On 02/11/2018 20:42, Matthew Knepley wrote:
On Fri, Nov 2, 2018 at 1:56 PM Lawrence Mitchell <wence@gmx.li <mailto:wence@gmx.li>> wrote:
> On 2 Nov 2018, at 17:53, Matthew Knepley <knepley@gmail.com <mailto: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
The log seems to say:
firedrake/spatialindex.c:614:10: fatal error: 'spatialindex/capi/sidx_api.h' file not found #include "spatialindex/capi/sidx_api.h"
which suggests libspatialindex wasn't installed (properly/at all) in your virtual env. Notably you should have a include/spatialindex in your virtual env. I'm not sure how to fix that. If you don't want to wait for Lawrence or David, I would try reinstalling like in the script (cf below), but without any guarantee. Otherwise restarting the installation from scratch is usually a good idea when things get too messed up. If you use the --venv-name option with the firedrake-install script, you can install Firedrake in a different directory so you can come back to your broken install later! def build_and_install_libspatialindex(): log.info("Installing libspatialindex") if os.path.exists("libspatialindex"): log.info("Updating the git repository for libspatialindex") with directory("libspatialindex"): check_call(["git", "fetch"]) git_sha = check_output(["git", "rev-parse", "HEAD"]) git_sha_new = check_output(["git", "rev-parse", "@{u}"]) libspatialindex_changed = git_sha != git_sha_new if libspatialindex_changed: check_call(["git", "reset", "--hard"]) check_call(["git", "pull"]) else: git_clone("git+https://github.com/firedrakeproject/libspatialindex.git") libspatialindex_changed = True if libspatialindex_changed: with directory("libspatialindex"): # Clean source directory check_call(["git", "reset", "--hard"]) check_call(["git", "clean", "-f", "-x", "-d"]) # Patch Makefile.am to skip building test check_call(["sed", "-i", "-e", "/^SUBDIRS/s/ test//", "Makefile.am"]) # Build and install check_call(["./autogen.sh"]) check_call(["./configure", "--prefix=" + firedrake_env, "--enable-shared", "--disable-static"]) check_call(["make"]) check_call(["make", "install"]) else: log.info("No need to rebuild libspatialindex") -- Nicolas
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/%7Eknepley/>
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