/MUMPS_5.6.2.tar.gz'] scalapack ['git clone https://github.com/Reference-ScaLAPACK/scalapack', 'https://github.com/Reference-ScaLAPACK/scalapack/archive/5bad7487f496c811192334640ce4d3fc5f88144b.tar.gz'] pastix ['https://web.cels.anl.gov/projects/petsc/download/externalpackages/pastix_5.2.3.tar.bz2'] superlu_dist ['git clone https://github.com/xiaoyeli/superlu_dist', 'https://github.com/xiaoyeli/superlu_dist/archive/v8.2.1.tar.gz'] triangle ['git clone https://bitbucket.org/petsc/pkg-triangle', 'https://bitbucket.org/petsc/pkg-triangle/get/v1.3-p2.tar.gz'] ctetgen ['git clone https://bitbucket.org/petsc/ctetgen', 'https://bitbucket.org/petsc/ctetgen/get/ctetgen-0.11.tar.gz'] fftw ['https://www.fftw.org/fftw-3.3.10.tar.gz', 'https://web.cels.anl.gov/projects/petsc/download/externalpackages/fftw-3.3.10.tar.gz'] hpddm ['git clone https://github.com/hpddm/hpddm', 'https://github.com/hpddm/hpddm/archive/201eecd26177f88d7bb6287251877d8013fb64d2.tar.gz'] libpng ['https://sourceforge.net/projects/libpng/files/libpng16/1.6.40/libpng-1.6.40.tar.gz', 'https://web.cels.anl.gov/projects/petsc/download/externalpackages/libpng-1.6.40.tar.gz'] mmg ['git clone https://github.com/MmgTools/mmg.git', 'https://github.com/MmgTools/mmg/archive/cc54b4174871212cd32595c5dca732d40e01e90b.tar.gz'] p4est ['git clone https://github.com/cburstedde/p4est', 'https://github.com/cburstedde/p4est/archive/56b58bd7a5462ef85e136cea9fd9ee6bf9558e71.tar.gz'] parmmg ['git clone https://github.com/MmgTools/ParMmg.git', 'https://github.com/MmgTools/ParMmg/archive/eaebcbe53488f11ce68325502c9f760ed250e0b3.tar.gz'] pragmatic ['git clone https://github.com/meshadaptation/pragmatic.git', 'https://github.com/meshadaptation/pragmatic/archive/ef941eddf50a6de307a5d6b54b5d44504dd3ce89.tar.gz'] tetgen ['http://www.tetgen.org/1.5/src/tetgen1.6.0.tar.gz', 'https://web.cels.anl.gov/projects/petsc/download/externalpackages/tetgen1.6.0.tar.gz'] Then run the script again
Download the pkgs
Download the script to download pkgs
yang@606d6cb4b0c4:~/opt/firedrake$ curl -L -O https://zzyang.net/firedrake-notes/_downloads/15cd80c553ab2d83b1094de3a5a5aa5c/download_petsc_pkgs.py % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 2930 100 2930 0 0 4494 0 --:--:-- --:--:-- --:--:-- 4493
Run the download script
This process may take several minutes depending on the network
yang@606d6cb4b0c4:~/opt/firedrake$ python3 download_petsc_pkgs.py -d $HOME/opt/firedrake/pkgs pkgs_info.txt Downloading 27 packages to /home/yang/opt/firedrake/pkgs... [01/27] Download mpich... [1/3] curl -L -O https://github.com/pmodels/mpich/releases/download/v4.1.2/mpich-4.1.2.tar.gz [02/27] Download hwloc... [1/2] curl -L -O https://download.open-mpi.org/release/hwloc/v2.10/hwloc-2.10.0.tar.gz ...... [26/27] Download pragmatic... [1/2] git clone https://github.com/meshadaptation/pragmatic.git [27/27] Download tetgen... [1/2] curl -L -O http://www.tetgen.org/1.5/src/tetgen1.6.0.tar.gz All packages downloaded successfully.
Clean the installation of the first time
yang@606d6cb4b0c4:~/opt/firedrake$ rm -rf firedrake-real-int32
Run the install script for the second time
This may take half to one hour to finish depending on the performance of the computer and the network.
yang@606d6cb4b0c4:~/opt/firedrake$ bash install.sh
Activate the env to use firedrake according to the output of the last step
yang@606d6cb4b0c4:~/opt/firedrake$ source $HOME/opt/firedrake/firedrake-real-int32/bin/activate
1.1.4. Some notes on PETSc#
Enable PETSc with X
Install
libx11-devsudo apt install libx11-dev
Enable
--with-x=1optionThis option is turned off in firedrake by default. If you need to turn it on, you can use the following command to enable it before run the install script.
sed -i.bak -e 's/\(--with-x=\)0/\11/g' firedrake-install
Add
binpath of petsc toPATHThe
bindirectory of petsc provides some useful tools, but it is not added to thePATHby default. We can define commandadd-petsc-bin.alias add-petsc-bin='export \ PATH=$PATH:$(dirname $(which python))/../src/petsc/lib/petsc/bin:$(\ dirname $(which python))/../src/petsc/default/bin'
Executing it in activated firedrake env will add the petsc/bin to
PATH.
