December 2016 - firedrake - imperial.ac.uk

Re: [firedrake] fire-drake installer issue
by David Ham 20 Dec '16

20 Dec '16

Dear Simon, What happens if you just run: pip install --user virtualenv yourself? Essentially I'm trying to identify whether it's a problem with your pip install (since that line doesn't really have much to do with Firedrake itself). Additionally, can you please let us know which release of which distribution you are running. Regards, David On Tue, 20 Dec 2016 at 12:35 Simon Dodd <S.Dodd(a)bath.ac.uk> wrote: > Hello, > > I am trying to run the firedrake installer and it gets stuck on > downloading virtualenv: > > Original-Maintainer: Mark Brown <broonie(a)debian.org> > installed. > Installing virtualenv. > Downloading/unpacking virtualenv > Cannot fetch index base URL http://pypi.python.org/simple/ > Could not find any downloads that satisfy the requirement virtualenv > No distributions at all found for virtualenv > Storing complete log in /u/t/enxspd/.pip/pip.log > Traceback (most recent call last): > File "./firedrake-install", line 1134, in <module> > check_call(["pip", "install", "--user", "virtualenv"]) > File "./firedrake-install", line 342, in check_call > subprocess.check_call(arguments, env=env) > File "/usr/lib/python2.7/subprocess.py", line 511, in check_call > raise CalledProcessError(retcode, cmd) > subprocess.CalledProcessError: Command '['pip', 'install', '--user', > 'virtualenv']' returned non-zero exit status 1 > > Looks like it cannot find the package. I check the link and it's an https > site, not http? > > Any help would be appreciated. > > Thanks > > Simon > > Simon Dodd > Computing Services Supporter (Science) > Bath University Computing Services > Room: 3 West 4.3a > Phone: 01225 38 5858 > > For IT requests, please use the help form: > > https://bath.topdesk.net > > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake > -- Dr David Ham Department of Mathematics Imperial College London

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fire-drake installer issue
by Simon Dodd 20 Dec '16

20 Dec '16

Hello, I am trying to run the firedrake installer and it gets stuck on downloading virtualenv: Original-Maintainer: Mark Brown <broonie(a)debian.org> installed. Installing virtualenv. Downloading/unpacking virtualenv Cannot fetch index base URL http://pypi.python.org/simple/ Could not find any downloads that satisfy the requirement virtualenv No distributions at all found for virtualenv Storing complete log in /u/t/enxspd/.pip/pip.log Traceback (most recent call last): File "./firedrake-install", line 1134, in <module> check_call(["pip", "install", "--user", "virtualenv"]) File "./firedrake-install", line 342, in check_call subprocess.check_call(arguments, env=env) File "/usr/lib/python2.7/subprocess.py", line 511, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['pip', 'install', '--user', 'virtualenv']' returned non-zero exit status 1 Looks like it cannot find the package. I check the link and it's an https site, not http? Any help would be appreciated. Thanks Simon Simon Dodd Computing Services Supporter (Science) Bath University Computing Services Room: 3 West 4.3a Phone: 01225 38 5858 For IT requests, please use the help form: https://bath.topdesk.net

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Re: [firedrake] Firedrake install on a cluster
by David Ham 20 Dec '16

20 Dec '16

Dear Tomasz, I'm sorry to hear you are having difficulty at Marin. I'm afraid to say that the description provided by your tech support is so general that it is very difficult to even understand what the problem they are having is. That said, there are a few comments I can glean which might help you: 1. Firedrake basically* does not install anything in the users home directory. Since tech support provide no information about what the error is, it's impossible for me to draw any inference about why they believe otherwise. (* If virtualenv is not already installed then Firedrake does in fact execute "pip install virtualenv" as the installing user, however this virtualenv package is only used by the install script so does not explain what tech support are reporting). 2. The usual use case for Firedrake, even on clusters, is to run firedrake-install yourself. This enables you to upgrade whenever you want and to switch branches as and when necessary. When working on a cluster, you might need some help from the cluster support to have compiled dependencies installed, to set the right environment variables and maybe to build PETSc. However there is usually no advantage and several drawbacks in a central install. 3. I notice that we have had no requests for support from the cluster admins at Marin. There are no github issues or messages on the list or chat raising specific bugs. It is exceptionally difficult for us to assist with issues we don't even know exist. Regards, David On Tue, 20 Dec 2016 at 09:13 Tomasz Salwa [RPG] <mmtjs(a)leeds.ac.uk> wrote: Dear all, We have been trying to install Firedrake on a local cluster at MARIN, with little success. Perhaps you can give a hint? I attach below the reply from the IT man with a rough problem description. Regards, Tomasz Good afternoon, It seems the install of Firedrake we did earlier in Marclus3 is not working for the students. The only explanation I can think of is that besides writing data in the install dir several things are also written in the user home dir during installation. I have not been able to exactly track down what data that could be... All in all, unfortunately I need to conclude that at the moment we simply can't support running Firedrake on our cluster(s) It's setup and running is simply not suited to our Linux distribution and our cluster setup. Regards, -- Jan-Albert -- Dr David Ham Department of Mathematics Imperial College London

