"Failed to clone libsupermesh branch master"

[MaihgrUmosch]

The following is the traceback during the attempt to install libsupermesh after running firedrake-install or -update.

`Traceback (most recent call last): File "/home/epipremnum/firedrake/src/../bin/firedrake-update", line 876, in git_clone check_call(["git", "clone", "-q", "--recursive", git_url(plain_url, "ssh")]) File "/home/epipremnum/firedrake/src/../bin/firedrake-update", line 655, in check_call Traceback (most recent call last): File "/home/epipremnum/firedrake/src/../bin/firedrake-update", line 876, in git_clone check_call(["git", "clone", "-q", "--recursive", git_url(plain_url, "ssh")]) File "/home/epipremnum/firedrake/src/../bin/firedrake-update", line 655, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/lib/python3.10/subprocess.py", line 420, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/lib/python3.10/subprocess.py", line 524, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['git', 'clone', '-q', '--recursive', 'git@bitbucket.org:libsupermesh/libsupermesh.git']' returned non-zero exit status 128.

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/epipremnum/firedrake/src/../bin/firedrake-update", line 2014, in build_and_install_libsupermesh() File "/home/epipremnum/firedrake/src/../bin/firedrake-update", line 1262, in build_and_install_libsupermesh git_clone(url) File "/home/epipremnum/firedrake/src/../bin/firedrake-update", line 882, in git_clone check_call(["git", "clone", "-q", "--recursive", git_url(plain_url, "https")]) File "/home/epipremnum/firedrake/src/../bin/firedrake-update", line 655, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/lib/python3.10/subprocess.py", line 420, in check_output return run(popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/lib/python3.10/subprocess.py", line 524, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['git', 'clone', '-q', '--recursive', 'https://bitbucket.org/libsupermesh/libsupermesh.git']' returned non-zero exit status 128.log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/lib/python3.10/subprocess.py", line 420, in check_output return run(popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/lib/python3.10/subprocess.py", line 524, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['git', 'clone', '-q', '--recursive', 'git@bitbucket.org:libsupermesh/libsupermesh.git']' returned non-zero exit status 128.

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/epipremnum/firedrake/src/../bin/firedrake-update", line 2014, in build_and_install_libsupermesh() File "/home/epipremnum/firedrake/src/../bin/firedrake-update", line 1262, in build_and_install_libsupermesh git_clone(url) File "/home/epipremnum/firedrake/src/../bin/firedrake-update", line 882, in git_clone check_call(["git", "clone", "-q", "--recursive", git_url(plain_url, "https")]) File "/home/epipremnum/firedrake/src/../bin/firedrake-update", line 655, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/lib/python3.10/subprocess.py", line 420, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/lib/python3.10/subprocess.py", line 524, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['git', 'clone', '-q', '--recursive', 'https://bitbucket.org/libsupermesh/libsupermesh.git']' returned non-zero exit status 128.`

[JDBetteridge]

Seems like a flakey internet connection, or bitbucket were experiencing issues.

Could you try again to see if the issue is now resolved?

[MaihgrUmosch]

Could well have been flakey internet connection, although the connection is currently stable but firedrake update is not even starting, seems like I'm missing something obvious here:

firedrake-update --install thetis Running /home/.../firedrake/bin/firedrake-update --install thetis Traceback (most recent call last): File "/home/~/firedrake/bin/firedrake-update", line 1724, in run_pip(["install", "-U", "setuptools==59.2.0"]) # Unpin this when numpy will build with latest setuptools File "/home/.../firedrake/bin/firedrake-update", line 958, in run_pip check_call(pip + args) File "/home/.../firedrake/bin/firedrake-update", line 655, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=os.environ).decode()) File "/usr/lib/python3.9/subprocess.py", line 424, in check_output return run(*popenargs, stdout=PIPE, timeout=timeout, check=True, File "/usr/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['/home/.../firedrake/bin/python', '-m', 'pip', 'install', '-U', 'setuptools==59.2.0']' returned non-zero exit status 1.

Kind regards

[JDBetteridge]

What do you see if you try running

pip install -U setuptools==59.2.0

manually in the activated virtual environment?

[MaihgrUmosch]

Originally:

"No module named distutils.cmd"

Tried install using sudo apt install python3-distutils or python3.7-distutils or python3.9-distutils but with no luck inside the venv

[MaihgrUmosch]

