packages that need to be installed inside the firedrake environment

[rhaynes74]

Hi folks, the install instructions were unclear about the packages that need to be installed (by pip say) after the activation of the firedrake environment. What about mpi libraries? others?

[connorjward]

The installation script will install everything that you need in order to run Firedrake. We install MPI (specifically MPICH) as part of installing PETSc so running mpiexec -np <N> python myfiredrakescript.py should simply work (with an activated venv).

[rhaynes74]

Ok - thanks. The reason I asked is the following failed testing after install (install was successful).

cd $VIRTUAL_ENV/src/firedrake
pytest tests/regression/ -k "poisson_strong or stokes_mini or dg_advection"
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
============================= test session starts ==============================
platform darwin -- Python 3.11.3, pytest-7.3.1, pluggy-1.0.0
rootdir: /Users/rhaynes/firedrake/src/firedrake
configfile: setup.cfg
plugins: nbval-0.10.0, mpi-0.1, xdist-3.2.1, anyio-3.6.2
collected 3154 items / 3127 deselected / 27 selected

tests/regression/test_dg_advection.py .F.F [ 14%]
tests/regression/test_poisson_strong_bcs.py ................F [ 77%]
tests/regression/test_poisson_strong_bcs_nitsche.py .... [ 92%]
tests/regression/test_stokes_mini.py .. [100%]

=================================== FAILURES ===================================
________________ test_dg_advection_icosahedral_sphere_parallel _________________

args = (), kwargs = {}

def parallel_callback(*args, **kwargs):

   subprocess.run(cmd, check=True)

../pytest-mpi/pytest_mpi.py:62:

---

input = None, capture_output = False, timeout = None, check = True
popenargs = (['mpiexec', '-n', '1', '-genv', '_PYTEST_MPI_CHILD_PROCESS', '1', ...],)
kwargs = {}
process = <Popen: returncode: 15 args: ['mpiexec', '-n', '1', '-genv', '_PYTEST_MPI_CH...>
stdout = None, stderr = None, retcode = 15

def run(*popenargs,
        input=None, capture_output=False, timeout=None, check=False, **kwargs):
    """Run command with arguments and return a CompletedProcess instance.

    The returned instance will have attributes args, returncode, stdout and
    stderr. By default, stdout and stderr are not captured, and those attributes
    will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
    or pass capture_output=True to capture both.

    If check is True and the exit code was non-zero, it raises a
    CalledProcessError. The CalledProcessError object will have the return code
    in the returncode attribute, and output & stderr attributes if those streams
    were captured.

    If timeout is given, and the process takes too long, a TimeoutExpired
    exception will be raised.

    There is an optional argument "input", allowing you to
    pass bytes or a string to the subprocess's stdin.  If you use this argument
    you may not also use the Popen constructor's "stdin" argument, as
    it will be used internally.

    By default, all communication is in bytes, and therefore any "input" should
    be bytes, and the stdout and stderr will be bytes. If in text mode, any
    "input" should be a string, and stdout and stderr will be strings decoded
    according to locale encoding, or by "encoding" if set. Text mode is
    triggered by setting any of text, encoding, errors or universal_newlines.

    The other arguments are the same as for the Popen constructor.
    """
    if input is not None:
        if kwargs.get('stdin') is not None:
            raise ValueError('stdin and input arguments may not both be used.')
        kwargs['stdin'] = PIPE

    if capture_output:
        if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
            raise ValueError('stdout and stderr arguments may not be used '
                             'with capture_output.')
        kwargs['stdout'] = PIPE
        kwargs['stderr'] = PIPE

    with Popen(*popenargs, **kwargs) as process:
        try:
            stdout, stderr = process.communicate(input, timeout=timeout)
        except TimeoutExpired as exc:
            process.kill()
            if _mswindows:
                # Windows accumulates the output in a single blocking
                # read() call run on child threads, with the timeout
                # being done in a join() on those threads.  communicate()
                # _after_ kill() is required to collect that and add it
                # to the exception.
                exc.stdout, exc.stderr = process.communicate()
            else:
                # POSIX _communicate already populated the output so
                # far into the TimeoutExpired exception.
                process.wait()
            raise
        except:  # Including KeyboardInterrupt, communicate handled that.
            process.kill()
            # We don't call process.wait() as .__exit__ does that for us.
            raise
        retcode = process.poll()
        if check and retcode:

          raise CalledProcessError(retcode, process.args,

                                     output=stdout, stderr=stderr)

