May 2016 - firedrake - imperial.ac.uk

problem with firedake installation
by Teresa Kyrke-Smith 26 May '16

26 May '16

Hello, I work with Patrick Farrell and he sent me a code to run in firedrake. I installed it on my ubuntu system using the instructions on your website, installing it in a python virtual environment (unsetting my environmental variable $PETSC_DIR to do this as it came up with a warning about that). The installation seemed to work, but when I test the installation I get errors. Terminal output pasted below. Is this something to do with having the virtual environment and where it is trying to access python/petsc? How should I fix it? Many thanks for your help in advance. Teresa (firedrake) terkyr@tksbeast:~/firedrake/src/firedrake$ make alltest Building extension modules Linting firedrake codebase Linting firedrake test suite Linting firedrake scripts Running all regression tests ============================================================================== test session starts =============================================================================== platform linux2 -- Python 2.7.6, pytest-2.9.1, py-1.4.31, pluggy-0.3.1 benchmark: 3.0.0 (defaults: timer=time.time disable_gc=False min_rounds=5 min_time=5.00us max_time=1.00s calibration_precision=10 warmup=False warmup_iterations=1) rootdir: /home/terkyr/firedrake/src/firedrake, inifile: plugins: xdist-1.14, benchmark-3.0.0 collected 0 items / 1 errors ===================================================================================== ERRORS ===================================================================================== _______________________________________________________________________________ ERROR collecting ________________________________________________________________________________ ../../local/lib/python2.7/site-packages/py/_path/common.py:332: in visit for x in Visitor(fil, rec, ignore, bf, sort).gen(self): ../../local/lib/python2.7/site-packages/py/_path/common.py:368: in gen if p.check(dir=1) and (rec is None or rec(p))]) ../../local/lib/python2.7/site-packages/_pytest/main.py:647: in _recurse ihook = self.gethookproxy(path) ../../local/lib/python2.7/site-packages/_pytest/main.py:550: in gethookproxy my_conftestmodules = pm._getconftestmodules(fspath) ../../local/lib/python2.7/site-packages/_pytest/config.py:297: in _getconftestmodules mod = self._importconftest(conftestpath) ../../local/lib/python2.7/site-packages/_pytest/config.py:322: in _importconftest raise ConftestImportFailure(conftestpath, sys.exc_info()) E ConftestImportFailure: (local('/home/terkyr/firedrake/src/firedrake/tests/extrusion/conftest.py'), (<type 'exceptions.ImportError'>, ImportError('cannot import name map_expr_dags',), <traceback object at 0x2b67296b77a0>)) ============================================================================ 1 error in 0.38 seconds ============================================================================= make: *** [test] Error 1 -- Dr Teresa Kyrke-Smith Glaciologist British Antarctic Survey Cambridge +44 1223 221644 terkyr(a)bas.ac.uk<mailto:terkyr@bas.ac.uk> ________________________________ This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system. ________________________________

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Applying DirichletBCs to arbitrary \Gamma_{inflow} regions
by Justin Chang 26 May '16

26 May '16

Hi all, I am attempting to simulate a chaotic advection equation where the velocity vector field is based on the Arnold–Beltrami–Childress (ABC) flow equation: v_x = A*sin(z) + C*cos(y) v_x = B*sin(x) + A*cos(z) v_x = C*sin(y) + B*cos(x) Right now I have the following: from firedrake import * mesh = UnitCubeMesh(20,20,20) A = 0.08 B = 0.1 C = 0.15 V = VectorFunctionSpace(mesh, "CG", 1) velocity = Function(V) velocity.interpolate(Expression(( "A*sin(2*pi*x[2])+C*cos(2*pi*x[1])", "B*sin(2*pi*x[0])+A*cos(2*pi*x[2])", "C*sin(8*pi*x[1])+B*cos(8*pi*x[0])"), A=A,B=B,C=C)) Where A,B,C are user-defined constants (will add such constants inside all sin and cos functions later). I want to have DirichletBC's only applied to faces and regions where the velocity points into the cube (i.e., the "upstream" location). The region locations and sizes will vary depending on the constants chosen. Yes I could create separate GMSH files and manually determine where these "inflow" regions will be for every set of A/B/C/etc constants, but I was wondering if there's a way to automate this the Firedrake way, particularly if these constants will vary as a function of time. Thanks, Justin

