April 2017 - firedrake - imperial.ac.uk

Present installation issues with PETSc build
by Lawrence Mitchell 15 May '17

15 May '17

Dear firedrakers, some of you attempting to install or update recently may have seen that the PETSc build fails (attempting to install Eigen). This is a reported bug in the PETSc installer, we hope that it will be fixed in the next day or so. As a short-term workaround, you can disable the installation of Eigen when running firedrake-install or firedrake-update like so: $ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-install or $ PETSC_CONFIGURE_OPTIONS="--download-eigen=0" firedrake-update This will disable the ability to solve problems using hybridisation methods, but Firedrake will otherwise be functional. A subsequent call to firedrake-install or firedrake-update without setting PETSC_CONFIGURE_OPTIONS will subsequently download and install Eigen, you can do this when the problem is fixed. I will update this thread when the bug fix arrives in PETSc and we have confirmed it works for us. Thanks, and apologies for any problems this might be causing, Lawrence

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Lagrange multipliers
by James Jackaman 29 Apr '17

29 Apr '17

Dear all, I'm currently working on an Firedrake implementation which utilises Lagrange multipliers, in the spirit of the Poisson equation with pure Neumann boundary conditions where the average value of the solution is constrained by a Lagrange multiplier. I have attempted to translate the Fenics demo, see https://fenicsproject.org/olddocs/dolfin/1.6.0/python/demo/documented/neuma…, into Firedrake with no success, see neumann-poisson.py in the attached gist. I believe there may be a problem with the function space of real constants /FunctionSpace(mesh,"R",0)/, see real_solver.py in the attached gist which returns u=0 instead of u=1. How can I modify my example codes in the gist such that they behave as expected, or alternatively how can I implement the Poisson equation with pure Neumann boundary conditions using Lagrange multipliers in Firedrake? Gist: https://gist.github.com/j130792/64d12e84cf5ede2b327d1859a36dc36d Thanks for your help, James

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a question on plotting
by Francis Poulin 26 Apr '17

26 Apr '17

Hello, I am trying to fix up some plots based on Colin's Camassa-Holm demo. http://firedrakeproject.org/demos/camassaholm.py.html I have two questions on plotting. 1. How do we set the y-limits in the context of the plot function? In matplotlib I would do ylim([0,1]) for example but that doesn't seem to work in this context. 2. If I wanted to make a Hovmoeller plot instead of a move I would like to be able to store the snapshots into an array and then plot those. Does someone have a suggestion on how one can do this easily? Cheers, 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

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Problem installing firedrake with Intel compiler
by Buesing, Henrik 20 Apr '17

20 Apr '17

Dear all, I am trying to install Firedrake with Intel Compiler 16.0.2 20160204 and intelmpi/2017. I run into an error while compiling HDF5 (see [1] and attached firedrake-install.log). Any idea what could be wrong? Thank you! Henrik [1] /usr/bin/ld: ../../test/.libs/libh5test.a(h5test.o): undefined reference to symbol '__intel_sse2_strlen' /opt/intel/Compiler/16.0/2.181/rwthlnk/compiler/lib/intel64_lin/libintlc.so.5: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status gmake[2]: *** [fortranlib_test] Error 1 gmake[1]: *** [all-recursive] Error 1 gmake: *** [all-recursive] Error 1 -- Dipl.-Math. Henrik Büsing Institute for Applied Geophysics and Geothermal Energy E.ON Energy Research Center RWTH Aachen University ------------------------------------------------------ Mathieustr. 10 | Tel +49 (0)241 80 49907 52074 Aachen, Germany | Fax +49 (0)241 80 49889 ------------------------------------------------------ http://www.eonerc.rwth-aachen.de/GGE hbuesing(a)eonerc.rwth-aachen.de ------------------------------------------------------

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Re: [firedrake] Lagrange multipliers
by Andrew McRae 20 Apr '17

20 Apr '17

Hi James, I will let David or Lawrence answer your question properly, as I'm not sure about the current status of the Real function space in Firedrake. (There is an open pull request here: https://github.com/firedrakeproject/firedrake/pull/909, but this is somewhat out of date) However, you might be able to solve your problem an alternative way, using the nullspace feature, as described here: http://www.firedrakeproject.org/solving-interface.html#solving-singular-sys… . Best, Andrew On 19 April 2017 at 15:09, James Jackaman <wb816921(a)live.reading.ac.uk> wrote: > Dear all, > > > I'm currently working on an Firedrake implementation which utilises > Lagrange multipliers, in the spirit of the Poisson equation with pure > Neumann boundary conditions where the average value of the solution is > constrained by a Lagrange multiplier. > > I have attempted to translate the Fenics demo, see > https://fenicsproject.org/olddocs/dolfin/1.6.0/python/ > demo/documented/neumann-poisson/python/documentation.html, into Firedrake > with no success, see neumann-poisson.py in the attached gist. > > I believe there may be a problem with the function space of real constants * > FunctionSpace(mesh,"R",0)*, see real_solver.py in the attached gist which > returns u=0 instead of u=1. > > How can I modify my example codes in the gist such that they behave as > expected, or alternatively how can I implement the Poisson equation with > pure Neumann boundary conditions using Lagrange multipliers in Firedrake? > > > Gist: https://gist.github.com/j130792/64d12e84cf5ede2b327d1859a36dc36d > > > Thanks for your help, > > James >

