April 2016 - firedrake - imperial.ac.uk

Re: [firedrake] volume integration splitting
by Colin Cotter 14 Apr '16

14 Apr '16

Hi Onno, Not really, I expect you are thinking of something related to water waves? I was hoping that many issues relating to free surface might be helped by defining function spaces that are constant throughout the column, to facilitate coupling between free surface and the bulk. We discussed this a while back, but nothing was implemented. all the best --cjc On 14 April 2016 at 15:36, Onno Bokhove <O.Bokhove(a)leeds.ac.uk> wrote: > Hi (-), > > > Can one in Firedrake split a volume integration in 3D, > > in a horizontal part (dx dy) and a vertical part (dz), > > as follows: > > \int_x\int_y f(x,y,t) [ \int_z g(x,y,z,) dz ] dy dx > > > instead of > > > \iiint f(x,y,t) g(x,y,z,t) dx dy dz > > ? > > > Best wishes, > > > Onno > > > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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Re: [firedrake] firedrake installation error
by Hiroe Yamazaki 14 Apr '16

14 Apr '16

Problem solved and the firedrake re-installation is completed. Thanks for all your help! Hiroe On 13 April 2016 at 08:48, Ham, David A <david.ham(a)imperial.ac.uk> wrote: > Hi Hiroe, > > A couple of thing to try. First, just in case, start with apt-get update . > Then chase pointers, so if linux-image-3.13.0-66-generic is not going to be > installed, try explicitly asking for that one, and apt should tell you why > it wasn't going to be installed. You should hopefully be able to iterate > this process until you get to something which you have to install or remove, > and then things will hopefully work. > > Regards, > > David > > On Tue, 12 Apr 2016 at 20:06 Yamazaki, Hiroe <h.yamazaki(a)imperial.ac.uk> > wrote: >> >> Hi Lawrence, >> >> > Maybe someone else will have an idea. I guess you could try the >> > proposed >> > attempt: "apt-get -f install" >> >> Thanks, hope someone can help me. I tried apt-get -f install for both >> cmake and cmake-data but in both cases I got the same dependency error >> with "linux-image-3.13.0-66-generic". >> >> Hiroe >> >> On 12 April 2016 at 18:49, Mitchell, Lawrence >> <lawrence.mitchell(a)imperial.ac.uk> wrote: >> > >> > >> > On 12/04/16 18:34, Hiroe Yamazaki wrote: >> >> Hi Lawrence, >> >> >> >> I tried apt-get -f install cmake but my machine is complaining like >> >> this: >> >> >> >> The following packages have unmet dependencies. >> >> cmake : Depends: cmake-data (>= 2.8.12.2) but it is not going to be >> >> installed >> >> linux-image-extra-3.13.0-66-generic : Depends: >> >> linux-image-3.13.0-66-generic but it is not going to be installed >> >> linux-image-generic : Depends: linux-image-3.13.0-66-generic but it >> >> is not going to be installed >> >> E: Unmet dependencies. Try 'apt-get -f install' with no packages (or >> >> specify a solution). >> >> >> >> Can you specify a solution? >> > >> > I can't immediately, unfortunately, I never know how to get apt out of >> > one of these installation dependency resolution problems. Maybe >> > someone else will have an idea. I guess you could try the proposed >> > attempt: "apt-get -f install" >> > >> > Lawrence >> > >> >> _______________________________________________ >> firedrake mailing list >> firedrake(a)imperial.ac.uk >> https://mailman.ic.ac.uk/mailman/listinfo/firedrake

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volume integration splitting
by Onno Bokhove 14 Apr '16

14 Apr '16

Hi (-), Can one in Firedrake split a volume integration in 3D, in a horizontal part (dx dy) and a vertical part (dz), as follows: \int_x\int_y f(x,y,t) [ \int_z g(x,y,z,) dz ] dy dx instead of \iiint f(x,y,t) g(x,y,z,t) dx dy dz ? Best wishes, Onno

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Re: [firedrake] firedrake installation error
by David Ham 13 Apr '16