E subprocess.CalledProcessError: Command '['mpiexec', '-n', '1', '-genv', '_PYTEST_MPI_CHILD_PROCESS', '1', 'python', '-m', 'pytest', '--runxfail', '-s', '-q', '/Users/rhaynes/firedrake/src/firedrake/tests/regression/test_dg_advection.py::test_dg_advection_icosahedral_sphere_parallel', ':', '-n', '2', 'python', '-m', 'pytest', '--runxfail', '-s', '-q', '/Users/rhaynes/firedrake/src/firedrake/tests/regression/test_dg_advection.py::test_dg_advection_icosahedral_sphere_parallel', '--tb=no', '--no-summary', '--no-header', '--disable-warnings', '--show-capture=no']' returned non-zero exit status 15.

/opt/homebrew/Cellar/[email protected]/3.11.3/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py:571: CalledProcessError
----------------------------- Captured stderr call -----------------------------
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
Fatal error in internal_Init_thread: Other MPI error, error stack:
internal_Init_thread(67)...........: MPI_Init_thread(argc=0x0, argv=0x0, required=3, provided=0x16aeb15f0) failed
MPII_Init_thread(234)..............:
MPID_Init(67)......................:
init_world(171)....................: channel initialization failed
MPIDI_CH3_Init(84).................:
MPID_nem_init(314).................:
MPID_nem_tcp_init(175).............:
MPID_nem_tcp_get_business_card(397):
GetSockInterfaceAddr(370)..........: gethostbyname failed, segrprolt092 (errno 0)
___________________ test_dg_advection_cubed_sphere_parallel ____________________

args = (), kwargs = {}

def parallel_callback(*args, **kwargs):

   subprocess.run(cmd, check=True)

../pytest-mpi/pytest_mpi.py:62:

---

input = None, capture_output = False, timeout = None, check = True
popenargs = (['mpiexec', '-n', '1', '-genv', '_PYTEST_MPI_CHILD_PROCESS', '1', ...],)
kwargs = {}
process = <Popen: returncode: 15 args: ['mpiexec', '-n', '1', '-genv', '_PYTEST_MPI_CH...>
stdout = None, stderr = None, retcode = 15

def run(*popenargs,
        input=None, capture_output=False, timeout=None, check=False, **kwargs):
    """Run command with arguments and return a CompletedProcess instance.

    The returned instance will have attributes args, returncode, stdout and
    stderr. By default, stdout and stderr are not captured, and those attributes
    will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
    or pass capture_output=True to capture both.

    If check is True and the exit code was non-zero, it raises a
    CalledProcessError. The CalledProcessError object will have the return code
    in the returncode attribute, and output & stderr attributes if those streams
    were captured.

    If timeout is given, and the process takes too long, a TimeoutExpired
    exception will be raised.

    There is an optional argument "input", allowing you to
    pass bytes or a string to the subprocess's stdin.  If you use this argument
    you may not also use the Popen constructor's "stdin" argument, as
    it will be used internally.

    By default, all communication is in bytes, and therefore any "input" should
    be bytes, and the stdout and stderr will be bytes. If in text mode, any
    "input" should be a string, and stdout and stderr will be strings decoded
    according to locale encoding, or by "encoding" if set. Text mode is
    triggered by setting any of text, encoding, errors or universal_newlines.