(firedrake) epipremnum@epipremnum-linux:$ pip install -U setuptools=59.2.0 Traceback (most recent call last): File "/home/epipremnum/Programs/Firedrake/firedrake/bin/pip", line 5, in <module> from pip._internal.cli.main import main File "/home/epipremnum/Programs/Firedrake/firedrake/lib/python3.9/site-packages/pip/_internal/cli/main.py", line 9, in <module> from pip._internal.cli.autocompletion import autocomplete File "/home/epipremnum/Programs/Firedrake/firedrake/lib/python3.9/site-packages/pip/_internal/cli/autocompletion.py", line 10, in <module> from pip._internal.cli.main_parser import create_main_parser File "/home/epipremnum/Programs/Firedrake/firedrake/lib/python3.9/site-packages/pip/_internal/cli/main_parser.py", line 9, in <module> from pip._internal.build_env import get_runnable_pip File "/home/epipremnum/Programs/Firedrake/firedrake/lib/python3.9/site-packages/pip/_internal/build_env.py", line 19, in <module> from pip._internal.cli.spinners import open_spinner File "/home/epipremnum/Programs/Firedrake/firedrake/lib/python3.9/site-packages/pip/_internal/cli/spinners.py", line 9, in <module> from pip._internal.utils.logging import get_indentation File "/home/epipremnum/Programs/Firedrake/firedrake/lib/python3.9/site-packages/pip/_internal/utils/logging.py", line 29, in <module> from pip._internal.utils.misc import ensure_dir File "/home/epipremnum/Programs/Firedrake/firedrake/lib/python3.9/site-packages/pip/_internal/utils/misc.py", line 43, in <module> from pip._internal.locations import get_major_minor_version File "/home/epipremnum/Programs/Firedrake/firedrake/lib/python3.9/site-packages/pip/_internal/locations/__init__.py", line 66, in <module> from . import _distutils File "/home/epipremnum/Programs/Firedrake/firedrake/lib/python3.9/site-packages/pip/_internal/locations/_distutils.py", line 20, in <module> from distutils.cmd import Command as DistutilsCommand ModuleNotFoundError: No module named 'distutils.cmd'

(firedrake) epipremnum@epipremnum-linux:$ sudo apt install python3-distutils [sudo] password for epipremnum: Reading package lists... Done Building dependency tree... Done Reading state information... Done python3-distutils is already the newest version (3.10.6-1~22.04). The following packages were automatically installed and are no longer required: cryptsetup-run libabsl20200923 libaom0 libavif9 libcbor0.6 libclang1-11 libcmark-gfm-extensions0 libcmark-gfm0 libcmis-0.5-5v5 libcodec2-0.9 libdav1d4 libflashrom1 libftdi1-2 libfwupdplugin1 libgdal28 libgeos-3.9.0 libglew2.1 libgmsh4 libgraphblas3 libhypre libicu67 libidn11 libigdgmm11 libjsoncpp24 libkdecorations2private8 libkf5pulseaudioqt2 libllvm11 libllvm12 libmbedcrypto3 libmbedtls12 libmbedx509-0 libmumps-5.3 libntfs-3g883 liborcus-0.16-0 liborcus-parser-0.16-0 libpdal-base12 libpdal-util12 libperl5.32 libpetsc-real3.14 libpetsc-real3.14-dev libpetsc3.14-dev-common libpetsc3.14-dev-examples libplacebo72 libpoppler111 libpython3.9 libpython3.9-dev libpython3.9-minimal libpython3.9-stdlib libqgis-3d3.10.14 libqgis-analysis3.10.14 libqgis-app3.10.14 libqgis-core3.10.14 libqgis-gui3.10.14 libqgis-native3.10.14 libqgis-server3.10.14 libqgisgrass7-3.10.14 libqgispython3.10.14 libsuperlu-dist6 libtinyxml2-8 libvpx6 libx264-160 libx265-192 libxmlb1 linux-headers-5.13.0-30 ltrace perl-modules-5.32 python3-argcomplete python3-argh python3-mistune python3-regex python3-retrying python3-simplejson python3-typed-ast python3.9 python3.9-dev python3.9-minimal qml-module-qtwebkit xul-ext-ubufox xwayland Use 'sudo apt autoremove' to remove them. 0 to upgrade, 0 to newly install, 0 to remove and 6 not to upgrade.

(firedrake) epipremnum@epipremnum-linux:$ sudo apt install python3.9-distutils Reading package lists... Done Building dependency tree... Done Reading state information... Done Package python3.9-distutils is not available, but is referred to by another package. This may mean that the package is missing, has been obsoleted, or is only available from another source

E: Package 'python3.9-distutils' has no installation candidate

[JDBetteridge]

It sounds like you have a broken Python install. Perhaps system Python has been updated since you created your original Firedrake installation.

You should be able to establish whether it is a system problem by creating a new empty venv:

python -m venv test_environment
source ./test_environment/bin/activate

An then trying to run the command above:

pip install -U setuptools==59.2.0

[MaihgrUmosch]

This worked but only by calling python3. python isn't a recognised command.

The result was setuptool 59.6 being uninstalled for 59.2

[MaihgrUmosch]

But inside Firedrake venv it is:

python --version Python 3.9.7

[JDBetteridge]

I forget sometimes that on some OS's python is still considered Python2!

If the Python version inside the venv is 3.9.7, what is the version outside the venv?

If it's 3.10 or 3.11 (or any other major version) we don't support updating Firedrake through a major version change, your only option is to reinstall Firedrake from scratch by following the instructions here.

[MaihgrUmosch]

Thanks for your help JD.