August 2019 - firedrake - imperial.ac.uk

Re: [firedrake] Installing firedrake on a HPC system without package manager
by Lawrence Mitchell 30 Aug '19

30 Aug '19

Hi Niall, (adding in firedrake cc again) > On 1 Aug 2019, at 15:43, Madden, Niall <niall.madden(a)nuigalway.ie> wrote: > > Hi Lawrence, > Thanks for the swift reply. I don't want to reply to the whole list with too much specific information on the system Please do reply with the list. That way others who might be able to help will see things. >> Can you give us some details on this system? Is it a cray, for example? > The system is ICHEC's "kay" - Ireland's national supercomputer for academic purposes: > https://www.ichec.ie/about/infrastructure/kay > >> Normally we find when building on supercomputers (contrary to the one-shot "firedrake-install" unfortunately), >> that it is best to build PETSc by hand. One then sets the appropriate environment variables and runs >> firedrake-install --honour-petsc-dir. This might be the best step forward. > > Thanks for the tip. I tried compiling PETSc myself: > > git clone https://github.com/firedrakeproject/petsc.git (but should I be cloning fromhttps://bitbucket.org/petsc/petsc ?) No, cloning from the firedrakeproject "fork" is correct. We keep a (reasonably up to date) version of petsc that is known good with all Firedrake components there: it isn't otherwise special. > ./configure --with-c2html=0 --download-chaco --download-metis --download-parmetis --download-scalapack --download-hypre --download-mumps --download-netcdf --download-hdf5 --download-pnetcdf --download-exodusii --download-mpich --download-suitesparse=1 --download-petsc4py=1 --download-mpi4py=1 --download-fblaslapack --download-zlib > > Then I set PETSC_DIR and PETSC_ARCH, and PYTHONPATH > > Then I try to install Firedrake with > python3 firedrake-install --no-package-manager -v --disable-ssh --honour-petsc-dir --honour-pythonpath > > But it eventually fails compiling libspatialindex > for reasons that seem to be related to the mpicxx , but it is a little opaque: > undefined reference to `psm2_info_query(a)PSM2_1.0' Can you attach the contents of firedrake-install.log (maybe gzip it since it is likely to be large). Thanks, Lawrence

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Problem installing Firedrake on Ubuntu 18.04
by Karin&NiKo 29 Aug '19

29 Aug '19

Dear Firedrake team, I am having big troubles in installing Firedrake on Ubuntu 18.04. - First I would like to report the error that I get when running : python3 ./firedrake-install --disable-ssh. Let me point that I run it behind a proxy but setting http_proxy seems to work, at least for several steps on the installation process. You can find the log as attached file.I have tried to run this script as a simple user or as root but i get the same error message. I also attach the echo of the script from the shell because it seems to me that they give some contreversial information of the origin of the error. - Second, I would like to know if there is a way to rerun the installation script *without* erasing the directory that the previous failed execution created. Indeed the script complains that "Specified venv '/home/xxxxx/dev/Firedrake/firedrake' already exists. Can't install into existing venv '/home/xxxxxx/dev/Firedrake/firedrake'" and the only solution I found is to erase the folder and rerun the script from the begining, meaning downloading again all that I have already downloaded. I thank you in advance for your help, Nicolas

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Re: [firedrake] Error instalation
by Sagiyama, Koki 28 Aug '19

28 Aug '19

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(a)gmail.com> Sent: Tuesday, August 27, 2019 4:36:36 PM To: Sagiyama, Koki <k.sagiyama(a)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(a)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(a)imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk> <firedrake-bounces(a)imperial.ac.uk<mailto:firedrake-bounces@imperial.ac.uk>> on behalf of Emmanuel Yarleque Medina <eyarmed(a)gmail.com<mailto:eyarmed@gmail.com>> Sent: Friday, August 23, 2019 7:35:22 PM To: firedrake <firedrake(a)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

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Re: [firedrake] firedrake Digest, Vol 32, Issue 9
by Sander Rhebergen 28 Aug '19