    The other arguments are the same as for the Popen constructor.
    """
    if input is not None:
        if kwargs.get('stdin') is not None:
            raise ValueError('stdin and input arguments may not both be used.')
        kwargs['stdin'] = PIPE

    if capture_output:
        if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
            raise ValueError('stdout and stderr arguments may not be used '
                             'with capture_output.')
        kwargs['stdout'] = PIPE
        kwargs['stderr'] = PIPE

    with Popen(*popenargs, **kwargs) as process:
        try:
            stdout, stderr = process.communicate(input, timeout=timeout)
        except TimeoutExpired as exc:
            process.kill()
            if _mswindows:
                # Windows accumulates the output in a single blocking
                # read() call run on child threads, with the timeout
                # being done in a join() on those threads.  communicate()
                # _after_ kill() is required to collect that and add it
                # to the exception.
                exc.stdout, exc.stderr = process.communicate()
            else:
                # POSIX _communicate already populated the output so
                # far into the TimeoutExpired exception.
                process.wait()
            raise
        except:  # Including KeyboardInterrupt, communicate handled that.
            process.kill()
            # We don't call process.wait() as .__exit__ does that for us.
            raise
        retcode = process.poll()
        if check and retcode:

          raise CalledProcessError(retcode, process.args,

                                     output=stdout, stderr=stderr)

E subprocess.CalledProcessError: Command '['mpiexec', '-n', '1', '-genv', '_PYTEST_MPI_CHILD_PROCESS', '1', 'python', '-m', 'pytest', '--runxfail', '-s', '-q', '/Users/rhaynes/firedrake/src/firedrake/tests/regression/test_dg_advection.py::test_dg_advection_cubed_sphere_parallel', ':', '-n', '2', 'python', '-m', 'pytest', '--runxfail', '-s', '-q', '/Users/rhaynes/firedrake/src/firedrake/tests/regression/test_dg_advection.py::test_dg_advection_cubed_sphere_parallel', '--tb=no', '--no-summary', '--no-header', '--disable-warnings', '--show-capture=no']' returned non-zero exit status 15.

/opt/homebrew/Cellar/[email protected]/3.11.3/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py:571: CalledProcessError
----------------------------- Captured stderr call -----------------------------
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
Fatal error in internal_Init_thread: Other MPI error, error stack:
internal_Init_thread(67)...........: MPI_Init_thread(argc=0x0, argv=0x0, required=3, provided=0x16b7a9600) failed
MPII_Init_thread(234)..............:
MPID_Init(67)......................:
init_world(171)....................: channel initialization failed
MPIDI_CH3_Init(84).................:
MPID_nem_init(314).................:
MPID_nem_tcp_init(175).............:
MPID_nem_tcp_get_business_card(397):
GetSockInterfaceAddr(370)..........: gethostbyname failed, segrprolt092 (errno 0)
____________________ test_poisson_analytic_linear_parallel _____________________

args = (), kwargs = {}

def parallel_callback(*args, **kwargs):

   subprocess.run(cmd, check=True)

../pytest-mpi/pytest_mpi.py:62:

---

input = None, capture_output = False, timeout = None, check = True
popenargs = (['mpiexec', '-n', '1', '-genv', '_PYTEST_MPI_CHILD_PROCESS', '1', ...],)
kwargs = {}
process = <Popen: returncode: 15 args: ['mpiexec', '-n', '1', '-genv', '_PYTEST_MPI_CH...>
stdout = None, stderr = None, retcode = 15

def run(*popenargs,
        input=None, capture_output=False, timeout=None, check=False, **kwargs):
    """Run command with arguments and return a CompletedProcess instance.

    The returned instance will have attributes args, returncode, stdout and
    stderr. By default, stdout and stderr are not captured, and those attributes
    will be None. Pass stdout=PIPE and/or stderr=PIPE in order to capture them,
    or pass capture_output=True to capture both.