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Re: [firedrake] firedrake_adjoint
by David Ham 13 Apr '17

13 Apr '17

Hi George, I think I don't quite understand what you mean. Can you write out mathematically what you're after and I'll try to understand if it's something we can extract from Dolfin-Adjoint? In addition, I need to apologise in advance because I'm off sailing all of next week so I shan't be very responsive. I will be back online in a week's time. Regards, David On Mon, 10 Apr 2017 at 18:29 George Ovchinnikov <lives9(a)gmail.com> wrote: > Dear colleagues, sorry for hijacking the thread, but could you explain to > me, how to compute residue of adjoint functional, if possible, with > firedrake-adjoint? > > I've seen in the documentation that > > J = Functional(inner(u, u)*dx*dt[FINISH_TIME])for (variable, solution) in compute_adjoint(J): > > provides the solution of adjoint problem, but for residual I need not only > solution, but also a set of adjoint equations. > > Sincerely, > George > > > > On 10.04.2017 17:32, Buesing, Henrik wrote: > > Yes! I opened a github issue here > <https://github.com/firedrakeproject/firedrake/issues/1042>. I guess the > markdown messes with the python code. Sorry, for that. > > Henrik > > > > > > -- > > Dipl.-Math. Henrik Büsing > > Institute for Applied Geophysics and Geothermal Energy > > E.ON Energy Research Center > > RWTH Aachen University > > > > Mathieustr. | Tel +49 (0)241 80 49907 <+49%20241%208049907> > > 52074 Aachen, Germany | Fax +49 (0)241 80 49889 <+49%20241%208049889> > > > > http://www.eonerc.rwth-aachen.de/GGE > > hbuesing(a)eonerc.rwth-aachen.de > > > > *Von:* firedrake-bounces(a)imperial.ac.uk [ > mailto:firedrake-bounces@imperial.ac.uk <firedrake-bounces(a)imperial.ac.uk>] > *Im Auftrag von *David Ham > *Gesendet:* Montag, 10. April 2017 11:57 > *An:* firedrake <firedrake(a)imperial.ac.uk> <firedrake(a)imperial.ac.uk> > *Betreff:* Re: [firedrake] firedrake_adjoint > > > > Hi Henrik, > > > > That sounds like a bug. Can you create a minimal failing example and file > a github issue please? > > > > Regards, > > > > David > > > > On Mon, 10 Apr 2017 at 10:48 Buesing, Henrik < > HBuesing(a)eonerc.rwth-aachen.de> wrote: > > Dear all, > > > > If I include > > > > *from firedrake*_*adjoint import ** > > > > in my firedrake program, my forward problem does not converge any more. If > I do nothing else than loading firedrake_adjoint, should the forward > problem not run as before? Note, that I set all the solver options from the > command line and not in the program itself. Thus, in the program I just have > > > > *solver = NonlinearVariationalSolver(problem,options_prefix="")* > > Thank you! > Henrik > > > > > > -- > > Dipl.-Math. Henrik Büsing > > Institute for Applied Geophysics and Geothermal Energy > > E.ON Energy Research Center > > RWTH Aachen University > > ------------------------------------------------------ > > Mathieustr. 10 | Tel +49 (0)241 80 49907 > <+49%20241%208049907> > > 52074 Aachen, Germany | Fax +49 (0)241 80 49889 > <+49%20241%208049889> > > ------------------------------------------------------ > > http://www.eonerc.rwth-aachen.de/GGE > > hbuesing(a)eonerc.rwth-aachen.de > > ------------------------------------------------------ > > > > -- > > Dr David Ham > > Department of Mathematics > > Imperial College London > > > > _______________________________________________ > firedrake mailing listfiredrake@imperial.ac.ukhttps://mailman.ic.ac.uk/mailman/listinfo/firedrake > > > -- Dr David Ham Department of Mathematics Imperial College London

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Re: [firedrake] Welcome to Firedake
by David Ham 12 Apr '17

