Dear Emmanuel,
It seems that you are trying to use a pre-installed PETSc, but the installer is unable to find some file (`hdf5.h`).
Could you tell us the configuration options you used to install PETSc?
When we make `firedrake-install` do all the installation work, it asks PETSc to install a number of dependencies (including hdf5), so if we want to build PETSc separately, we must configure it with correct options as
`firedrake-install` would.
You can see those options by running:
python3 firedrake-install --show-petsc-configure-options
python3 firedrake-install --show-petsc-configure-options
To ensure compatibility with all firedrake components, we also recommend that PETSc be downloaded from the following branch (if you have not done so), which we try to keep up-to-date with the upstream PETSc as frequently as possible:
https://github.com/firedrakeproject/petsc.git
 |
github.com
Mirror of https://bitbucket.org/petsc/petsc. Contribute to firedrakeproject/petsc development by creating an account on GitHub.
|
|
Regards,
Koki
From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Emmanuel Yarleque Medina <eyarmed@gmail.com>
Sent: Friday, August 23, 2019 7:35:22 PM
To: firedrake <firedrake@imperial.ac.uk>
Subject: [firedrake] Error instalation
Sent: Friday, August 23, 2019 7:35:22 PM
To: firedrake <firedrake@imperial.ac.uk>
Subject: [firedrake] Error instalation
Hi users,
I have the following error installing Firedrake on ubuntu 16.04
(firedrake) hpc@hpc:~/firedrake/src/firedrake$ make alltest
Building extension modules
Traceback (most recent call last):
File "setup.py", line 8, in <module>
import petsc4py
ImportError: No module named 'petsc4py'
Linting firedrake codebase
Linting firedrake test suite
Linting firedrake scripts
Running all regression tests
============================================ test session starts ============================================
platform linux -- Python 3.5.2, pytest-5.1.1, py-1.8.0, pluggy-0.12.0
rootdir: /home/hpc/firedrake/src/firedrake, inifile: setup.cfg
plugins: forked-1.0.2, xdist-1.29.0
collected 0 items / 1 errors
================================================== ERRORS ===================================================
_______________________________________ ERROR collecting test session _______________________________________
../../lib/python3.5/site-packages/_pytest/config/__init__.py:436: in _importconftest
return self._conftestpath2mod[conftestpath]
E KeyError: local('/home/hpc/firedrake/src/firedrake/tests/extrusion/conftest.py')
During handling of the above exception, another exception occurred:
../../lib/python3.5/site-packages/_pytest/config/__init__.py:442: in _importconftest
mod = conftestpath.pyimport()
../../lib/python3.5/site-packages/py/_path/local.py:701: in pyimport
__import__(modname)
<frozen importlib._bootstrap>:969: in _find_and_load
???
<frozen importlib._bootstrap>:958: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:673: in _load_unlocked
???
../../lib/python3.5/site-packages/_pytest/assertion/rewrite.py:140: in exec_module
exec(co, module.__dict__)
tests/extrusion/conftest.py:2: in <module>
from firedrake import ExtrudedMesh, UnitSquareMesh, UnitIntervalMesh
firedrake/__init__.py:5: in <module>
if "PETSC_DIR" in os.environ and not config["options"]["honour_petsc_dir"]:
E TypeError: 'NoneType' object is not subscriptable
During handling of the above exception, another exception occurred:
../../lib/python3.5/site-packages/py/_path/common.py:377: in visit
for x in Visitor(fil, rec, ignore, bf, sort).gen(self):
../../lib/python3.5/site-packages/py/_path/common.py:418: in gen
dirs = self.optsort([p for p in entries
../../lib/python3.5/site-packages/py/_path/common.py:419: in <listcomp>
if p.check(dir=1) and (rec is None or rec(p))])
../../lib/python3.5/site-packages/_pytest/main.py:606: in _recurse
ihook = self.gethookproxy(dirpath)
../../lib/python3.5/site-packages/_pytest/main.py:424: in gethookproxy
my_conftestmodules = pm._getconftestmodules(fspath)