    If check is True and the exit code was non-zero, it raises a
    CalledProcessError. The CalledProcessError object will have the return code
    in the returncode attribute, and output & stderr attributes if those streams
    were captured.

    If timeout is given, and the process takes too long, a TimeoutExpired
    exception will be raised.

    There is an optional argument "input", allowing you to
    pass bytes or a string to the subprocess's stdin.  If you use this argument
    you may not also use the Popen constructor's "stdin" argument, as
    it will be used internally.

    By default, all communication is in bytes, and therefore any "input" should
    be bytes, and the stdout and stderr will be bytes. If in text mode, any
    "input" should be a string, and stdout and stderr will be strings decoded
    according to locale encoding, or by "encoding" if set. Text mode is
    triggered by setting any of text, encoding, errors or universal_newlines.

    The other arguments are the same as for the Popen constructor.
    """
    if input is not None:
        if kwargs.get('stdin') is not None:
            raise ValueError('stdin and input arguments may not both be used.')
        kwargs['stdin'] = PIPE

    if capture_output:
        if kwargs.get('stdout') is not None or kwargs.get('stderr') is not None:
            raise ValueError('stdout and stderr arguments may not be used '
                             'with capture_output.')
        kwargs['stdout'] = PIPE
        kwargs['stderr'] = PIPE

    with Popen(*popenargs, **kwargs) as process:
        try:
            stdout, stderr = process.communicate(input, timeout=timeout)
        except TimeoutExpired as exc:
            process.kill()
            if _mswindows:
                # Windows accumulates the output in a single blocking
                # read() call run on child threads, with the timeout
                # being done in a join() on those threads.  communicate()
                # _after_ kill() is required to collect that and add it
                # to the exception.
                exc.stdout, exc.stderr = process.communicate()
            else:
                # POSIX _communicate already populated the output so
                # far into the TimeoutExpired exception.
                process.wait()
            raise
        except:  # Including KeyboardInterrupt, communicate handled that.
            process.kill()
            # We don't call process.wait() as .__exit__ does that for us.
            raise
        retcode = process.poll()
        if check and retcode:

          raise CalledProcessError(retcode, process.args,

                                     output=stdout, stderr=stderr)

E subprocess.CalledProcessError: Command '['mpiexec', '-n', '1', '-genv', '_PYTEST_MPI_CHILD_PROCESS', '1', 'python', '-m', 'pytest', '--runxfail', '-s', '-q', '/Users/rhaynes/firedrake/src/firedrake/tests/regression/test_poisson_strong_bcs.py::test_poisson_analytic_linear_parallel', ':', '-n', '1', 'python', '-m', 'pytest', '--runxfail', '-s', '-q', '/Users/rhaynes/firedrake/src/firedrake/tests/regression/test_poisson_strong_bcs.py::test_poisson_analytic_linear_parallel', '--tb=no', '--no-summary', '--no-header', '--disable-warnings', '--show-capture=no']' returned non-zero exit status 15.

/opt/homebrew/Cellar/[email protected]/3.11.3/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py:571: CalledProcessError
----------------------------- Captured stderr call -----------------------------
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
0.00s - Debugger warning: It seems that frozen modules are being used, which may
0.00s - make the debugger miss breakpoints. Please pass -Xfrozen_modules=off
0.00s - to python to disable frozen modules.
0.00s - Note: Debugging will proceed. Set PYDEVD_DISABLE_FILE_VALIDATION=1 to disable this validation.
Fatal error in internal_Init_thread: Other MPI error, error stack:
internal_Init_thread(67)...........: MPI_Init_thread(argc=0x0, argv=0x0, required=3, provided=0x16b1815f0) failed
MPII_Init_thread(234)..............:
MPID_Init(67)......................:
init_world(171)....................: channel initialization failed
MPIDI_CH3_Init(84).................:
MPID_nem_init(314).................:
MPID_nem_tcp_init(175).............:
MPID_nem_tcp_get_business_card(397):
GetSockInterfaceAddr(370)..........: gethostbyname failed, segrprolt092 (errno 0)
=============================== warnings summary ===============================
tests/regression/test_dg_advection.py::test_dg_advection_icosahedral_sphere
tests/regression/test_dg_advection.py::test_dg_advection_icosahedral_sphere
/Users/rhaynes/firedrake/src/loopy/loopy/target/c/compyte/dtypes.py:184: DeprecationWarning: np.bool8 is a deprecated alias for np.bool_. (Deprecated NumPy 1.24)
reg.get_or_register_dtype("bool", np.bool8)