2 1

Re: [firedrake] installation Linux
by David Ham 26 May '16

26 May '16

Hi Floriane, That error is a PETSc configure error so you have to provide any options that it wants by setting the PETSC_CONFIGURE_OPTIONS environment variable to contain those options. Regards, David On Wed, 25 May 2016 at 10:14 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> wrote: > Dear David, > > > I could fixed the issue by loading the MPI module in my terminal. However > I now get an issue with BLAS (see error below). I tried to use the argument > --with-blas-lib=<lib> but it is not recognized ( error: " > firedrake-install: error: unrecognized arguments: > --with-blas-lib=/home/fgidel/BLAS-3.6.0/blas_LINUX.a " ). > > > How can I indicate the library containing BLAS then? > > > Thanks, > Floriane > > > > ******************************************************************************* > UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log > for details): > > ------------------------------------------------------------------------------- > Could not find a functional BLAS. Run with --with-blas-lib=<lib> to > indicate the library containing BLAS. > Or --download-fblaslapack=1 to have one automatically downloaded and > installed > > > ******************************************************************************* > > Traceback (most recent call last): > File "<string>", line 1, in <module> > File "/tmp/pip-3EIjIm-build/setup.py", line 302, in <module> > > **metadata) > File "/usr/lib64/python2.7/distutils/core.py", line 152, in setup > dist.run_commands() > File "/usr/lib64/python2.7/distutils/dist.py", line 953, in > run_commands > self.run_command(cmd) > File "/usr/lib64/python2.7/distutils/dist.py", line 972, in > run_command > cmd_obj.run() > File "/tmp/pip-3EIjIm-build/setup.py", line 218, in run > config(prefix, self.dry_run) > File "/tmp/pip-3EIjIm-build/setup.py", line 148, in config > > if status != 0: raise RuntimeError(status) > RuntimeError: 256 > > ---------------------------------------- > Command "/home/fgidel/firedrake/bin/python -u -c "import setuptools, > tokenize;__file__='/tmp/pip-3EIjIm-build/setup.py';exec(compile(getattr(tokenize, > 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" > install --record /tmp/pip-Zetm3L-record/install-record.txt > --single-version-externally-managed --compile --install-headers > /home/fgidel/firedrake/include/site/python2.7/petsc" failed with error code > 1 in /tmp/pip-3EIjIm-build/ > > Traceback (most recent call last): > File "firedrake-install", line 884, in <module> > > install("petsc/") > File "firedrake-install", line 491, in install > run_pip_install(["--ignore-installed", package]) > File "firedrake-install", line 354, in run_pip_install > check_call(pipinstall + pipargs) > File "firedrake-install", line 205, in check_call > subprocess.check_call(arguments, env=env) > File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call > raise CalledProcessError(retcode, cmd) > subprocess.CalledProcessError: Command '['/home/fgidel/firedrake/bin/pip', > 'install', '--no-deps', '--ignore-installed', 'petsc/']' returned non-zero > exit status 1 > *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > de la part de David Ham <David.Ham(a)imperial.ac.uk> > *Envoyé :* mercredi 18 mai 2016 12:59:51 > > *À :* firedrake > *Objet :* Re: [firedrake] installation Linux > Hi Floriane, > > OK. This is a bit more mysterious can you: > > 1. Check that mpicc works from the command line. > > 2. Try to install with the --log option and post the resulting log file so > we can see exactly what goes wrong. > > Thanks, > > David > > On Tue, 17 May 2016 at 15:43 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> > wrote: > >> Dear David, >> >> >> I have checked and yet openmpi-devel is installed, and MPI is also >> installed but as part of another software (specific to MARIN). I know the >> path to MPI, so is there a way to specify it during the installation of >> Firedrake? But shouldn't it work anyway since openmpi-devel is installed as >> well? >> >> >> Thanks, >> Floriane >> ------------------------------ >> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >> de la part de David Ham <David.Ham(a)imperial.ac.uk> >> *Envoyé :* mardi 17 mai 2016 13:48:26 >> >> *À :* firedrake >> *Objet :* Re: [firedrake] installation Linux >> Hi Floriane, >> >> The error message says that you don't have MPI installed. A quick google >> suggests that the package you need for scientific Linux might be >> openmpi-devel. >> >> Regards, >> >> David >> >> On Tue, 17 May 2016 at 13:38 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >> wrote: >> >>> Dear David, >>> >>> >>> Indeed, pip was not installed correctly. This is now fixed but another >>> error occurs during the installation of Firedrake: >>> >>> >>> >>> >>> >>> ******************************************************************************* >>> UNABLE to CONFIGURE with GIVEN OPTIONS (see >>> configure.log for details): >>> >>> ------------------------------------------------------------------------------- >>> Did not find package MPI needed by hdf5. >>> Enable the package using --with-mpi >>> >>> ******************************************************************************* >>> >>> >>> Traceback (most recent call last): >>> File "<string>", line 1, in <module> >>> File "/tmp/pip-nn0xv2-build/setup.py", line 302, in <module> >>> **metadata) >>> File "/usr/lib64/python2.7/distutils/core.py", line 152, in setup >>> dist.run_commands() >>> File "/usr/lib64/python2.7/distutils/dist.py", line 953, in >>> run_commands >>> self.run_command(cmd) >>> File "/usr/lib64/python2.7/distutils/dist.py", line 972, in >>> run_command >>> cmd_obj.run() >>> File "/tmp/pip-nn0xv2-build/setup.py", line 218, in run >>> config(prefix, self.dry_run) >>> File "/tmp/pip-nn0xv2-build/setup.py", line 148, in config >>> if status != 0: raise RuntimeError(status) >>> RuntimeError: 256 >>> >>> ---------------------------------------- >>> Command "/home/fgidel/firedrake/bin/python -u -c "import setuptools, >>> tokenize;__file__='/tmp/pip-nn0xv2-build/setup.py';exec(compile(getattr(tokenize, >>> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" >>> install --record /tmp/pip-_EAAFI-record/install-record.txt >>> --single-version-externally-managed --compile --install-headers >>> /home/fgidel/firedrake/include/site/python2.7/petsc" failed with error code >>> 1 in /tmp/pip-nn0xv2-build/ >>> >>> Traceback (most recent call last): >>> File "firedrake-install", line 876, in <module> >>> install("petsc/") >>> File "firedrake-install", line 491, in install >>> run_pip_install(["--ignore-installed", package]) >>> File "firedrake-install", line 354, in run_pip_install >>> check_call(pipinstall + pipargs) >>> >>> File "firedrake-install", line 205, in check_call >>> subprocess.check_call(arguments, env=env) >>> File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call >>> raise CalledProcessError(retcode, cmd) >>> subprocess.CalledProcessError: Command >>> '['/home/fgidel/firedrake/bin/pip', 'install', '--no-deps', >>> '--ignore-installed', 'petsc/']' returned non-zero exit status 1 >>> >>> >>> >>> >>> Do you know what's missing? >>> >>> >>> Best wishes, >>> >>> >>> Floriane >>> >>> >>> ------------------------------ >>> *De :* firedrake-bounces(a)imperial.ac.uk < >>> firedrake-bounces(a)imperial.ac.uk> de la part de David Ham < >>> David.Ham(a)imperial.ac.uk> >>> *Envoyé :* mercredi 11 mai 2016 11:05:33 >>> *À :* firedrake >>> >>> *Objet :* Re: [firedrake] installation Linux >>> Hi Floriane, >>> >>> That error strongly suggests that pip is not installed. Can you please >>> tell us what the result of: >>> >>> pip install --user virtualenv >>> >>> is? >>> >>> In addition, I notice that you are installing Firedrake as root. We >>> recommend in the strongest possible terms that you do not do this. You >>> should install Firedrake yourself as your normal user. >>> >>> Regards, >>> >>> David >>> >>> On Wed, 11 May 2016 at 10:58 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >>> wrote: >>> >>>> Dear all, >>>> >>>> The IT team is still struggling to install Firedrake on the linux >>>> machine. This is the error that they get: >>>> >>>> root@lin0320 ~ # firedrake-install --no-package-manager >>>> -bash: firedrake-install: command not found >>>> root@lin0320 ~ # python firedrake-install --no-package-manager apt-get >>>> not found or disabled. Proceeding on the rash assumption that your compiled >>>> dependencies are in place. >>>> If this is not the case, please install the following and try again: >>>> * A C and C++ compiler (for example gcc/g++ or clang), GNU make >>>> * A Fortran compiler (for PETSc) >>>> * MPI >>>> * Blas and Lapack >>>> * Git, Mercurial >>>> * Python version 2.7 >>>> * pip and the Python headers >>>> * CMake >>>> * libspatialindex and headers >>>> * zlib >>>> Installing virtualenv. >>>> Traceback (most recent call last): >>>> File "firedrake-install", line 813, in <module> >>>> check_call(["pip", "install", "--user", "virtualenv"]) >>>> File "firedrake-install", line 205, in check_call >>>> subprocess.check_call(arguments, env=env) >>>> File "/usr/lib64/python2.7/subprocess.py", line 537, in check_call >>>> retcode = call(*popenargs, **kwargs) >>>> File "/usr/lib64/python2.7/subprocess.py", line 524, in call >>>> return Popen(*popenargs, **kwargs).wait() >>>> File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__ >>>> errread, errwrite) >>>> File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child >>>> raise child_exception >>>> OSError: [Errno 2] No such file or directory >>>> >>>> >>>> Do you have any suggestion? >>>> Thanks, >>>> Floriane >>>> ________________________________________ >>>> De : firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >>>> de la part de Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >>>> Envoyé : mardi 10 mai 2016 09:46:54 >>>> À : firedrake(a)imperial.ac.uk >>>> Objet : Re: [firedrake] installation Linux >>>> >>>> Ok, thanks! >>>> >>>> Floriane >>>> >>>> ________________________________________ >>>> De : firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >>>> de la part de Lawrence Mitchell <lawrence.mitchell(a)imperial.ac.uk> >>>> Envoyé : mardi 10 mai 2016 09:42:37 >>>> À : firedrake(a)imperial.ac.uk >>>> Objet : Re: [firedrake] installation Linux >>>> >>>> On 10/05/16 09:34, Floriane Gidel [RPG] wrote: >>>> > Hi David, >>>> > >>>> > >>>> > Thanks for your reply. I am now based at MARIN where I work on a >>>> > machine with Scientific Linux release 7.2 (Nitrogen). Which packages >>>> > do I need in that case? >>>> >>>> The same as on CentOS (SL is basically the same, just with a different >>>> badge). I'm not sure what those are called. They probably have very >>>> similar names to the packages on ubuntu. >>>> >>>> Lawrence >>>> >>>> >>>> _______________________________________________ >>>> firedrake mailing list >>>> firedrake(a)imperial.ac.uk >>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>>> >>>> _______________________________________________ >>>> firedrake mailing list >>>> firedrake(a)imperial.ac.uk >>>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>>> >>>

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Re: [firedrake] installation Linux
by David Ham 25 May '16

