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A repository of Spack packages for installing Firedrake

Python 94.03% Shell 5.97%

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b17jps1 lrtfm mfkiwl jaroslavhron

firedrake-spack's Issues

The file was installed in python path, and will result in error in import.

Thanks for creating this repo to install firedrake with spack.

After install the testing version, I get the following errors when import firedrake.

zzyang@MathWorkstation: ~
$ python
Python 3.8.10 (default, Jun  4 2021, 19:24:32)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import firedrake
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/lib/python3.8/site-packages/firedrake-0+untagged.1.gc3b5440-py3.8-linux-x86_64.egg/firedrake/__init__.py", line 28, in <module>
    firedrake_configuration.setup_cache_dirs()
  File "/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/lib/python3.8/site-packages/firedrake-0+untagged.1.gc3b5440-py3.8-linux-x86_64.egg/firedrake_configuration/__init__.py", line 43, in setup_cache_dirs
    os.environ["PYOP2_CACHE_DIR"] = os.path.join(config["options"]["cache_dir"], "pyop2")
KeyError: 'cache_dir'

Then I copy the file to the python path, and another error shows up.

zzyang@MathWorkstation: ~
$ cp /home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/py-firedrake-testing-5wii6ngzbo7qi325hd73h2wypcy56qpv/.configuration.json /home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/lib/python3.8/site-packages/firedrake-0+untagged.1.gc3b5440-py3.8-linux-x86_64.egg/firedrake_configuration/configuration.json
zzyang@MathWorkstation: ~
$ python
Python 3.8.10 (default, Jun  4 2021, 19:24:32)
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import firedrake
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/lib/python3.8/site-packages/firedrake-0+untagged.1.gc3b5440-py3.8-linux-x86_64.egg/firedrake/__init__.py", line 39, in <module>
    from pyop2 import op2                        # noqa: F401
  File "/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/py-pyop2-master-qfjxifxctyo4eha6v6cgbbha7dnjr5ww/lib/python3.8/site-packages/pyop2/__init__.py", line 4, in <module>
    from pyop2.op2 import *  # noqa
  File "/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/py-pyop2-master-qfjxifxctyo4eha6v6cgbbha7dnjr5ww/lib/python3.8/site-packages/pyop2/op2.py", line 42, in <module>
    from pyop2.sequential import par_loop, Kernel  # noqa: F401
  File "/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/py-pyop2-master-qfjxifxctyo4eha6v6cgbbha7dnjr5ww/lib/python3.8/site-packages/pyop2/sequential.py", line 42, in <module>
    from pyop2 import base
  File "/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/py-pyop2-master-qfjxifxctyo4eha6v6cgbbha7dnjr5ww/lib/python3.8/site-packages/pyop2/base.py", line 64, in <module>
    import loopy
  File "/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/py-loopy-firedrake-ldx2zmspv6acaeokaegnk276oyzl4gv3/lib/python3.8/site-packages/loopy/__init__.py", line 27, in <module>
    from loopy.translation_unit import for_each_kernel
  File "/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/py-loopy-firedrake-ldx2zmspv6acaeokaegnk276oyzl4gv3/lib/python3.8/site-packages/loopy/translation_unit.py", line 43, in <module>
    from pyrsistent import pmap, PMap
ModuleNotFoundError: No module named 'pyrsistent'

I think this one can be fixed by add depends in the package file.

The first error maybe caused by installing the files in python path other than firedrake path?
How can I install the file in the proper palce?

zzyang@MathWorkstation: ~
$ find /home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8* -name '*firedrake*'
/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/bin/firedrake-clean
/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/bin/firedrake-install
/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/bin/firedrake-preprocess-bibtex
/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/bin/firedrake-status
/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/bin/firedrake-zenodo
/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/lib/python3.8/site-packages/firedrake-0+untagged.1.gc3b5440-py3.8-linux-x86_64.egg
/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/lib/python3.8/site-packages/firedrake-0+untagged.1.gc3b5440-py3.8-linux-x86_64.egg/EGG-INFO/scripts/firedrake-clean
/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/lib/python3.8/site-packages/firedrake-0+untagged.1.gc3b5440-py3.8-linux-x86_64.egg/EGG-INFO/scripts/firedrake-install
/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/lib/python3.8/site-packages/firedrake-0+untagged.1.gc3b5440-py3.8-linux-x86_64.egg/EGG-INFO/scripts/firedrake-preprocess-bibtex
/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/lib/python3.8/site-packages/firedrake-0+untagged.1.gc3b5440-py3.8-linux-x86_64.egg/EGG-INFO/scripts/firedrake-status
/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/lib/python3.8/site-packages/firedrake-0+untagged.1.gc3b5440-py3.8-linux-x86_64.egg/EGG-INFO/scripts/firedrake-zenodo
/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/lib/python3.8/site-packages/firedrake-0+untagged.1.gc3b5440-py3.8-linux-x86_64.egg/firedrake
/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/lib/python3.8/site-packages/firedrake-0+untagged.1.gc3b5440-py3.8-linux-x86_64.egg/firedrake_citations
/home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/python-3.8.10-w53qlewfh5ywh4sc4zicthpizfgh32jy/lib/python3.8/site-packages/firedrake-0+untagged.1.gc3b5440-py3.8-linux-x86_64.egg/firedrake_configuration
zzyang@MathWorkstation: ~
$ ls /home/zzyang/spack/opt/spack/linux-rhel7-skylake_avx512/gcc-9.3.0/py-firedrake-testing-5wii6ngzbo7qi325hd73h2wypcy56qpv/lib/python3.8/site-packages/
zzyang@MathWorkstation: ~
$

Some options related to `64-bit-indices` and `complex`

First, thank you for your team making this tool available.