tests/regression/test_dg_advection.py: 44 warnings
tests/regression/test_poisson_strong_bcs.py: 148 warnings
tests/regression/test_poisson_strong_bcs_nitsche.py: 68 warnings
tests/regression/test_stokes_mini.py: 141 warnings
/Users/rhaynes/firedrake/src/ufl/ufl/core/expr.py:276: DeprecationWarning: Expr.ufl_domain() is deprecated, please use extract_unique_domain(expr) instead.
warnings.warn("Expr.ufl_domain() is deprecated, please "

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/regression/test_dg_advection.py::test_dg_advection_icosahedral_sphere_parallel - subprocess.CalledProcessError: Command '['mpiexec', '-n', '1', '-genv', '_P...
FAILED tests/regression/test_dg_advection.py::test_dg_advection_cubed_sphere_parallel - subprocess.CalledProcessError: Command '['mpiexec', '-n', '1', '-genv', '_P...
FAILED tests/regression/test_poisson_strong_bcs.py::test_poisson_analytic_linear_parallel - subprocess.CalledProcessError: Command '['mpiexec', '-n', '1', '-genv', '_P...
==== 3 failed, 24 passed, 3127 deselected, 403 warnings in 72.44s (0:01:12) ====
(firedrake)
firedrake/src/firedrake master ✔

[connorjward]

Odd. What do you get with which mpiexec? And did you pass any MPI-related options to firedrake-install? Have you set any pertinent environment variables?

[rhaynes74]

No PETSc flags which mpiexec /Users/rhaynes/firedrake/bin/mpiexec (firedrake) firedrake/src/firedrake  master ✔ based on suggestions from homebrew I have : export PATH="/usr/local/opt/python/libexec/bin:$PATH" export PKG_CONFIG_PATH="/opt/homebrew/opt/zlib/lib/pkgconfig" export PATH="/opt/homebrew/opt/flex/bin:$PATH" export LDFLAGS="-L/opt/homebrew/opt/flex/lib" export CPPFLAGS="-I/opt/homebrew/opt/flex/include" export PATH="/opt/homebrew/opt/bison/bin:$PATH" export LDFLAGS="-L/opt/homebrew/opt/bison/lib" in my .zshrc Install is on a new macbook pro m2. Sincerely, Dr. Ronald D. Haynes Professor, Department of Mathematics and Statistics Chair, MSc and Phd Scientific Computing Programs Memorial University of Newfoundland We acknowledge that the lands on which Memorial University’s campuses are situated are in the traditional territories of diverse Indigenous groups, and we acknowledge with respect the diverse histories and cultures of the Beothuk, Mi’kmaq, Innu, and Inuit of this province.

…

On May 6, 2023 at 9:34 AM -0230, Connor Ward ***@***.***>, wrote: Odd. What do you get with which mpiexec? And did you pass any MPI-related options to firedrake-install? Have you set any pertinent environment variables? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***>

[connorjward]

Please can you share (if it still exists) your firedrake-install.log.

Please also try running a Firedrake script (perhaps one of the demos) with mpiexec. Something like the error that you have can occur if one is using OpenMPI instead of MPICH, but that should only prevent parallel tests. Scripts should still work.

[rhaynes74]

Hi - here is the link to the .log file:

log file