25 May '16

Hi Floriane, OK. This is a bit more mysterious can you: 1. Check that mpicc works from the command line. 2. Try to install with the --log option and post the resulting log file so we can see exactly what goes wrong. Thanks, David On Tue, 17 May 2016 at 15:43 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> wrote: > Dear David, > > > I have checked and yet openmpi-devel is installed, and MPI is also > installed but as part of another software (specific to MARIN). I know the > path to MPI, so is there a way to specify it during the installation of > Firedrake? But shouldn't it work anyway since openmpi-devel is installed as > well? > > > Thanks, > Floriane > ------------------------------ > *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > de la part de David Ham <David.Ham(a)imperial.ac.uk> > *Envoyé :* mardi 17 mai 2016 13:48:26 > > *À :* firedrake > *Objet :* Re: [firedrake] installation Linux > Hi Floriane, > > The error message says that you don't have MPI installed. A quick google > suggests that the package you need for scientific Linux might be > openmpi-devel. > > Regards, > > David > > On Tue, 17 May 2016 at 13:38 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> > wrote: > >> Dear David, >> >> >> Indeed, pip was not installed correctly. This is now fixed but another >> error occurs during the installation of Firedrake: >> >> >> >> >> >> ******************************************************************************* >> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log >> for details): >> >> ------------------------------------------------------------------------------- >> Did not find package MPI needed by hdf5. >> Enable the package using --with-mpi >> >> ******************************************************************************* >> >> >> Traceback (most recent call last): >> File "<string>", line 1, in <module> >> File "/tmp/pip-nn0xv2-build/setup.py", line 302, in <module> >> **metadata) >> File "/usr/lib64/python2.7/distutils/core.py", line 152, in setup >> dist.run_commands() >> File "/usr/lib64/python2.7/distutils/dist.py", line 953, in >> run_commands >> self.run_command(cmd) >> File "/usr/lib64/python2.7/distutils/dist.py", line 972, in >> run_command >> cmd_obj.run() >> File "/tmp/pip-nn0xv2-build/setup.py", line 218, in run >> config(prefix, self.dry_run) >> File "/tmp/pip-nn0xv2-build/setup.py", line 148, in config >> if status != 0: raise RuntimeError(status) >> RuntimeError: 256 >> >> ---------------------------------------- >> Command "/home/fgidel/firedrake/bin/python -u -c "import setuptools, >> tokenize;__file__='/tmp/pip-nn0xv2-build/setup.py';exec(compile(getattr(tokenize, >> 'open', open)(__file__).read().replace('\r\n', '\n'), __file__, 'exec'))" >> install --record /tmp/pip-_EAAFI-record/install-record.txt >> --single-version-externally-managed --compile --install-headers >> /home/fgidel/firedrake/include/site/python2.7/petsc" failed with error code >> 1 in /tmp/pip-nn0xv2-build/ >> >> Traceback (most recent call last): >> File "firedrake-install", line 876, in <module> >> install("petsc/") >> File "firedrake-install", line 491, in install >> run_pip_install(["--ignore-installed", package]) >> File "firedrake-install", line 354, in run_pip_install >> check_call(pipinstall + pipargs) >> >> File "firedrake-install", line 205, in check_call >> subprocess.check_call(arguments, env=env) >> File "/usr/lib64/python2.7/subprocess.py", line 542, in check_call >> raise CalledProcessError(retcode, cmd) >> subprocess.CalledProcessError: Command >> '['/home/fgidel/firedrake/bin/pip', 'install', '--no-deps', >> '--ignore-installed', 'petsc/']' returned non-zero exit status 1 >> >> >> >> >> Do you know what's missing? >> >> >> Best wishes, >> >> >> Floriane >> >> >> ------------------------------ >> *De :* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >> de la part de David Ham <David.Ham(a)imperial.ac.uk> >> *Envoyé :* mercredi 11 mai 2016 11:05:33 >> *À :* firedrake >> >> *Objet :* Re: [firedrake] installation Linux >> Hi Floriane, >> >> That error strongly suggests that pip is not installed. Can you please >> tell us what the result of: >> >> pip install --user virtualenv >> >> is? >> >> In addition, I notice that you are installing Firedrake as root. We >> recommend in the strongest possible terms that you do not do this. You >> should install Firedrake yourself as your normal user. >> >> Regards, >> >> David >> >> On Wed, 11 May 2016 at 10:58 Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >> wrote: >> >>> Dear all, >>> >>> The IT team is still struggling to install Firedrake on the linux >>> machine. This is the error that they get: >>> >>> root@lin0320 ~ # firedrake-install --no-package-manager >>> -bash: firedrake-install: command not found >>> root@lin0320 ~ # python firedrake-install --no-package-manager apt-get >>> not found or disabled. Proceeding on the rash assumption that your compiled >>> dependencies are in place. >>> If this is not the case, please install the following and try again: >>> * A C and C++ compiler (for example gcc/g++ or clang), GNU make >>> * A Fortran compiler (for PETSc) >>> * MPI >>> * Blas and Lapack >>> * Git, Mercurial >>> * Python version 2.7 >>> * pip and the Python headers >>> * CMake >>> * libspatialindex and headers >>> * zlib >>> Installing virtualenv. >>> Traceback (most recent call last): >>> File "firedrake-install", line 813, in <module> >>> check_call(["pip", "install", "--user", "virtualenv"]) >>> File "firedrake-install", line 205, in check_call >>> subprocess.check_call(arguments, env=env) >>> File "/usr/lib64/python2.7/subprocess.py", line 537, in check_call >>> retcode = call(*popenargs, **kwargs) >>> File "/usr/lib64/python2.7/subprocess.py", line 524, in call >>> return Popen(*popenargs, **kwargs).wait() >>> File "/usr/lib64/python2.7/subprocess.py", line 711, in __init__ >>> errread, errwrite) >>> File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child >>> raise child_exception >>> OSError: [Errno 2] No such file or directory >>> >>> >>> Do you have any suggestion? >>> Thanks, >>> Floriane >>> ________________________________________ >>> De : firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >>> de la part de Floriane Gidel [RPG] <mmfg(a)leeds.ac.uk> >>> Envoyé : mardi 10 mai 2016 09:46:54 >>> À : firedrake(a)imperial.ac.uk >>> Objet : Re: [firedrake] installation Linux >>> >>> Ok, thanks! >>> >>> Floriane >>> >>> ________________________________________ >>> De : firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> >>> de la part de Lawrence Mitchell <lawrence.mitchell(a)imperial.ac.uk> >>> Envoyé : mardi 10 mai 2016 09:42:37 >>> À : firedrake(a)imperial.ac.uk >>> Objet : Re: [firedrake] installation Linux >>> >>> On 10/05/16 09:34, Floriane Gidel [RPG] wrote: >>> > Hi David, >>> > >>> > >>> > Thanks for your reply. I am now based at MARIN where I work on a >>> > machine with Scientific Linux release 7.2 (Nitrogen). Which packages >>> > do I need in that case? >>> >>> The same as on CentOS (SL is basically the same, just with a different >>> badge). I'm not sure what those are called. They probably have very >>> similar names to the packages on ubuntu. >>> >>> Lawrence >>> >>> >>> _______________________________________________ >>> firedrake mailing list >>> firedrake(a)imperial.ac.uk >>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>> >>> _______________________________________________ >>> firedrake mailing list >>> firedrake(a)imperial.ac.uk >>> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >>> >>

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Re: [firedrake] Failed update
by Fabio Luporini 24 May '16

