On Fri, Nov 2, 2018 at 1:56 PM Lawrence Mitchell <wence@gmx.li> wrote:
On 2 Nov 2018, at 17:53, Matthew Knepley <knepley@gmail.com> wrote: ...
Successfully cloned repository libspatialindex Checking out branch master Successfully checked out branch master Traceback (most recent call last): File "../bin/firedrake-update", line 1207, in <module> build_and_install_libspatialindex() File "../bin/firedrake-update", line 808, in build_and_install_libspatialindex check_call(["./autogen.sh"]) File "../bin/firedrake-update", line 435, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode()) File "/Users/knepley/MacSoftware/lib/python3.6/subprocess.py", line 336, in check_output **kwargs).stdout File "/Users/knepley/MacSoftware/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['./autogen.sh']' returned non-zero exit status 1.
Update log saved in firedrake-update.log
Here is the log.
Ah ha! You need autotools, but do not check up front :) We get farther
When you first ran "firedrake-install" you said --no-package-manager, so we assumed that you had all the things we need.
(firedrake) 127:/PETSc3/fem$ export PATH=${PATH}:${HOME}/MacSoftware/bin (firedrake) :/PETSc3/fem$ which libtoolize /Users/knepley/MacSoftware/bin/libtoolize (firedrake) :/PETSc3/fem$ firedrake-update --honour-pythonpath Running /PETSc3/fem/firedrake/bin/firedrake-update --honour-pythonpath Updating the git repository for firedrake Creating firedrake-update script. Running ../bin/firedrake-update --no-update-script --honour-pythonpath Xcode and homebrew installation disabled. Proceeding on the rash assumption that packaged dependencies are in place. Finding dependencies of PyOP2
Finding dependencies of firedrake
Updating the git repository for petsc4py Updating the git repository for COFFEE Updating the git repository for ufl Updating the git repository for fiat Updating the git repository for FInAT Updating the git repository for tsfc Updating the git repository for PyOP2 Updating the git repository for firedrake Installing pip dependencies for COFFEE Installing pip dependencies for ufl No dependencies found. Skipping. Installing pip dependencies for fiat No dependencies found. Skipping. Installing pip dependencies for FInAT Installing pip dependencies for tsfc Installing pip dependencies for PyOP2 Installing pip dependencies for firedrake Installing h5py Updating the git repository for h5py No need to rebuild h5py Installing libspatialindex Updating the git repository for libspatialindex No need to rebuild libspatialindex Cleaning COFFEE Installing COFFEE/ Cleaning ufl Installing ufl/ Cleaning fiat Installing fiat/ Cleaning FInAT Installing FInAT/ Cleaning tsfc Installing tsfc/ Cleaning PyOP2 Traceback (most recent call last): File "../bin/firedrake-update", line 1216, in <module> clean(p) File "../bin/firedrake-update", line 633, in clean check_call(["python", "setup.py", "clean"]) File "../bin/firedrake-update", line 435, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode()) File "/Users/knepley/MacSoftware/lib/python3.6/subprocess.py", line 336, in check_output **kwargs).stdout File "/Users/knepley/MacSoftware/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['python', 'setup.py', 'clean']' returned non-zero exit status 1.
Update log saved in firedrake-update.log
Here is the log.
I see. My petsc4py is not visible in this venv. WIll fix that.
We should have installed petsc4py, but obviously didn't and then the firedrake-update has some logic to not rebuild it.
Just "pip install -U --no-deps firedrake/src/petsc4py"
That worked. We are almost there. However, I cannot interpret the error here: (firedrake) :/PETSc3/fem$ firedrake-update --honour-pythonpath Running /PETSc3/fem/firedrake/bin/firedrake-update --honour-pythonpath Updating the git repository for firedrake Creating firedrake-update script. Running ../bin/firedrake-update --no-update-script --honour-pythonpath Xcode and homebrew installation disabled. Proceeding on the rash assumption that packaged dependencies are in place. Finding dependencies of PyOP2 Finding dependencies of firedrake Updating the git repository for petsc4py Updating the git repository for COFFEE Updating the git repository for ufl Updating the git repository for fiat Updating the git repository for FInAT Updating the git repository for tsfc Updating the git repository for PyOP2 Updating the git repository for firedrake Installing pip dependencies for COFFEE Installing pip dependencies for ufl No dependencies found. Skipping. Installing pip dependencies for fiat No dependencies found. Skipping. Installing pip dependencies for FInAT Installing pip dependencies for tsfc Installing pip dependencies for PyOP2 Installing pip dependencies for firedrake Installing h5py Updating the git repository for h5py No need to rebuild h5py Installing libspatialindex Updating the git repository for libspatialindex No need to rebuild libspatialindex Cleaning COFFEE Installing COFFEE/ Cleaning ufl Installing ufl/ Cleaning fiat Installing fiat/ Cleaning FInAT Installing FInAT/ Cleaning tsfc Installing tsfc/ Cleaning PyOP2 Installing PyOP2/ Cleaning firedrake Installing firedrake/ Traceback (most recent call last): File "../bin/firedrake-update", line 1217, in <module> install(p+"/") File "../bin/firedrake-update", line 625, in install run_pip_install(["-e", package]) File "../bin/firedrake-update", line 597, in run_pip_install check_call(pipinstall + pipargs) File "../bin/firedrake-update", line 435, in check_call log.debug(subprocess.check_output(arguments, stderr=subprocess.STDOUT, env=env).decode()) File "/Users/knepley/MacSoftware/lib/python3.6/subprocess.py", line 336, in check_output **kwargs).stdout File "/Users/knepley/MacSoftware/lib/python3.6/subprocess.py", line 418, in run output=stdout, stderr=stderr) subprocess.CalledProcessError: Command '['/PETSc3/fem/firedrake/bin/python', '-m', 'pip', 'install', '--no-binary', 'mpi4py', '--no-deps', '-vvv', '-e', 'firedrake/']' returned non-zero exit status 1. Update log saved in firedrake-update.log Here is the log. Thanks, Matt Lawrence
-- What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead. -- Norbert Wiener https://www.cse.buffalo.edu/~knepley/ <http://www.cse.buffalo.edu/~knepley/>