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Firedrake install on a cluster
by Tomasz Salwa [RPG] 20 Dec '16

20 Dec '16

Dear all, We have been trying to install Firedrake on a local cluster at MARIN, with little success. Perhaps you can give a hint? I attach below the reply from the IT man with a rough problem description. Regards, Tomasz Good afternoon, It seems the install of Firedrake we did earlier in Marclus3 is not working for the students. The only explanation I can think of is that besides writing data in the install dir several things are also written in the user home dir during installation. I have not been able to exactly track down what data that could be... All in all, unfortunately I need to conclude that at the moment we simply can't support running Firedrake on our cluster(s) It's setup and running is simply not suited to our Linux distribution and our cluster setup. Regards, -- Jan-Albert

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Firedrake '17 registration is open
by David Ham 19 Dec '16

19 Dec '16

Dear Firedrakers, Registration is now open for Firedrake '17. Early registration is open until 10 February and costs £40 for students, £50 for others. After 10 February, registration will rise to £75 for everyone. Registration and abstract submission are available at: http://firedrakeproject.org/firedrake_17.html I hope to see many of you there. Regards, David -- Dr David Ham Department of Mathematics Imperial College London

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Firedrake '17 submissions are now open.
by David Ham 16 Dec '16

16 Dec '16

Dear Firedrakers, The first Firedrake user and developer workshop will be held at Imperial College London on 27 and 28 March 2017. The workshop will be an opportunity for the Firedrake community to communicate new applications and developments in Firedrake, a chance for face-to-face time with the developer team, and will feature a tutorial for new users. Submissions of oral and poster contributions are now open. More information on this and the workshop in general are available at http://www.firedrakeproject.org/firedrake_17.html Regards, David -- Dr David Ham Department of Mathematics Imperial College London

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Re: [firedrake] Firedrake
by Lawrence Mitchell 12 Dec '16

12 Dec '16

Dear Patrick, Thomas, [note: writing email directly to me to try and solve problems with Firedrake is not the way to get a fast response. Please send issues to the Firedrake mailing list (cc'd now)] > On 11 Dec 2016, at 11:20, Patrick Farrell <patrick.farrell(a)maths.ox.ac.uk> wrote: > > Dear Lawrence, > > A colleague of mine, Thomas Surowiec, is trying to install firedrake on OSX 10.10.3. > Unfortunately the firedrake-install script isn't working out of the box. > > It appears that OSX has decided to put mpif90 in /usr/local/Cellar/open-mpi/1.10.2/bin/mpif90, > but the PETSc compilation is looking for it in /usr/local/bin/. Any idea why, or what we can > do? What does: $ env $ which mpif90 $ which gfortran $ which python $ cat > foo.f90 << \EOF program main use mpi end $ mpif90 foo.f90 Give? It looks like the MPI compiler is somehow not working? > > > -------- Forwarded Message -------- > Subject: Re: Firedrake > Date: Sun, 11 Dec 2016 12:06:26 +0100 > From: Thomas Surowiec <thomas.surowiec(a)gmail.com> > To: Patrick Farrell <patrick.farrell(a)maths.ox.ac.uk> > > Still a mess. It went a few steps further, but there were problems with the security features. In case you're interested the complete output is below. Are there now several half compiled versions and folders associated with fenics and firedrake on my system? Is there anyway to delete all of them and start over? Other than the homebrew dependencies, firedrake-install puts *everything* inside the "firedrake" subdirectory of the working directory that you ran firedrake-install in. You can safely just delete this subtree. > ThomasSsMacBook:~ anounz$ /usr/bin/python firedrake-install All of our testing is done with the homebrew python, rather than the system python. I do not know if this will cause issues, but all of us with Mac systems use the python that homebrew puts in /usr/local/bin. Lawrence

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FInAT has landed!
by Homolya, Miklós 12 Dec '16