12 Apr '17

Hi Diana, We have to confess that we don't understand this error. However it's actually in an optional piece of functionality which is only require to make online matplotlib plots work with iPython on the Mac. As a workaround, we're going to add an option to firedrake-install to disable this functionality. Hopefully this will make your install work. I'll let you know when it's in (hopefully later today). Regards, David On Fri, 7 Apr 2017 at 10:03 Barac Diana <diana.barac(a)bsse.ethz.ch> wrote: > Dear David, > > Thank you for the quick reply. I have attached the log file to this email. > The user baracd is an administrator and the output I get is: > > bs-mbpr85:~ baracd$ ls -l > '/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/_CodeSignature/CodeResources' > > -rw-r--r-- 1 root wheel 3224 Jan 13 08:16 > /System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/_CodeSignature/CodeResources > > > Many Thanks, > > Diana > > > > > From: David Ham <David.Ham(a)imperial.ac.uk> > Date: Thursday, 6 April 2017 at 18:10 > To: Mitarbeiter <diana.barac(a)bsse.ethz.ch>, firedrake < > firedrake(a)imperial.ac.uk> > Subject: Re: Welcome to Firedake > > Dear Diana, > > I'm copying this onto the Firedrake list - it's definitely not a usual > error and we might need some input from the rest of the team. > > In essence, Python on Macs is a little different from Python on other > platforms because of the way that Macs deal with applications. This means > our install script has to do a little modification of the virtualenv after > it is set up. In this case this is failing, seemingly because of some > permissions issue. Can you provide the following additional information: > > 1. I see that you ran with --log, can you attach the log file for the last > failure please (this gives us the full verbose output)? > > 2. Can you confirm whether or not the user baracd is an administrator on > this machine? > > 3. Just to sanity check, can you give us the output of: > > ls -l > '/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/_CodeSignature/CodeResources' > > Many thanks, > > David > > On Thu, 6 Apr 2017 at 16:02 Barac Diana <diana.barac(a)bsse.ethz.ch> wrote: > > Dear David, > > Thank you very much for the personalised welcome. I am very much looking > forward to using Firedrake and interacting/contributing to the community. > > At the moment I am having some problems with the installation. When I try > and install it using the terminal I get the following: > > bs-mbpr85:Applications baracd$ python firedrake-install -v --log > > Installing command line tools... > > Installing required packages via homebrew. You can safely ignore warnings > that packages are already installed > > Specified virtualenv '/Users/baracd/Applications/firedrake' already exists > > Can't install into existing virtualenv > '/Users/baracd/Applications/firedrake' > > bs-mbpr85:Applications baracd$ python firedrake-install -v --log > > Installing command line tools... > > Installing required packages via homebrew. You can safely ignore warnings > that packages are already installed > > Creating firedrake virtualenv in '/Users/baracd/Applications/firedrake'. > > /Users/baracd/Applications/firedrake/bin/pip install -U setuptools > > /Users/baracd/Applications/firedrake/bin/pip install -U pip > > Traceback (most recent call last): > > File "firedrake-install", line 1187, in <module> > > framework = fix_osx_virtualenv_python() > > File "firedrake-install", line 1139, in fix_osx_virtualenv_python > > shutil.copytree(appsrc, appdest) > > File > "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", > line 208, in copytree > > raise Error, errors > > shutil.Error: > [('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/_CodeSignature/CodeResources', > '/Users/baracd/Applications/firedrake/Python.app/Contents/_CodeSignature/CodeResources', > "[Errno 1] Operation not permitted: > '/Users/baracd/Applications/firedrake/Python.app/Contents/_CodeSignature/CodeResources'"), > ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/_CodeSignature', > '/Users/baracd/Applications/firedrake/Python.app/Contents/_CodeSignature', > "[Errno 1] Operation not permitted: > '/Users/baracd/Applications/firedrake/Python.app/Contents/_CodeSignature'"), > ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Info.plist', > '/Users/baracd/Applications/firedrake/Python.app/Contents/Info.plist', > "[Errno 1] Operation not permitted: > '/Users/baracd/Applications/firedrake/Python.app/Contents/Info.plist'"), > ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python', > '/Users/baracd/Applications/firedrake/Python.app/Contents/MacOS/Python', > "[Errno 1] Operation not permitted: > '/Users/baracd/Applications/firedrake/Python.app/Contents/MacOS/Python'"), > ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS', > '/Users/baracd/Applications/firedrake/Python.app/Contents/MacOS', "[Errno > 1] Operation not permitted: > '/Users/baracd/Applications/firedrake/Python.app/Contents/MacOS'"), > ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/PkgInfo', > '/Users/baracd/Applications/firedrake/Python.app/Contents/PkgInfo', "[Errno > 1] Operation not permitted: > '/Users/baracd/Applications/firedrake/Python.app/Contents/PkgInfo'"), > ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources/PythonApplet.icns', > '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources/PythonApplet.icns', > "[Errno 1] Operation not permitted: > '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources/PythonApplet.icns'"), > ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources/PythonInterpreter.icns', > '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns', > "[Errno 1] Operation not permitted: > '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources/PythonInterpreter.icns'"), > ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/Resources', > '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources', > "[Errno 1] Operation not permitted: > '/Users/baracd/Applications/firedrake/Python.app/Contents/Resources'"), > ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/version.plist', > '/Users/baracd/Applications/firedrake/Python.app/Contents/version.plist', > "[Errno 1] Operation not permitted: > '/Users/baracd/Applications/firedrake/Python.app/Contents/version.plist'"), > ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents', > '/Users/baracd/Applications/firedrake/Python.app/Contents', "[Errno 1] > Operation not permitted: > '/Users/baracd/Applications/firedrake/Python.app/Contents'"), > ('/System/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app', > '/Users/baracd/Applications/firedrake/Python.app', "[Errno 1] Operation not > permitted: '/Users/baracd/Applications/firedrake/Python.app'")] > > I asked the IT helpdesk at my university but they were not able to resolve > the issue. Would you know if this is simple to fix or whether I should > message the community about it? > > Best regards, > Diana > > From: David Ham <David.Ham(a)imperial.ac.uk> > Date: Thursday, 6 April 2017 at 15:41 > To: Mitarbeiter <diana.barac(a)bsse.ethz.ch> > Subject: Welcome to Firedake > > Dear Ms Barac, > > Thanks for subscribing to the Firedrake mailing list. I took the liberty > of Googling what you're working on, and it sounds like an amazing and > exciting PDE application. > > I hope you'll find the Firedrake community welcoming and helpful and that > Firedrake will be a good tool for your work. Please don't hesitate to ask > questions on the mailing list, or on GitHub. Another good option which many > of our users use is to ask questions interactively on our slack channels. > You can sign up to those at: http://www.firedrakeproject.org/contact.html > > We look forward to hearing from you by whichever route. > > Regards, > > David > -- > Dr David Ham > Department of Mathematics > Imperial College London > > -- > Dr David Ham > Department of Mathematics > Imperial College London > -- Dr David Ham Department of Mathematics Imperial College London