24 May '16

2016-05-24 19:16 GMT+02:00 Homolya, Miklós <m.homolya14(a)imperial.ac.uk>: > Is there any connection between the installation problem on CentOS and the > traceback below? (I struggle to see any.) > > > The traceback suggests a bug in COFFEE. If you're installation is > up-to-date, please file a bug here: > https://github.com/coneoproject/COFFEE/issues/new > > (If not up-to-date, please update, the bug might have been fixed already.) > > > Also, please run firedrake-clean after the update. Thanks > > With regard to the installation on CentOS: > > > python firedrake-install --no-package-manager > > > is the right thing to do. Beforehand you should make sure that the > following system packages are installed: > > * A C and C++ compiler (for example gcc/g++ or clang), GNU make > * A Fortran compiler (for PETSc) > * MPI > * Blas and Lapack > * Git, Mercurial > * Python version 2.7 > * pip and the Python headers > * autoconf, automake, libtool > * CMake > * zlib > (Also printed by the install script.) > > > Please don't run firedrake-install as root. > > If there are still any problems with the installation, please send us the > log (you get that by adding the --log option to firedrake-install), > otherwise we cannot possibly figure out what could have gone wrong. > > > Thanks, > Miklós > > ------------------------------ > *From:* firedrake-bounces(a)imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk> > on behalf of Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> > *Sent:* 24 May 2016 18:02:32 > *To:* firedrake > *Subject:* Re: [firedrake] Failed update > > Dear all, > > We are still struggling with the installation of firedrake on a linux > machine (running Centos). > > The only person with access rights on the machine is an IT who just told > me that he cannot install using the installation script because it crashes > immediately. As a first step, I asked him to run > > firedrake-install --no-package-manager > > but I am also asking for your help if you identify which dependency is > missing by the error below. > > Thank you, > > Anna. > > --------------------- > > Traceback (most recent call last): > File "nozzle_nsch.py", line 164, in <module> > solve(F_u == 0, u, bcs = [bc0,bc2,bc3,bc4, phi_bc, > mu_bc],solver_parameters={'pc_type': 'lu', 'pc_factor_mat_solver_package': > 'mumps'} ) # > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/solving.py", > line 118, in solve > _solve_varproblem(*args, **kwargs) > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/solving.py", > line 160, in _solve_varproblem > options_prefix=options_prefix) > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/variational_solver.py", > line 125, in __init__ > ctx = solving_utils._SNESContext(problem) > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/solving_utils.py", > line 106, in __init__ > for problem in problems) > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/solving_utils.py", > line 106, in <genexpr> > for problem in problems) > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/assemble.py", > line 66, in assemble > inverse=inverse, nest=nest) > File "<decorator-gen-295>", line 2, in _assemble > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/utils.py", > line 62, in wrapper > return f(*args, **kwargs) > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/assemble.py", > line 100, in _assemble > inverse=inverse) > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/tsfc_interface.py", > line 243, in compile_form > number_map).kernels > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", > line 203, in __new__ > obj = make_obj() > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", > line 193, in make_obj > obj.__init__(*args, **kwargs) > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/tsfc_interface.py", > line 174, in __init__ > kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts), > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/backends.py", > line 118, in __call__ > return t(*args, **kwargs) > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", > line 203, in __new__ > obj = make_obj() > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", > line 193, in make_obj > obj.__init__(*args, **kwargs) > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/base.py", > line 3848, in __init__ > self._code = self._ast_to_c(self._ast, self._opts) > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/host.py", > line 60, in _ast_to_c > ast_handler.plan_cpu(self._opts) > File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/plan.py", > line 184, in plan_cpu > _generate_cpu_code(self, kernel, **params) > File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/plan.py", > line 110, in _generate_cpu_code > loop_opt.eliminate_zeros() > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/optimizer.py", > line 167, in eliminate_zeros > self.nz_syms = zls.reschedule(self.header) > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/scheduler.py", > line 852, in reschedule > nz_syms, nz_info = self._reschedule_itspace(root, candidates) > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/scheduler.py", > line 728, in _reschedule_itspace > dim_size = tuple(((0, dict(i)[l.dim][0]), l.dim) for l in loops) > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/scheduler.py", > line 728, in <genexpr> > dim_size = tuple(((0, dict(i)[l.dim][0]), l.dim) for l in loops) > KeyError: 'k' > Exception AttributeError: "'NonlinearVariationalSolver' object has no > attribute '_parameters'" in <bound method > NonlinearVariationalSolver.__del__ of > <firedrake.variational_solver.NonlinearVariationalSolver object at > 0x7f2dc6cfc510>> ignored > > > > On 24/05/16 06:45, Homolya, Miklós wrote: > > It seems that the new COFFEE dependency GLPK is not found, which should be > installed automatically by the update script. > > Can you verify that your installation is in virtualenv, not global? > > Can you run firedrake-update again and send its output? > > Get Outlook for Android <https://aka.ms/ghei36> > > From: Fryderyk Wilczynski > Sent: Tuesday, 24 May, 06:25 > Subject: [firedrake] Failed update > To: firedrake > > Dear Firedrakes, > > we suspect some mistake has been made when we tried updating Firedrake > yesterday. I tried running some sample scripts from the documentation page > and get the following exception > > mat-lin4123.leeds.ac.uk% (19) python benney_luke.py > > COFFEE finished in 0.0112019 seconds (flops: 0 -> 0) > > COFFEE finished in 0.00383806 seconds (flops: 0 -> 0) > > compute_form_data finished in 0.057472 seconds. > > compile_integral finished in 0.0535629 seconds. > > TSFC finished in 0.111062 seconds. > > Traceback (most recent call last): > > File "benney_luke.py", line 133, in <module> > > phi_solver_h = NonlinearVariationalSolver(phi_problem_h) > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/variational_solver.py", > line 125, in __init__ > > ctx = solving_utils._SNESContext(problem) > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/solving_utils.py", > line 106, in __init__ > > for problem in problems) > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/solving_utils.py", > line 106, in <genexpr> > > for problem in problems) > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/assemble.py", > line 66, in assemble > > inverse=inverse, nest=nest) > > File "<decorator-gen-295>", line 2, in _assemble > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/utils.py", > line 62, in wrapper > > return f(*args, **kwargs) > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/assemble.py", > line 100, in _assemble > > inverse=inverse) > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/tsfc_interface.py", > line 243, in compile_form > > number_map).kernels > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", > line 203, in __new__ > > obj = make_obj() > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", > line 193, in make_obj > > obj.__init__(*args, **kwargs) > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/tsfc_interface.py", > line 174, in __init__ > > kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts), > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/backends.py", > line 118, in __call__ > > return t(*args, **kwargs) > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", > line 203, in __new__ > > obj = make_obj() > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", > line 193, in make_obj > > obj.__init__(*args, **kwargs) > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/base.py", > line 3848, in __init__ > > self._code = self._ast_to_c(self._ast, self._opts) > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/host.py", > line 60, in _ast_to_c > > ast_handler.plan_cpu(self._opts) > > File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/plan.py", > line 184, in plan_cpu > > _generate_cpu_code(self, kernel, **params) > > File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/plan.py", > line 106, in _generate_cpu_code > > loop_opt.rewrite(rewrite) > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/optimizer.py", > line 120, in rewrite > > ew.SGrewrite() > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/rewriter.py", > line 497, in SGrewrite > > prob.solve(ilp.GLPK(msg=0)) > > File "/opt/firedrake/1605.1/lib/python2.7/site-packages/pulp/pulp.py", > line 1643, in solve > > status = solver.actualSolve(self, **kwargs) > > File > "/opt/firedrake/1605.1/lib/python2.7/site-packages/pulp/solvers.py", line > 346, in actualSolve > > raise PulpSolverError("PuLP: cannot execute "+self.path) > > pulp.solvers.PulpSolverError: PuLP: cannot execute glpsol > > Exception AttributeError: "'NonlinearVariationalSolver' object has no > attribute '_parameters'" in <bound method > NonlinearVariationalSolver.__del__ of > <firedrake.variational_solver.NonlinearVariationalSolver object at > 0x7f3e2ea40710>> ignored > > > Would you be able to help us identify what is going wrong and how to fix > it? > > Thanks, > > Fryderyk > > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > >

1 0

Failed update
by Fryderyk Wilczynski 24 May '16

24 May '16

Dear Firedrakes, we suspect some mistake has been made when we tried updating Firedrake yesterday. I tried running some sample scripts from the documentation page and get the following exception mat-lin4123.leeds.ac.uk% (19) python benney_luke.py COFFEE finished in 0.0112019 seconds (flops: 0 -> 0) COFFEE finished in 0.00383806 seconds (flops: 0 -> 0) compute_form_data finished in 0.057472 seconds. compile_integral finished in 0.0535629 seconds. TSFC finished in 0.111062 seconds. Traceback (most recent call last): File "benney_luke.py", line 133, in <module> phi_solver_h = NonlinearVariationalSolver(phi_problem_h) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/variational_solver.py", line 125, in __init__ ctx = solving_utils._SNESContext(problem) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/solving_utils.py", line 106, in __init__ for problem in problems) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/solving_utils.py", line 106, in <genexpr> for problem in problems) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/assemble.py", line 66, in assemble inverse=inverse, nest=nest) File "<decorator-gen-295>", line 2, in _assemble File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/utils.py", line 62, in wrapper return f(*args, **kwargs) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/assemble.py", line 100, in _assemble inverse=inverse) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/tsfc_interface.py", line 243, in compile_form number_map).kernels File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", line 203, in __new__ obj = make_obj() File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", line 193, in make_obj obj.__init__(*args, **kwargs) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/firedrake/tsfc_interface.py", line 174, in __init__ kernels.append(KernelInfo(kernel=Kernel(ast, ast.name, opts=opts), File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/backends.py", line 118, in __call__ return t(*args, **kwargs) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", line 203, in __new__ obj = make_obj() File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/caching.py", line 193, in make_obj obj.__init__(*args, **kwargs) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/base.py", line 3848, in __init__ self._code = self._ast_to_c(self._ast, self._opts) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/PyOP2-0.13.0_19_g2062a47-py2.7-linux-x86_64.egg/pyop2/host.py", line 60, in _ast_to_c ast_handler.plan_cpu(self._opts) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/plan.py", line 184, in plan_cpu _generate_cpu_code(self, kernel, **params) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/plan.py", line 106, in _generate_cpu_code loop_opt.rewrite(rewrite) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/optimizer.py", line 120, in rewrite ew.SGrewrite() File "/opt/firedrake/1605.1/lib/python2.7/site-packages/coffee/rewriter.py", line 497, in SGrewrite prob.solve(ilp.GLPK(msg=0)) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/pulp/pulp.py", line 1643, in solve status = solver.actualSolve(self, **kwargs) File "/opt/firedrake/1605.1/lib/python2.7/site-packages/pulp/solvers.py", line 346, in actualSolve raise PulpSolverError("PuLP: cannot execute "+self.path) pulp.solvers.PulpSolverError: PuLP: cannot execute glpsol Exception AttributeError: "'NonlinearVariationalSolver' object has no attribute '_parameters'" in <bound method NonlinearVariationalSolver.__del__ of <firedrake.variational_solver.NonlinearVariationalSolver object at 0x7f3e2ea40710>> ignored Would you be able to help us identify what is going wrong and how to fix it? Thanks, Fryderyk