28 Aug '19

Hi Matt, Thanks for the explanation. I'm new to this formulation as well and not sure about the best way to address the solver part, but I will try out your suggestions. Sander ________________________________ From: firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> on behalf of firedrake-request(a)imperial.ac.uk <firedrake-request(a)imperial.ac.uk> Sent: Tuesday, August 27, 2019 7:00 AM To: firedrake(a)imperial.ac.uk Subject: firedrake Digest, Vol 32, Issue 9 Send firedrake mailing list submissions to firedrake(a)imperial.ac.uk To subscribe or unsubscribe via the World Wide Web, visit https://mailman.ic.ac.uk/mailman/listinfo/firedrake or, via email, send a message with subject or body 'help' to firedrake-request(a)imperial.ac.uk You can reach the person managing the list at firedrake-owner(a)imperial.ac.uk When replying, please edit your Subject line so it is more specific than "Re: Contents of firedrake digest..." Today's Topics: 1. nullspace within nonlinearvariationalsolver? (Sander Rhebergen) 2. Re: nullspace within nonlinearvariationalsolver? (Matthew Knepley) ---------------------------------------------------------------------- Message: 1 Date: Mon, 26 Aug 2019 21:37:11 +0000 From: Sander Rhebergen <srhebergen(a)uwaterloo.ca> To: "firedrake(a)imperial.ac.uk" <firedrake(a)imperial.ac.uk> Subject: [firedrake] nullspace within nonlinearvariationalsolver? Message-ID: <d728cc7c78d84497a4a45da641289f9d(a)uwaterloo.ca> Content-Type: text/plain; charset="iso-8859-1" Hello, Is it possible to set a constant nullspace for a NonlinearVariationalSolver? I tried the following: order = 2 V3 = FunctionSpace(mesh, "CG", order) V1 = FunctionSpace(mesh, "BDM", order) V2 = FunctionSpace(mesh, "DG", order-1) W = MixedFunctionSpace([V3, V1, V2]) v_basis = VectorSpaceBasis(constant=True) null_space = MixedVectorSpaceBasis(W, [W.sub(0), W.sub(1), v_basis]) # Build Nonlinear Solver uprob = NonlinearVariationalProblem(L, w1) usolver = NonlinearVariationalSolver(uprob, nullspace=null_space, solver_parameters = { 'snes_max_it': '50', 'snes_rtol': '1e-12', 'mat_type': 'aij', 'ksp_type': 'preonly', 'pc_type': 'lu', 'snes_monitor': True, 'snes_view': False, 'snes_converged_reason': True, 'ksp_converged_reason': True}) but the linear solver did not converge: 0 SNES Function norm 7.964422825545e-02 Linear firedrake_1_ solve did not converge due to DIVERGED_PCSETUP_FAILED iterations 0 PCSETUP_FAILED due to FACTOR_NUMERIC_ZEROPIVOT Nonlinear firedrake_1_ solve did not converge due to DIVERGED_LINEAR_SOLVE iterations 0 I can send the full code if necessary. I'm trying to solve Navier-Stokes in velocity-vorticity-pressure formulation (https://arxiv.org/pdf/1604.00257.pdf) but the solver doesn't converge. If I add a small parameter times a pressure mass-matrix, the solver converges, but I was hoping to avoid doing this. Thanks, Sander

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Error instalation
by Emmanuel Yarleque Medina 27 Aug '19

27 Aug '19

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

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nullspace within nonlinearvariationalsolver?
by Sander Rhebergen 26 Aug '19

26 Aug '19

Hello, Is it possible to set a constant nullspace for a NonlinearVariationalSolver? I tried the following: order = 2 V3 = FunctionSpace(mesh, "CG", order) V1 = FunctionSpace(mesh, "BDM", order) V2 = FunctionSpace(mesh, "DG", order-1) W = MixedFunctionSpace([V3, V1, V2]) v_basis = VectorSpaceBasis(constant=True) null_space = MixedVectorSpaceBasis(W, [W.sub(0), W.sub(1), v_basis]) # Build Nonlinear Solver uprob = NonlinearVariationalProblem(L, w1) usolver = NonlinearVariationalSolver(uprob, nullspace=null_space, solver_parameters = { 'snes_max_it': '50', 'snes_rtol': '1e-12', 'mat_type': 'aij', 'ksp_type': 'preonly', 'pc_type': 'lu', 'snes_monitor': True, 'snes_view': False, 'snes_converged_reason': True, 'ksp_converged_reason': True}) but the linear solver did not converge: 0 SNES Function norm 7.964422825545e-02 Linear firedrake_1_ solve did not converge due to DIVERGED_PCSETUP_FAILED iterations 0 PCSETUP_FAILED due to FACTOR_NUMERIC_ZEROPIVOT Nonlinear firedrake_1_ solve did not converge due to DIVERGED_LINEAR_SOLVE iterations 0 I can send the full code if necessary. I'm trying to solve Navier-Stokes in velocity-vorticity-pressure formulation (https://arxiv.org/pdf/1604.00257.pdf) but the solver doesn't converge. If I add a small parameter times a pressure mass-matrix, the solver converges, but I was hoping to avoid doing this. Thanks, Sander

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Integrate solution over internal (unmarked) line
by Jessica Williams 23 Aug '19

23 Aug '19

I was just wondering whether there’s a simple way to integrate a 2D solution, p(x,y), over an arbitrary line segment, e.g., p(0 <= x <= 1, y = 1)? I imagine p will have to be interpolated along relevant points, but not sure how best to do this. Many thanks.

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Firedrake 19 abstract deadline this Friday!
by Lawrence Mitchell 12 Aug '19

12 Aug '19

Dear all, for those of you still preparing your abstracts for the Firedrake meeting, and I know you're out there, note that the abstract submission deadline is: *** This Friday (16th August) *** This is also the day the early registration closes. Look forward to a glut of submissions! Cheers, Lawrence

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Re: [firedrake] question about surface integral
by Ham, David A 06 Aug '19

06 Aug '19

Hi Serdan, All integrals in Firedrake are evaluated with quadrature. By default, UFL estimates the degree of quadrature required, but you can force the quadrature degree by passing it to the measure. E.g. `ds(degree=4)`. If you want to understand the design philosophy of Firedrake, the place to go is Rathgeber (2016). https://doi.org/10.1145/2998441 . Is that what you mean by “theory guide”? Regards, David From: <firedrake-bounces(a)imperial.ac.uk> on behalf of Shaerdan Shataer <ss2571(a)bath.ac.uk> Date: Tuesday, 6 August 2019 at 11:24 To: firedrake <firedrake(a)imperial.ac.uk> Subject: [firedrake] question about surface integral Dear all, Does anyone know how does firedrake evaluate surface integrals? Is it Gaussian quadrature? Can I find the detail somewhere? p.s. can I find a theory guide about firedrake anywhere? Many thanks, Kind regards, Serdan

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question about surface integral
by Shaerdan Shataer 06 Aug '19

06 Aug '19

Dear all, Does anyone know how does firedrake evaluate surface integrals? Is it Gaussian quadrature? Can I find the detail somewhere? p.s. can I find a theory guide about firedrake anywhere? Many thanks, Kind regards, Serdan

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