../../lib/python3.5/site-packages/_pytest/config/__init__.py:420: in _getconftestmodules
mod = self._importconftest(conftestpath.realpath())
../../lib/python3.5/site-packages/_pytest/config/__init__.py:450: in _importconftest
raise ConftestImportFailure(conftestpath, sys.exc_info())
E _pytest.config.ConftestImportFailure: (local('/home/hpc/firedrake/src/firedrake/tests/extrusion/conftest.py'), (<class 'TypeError'>, TypeError("'NoneType' object is not subscriptable",), <traceback object at 0x7f4728146088>))
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
============================================= 1 error in 0.29s ==============================================
Makefile:64: recipe for target 'test' failed
make: *** [test] Error 2
Building extension modules
Traceback (most recent call last):
File "setup.py", line 8, in <module>
import petsc4py
ImportError: No module named 'petsc4py'
Linting firedrake codebase
Linting firedrake test suite
Linting firedrake scripts
Running all regression tests
============================================ test session starts ============================================
platform linux -- Python 3.5.2, pytest-5.1.1, py-1.8.0, pluggy-0.12.0
rootdir: /home/hpc/firedrake/src/firedrake, inifile: setup.cfg
plugins: forked-1.0.2, xdist-1.29.0
collected 0 items / 1 errors
================================================== ERRORS ===================================================
_______________________________________ ERROR collecting test session _______________________________________
../../lib/python3.5/site-packages/_pytest/config/__init__.py:436: in _importconftest
return self._conftestpath2mod[conftestpath]
E KeyError: local('/home/hpc/firedrake/src/firedrake/tests/extrusion/conftest.py')
During handling of the above exception, another exception occurred:
../../lib/python3.5/site-packages/_pytest/config/__init__.py:442: in _importconftest
mod = conftestpath.pyimport()
../../lib/python3.5/site-packages/py/_path/local.py:701: in pyimport
__import__(modname)
<frozen importlib._bootstrap>:969: in _find_and_load
???
<frozen importlib._bootstrap>:958: in _find_and_load_unlocked
???
<frozen importlib._bootstrap>:673: in _load_unlocked
???
../../lib/python3.5/site-packages/_pytest/assertion/rewrite.py:140: in exec_module
exec(co, module.__dict__)
tests/extrusion/conftest.py:2: in <module>
from firedrake import ExtrudedMesh, UnitSquareMesh, UnitIntervalMesh
firedrake/__init__.py:5: in <module>
if "PETSC_DIR" in os.environ and not config["options"]["honour_petsc_dir"]:
E TypeError: 'NoneType' object is not subscriptable
During handling of the above exception, another exception occurred:
../../lib/python3.5/site-packages/py/_path/common.py:377: in visit
for x in Visitor(fil, rec, ignore, bf, sort).gen(self):
../../lib/python3.5/site-packages/py/_path/common.py:418: in gen
dirs = self.optsort([p for p in entries
../../lib/python3.5/site-packages/py/_path/common.py:419: in <listcomp>
if p.check(dir=1) and (rec is None or rec(p))])
../../lib/python3.5/site-packages/_pytest/main.py:606: in _recurse
ihook = self.gethookproxy(dirpath)
../../lib/python3.5/site-packages/_pytest/main.py:424: in gethookproxy
my_conftestmodules = pm._getconftestmodules(fspath)
../../lib/python3.5/site-packages/_pytest/config/__init__.py:420: in _getconftestmodules
mod = self._importconftest(conftestpath.realpath())
../../lib/python3.5/site-packages/_pytest/config/__init__.py:450: in _importconftest
raise ConftestImportFailure(conftestpath, sys.exc_info())
E _pytest.config.ConftestImportFailure: (local('/home/hpc/firedrake/src/firedrake/tests/extrusion/conftest.py'), (<class 'TypeError'>, TypeError("'NoneType' object is not subscriptable",), <traceback object at 0x7f4728146088>))
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Interrupted: 1 errors during collection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
============================================= 1 error in 0.29s ==============================================
Makefile:64: recipe for target 'test' failed
make: *** [test] Error 2