3 3

Re: [firedrake] aborted run
by David Ham 24 May '16

24 May '16

Hi Francis, This is a memory leak in PETSc. PETSc currently leaks about 400 bytes per halo exchange. Lawrence found the leak last week and sent PETSc a fix. PETSc have responded so hopefully a fix will go into PETSc in the next few days. Regards, David On Tue, 24 May 2016 at 03:20 Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Hello, > > Minor update. > > The run with cpu=4 has gone beyond the point where the cpu=2 case > crashes. I guess it's good news that it didn't stop but I am still not > sure as to why. > > Francis > > > > > ------------------ > Francis Poulin > Associate Professor > Department of Applied Mathematics > University of Waterloo > > email: fpoulin(a)uwaterloo.ca > Web: https://uwaterloo.ca/poulin-research-group/ > Telephone: +1 519 888 4567 x32637 > > ------------------------------ > *From:* Francis Poulin > *Sent:* Sunday, May 22, 2016 4:59 PM > *To:* firedrake(a)imperial.ac.uk > *Subject:* RE: [firedrake] aborted run > > Hello Everyone, > > Thanks Colin and David for the helpful advice. > > *David: *I'm glad to know that things should scale much better than > this. On my laptop that only has 4 cores, I did a some tests to see how > long it took to output one day (100 time steps). > > cpu = 4: > time: initially 24, then 25 and 26. Approximately 25. > memory: initially 6%, then 8% > > cpu = 2: > time: about 36 between outputs > > cpu = 1: > time: about 64 between outputs > > Going from 1 to 2 cores is pretty efficient, about 90%, but then going to > 4 we get 67%. Maybe it's because of the architecture. I'm not sure. > > > *Colin:* Following what you set up initially we are choosing the > following function spaces. > > Vdg = FunctionSpace(mesh,"DG",1) # DG elements for > Potential Vorticity (PV) > Vcg = FunctionSpace(mesh,"CG",1) # CG elements for > Streamfunction > Vu = VectorFunctionSpace(mesh,"DG",1, dim=2) # DG elements for > velocity > > So velocity is already a DG space and the same degree at the PV space. Is > there something here that I'm not getting? > > As for the projection vs interpolate, we have the following two lines that > project. > > v = Function(Vu, name='velocity').project(gradperp_h(psi0)) > > v.project(gradperp_h(psi0)) > > It seems easy enough to change project to interpolate and I will give that > a try. > > I can appreciate that maybe ilu is using a lot of memory but should it be > using more memory as time passes? Significantly more memory. I would > think that it's not allocating anymore arrays and it's solving the same > problem at every step which does not change much in the first 40 days. Is > there a reason to think why at day 32 suddenly uses so much more > memory? > > I am doing the cpu = 4 test case right now and I do see a steady increase > in the percentage of memory usage: 6, 8 and now 8.7. I have 16 GB of memory > and the increase seems very dramatic to me but I don't have that much > experience using PETSc so maybe this is to be expected. > > If there is a possibility to use AMG to speed things up and improve the > efficiency I am very keen to try it. I presume this requires using a > different branch of the gitrepo? > > Best regards, > Francis > > ------------------ > Francis Poulin > Associate Professor > Department of Applied Mathematics > University of Waterloo > > email: fpoulin(a)uwaterloo.ca > Web: https://uwaterloo.ca/poulin-research-group/ > Telephone: +1 519 888 4567 x32637 > > ------------------------------ > *From:* firedrake-bounces(a)imperial.ac.uk [firedrake-bounces(a)imperial.ac.uk] > on behalf of Colin Cotter [colin.cotter(a)imperial.ac.uk] > *Sent:* Sunday, May 22, 2016 2:11 PM > *To:* firedrake > *Subject:* Re: [firedrake] aborted run > > ... in which case we should get you set up with AMG for the PV inversion > as well. > > all the best > --cjc > On 22 May 2016 at 11:34, Ham, David A <david.ham(a)imperial.ac.uk> wrote: > >> Additionally, that's something like half a million cells, so you should >> be able to go faster by using more cores. Depending on your discretisation, >> 10-20 cores probably makes sense for that problem. >> >> Regards, >> >> David >> >> On Sun, 22 May 2016 at 08:24 Cotter, Colin J <colin.cotter(a)imperial.ac.uk> >> wrote: >> > Hi Francis, >>> This is because the solver inside the projection is using ilu and it >>> is running out of memory. More scalable solvers are available but in this >>> case I would suggest making the velocity space into a DG vector function >>> space large enough to contain your grad perp (same degree as the pv space >>> works) and then using interpolate instead of project, which produces the >>> same result mathematically but can then be computed locally. This wasn't >>> previously possible which is why we put project. >>> >>> All the best >>> Cjc >>> >>> On Sunday, 22 May 2016, Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: >>> >>>> Hello, >>>> >>>> First, sorry to trouble you on the weekend, if you are reading this on >>>> the weekend that is. Second, Jemma and I have had some success with our 3D >>>> QG model. You can seem the result of the instability of a barotropic jet a >>>> very course 50x50x50 run at the following link. The movie needs a lot of >>>> fixing up but energy and enstrophy are nearly conserved so somethings are >>>> going pretty well. >>>> >>>> https://www.youtube.com/watch?v=CbqdA3a9DZg >>>> >>>> I decide to try a finer resolution case, 100x100x50, in hopes of having >>>> a better data set to work with. >>>> >>>> I am using a time step of 0.01 and it does 1 time unit on 2 cores on my >>>> laptop in over an hour. Not sure if that is very fast or not but it was >>>> working away up until it died. Below you see the last few outputs of the >>>> energies before things went all pear shaped. >>>> >>>> I have a fixed time step and so can believe that maybe the CFL >>>> condition was violated but for a 2D case I did a 200x200 run with the same >>>> time step so I'm not convinced that the CFL condition is violated. >>>> >>>> Given the output, does anyone have any ideas on what might have gone >>>> wrong? >>>> >>>> It would be great to restart from the last