(Resending as Emmanuel's email address was somehow not included in the To/Cc list) Hi Emmanuel, Thinking about what Nacime said, I wonder if you have multiple PETSc installations. The following environment variables were used when you attempted to install firedrake: PETSC_DIR=/home/hpc/petsc-3.11.3 PETSC_ARCH=arch-FreeFem-sources Are these pointing to the PETSc you installed with the configuration options you mentioned earlier? (It seems, as Nacime pointed out, that this is one automatically(?) installed by FreeFem.) Thanks, Koki ________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Sagiyama, Koki <k.sagiyama@imperial.ac.uk> Sent: Wednesday, August 28, 2019 3:40:06 PM To: Nacime Bouziani <nacime.bouziani@gmail.com> Cc: firedrake <firedrake@imperial.ac.uk> Subject: Re: [firedrake] Error instalation Hi Emmanuel, Thinking about what Nacime said, I wonder if you have multiple PETSc installations. The following environment variables were used when you attempted to install firedrake: PETSC_DIR=/home/hpc/petsc-3.11.3 PETSC_ARCH=arch-FreeFem-sources Are these pointing to the PETSc you installed with the configuration options you mentioned earlier? (It seems, as Nacime pointed out, that this is one automatically(?) installed by FreeFem.) Thanks, Koki ________________________________ From: Nacime Bouziani <nacime.bouziani@gmail.com> Sent: Wednesday, August 28, 2019 1:17:48 PM To: Sagiyama, Koki <k.sagiyama@imperial.ac.uk> Cc: Emmanuel Yarleque Medina <eyarmed@gmail.com>; firedrake <firedrake@imperial.ac.uk> Subject: Re: [firedrake] Error instalation Hi again, Just to precise, by "working" I meant both installations were done successfully. Regards. Nacime BOUZIANI Le mer. 28 août 2019 à 14:16, Nacime Bouziani <nacime.bouziani@gmail.com<mailto:nacime.bouziani@gmail.com>> a écrit : Hi Both, When you have installed FreeFem it has installed installed PETSc as well as h5py. I did have a similar problem, I realised that if I started to first install Firedrake and then freefem it was working, if that is useful. Sorry I do not much about that. Regards. Nacime BOUZIANI Le mer. 28 août 2019 à 10:20, Sagiyama, Koki <k.sagiyama@imperial.ac.uk<mailto:k.sagiyama@imperial.ac.uk>> a écrit : Hi Emmanuel, (Added firedrake back so that others can also help.) So this is where your installation fails: mpicc -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC -DH5_USE_16_API -I./h5py -I/home/hpc/petsc-3.11.3/arch-FreeFem-sources/include -I/home/hpc/firedrake/src/h5py/lzf -I/home/hpc/firedrake/lib/python3.5/site-packages/numpy/core/include -I/home/hpc/firedrake/lib/python3.5/site-packages/mpi4py/include -I/home/hpc/firedrake/include -I/usr/include/python3.5m -c /home/hpc/firedrake/src/h5py/h5py/defs.c -o build/temp.linux-x86_64-3.5/home/hpc/firedrake/src/h5py/h5py/defs.o with this error: /home/hpc/firedrake/src/h5py/h5py/api_compat.h:27:18: fatal error: hdf5.h: Arquivo ou diretório não encontrado I think `-I/home/hpc/petsc-3.11.3/arch-FreeFem-sources/include` is the correct flag to find `hdf5.h,` so I don't know why it failed. Does anyone have any idea? Thanks, Koki ________________________________ From: Emmanuel Yarleque Medina <eyarmed@gmail.com<mailto:eyarmed@gmail.com>> Sent: Tuesday, August 27, 2019 4:36:36 PM To: Sagiyama, Koki <k.sagiyama@imperial.ac.uk<mailto:k.sagiyama@imperial.ac.uk>> Subject: Re: [firedrake] Error instalation Hi Koki, the configuration of Petsc, for example I installed it with the following configuration: ./configure --with-cc=gcc --with-fc=gfortran --download-mpich --download-fblaslapack --download-mumps --download-scalapack --download-hypre --download-metis --download-parmetis --download-arpack --download-hdf5 --download-eigen --download-ptscotch --download-suitesparse --with-scalar-type=real --with-debugging=no El mar., 27 ago. 2019 a las 12:59, Sagiyama, Koki (<k.sagiyama@imperial.ac.uk<mailto:k.sagiyama@imperial.ac.uk>>) escribió: 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 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 [https://avatars0.githubusercontent.com/u/5558005?s=400&v=4]<https://github.com/firedrakeproject/petsc.git> firedrakeproject/petsc<https://github.com/firedrakeproject/petsc.git> github.com<http://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<mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces@imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk>> on behalf of Emmanuel Yarleque Medina <eyarmed@gmail.com<mailto:eyarmed@gmail.com>> Sent: Friday, August 23, 2019 7:35:22 PM To: firedrake <firedrake@imperial.ac.uk<mailto: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 _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk<mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake