This is my installation error: 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 Traceback (most recent call last): File "/usr/lib/python3.5/runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "/usr/lib/python3.5/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/emmanuel/firedrake/lib/python3.5/site-packages/pytest.py", line 7, in <module> from _pytest.assertion import register_assert_rewrite File "/home/emmanuel/firedrake/lib/python3.5/site-packages/_pytest/assertion/__init__.py", line 12, in <module> from _pytest.assertion import rewrite File "/home/emmanuel/firedrake/lib/python3.5/site-packages/_pytest/assertion/rewrite.py", line 24, in <module> from _pytest.pathlib import fnmatch_ex File "/home/emmanuel/firedrake/lib/python3.5/site-packages/_pytest/pathlib.py", line 26, in <module> from pathlib2 import Path, PurePath ImportError: No module named 'pathlib2' Makefile:60: recipe for target 'test' failed make: *** [test] Error 1 (firedrake) emmanuel@emmanuel:~/firedrake/src/firedrake$ (firedrake) emmanuel@emmanuel:~/firedrake/src/firedrake$ (firedrake) emmanuel@emmanuel:~/firedrake/src/firedrake$ (firedrake) emmanuel@emmanuel:~/firedrake/src/firedrake$ sudo su [sudo] senha para emmanuel: root@emmanuel:/home/emmanuel/firedrake/src/firedrake# root@emmanuel:/home/emmanuel/firedrake/src/firedrake# root@emmanuel:/home/emmanuel/firedrake/src/firedrake# root@emmanuel:/home/emmanuel/firedrake/src/firedrake# make alltest Building extension modules Traceback (most recent call last): File "setup.py", line 31, in <module> import versioneer File "/home/emmanuel/firedrake/src/firedrake/versioneer.py", line 1658 file=sys.stderr) ^ SyntaxError: invalid syntax Linting firedrake codebase /usr/bin/python: No module named flake8 Makefile:8: recipe for target 'lint' failed make: *** [lint] Error 1
Dear Emmanuel,
On 7 Nov 2018, at 00:47, Emmanuel Yarleque Medina <eyarmed@gmail.com> wrote:
This is my installation error:
Your installation log indicates that petsc4py failed to build: creating build/temp.linux-x86_64-3.5 creating build/temp.linux-x86_64-3.5/arch-linux2-c-debug creating build/temp.linux-x86_64-3.5/arch-linux2-c-debug/src /home/emmanuel/Area_de_Trabalho/petsc-3.9.0/arch-linux2-c-debug/bin/mpicc -pthread -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -g3 -fPIC -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fdebug-prefix-map=/build/python3.5-nLrllb/python3.5-3.5.3=. -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -DPETSC_DIR=/home/emmanuel/Area_de_Trabalho/petsc-3.9.0 -I/home/emmanuel/Area_de_Trabalho/petsc-3.9.0/arch-linux2-c-debug/include/eigen3 -I/home/emmanuel/Area_de_Trabalho/petsc-3.9.0/arch-linux2-c-debug/include -I/home/emmanuel/Area_de_Trabalho/petsc-3.9.0/include -Isrc/include -I/home/emmanuel/firedrake/lib/python3.5/site-packages/numpy/core/include -I/home/emmanuel/firedrake/include -I/usr/include/python3.5m -c src/PETSc.c -o build/temp.linux-x86_64-3.5/arch-linux2-c-debug/src/PETSc.o In file included from src/PETSc.c:4:0: src/petsc4py.PETSc.c:3176:70: error: unknown type name ‘PCPatchConstructType’ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_PCPatchConstructType(PCPatchConstructType value); ... I see you ran firedrake-install with --honour-petsc-dir. While this is a supported route, we do have particular requirements on how recent the PETSc you use is (and what packages it builds with). It looks like the PETSc you are using is too old for the version of petsc4py we want. You have a few options, in order of easiest to hardest: 1. Run firedrake-install without --honour-petsc-dir. This installs a known-compatible version of PETSc inside the firedrake virtualenv (it doesn't interfere with anything else you use). 2. Build the version of PETSc we know is good yourself: clone github.com/firedrakeproject/petsc.git. The firedrake branch in this repository tracks PETSc master with some (small) delays. 3. Build a more modern PETSc (probably the master branch). Thanks, Lawrence
Thanks, I'll check it out. Em qua, 7 de nov de 2018 às 08:54, Lawrence Mitchell <wence@gmx.li> escreveu:
Dear Emmanuel,
On 7 Nov 2018, at 00:47, Emmanuel Yarleque Medina <eyarmed@gmail.com> wrote:
This is my installation error:
Your installation log indicates that petsc4py failed to build:
creating build/temp.linux-x86_64-3.5 creating build/temp.linux-x86_64-3.5/arch-linux2-c-debug creating build/temp.linux-x86_64-3.5/arch-linux2-c-debug/src
/home/emmanuel/Area_de_Trabalho/petsc-3.9.0/arch-linux2-c-debug/bin/mpicc -pthread -Wall -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -fstack-protector -g3 -fPIC -Wno-unused-result -Wsign-compare -DNDEBUG -g -fwrapv -O2 -Wall -g -fdebug-prefix-map=/build/python3.5-nLrllb/python3.5-3.5.3=. -fstack-protector-strong -Wformat -Werror=format-security -g -flto -fuse-linker-plugin -ffat-lto-objects -DPETSC_DIR=/home/emmanuel/Area_de_Trabalho/petsc-3.9.0 -I/home/emmanuel/Area_de_Trabalho/petsc-3.9.0/arch-linux2-c-debug/include/eigen3 -I/home/emmanuel/Area_de_Trabalho/petsc-3.9.0/arch-linux2-c-debug/include -I/home/emmanuel/Area_de_Trabalho/petsc-3.9.0/include -Isrc/include -I/home/emmanuel/firedrake/lib/python3.5/site-packages/numpy/core/include -I/home/emmanuel/firedrake/include -I/usr/include/python3.5m -c src/PETSc.c -o build/temp.linux-x86_64-3.5/arch-linux2-c-debug/src/PETSc.o In file included from src/PETSc.c:4:0: src/petsc4py.PETSc.c:3176:70: error: unknown type name ‘PCPatchConstructType’ static CYTHON_INLINE PyObject* __Pyx_PyInt_From_PCPatchConstructType(PCPatchConstructType value);
...
I see you ran firedrake-install with --honour-petsc-dir. While this is a supported route, we do have particular requirements on how recent the PETSc you use is (and what packages it builds with). It looks like the PETSc you are using is too old for the version of petsc4py we want. You have a few options, in order of easiest to hardest:
1. Run firedrake-install without --honour-petsc-dir. This installs a known-compatible version of PETSc inside the firedrake virtualenv (it doesn't interfere with anything else you use).
2. Build the version of PETSc we know is good yourself: clone github.com/firedrakeproject/petsc.git. The firedrake branch in this repository tracks PETSc master with some (small) delays.
3. Build a more modern PETSc (probably the master branch).
Thanks,
Lawrence
participants (2)
-
Emmanuel Yarleque Medina
-
Lawrence Mitchell