output and see whether this >>>> happens every time. Unfortunately we haven't gotten to that stage yet but >>>> we really should do that next. >>>> >>>> Cheers, Francis >>>> >>>> >>>> ... >>>> 33.98 16.504104156 39.1507283386 55.6548324946 33.3509321074 >>>> 33.99 16.504103109 39.1507164876 55.6548195966 33.3509288412 >>>> 34.0 16.5041020578 39.1507045844 55.6548066422 33.3509255645 >>>> Traceback (most recent call last): >>>> File "qg3d_jet.py", line 151, in <module> >>>> v.project(gradperp_h(psi0)) >>>> File >>>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/function.py", >>>> line 277, in project >>>> return projection.project(b, self, *args, **kwargs) >>>> File >>>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/projection.py", >>>> line 101, in project >>>> form_compiler_parameters=form_compiler_parameters) >>>> File >>>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/solving.py", >>>> line 118, in solve >>>> _solve_varproblem(*args, **kwargs) >>>> File >>>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/solving.py", >>>> line 145, in _solve_varproblem >>>> solver.solve() >>>> File >>>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/variational_solver.py", >>>> line 185, in solve >>>> self.snes.solve(None, v) >>>> File "PETSc/SNES.pyx", line 520, in petsc4py.PETSc.SNES.solve >>>> (src/petsc4py.PETSc.c:168132) >>>> Traceback (most recent call last): >>>> File "qg3d_jet.py", line 151, in <module> >>>> v.project(gradperp_h(psi0)) >>>> File >>>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/function.py", >>>> line 277, in project >>>> return projection.project(b, self, *args, **kwargs) >>>> File >>>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/projection.py", >>>> line 101, in project >>>> form_compiler_parameters=form_compiler_parameters) >>>> File >>>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/solving.py", >>>> line 118, in solve >>>> _solve_varproblem(*args, **kwargs) >>>> File >>>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/solving.py", >>>> line 145, in _solve_varproblem >>>> solver.solve() >>>> File >>>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/variational_solver.py", >>>> line 185, in solve >>>> self.snes.solve(None, v) >>>> File "PETSc/SNES.pyx", line 520, in petsc4py.PETSc.SNES.solve >>>> (src/petsc4py.PETSc.c:168132) >>>> petsc4py.PETSc.Errorpetsc4py.PETSc.Error: error code 1 >>>> [0] SNESSolve() line 4008 in >>>> /tmp/pip-EZZoo0-build/src/snes/interface/snes.c >>>> [0] SNESSolve_KSPONLY() line 40 in >>>> /tmp/pip-EZZoo0-build/src/snes/impls/ksponly/ksponly.c >>>> [0] KSPSolve() line 600 in >>>> /tmp/pip-EZZoo0-build/src/ksp/ksp/interface/itfunc.c >>>> [0] KSPSetUpOnBlocks() line 220 in >>>> /tmp/pip-EZZoo0-build/src/ksp/ksp/interface/itfunc.c >>>> [0] PCSetUpOnBlocks() line 1001 in >>>> /tmp/pip-EZZoo0-build/src/ksp/pc/interface/precon.c >>>> [0] PCSetUpOnBlocks_BJacobi_Singleblock() line 650 in >>>> /tmp/pip-EZZoo0-build/src/ksp/pc/impls/bjacobi/bjacobi.c >>>> [0] KSPSetUp() line 390 in >>>> /tmp/pip-EZZoo0-build/src/ksp/ksp/interface/itfunc.c >>>> [0] PCSetUp() line 968 in >>>> /tmp/pip-EZZoo0-build/src/ksp/pc/interface/precon.c >>>> [0] PCSetUp_ILU() line 212 in >>>> /tmp/pip-EZZoo0-build/src/ksp/pc/impls/factor/ilu/ilu.c >>>> [0] MatILUFactorSymbolic() line 6594 in >>>> /tmp/pip-EZZoo0-build/src/mat/interface/matrix.c >>>> [0] MatILUFactorSymbolic_SeqBAIJ() line 370 in >>>> /tmp/pip-EZZoo0-build/src/mat/impls/baij/seq/baijfact2.c >>>> [0] MatILUFactorSymbolic_SeqBAIJ_ilu0() line 276 in >>>> /tmp/pip-EZZoo0-build/src/mat/impls/baij/seq/baijfact2.c >>>> [0] MatILUFactorSymbolic_SeqBAIJ_ilu0() line 276 in >>>> /tmp/pip-EZZoo0-build/src/mat/impls/baij/seq/baijfact2.c >>>> [0] Out of memory. Allocated: 0, Used by process: 2962321408 >>>> [0] Memory requested 584000046 >>>> : error code 1 >>>> [1] SNESSolve() line 4008 in >>>> /tmp/pip-EZZoo0-build/src/snes/interface/snes.c >>>> [1] SNESSolve_KSPONLY() line 40 in >>>> /tmp/pip-EZZoo0-build/src/snes/impls/ksponly/ksponly.c >>>> [1] KSPSolve() line 600 in >>>> /tmp/pip-EZZoo0-build/src/ksp/ksp/interface/itfunc.c >>>> [1] KSPSetUpOnBlocks() line 220 in >>>> /tmp/pip-EZZoo0-build/src/ksp/ksp/interface/itfunc.c >>>> [1] PCSetUpOnBlocks() line 1001 in >>>> /tmp/pip-EZZoo0-build/src/ksp/pc/interface/precon.c >>>> [1] PCSetUpOnBlocks_BJacobi_Singleblock() line 650 in >>>> /tmp/pip-EZZoo0-build/src/ksp/pc/impls/bjacobi/bjacobi.c >>>> [1] KSPSetUp() line 390 in >>>> /tmp/pip-EZZoo0-build/src/ksp/ksp/interface/itfunc.c >>>> [1] PCSetUp() line 968 in >>>> /tmp/pip-EZZoo0-build/src/ksp/pc/interface/precon.c >>>> [1] PCSetUp_ILU() line 212 in >>>> /tmp/pip-EZZoo0-build/src/ksp/pc/impls/factor/ilu/ilu.c >>>> [1] MatILUFactorSymbolic() line 6594 in >>>> /tmp/pip-EZZoo0-build/src/mat/interface/matrix.c >>>> [1] MatILUFactorSymbolic_SeqBAIJ() line 370 in >>>> /tmp/pip-EZZoo0-build/src/mat/impls/baij/seq/baijfact2.c >>>> [1] MatILUFactorSymbolic_SeqBAIJ_ilu0() line 276 in >>>> /tmp/pip-EZZoo0-build/src/mat/impls/baij/seq/baijfact2.c >>>> [1] MatILUFactorSymbolic_SeqBAIJ_ilu0() line 276 in >>>> /tmp/pip-EZZoo0-build/src/mat/impls/baij/seq/baijfact2.c >>>> [1] Out of memory. Allocated: 0, Used by process: 2943778816 >>>> [1] Memory requested 584000046 >>>> >>>> -------------------------------------------------------------------------- >>>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>>> with errorcode 1. >>>> >>>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>>> You may or may not see output from other processes, depending on >>>> exactly when Open MPI kills them. >>>> >>>> -------------------------------------------------------------------------- >>>> >>>> >>>> ------------------ >>>> Francis Poulin >>>> Associate Professor >>>> Department of Applied Mathematics >>>> University of Waterloo >>>> >>>> email: fpoulin(a)uwaterloo.ca >>>> Web: https://uwaterloo.ca/poulin-research-group/ >>>> Telephone: +1 519 888 4567 x32637 >>>> >>>> >>> >>> -- >>> http://www.imperial.ac.uk/people/colin.cotter >>> >>> www.cambridge.org/9781107663916 >>> >>> >>> >>> > > > -- > http://www.imperial.ac.uk/people/colin.cotter > > www.cambridge.org/9781107663916 > > >