1.1.5. Using firedrake in Jupyter-lab#
Install
jupyterlabpython3 -m pip install jupyterlab
Maybe you need add
$HOME/.local/binto environment variablePATH:export PATH=$PATH:$HOME/.local/bin
Configure jupyterlab
Generate config file for customizing jupyter lab:
jupyter lab --generate-config
Set password for jupyter lab:
jupyter lab password #
Configure Browser
In wsl-ubuntu, configure the browser like this:
export BROWSER="/path/to/chrome/or/firefox"
An example of chrome:
export BROWSER='/mnt/c/Program Files/Google/Chrome/Application/chrome.exe'
Now, you can type
jupyter-labto start jupyter. You will see jupyter in browser.Configure kernels
Activate env:
$ source /your/env/path/activate
Add kernels:
(your-venv)$ ipython kernel install --name "local-venv" --user
The output should looks like:
Installed kernelspec local-venv in /path/to/kernels/local-venvwhere the path
/path/to/kernels/local-venvshould have different name in your enviornment.Also, we can find the kernelspec path by run
jupyter kernelspec list, which will output all avaialbe kernels with its path.Now we need check the python path in
kernel.json, which is located in the above path. Make sure it is the python in your env. Otherwise, correct it.Add environment variables to
kernel.json:[1]An exmaple of
kernel.json:{ "argv": [ "/home/yzz/firedrake/real-int32-debug/bin/python", "-m", "ipykernel_launcher", "-f", "{connection_file}" ], "env": { "OMP_NUM_THREADS": "1", "PATH": "/home/yzz/firedrake/real-int32-debug/bin:${PATH}" }, "display_name": "firedrake-real-int32", "language": "python", "metadata": { "debugger": true } }
1.1.6. Update firedrake#
Generally, you can simply run firedrake-update in the activated environment to update firedrake.
If you want to rebuild PETSc (i.e., using the --rebuild option)
and you have used PETSC_CONFIGURE_OPTIONS and --with-blas during the installation,
you also need to use these two options when updating.
In addition, if you installed MKL using the aforementioned method, you may need to modify the firedrake-update script.
The example for firedrake/complex-int32-mkl-debug is as follows:
Modify
firedrake-updatesed -i.bak -e 's/\(--with-debugging=\)0/\11/g' -e 's/\({0}\/lib\)/\1\/intel64/g' \ -e 's/\(.*\)\(--C\)\(FLAGS=-I{}\/include\)\(.*\)/\1\2\3\4\n\1\2XX\3\4/' \ firedrake-update
Update
PETSC_CONFIGURE_OPTIONS=" \ --download-fftw --download-mmg --download-pragmatic --download-eigen \ --download-p4est --download-parmmg --download-triangle \ --download-tetgen --download-ctetgen --download-hpddm --download-libpng \ --download-slepc --download-scalapack --download-mumps \ --with-mkl_pardiso-dir=/opt/intel/oneapi/mkl/latest \ --with-mkl_cpardiso-dir=/opt/intel/oneapi/mkl/latest" \ firedrake-update --rebuild --no-update-script --with-blas=/opt/intel/oneapi/mkl/latest
1.2. Windows#
Install WSL (Windows Subsystem for Linux) on Windows (the system installed is Ubuntu by default) and then install Firedrake as before.
1.2.1. Install WSL#
To install WSL, please see https://docs.microsoft.com/zh-cn/windows/wsl/install.
1.2.2. Install Firedrake#
Follow the installation method for Ubuntu.
1.3. MacOS#
First, install Homebrew[2], and then use Homebrew to install python3. After that, install Firedrake directly, similar to Ubuntu.
Please install pkgconf before start the installation if you add package p4est for PETSc.
Install Homebrew
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
Install python3
When installing python3, you can choose the version you want to install. For example, you can install python3.11 as follows.
brew install python3 brew install m4
Note
If you using Xcode command line tool other then Xcode. You should install m4 using brew or patch the system with m4.
xcode-select -p # this will print the path to command line tools cd <the-path-to-command-line-tools> # should be /Library/Developer/CommandLineTools cd usr/bin ln -s gm4 m4 # need password for the system
Install firedrake
Now, you can follow the installation method for Ubuntu.
curl -O https://raw.githubusercontent.com/firedrakeproject/firedrake/master/scripts/firedrake-install $(brew --prefix)/bin/python3 firedrake-install
1.4. Linux Server#
If the server cannot access the network, please refer Installation without Network. The Firedrake team provides a way[3] to install Firedrake based on Spack[4], a package manager for HPC.