I try to install firedrake with this useful tool, and find some options that should be updated:

+int64 of PETSc should be added if +64-bit-indices is turned on.
+complex of PETSc should be added if +complex is turned on.
For PETSc +chaco is in conflict with +int64
py-pybind11 is one of the dependencies of firedrake.py-islpy.

In addition, I have a question about hypre. It seems hypre has options int64 and complex. If I want to use it in complex and int64 mode, must it be compiled in int64?

Installation issue: petsc

I get the exact same issue as in spack/spack#27851.
PETSC assumes mpiexec as executable.

I installed everything from scratch without trying to provide the system MPI (since I don't know how to do).

Any help?

Updating of loopy make `python -c "import firedrake"` failed

The command raises the error "ImportError: cannot import name 'CachedCombineMapper' from 'pymbolic.mapper' ". It seems that the new version loopy needs the develop version py-pymbolic and the package py-immutables.

Traceback after install firedrake:

[firedrake-real-int32] [z2yang@ws2 firedrake-real-int32]$ python -c "import firedrake"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/z2yang/opt/firedrake-real-int32/.spack-env/view/lib/python3.10/site-packages/firedrake/__init__.py", line 69, in <module>
    from pyop2 import op2                        # noqa: F401
  File "/home/z2yang/opt/firedrake-real-int32/.spack-env/view/lib/python3.10/site-packages/pyop2/__init__.py", line 4, in <module>
    from pyop2.op2 import *  # noqa
  File "/home/z2yang/opt/firedrake-real-int32/.spack-env/view/lib/python3.10/site-packages/pyop2/op2.py", line 38, in <module>
    from pyop2.configuration import configuration
  File "/home/z2yang/opt/firedrake-real-int32/.spack-env/view/lib/python3.10/site-packages/pyop2/configuration.py", line 38, in <module>
    from loopy.target.c import CWithGNULibcTarget
  File "/home/z2yang/opt/firedrake-real-int32/.spack-env/view/lib/python3.10/site-packages/loopy/__init__.py", line 24, in <module>
    from loopy.symbolic import (
  File "/home/z2yang/opt/firedrake-real-int32/.spack-env/view/lib/python3.10/site-packages/loopy/symbolic.py", line 43, in <module>
    from pymbolic.mapper import (
ImportError: cannot import name 'CachedCombineMapper' from 'pymbolic.mapper' (/home/z2yang/opt/firedrake-real-int32/.spack-env/view/lib/python3.10/site-packages/pymbolic/mapper/__init__.py)

Traceback after installing py-pymbolic@develop:

[firedrake-real-int32] [z2yang@ws2 firedrake-real-int32]$ python -c "import firedrake"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/z2yang/opt/firedrake-real-int32/.spack-env/view/lib/python3.10/site-packages/firedrake/__init__.py", line 69, in <module>
    from pyop2 import op2                        # noqa: F401
  File "/home/z2yang/opt/firedrake-real-int32/.spack-env/view/lib/python3.10/site-packages/pyop2/__init__.py", line 4, in <module>
    from pyop2.op2 import *  # noqa
  File "/home/z2yang/opt/firedrake-real-int32/.spack-env/view/lib/python3.10/site-packages/pyop2/op2.py", line 38, in <module>
    from pyop2.configuration import configuration
  File "/home/z2yang/opt/firedrake-real-int32/.spack-env/view/lib/python3.10/site-packages/pyop2/configuration.py", line 38, in <module>
    from loopy.target.c import CWithGNULibcTarget
  File "/home/z2yang/opt/firedrake-real-int32/.spack-env/view/lib/python3.10/site-packages/loopy/__init__.py", line 24, in <module>
    from loopy.symbolic import (
  File "/home/z2yang/opt/firedrake-real-int32/.spack-env/view/lib/python3.10/site-packages/loopy/symbolic.py", line 52, in <module>
    import immutables
ModuleNotFoundError: No module named 'immutables'

Parallel test failed when install firedrake by spack

I install firedrake by adding the following package to spack env:

spack add py-firedrake@develop%gcc +64-bit-indices+complex  ^openblas \
    ^petsc+mumps+scalapack+int64+complex+libyaml+parmmg+mmg \
    ^hypre+complex+int64+superlu-dist && \
spack add py-pygmsh py-meshio py-tqdm py-pyyaml

spack finished the installation by using openmpi.

When I test the installation by

pytest tests/regression/ -k "poisson_strong or stokes_mini or dg_advection" 2>&1

The parallel tests all failed.

Is this a known issue?

The spec of the env and the test log is attached.
firedrake-pytest-log.txt
firedrake-spec.txt

Then I create a new spack env to install firedrake with mpich, the test fails again. The errors are a little different:

==================================== ERRORS ====================================
___________ ERROR at setup of test_poisson_analytic_linear_parallel ____________

item = <Function test_poisson_analytic_linear_parallel>

    def pytest_runtest_setup(item):
        if item.get_closest_marker("parallel"):
            from mpi4py import MPI
            if MPI.COMM_WORLD.size > 1:
                # Turn on source hash checking
                from firedrake import parameters
                from functools import partial

                def _reset(check):
                    parameters["pyop2_options"]["check_src_hashes"] = check

                # Reset to current value when test is cleaned up
>               item.addfinalizer(partial(_reset,
                                          parameters["pyop2_options"]["check_src_hashes"]))
E               AssertionError: (<Function test_poisson_analytic_linear_parallel>, {})

tests/conftest.py:82: AssertionError
=========================== short test summary info ============================

firedrake-mpich-pytest.txt

Thanks for your attention!

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