2 1

Re: [firedrake] Laplace equation on subdomain
by David Ham 24 May '16

24 May '16

Well the following reproduces the reported error for me: from firedrake import * m = UnitSquareMesh(2, 2) fs = FunctionSpace(m, "CG", 1) v = TestFunction(fs) assemble(v*dS) On Tue, 26 Apr 2016 at 21:27 Andrew McRae <A.T.T.McRae(a)bath.ac.uk> wrote: > I didn't think this was true, unless something changed "recently". > > I can't test right now, but I'm quite confident I used to use continuous > functions in interior facet integrals on simplex meshes without needing a > restriction. > > However, I recall being forced to use restrictions on extruded meshes; I > never got to the bottom of why. Perhaps Miklós can comment (or state that > my recollection is nonsense)? > > On 26 April 2016 at 21:12, David Ham <David.Ham(a)imperial.ac.uk> wrote: > >> Hi Tomasz, >> >> This is a subtlety of UFL. *All* arguments and coefficients in an >> interior facet integral have to be "restricted". This even applies to ones >> which are continuous and for which the "+" and "-" restrictions are >> therefore the same. You can just arbitrarily decide to restrict the >> continuous things to the plus side, or take avg() of the lack of symmetry >> offends your sense of aesthetics. >> >> Regards, >> >> David >> > >> On Tue, 26 Apr 2016 at 15:46 Tomasz Salwa [RPG] <mmtjs(a)leeds.ac.uk> >> wrote: >> >>> Hi, >>> >>> >>> Previous problem continued. >>> >>> I have a working solver for separate subsystems in mixed function space >>> now. I'd like to introduce the coupling terms at the interface, but they >>> cause a UFL exception "Discontinuous type Argument must be restricted." >>> >>> Full code is here: https://bitbucket.org/mmtjs/lin_coupled_fd_2d >>> >>> >>> <https://bitbucket.org/mmtjs/lin_coupled_fd_2d> >>> >>> The relevant part from lib/coupled_system.py is: >>> >>> ... >>> >>> # define the normal vector at the interface >>> >>> self.n = fd.FacetNormal(self.mesh) >>> self.n_int = (self.B.I("+")*self.W.I("-") - >>> self.B.I("-")*self.W.I("+"))*self.n("+") # btw how can write this to file >>> to verify? >>> >>> ... >>> >>> # the second line causes exception (and later similar terms too) >>> >>> a_U = fd.dot( self.trial_s * self.B.I, self.v_s * self.B.I) * >>> fd.dx \ >>> + fd.dot( self.v_s, self.n_int ) * self.trial_f * >>> fd.dS >>> >>> >>> Regards, >>> >>> Tomasz >>> >>> >>> >>> ------------------------------ >>> *From:* firedrake-bounces(a)imperial.ac.uk < >>> firedrake-bounces(a)imperial.ac.uk> on behalf of Tomasz Salwa [RPG] < >>> mmtjs(a)leeds.ac.uk> >>> *Sent:* 21 April 2016 11:04 >>> >>> *To:* firedrake >>> *Subject:* Re: [firedrake] Laplace equation on subdomain >>> >>> >>> Cool, works now, dynamic case too. I'll do the same for the structural >>> part. >>> >>> >>> Cheers, >>> >>> Tomasz >>> >>> >>> ------------------------------ >>> *From:* firedrake-bounces(a)imperial.ac.uk < >>> firedrake-bounces(a)imperial.ac.uk> on behalf of David Ham < >>> David.Ham(a)imperial.ac.uk> >>> *Sent:* 21 April 2016 09:38 >>> *To:* firedrake >>> *Subject:* Re: [firedrake] Laplace equation on subdomain >>> Hi Tomasz, >>> >>> See the new pull request. In essence, the projection is not safe in the >>> indicator function case. >>> >>> Regards, >>> >>> David >>> >>> On Wed, 20 Apr 2016 at 15:53 Tomasz Salwa [RPG] <mmtjs(a)leeds.ac.uk> >>> wrote: >>> >>>> Hi David, >>>> >>>> >>>> Thank you, now it converges properly. >>>> >>>> However, I noticed that the error depends on the mesh resolution beyond >>>> the fluid subdomain, which I think should not be the case (at least when I >>>> refine it in x direction). Perhaps the solution is ok, but the source is in >>>> the way I impose the analytical one, or compute the error. Can you diagnose >>>> this? >>>> >>>> Bitbucket's repo is updated. >>>> >>>> >>>> Regards, >>>> >>>> Tomasz >>>> >>>> >>>> ------------------------------ >>>> *From:* firedrake-bounces(a)imperial.ac.uk < >>>> firedrake-bounces(a)imperial.ac.uk> on behalf of David Ham < >>>> David.Ham(a)imperial.ac.uk> >>>> *Sent:* 20 April 2016 10:05 >>>> >>>> *To:* firedrake >>>> *Subject:* Re: [firedrake] Laplace equation on subdomain >>>> Hi Tomasz, >>>> >>>> I have just put in a pull request fixing your problem. In essence, you >>>> were only applying half of the indicator function fix. In order to >>>> correctly use indicator functions to solve problems over a subdomain, it is >>>> necessary to *both* use the custom boundary condition to force the solution >>>> in the rest of the domain to zero *and* multiply the integrands in your >>>> forms by the indicator function. You were only doing the former and not the >>>> latter. Making this fix causes the error to drop to 10^-5. I haven't done a >>>> convergence test to check that the error converges at the right rate, but >>>> you should really do so. >>>> >>>> Regards, >>>> >>>> David >>>> >>>> On Tue, 19 Apr 2016 at 11:52 Tomasz Salwa [RPG] <mmtjs(a)leeds.ac.uk> >>>> wrote: >>>> >>>>> Hi David, >>>>> >>>>> >>>>> Here's the code: >>>>> >>>>> https://bitbucket.org/mmtjs/laplace_extended_domain >>>>> >>>>> >>>>> It's roughly the same as before, just with a gmsh-generated mesh. >>>>> >>>>> >>>>> Regards, >>>>> >>>>> Tomasz >>>>> >>>>> >>>>> ------------------------------ >>>>> *From:* firedrake-bounces(a)imperial.ac.uk < >>>>> firedrake-bounces(a)imperial.ac.uk> on behalf of David Ham < >>>>> David.Ham(a)imperial.ac.uk> >>>>> *Sent:* 19 April 2016 09:54 >>>>> *To:* firedrake >>>>> >>>>> *Subject:* Re: [firedrake] Laplace equation on subdomain >>>>> Hi Tomasz, >>>>> >>>>> Can you please post the code you are using for this (preferably by >>>>> pointing us to a git repo we can clone). I can't diagnose what is going >>>>> wrong just by looking at the visualisation, I'm afraid. >>>>> >>>>> Regards, >>>>> >>>>> David >>>>> >>>>> On Mon, 18 Apr 2016 at 12:12 Tomasz Salwa [RPG] <mmtjs(a)leeds.ac.uk> >>>>> wrote: >>>>> >>>>>> Hi, >>>>>> >>>>>> I plotted the difference between analytical and numerical solutions >>>>>> (see attached). It doesn't converge to the right solution with mesh >>>>>> refinement. Is it possible that the Neumann BC is not applied at the >>>>>> interface during the computation, although the extended Dirichlet BCs >>>>>> enforce resulting zero solution beyond the fluid subdomain? >>>>>> >>>>>> Cheers, >>>>>> Tomasz >>>>>> >>>>>> ________________________________________ >>>>>> From: firedrake-bounces(a)imperial.ac.uk < >>>>>> firedrake-bounces(a)imperial.ac.uk> on behalf of Lawrence Mitchell < >>>>>> lawrence.mitchell(a)imperial.ac.uk> >>>>>> Sent: 15 April 2016 16:00 >>>>>> To: firedrake(a)imperial.ac.uk >>>>>> Subject: Re: [firedrake] Laplace equation on subdomain >>>>>> >>>>>> > On 15 Apr 2016, at 15:54, Tomasz Salwa [RPG] <mmtjs(a)leeds.ac.uk> >>>>>> wrote: >>>>>> > >>>>>> > Hi David, >>>>>> > >>>>>> > It works partially, i.e. the nodes beyond the fluid subdomain are >>>>>> "turned off" now, but it looks like the interface is "smeared". I suspect >>>>>> that the assembled matrix's entries involve also integration over elements >>>>>> one layer beyond the subdomain boundary. Is it possible to exclude them? >>>>>> >>>>>> If you have neumann conditions on your subdomain boundary you've only >>>>>> constrained the gradient of the solution. Therefore on the boundary nodes >>>>>> you may have non-zero solution values. >>>>>> >>>>>> Because the domain you visualise in paraview extends outside the >>>>>> subdomain you'll have (in 1D) something like: >>>>>> >>>>>> >>>>>> ........ >>>>>> \............ >>>>>> ^ boundary node >>>>>> >>>>>> Note how the cell at the boundary has a non-zero coefficient value >>>>>> are one end, but a zero value at the other (assuming piecewise liners). >>>>>> Paraview will linearly interpolate this basis function when visualising, >>>>>> which may be the artefact you're seeing. >>>>>> >>>>>> Can you construct an analytic solution and determine that you >>>>>> converge at the correct rate as you refine the mesh? This is a safer test >>>>>> than eyeballing the solution. >>>>>> >>>>>> Lawrence >>>>>> >>>>>