Download spack
mkdir -p $HOME/opt cd $HOME/opt && \ git clone -c feature.manyFiles=true https://github.com/lrtfm/spack.git && \ pushd spack git checkout lrtfm/develop popd source $HOME/opt/spack/share/spack/setup-env.sh
Note
Add the following command to the file $HOME/.bashrc to add shell support for spack.
source $HOME/opt/spack/share/spack/setup-env.sh
Note
On some workstations, the content of the /tmp directory may not have execution permissions. You need to change the spack build directory as follows.
mkdir -p $HOME/.spack && \ cat > $HOME/.spack/config.yaml <<EOF config: build_stage: - \$user_cache_path/stage EOF
Download firedrake-spack
cd $HOME/opt && \ git clone https://github.com/lrtfm/firedrake-spack.git && \ pushd firedrake-spack && \ git checkout lrtfm/air-gapped-install && \ popd
Note
The current version of petsc in firedrakeproject will break when using some compilers: https://lists.mcs.anl.gov/pipermail/petsc-users/2023-April/048482.html. Patch has been added branch
lrtfm/air-gapped-installoffiredrake-spack.Create spack env and add packages
complex-int32
Create spack env
cd $HOME/opt && \ FIREDRAKE_ENV_NAME=firedrake-complex-int32 && \ spack env create -d $FIREDRAKE_ENV_NAME && \ spack env activate -p $FIREDRAKE_ENV_NAME && \ spack -e $SPACK_ENV config add concretizer:unify:true
Add firedrake repo
We add the firedrake repo to the created space env
cd $HOME/opt && \ spack repo add firedrake-spack
Add packages
spack add py-firedrake@develop%gcc +complex ^mpich ^openblas ^slepc+hpddm \ ^petsc+libpng+libyaml+parmmg+mmg+hpddm+tetgen+valgrind \ ^hypre+superlu-dist ^vtk@9.0.3 && \ spack add gmsh py-meshio py-tqdm py-pyyaml py-memory-profiler
real-int32
Create env
cd $HOME/opt && \ FIREDRAKE_ENV_NAME=firedrake-real-int32 && \ spack env create -d $FIREDRAKE_ENV_NAME && \ spack env activate -p $FIREDRAKE_ENV_NAME && \ spack -e $SPACK_ENV config add concretizer:unify:true
Add firedrake repo
cd $HOME/opt && \ spack repo add firedrake-spack
Add packages
Copy the follwing command into bash will raise error. Please copy line by line.
spack add py-firedrake@develop%gcc ^mpich ^openblas ^slepc+hpddm \ ^petsc+libpng+libyaml+parmmg+mmg+hpddm+tetgen+valgrind \ ^hypre+superlu-dist ^vtk@9.0.3 && \ spack add gmsh py-meshio py-tqdm py-pyyaml py-memory-profiler
Note
Installing
vtk@8.x.xandvtk@9.2.2(on some hosts) in spack will fail. We usevtk@9.0.3.(2023-04-30)
Make some packages as develop
This step can be skiped. With this step, we can update firedrake easily in spack.
spack develop py-firedrake@develop && \ spack develop libsupermesh@develop && \ spack develop petsc@develop && \ spack develop slepc@develop && \ spack develop py-fiat@develop && \ spack develop py-finat@develop && \ spack develop py-islpy@develop && \ spack develop py-petsc4py@develop && \ spack develop py-slepc4py@develop && \ spack develop py-pyadjoint@develop && \ spack develop py-pyop2@develop && \ spack develop py-coffee@develop && \ spack develop py-loopy@develop && \ spack develop py-cgen@develop && \ spack develop py-codepy@develop && \ spack develop py-genpy@develop && \ spack develop py-tsfc@develop && \ spack develop py-ufl@develop && \ spack develop chaco@petsc
Note
We do not need the following package when install
int64version:spack develop chaco@petsc
Concretize and install
spack concretize -f 2>&1 | tee $SPACK_ENV/spack-firedrake-develop.log && \ time spack install --fail-fast --show-log-on-error \ --log-file $SPACK_ENV/spack-firedrake-install.log --log-format cdash
1.5. Docker#
1.5.1. Images#
Firedrake team provides some docker images for users to use: https://hub.docker.com/u/firedrakeproject.
For Docker on a server, there may be issues related to file permissions. Try the following script:
firedrake-run