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Re: [firedrake] firedrake_adjoint
by David Ham 10 Apr '17

10 Apr '17

Hi Henrik, That sounds like a bug. Can you create a minimal failing example and file a github issue please? Regards, David On Mon, 10 Apr 2017 at 10:48 Buesing, Henrik <HBuesing(a)eonerc.rwth-aachen.de> wrote: > Dear all, > > > > If I include > > > > *from firedrake*_*adjoint import ** > > > > in my firedrake program, my forward problem does not converge any more. If > I do nothing else than loading firedrake_adjoint, should the forward > problem not run as before? Note, that I set all the solver options from the > command line and not in the program itself. Thus, in the program I just have > > > > > *solver = NonlinearVariationalSolver(problem,options_prefix="") * > Thank you! > Henrik > > > > > > -- > > Dipl.-Math. Henrik Büsing > > Institute for Applied Geophysics and Geothermal Energy > > E.ON Energy Research Center > > RWTH Aachen University > > ------------------------------------------------------ > > Mathieustr. 10 | Tel +49 (0)241 80 49907 > <+49%20241%208049907> > > 52074 Aachen, Germany | Fax +49 (0)241 80 49889 > <+49%20241%208049889> > > ------------------------------------------------------ > > http://www.eonerc.rwth-aachen.de/GGE > > hbuesing(a)eonerc.rwth-aachen.de > > ------------------------------------------------------ > > > -- Dr David Ham Department of Mathematics Imperial College London

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firedrake_adjoint
by Buesing, Henrik 10 Apr '17

10 Apr '17

Dear all, If I include from firedrake_adjoint import * in my firedrake program, my forward problem does not converge any more. If I do nothing else than loading firedrake_adjoint, should the forward problem not run as before? Note, that I set all the solver options from the command line and not in the program itself. Thus, in the program I just have solver = NonlinearVariationalSolver(problem,options_prefix="") Thank you! Henrik -- Dipl.-Math. Henrik Büsing Institute for Applied Geophysics and Geothermal Energy E.ON Energy Research Center RWTH Aachen University ------------------------------------------------------ Mathieustr. 10 | Tel +49 (0)241 80 49907 52074 Aachen, Germany | Fax +49 (0)241 80 49889 ------------------------------------------------------ http://www.eonerc.rwth-aachen.de/GGE hbuesing(a)eonerc.rwth-aachen.de ------------------------------------------------------

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Bug report
by Wingate, Beth 09 Apr '17

09 Apr '17

All, Once again I am failing to install petsc at all when I try to install firedrake. I’m including the firedrake install log. Thanks, Beth Beth Wingate b.wingate(a)exeter.ac.uk<mailto:b.wingate@exeter.ac.uk> The world is but a canvas to the imagination - Thoreau

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