2 2

Re: [firedrake] aborted run
by Colin Cotter 24 May '16

24 May '16

... in which case we should get you set up with AMG for the PV inversion as well. all the best --cjc On 22 May 2016 at 11:34, Ham, David A <david.ham(a)imperial.ac.uk> wrote: > Additionally, that's something like half a million cells, so you should be > able to go faster by using more cores. Depending on your discretisation, > 10-20 cores probably makes sense for that problem. > > Regards, > > David > > On Sun, 22 May 2016 at 08:24 Cotter, Colin J <colin.cotter(a)imperial.ac.uk> > wrote: > >> Hi Francis, >> This is because the solver inside the projection is using ilu and it is >> running out of memory. More scalable solvers are available but in this case >> I would suggest making the velocity space into a DG vector function space >> large enough to contain your grad perp (same degree as the pv space works) >> and then using interpolate instead of project, which produces the same >> result mathematically but can then be computed locally. This wasn't >> previously possible which is why we put project. >> >> All the best >> Cjc >> >> On Sunday, 22 May 2016, Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: >> >>> Hello, >>> >>> First, sorry to trouble you on the weekend, if you are reading this on >>> the weekend that is. Second, Jemma and I have had some success with our 3D >>> QG model. You can seem the result of the instability of a barotropic jet a >>> very course 50x50x50 run at the following link. The movie needs a lot of >>> fixing up but energy and enstrophy are nearly conserved so somethings are >>> going pretty well. >>> >>> https://www.youtube.com/watch?v=CbqdA3a9DZg >>> >>> I decide to try a finer resolution case, 100x100x50, in hopes of having >>> a better data set to work with. >>> >>> I am using a time step of 0.01 and it does 1 time unit on 2 cores on my >>> laptop in over an hour. Not sure if that is very fast or not but it was >>> working away up until it died. Below you see the last few outputs of the >>> energies before things went all pear shaped. >>> >>> I have a fixed time step and so can believe that maybe the CFL condition >>> was violated but for a 2D case I did a 200x200 run with the same time step >>> so I'm not convinced that the CFL condition is violated. >>> >>> Given the output, does anyone have any ideas on what might have gone >>> wrong? >>> >>> It would be great to restart from the last output and see whether this >>> happens every time. Unfortunately we haven't gotten to that stage yet but >>> we really should do that next. >>> >>> Cheers, Francis >>> >>> >>> ... >>> 33.98 16.504104156 39.1507283386 55.6548324946 33.3509321074 >>> 33.99 16.504103109 39.1507164876 55.6548195966 33.3509288412 >>> 34.0 16.5041020578 39.1507045844 55.6548066422 33.3509255645 >>> Traceback (most recent call last): >>> File "qg3d_jet.py", line 151, in <module> >>> v.project(gradperp_h(psi0)) >>> File >>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/function.py", >>> line 277, in project >>> return projection.project(b, self, *args, **kwargs) >>> File >>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/projection.py", >>> line 101, in project >>> form_compiler_parameters=form_compiler_parameters) >>> File >>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/solving.py", >>> line 118, in solve >>> _solve_varproblem(*args, **kwargs) >>> File >>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/solving.py", >>> line 145, in _solve_varproblem >>> solver.solve() >>> File >>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/variational_solver.py", >>> line 185, in solve >>> self.snes.solve(None, v) >>> File "PETSc/SNES.pyx", line 520, in petsc4py.PETSc.SNES.solve >>> (src/petsc4py.PETSc.c:168132) >>> Traceback (most recent call last): >>> File "qg3d_jet.py", line 151, in <module> >>> v.project(gradperp_h(psi0)) >>> File >>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/function.py", >>> line 277, in project >>> return projection.project(b, self, *args, **kwargs) >>> File >>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/projection.py", >>> line 101, in project >>> form_compiler_parameters=form_compiler_parameters) >>> File >>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/solving.py", >>> line 118, in solve >>> _solve_varproblem(*args, **kwargs) >>> File >>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/solving.py", >>> line 145, in _solve_varproblem >>> solver.solve() >>> File >>> "/home/fpoulin/software/firedrake/local/lib/python2.7/site-packages/firedrake/variational_solver.py", >>> line 185, in solve >>> self.snes.solve(None, v) >>> File "PETSc/SNES.pyx", line 520, in petsc4py.PETSc.SNES.solve >>> (src/petsc4py.PETSc.c:168132) >>> petsc4py.PETSc.Errorpetsc4py.PETSc.Error: error code 1 >>> [0] SNESSolve() line 4008 in >>> /tmp/pip-EZZoo0-build/src/snes/interface/snes.c >>> [0] SNESSolve_KSPONLY() line 40 in >>> /tmp/pip-EZZoo0-build/src/snes/impls/ksponly/ksponly.c >>> [0] KSPSolve() line 600 in >>> /tmp/pip-EZZoo0-build/src/ksp/ksp/interface/itfunc.c >>> [0] KSPSetUpOnBlocks() line 220 in >>> /tmp/pip-EZZoo0-build/src/ksp/ksp/interface/itfunc.c >>> [0] PCSetUpOnBlocks() line 1001 in >>> /tmp/pip-EZZoo0-build/src/ksp/pc/interface/precon.c >>> [0] PCSetUpOnBlocks_BJacobi_Singleblock() line 650 in >>> /tmp/pip-EZZoo0-build/src/ksp/pc/impls/bjacobi/bjacobi.c >>> [0] KSPSetUp() line 390 in >>> /tmp/pip-EZZoo0-build/src/ksp/ksp/interface/itfunc.c >>> [0] PCSetUp() line 968 in >>> /tmp/pip-EZZoo0-build/src/ksp/pc/interface/precon.c >>> [0] PCSetUp_ILU() line 212 in >>> /tmp/pip-EZZoo0-build/src/ksp/pc/impls/factor/ilu/ilu.c >>> [0] MatILUFactorSymbolic() line 6594 in >>> /tmp/pip-EZZoo0-build/src/mat/interface/matrix.c >>> [0] MatILUFactorSymbolic_SeqBAIJ() line 370 in >>> /tmp/pip-EZZoo0-build/src/mat/impls/baij/seq/baijfact2.c >>> [0] MatILUFactorSymbolic_SeqBAIJ_ilu0() line 276 in >>> /tmp/pip-EZZoo0-build/src/mat/impls/baij/seq/baijfact2.c >>> [0] MatILUFactorSymbolic_SeqBAIJ_ilu0() line 276 in >>> /tmp/pip-EZZoo0-build/src/mat/impls/baij/seq/baijfact2.c >>> [0] Out of memory. Allocated: 0, Used by process: 2962321408 >>> [0] Memory requested 584000046 >>> : error code 1 >>> [1] SNESSolve() line 4008 in >>> /tmp/pip-EZZoo0-build/src/snes/interface/snes.c >>> [1] SNESSolve_KSPONLY() line 40 in >>> /tmp/pip-EZZoo0-build/src/snes/impls/ksponly/ksponly.c >>> [1] KSPSolve() line 600 in >>> /tmp/pip-EZZoo0-build/src/ksp/ksp/interface/itfunc.c >>> [1] KSPSetUpOnBlocks() line 220 in >>> /tmp/pip-EZZoo0-build/src/ksp/ksp/interface/itfunc.c >>> [1] PCSetUpOnBlocks() line 1001 in >>> /tmp/pip-EZZoo0-build/src/ksp/pc/interface/precon.c >>> [1] PCSetUpOnBlocks_BJacobi_Singleblock() line 650 in >>> /tmp/pip-EZZoo0-build/src/ksp/pc/impls/bjacobi/bjacobi.c >>> [1] KSPSetUp() line 390 in >>> /tmp/pip-EZZoo0-build/src/ksp/ksp/interface/itfunc.c >>> [1] PCSetUp() line 968 in >>> /tmp/pip-EZZoo0-build/src/ksp/pc/interface/precon.c >>> [1] PCSetUp_ILU() line 212 in >>> /tmp/pip-EZZoo0-build/src/ksp/pc/impls/factor/ilu/ilu.c >>> [1] MatILUFactorSymbolic() line 6594 in >>> /tmp/pip-EZZoo0-build/src/mat/interface/matrix.c >>> [1] MatILUFactorSymbolic_SeqBAIJ() line 370 in >>> /tmp/pip-EZZoo0-build/src/mat/impls/baij/seq/baijfact2.c >>> [1] MatILUFactorSymbolic_SeqBAIJ_ilu0() line 276 in >>> /tmp/pip-EZZoo0-build/src/mat/impls/baij/seq/baijfact2.c >>> [1] MatILUFactorSymbolic_SeqBAIJ_ilu0() line 276 in >>> /tmp/pip-EZZoo0-build/src/mat/impls/baij/seq/baijfact2.c >>> [1] Out of memory. Allocated: 0, Used by process: 2943778816 >>> [1] Memory requested 584000046 >>> >>> -------------------------------------------------------------------------- >>> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD >>> with errorcode 1. >>> >>> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. >>> You may or may not see output from other processes, depending on >>> exactly when Open MPI kills them. >>> >>> -------------------------------------------------------------------------- >>> >>> >>> ------------------ >>> Francis Poulin >>> Associate Professor >>> Department of Applied Mathematics >>> University of Waterloo >>> >>> email: fpoulin(a)uwaterloo.ca >>> Web: https://uwaterloo.ca/poulin-research-group/ >>> Telephone: +1 519 888 4567 x32637 >>> >>> >> >> -- >> http://www.imperial.ac.uk/people/colin.cotter >> >> www.cambridge.org/9781107663916 >> >> >> >> -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

2 2

Re: [firedrake] Periodic 3D meshes
by David Ham 23 May '16

23 May '16

For the special case of a periodic box, doing it using mesh._from_cell_list and constructing the connectivity and coordinates yourself is not that hard. If you want a really big mesh, you probably want to use a small one and create a hierarchy to get a big one (for added bonus, you can use the hierarchy for GMG if you are so inclined). Regards, David On Mon, 23 May 2016 at 10:32 Andrew McRae <A.T.T.McRae(a)bath.ac.uk> wrote: > It's not currently implemented, but you're welcome to do so. > > The current periodic meshes are built in a roundabout way: to build a 2d > periodic mesh, a torus is constructed (this has the desired connectivity > but not the desired geometry), then the coordinates are replaced by the > coordinates of a rectangle. > > Related: there must be a way to build these directly, rather than via the > hack? I continued using the hack because I didn't know how to build a mesh > without going through mesh._from_cell_list. > > On 23 May 2016 at 09:18, Daniel Ruprecht <D.Ruprecht(a)leeds.ac.uk> wrote: > >> Dear Firedrakers, >> >> I am trying to set up a 3D cube mesh, periodic in all three directions, >> but can't find the correct class to call. At >> http://firedrakeproject.org/_modules/firedrake/utility_meshes.html only >> 2d periodic meshes are listed. >> >> Essentially, I'd like something like PeriodicUnitCubeMesh. How do I >> generate a mesh like this? >> >> Cheers, Daniel >> >> -- >> Dr. Daniel Ruprecht >> University Academic Fellow >> School of Mechanical Engineering, Room 4.50 >> University of Leeds >> Leeds LS2 9JT, UK >> Email: d.ruprecht(a)leeds.ac.uk >> Phone: +44 (0)113 343 22 01 >> >> >> _______________________________________________ >> firedrake mailing list >> firedrake(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake >> > >

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