12 Dec '16

Dear Firedrakers, An updated form compilation system has just been merged into Firedrake. FInAT, a new component, is a finite element library that is able to express structure in the finite elements themselves; this structure is then exploited by TSFC and COFFEE for optimisation. Most important benefits: - Automatic sum factorisation for Q/DQ elements. - Better code generation for vector/tensor elements and more compact element tables. So if you use CG/DG elements on non-simplex cells (quadrilaterals and extruded), you will likely see significant assembly time improvements, depending on polynomial order (higher gain with higher order). Sum factorisation for H(div)/H(curl) conforming elements (RTCF, RTCE, NCF, NCE) is not supported yet, nor for any elements on simplices. Update instructions: nothing special, just run firedrake-update. Best wishes, Miklós

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Re: [firedrake] Problems with NonlinearVariationalProblem
by Andrew McRae 11 Dec '16

11 Dec '16

Your F uses psi_non, a Function, and psi, a TrialFunction. Probably you meant to replace psi with phi, which was defined as a TestFunction? Best, Andrew On 11 December 2016 at 02:42, Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Hello Andrew, > > Thanks for pointing that out. > > I have looked at the Burger equation demo more and think I understand it > better. > > If you go to the following link you will see that there is a revised > version of the code. Now I solve the linear problem first, since that > should be used as an initial guess. Then I want to solve the Nonlinear > Variational Problem. > > https://github.com/francispoulin/firedrakeQG/blob/master/fofonoff_qg.py > > Unfortunately, I haven't figured out how to get the syntax correct. I'm > only using a Function, with the guess an the variable to determine, and a > Test Function. > > Any advice would be greatly appreciated. > > 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 <(519)%20888-4567> > > ------------------------------ > *From:* firedrake-bounces(a)imperial.ac.uk [firedrake-bounces(a)imperial.ac.uk] > on behalf of Andrew McRae [A.T.T.McRae(a)bath.ac.uk] > *Sent:* Friday, December 09, 2016 4:49 PM > *To:* Firedrake Project > *Subject:* Re: [firedrake] Problems with NonlinearVariationalProblem > > Hi Francis, > > The residual should be linear in the Test Function, and TrialFunctions > should not appear at all (a Function should be used instead). > > Best, > Andrew > > On 9 Dec 2016 8:58 p.m., "Francis Poulin" <fpoulin(a)uwaterloo.ca> wrote: > >> Hello, >> >> We have been following the documentation and examples to learn how to >> solve nonlinear problems in Firedrake. We want to solve the classical >> Fofonoff problem in a one-layer Quasi-Geostrophic problem. >> >> We have set up a nonlinear variational problem, following the >> Camassa-Holm demo. Unfortunately, whenever we try it we get an error >> saying that our for is not a linear form. Which is true, but since we are >> using NonlinearVariationalProblem, I presume this should be ok. >> >> Traceback (most recent call last): >> File "fofonoff_qg.py", line 41, in <module> >> psi_problem = NonlinearVariationalProblem(L, psi_soln, bcs=bc) >> File "/home/fpoulin/software/firedrake/src/firedrake/firedrake/variational_solver.py", >> line 47, in __init__ >> raise ValueError("Provided residual is not a linear form") >> ValueError: Provided residual is not a linear form >> >> Our code can be found on github. >> >> https://github.com/francispoulin/firedrakeQG/blob/master/fofonoff_qg.py >> >> If anyone has any advice or other examples that do this successfully, we >> would love to know more. >> >> 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 <(519)%20888-4567> >> >>

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Re: [firedrake] Problems with NonlinearVariationalProblem
by Andrew McRae 11 Dec '16

11 Dec '16

Hi Francis, The residual should be linear in the Test Function, and TrialFunctions should not appear at all (a Function should be used instead). Best, Andrew On 9 Dec 2016 8:58 p.m., "Francis Poulin" <fpoulin(a)uwaterloo.ca> wrote: > Hello, > > We have been following the documentation and examples to learn how to > solve nonlinear problems in Firedrake. We want to solve the classical > Fofonoff problem in a one-layer Quasi-Geostrophic problem. > > We have set up a nonlinear variational problem, following the Camassa-Holm > demo. Unfortunately, whenever we try it we get an error saying that our > for is not a linear form. Which is true, but since we are using > NonlinearVariationalProblem, I presume this should be ok. > > Traceback (most recent call last): > File "fofonoff_qg.py", line 41, in <module> > psi_problem = NonlinearVariationalProblem(L, psi_soln, bcs=bc) > File "/home/fpoulin/software/firedrake/src/firedrake/ > firedrake/variational_solver.py", line 47, in __init__ > raise ValueError("Provided residual is not a linear form") > ValueError: Provided residual is not a linear form > > Our code can be found on github. > > https://github.com/francispoulin/firedrakeQG/blob/master/fofonoff_qg.py > > If anyone has any advice or other examples that do this successfully, we > would love to know more. > > 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 <(519)%20888-4567> > >

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