13 Apr '16

Hi Hiroe, A couple of thing to try. First, just in case, start with apt-get update . Then chase pointers, so if linux-image-3.13.0-66-generic is not going to be installed, try explicitly asking for that one, and apt should tell you why it wasn't going to be installed. You should hopefully be able to iterate this process until you get to something which you have to install or remove, and then things will hopefully work. Regards, David On Tue, 12 Apr 2016 at 20:06 Yamazaki, Hiroe <h.yamazaki(a)imperial.ac.uk> wrote: > Hi Lawrence, > > > Maybe someone else will have an idea. I guess you could try the proposed > > attempt: "apt-get -f install" > > Thanks, hope someone can help me. I tried apt-get -f install for both > cmake and cmake-data but in both cases I got the same dependency error > with "linux-image-3.13.0-66-generic". > > Hiroe > > On 12 April 2016 at 18:49, Mitchell, Lawrence > <lawrence.mitchell(a)imperial.ac.uk> wrote: > > > > > > On 12/04/16 18:34, Hiroe Yamazaki wrote: > >> Hi Lawrence, > >> > >> I tried apt-get -f install cmake but my machine is complaining like > this: > >> > >> The following packages have unmet dependencies. > >> cmake : Depends: cmake-data (>= 2.8.12.2) but it is not going to be > >> installed > >> linux-image-extra-3.13.0-66-generic : Depends: > >> linux-image-3.13.0-66-generic but it is not going to be installed > >> linux-image-generic : Depends: linux-image-3.13.0-66-generic but it > >> is not going to be installed > >> E: Unmet dependencies. Try 'apt-get -f install' with no packages (or > >> specify a solution). > >> > >> Can you specify a solution? > > > > I can't immediately, unfortunately, I never know how to get apt out of > > one of these installation dependency resolution problems. Maybe > > someone else will have an idea. I guess you could try the proposed > > attempt: "apt-get -f install" > > > > Lawrence > > > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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Re: [firedrake] firedrake installation error
by Hiroe Yamazaki 12 Apr '16

12 Apr '16

Hi Lawrence, > Maybe someone else will have an idea. I guess you could try the proposed > attempt: "apt-get -f install" Thanks, hope someone can help me. I tried apt-get -f install for both cmake and cmake-data but in both cases I got the same dependency error with "linux-image-3.13.0-66-generic". Hiroe On 12 April 2016 at 18:49, Mitchell, Lawrence <lawrence.mitchell(a)imperial.ac.uk> wrote: > > > On 12/04/16 18:34, Hiroe Yamazaki wrote: >> Hi Lawrence, >> >> I tried apt-get -f install cmake but my machine is complaining like this: >> >> The following packages have unmet dependencies. >> cmake : Depends: cmake-data (>= 2.8.12.2) but it is not going to be >> installed >> linux-image-extra-3.13.0-66-generic : Depends: >> linux-image-3.13.0-66-generic but it is not going to be installed >> linux-image-generic : Depends: linux-image-3.13.0-66-generic but it >> is not going to be installed >> E: Unmet dependencies. Try 'apt-get -f install' with no packages (or >> specify a solution). >> >> Can you specify a solution? > > I can't immediately, unfortunately, I never know how to get apt out of > one of these installation dependency resolution problems. Maybe > someone else will have an idea. I guess you could try the proposed > attempt: "apt-get -f install" > > Lawrence >

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Re: [firedrake] firedrake installation error
by Hiroe Yamazaki 12 Apr '16

12 Apr '16

Hi Lawrence, I tried apt-get -f install cmake but my machine is complaining like this: The following packages have unmet dependencies. cmake : Depends: cmake-data (>= 2.8.12.2) but it is not going to be installed linux-image-extra-3.13.0-66-generic : Depends: linux-image-3.13.0-66-generic but it is not going to be installed linux-image-generic : Depends: linux-image-3.13.0-66-generic but it is not going to be installed E: Unmet dependencies. Try 'apt-get -f install' with no packages (or specify a solution). Can you specify a solution? Hiroe On 12 April 2016 at 18:22, Mitchell, Lawrence < lawrence.mitchell(a)imperial.ac.uk> wrote: > > > On 12/04/16 18:14, Hiroe Yamazaki wrote: > > Dear all, > > > > I re-installed firedrake on one of my Ubuntu machines by removing old > > firedrake which was installed manually and running firedrake-install. > > > > Unfortunately it stopped running half way through with the errors > > attached. I would appreciate any help to solve this. > > "CMake > 2.5 is needed to build METIS" > > Can you try upgrading the global cmake install to something more > modern than cmake 2.5 which is about 9 years old? > > Lawrence > >

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firedrake installation error
by Hiroe Yamazaki 12 Apr '16

12 Apr '16

Dear all, I re-installed firedrake on one of my Ubuntu machines by removing old firedrake which was installed manually and running firedrake-install. Unfortunately it stopped running half way through with the errors attached. I would appreciate any help to solve this. All the best, Hiroe

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Re: [firedrake] new firedrake install on El Capitan
by David Ham 10 Apr '16

10 Apr '16

Hi Jemma, Why are you installing in global mode? That's a little tested option which is basically only there for supercomputers. Using the usual virtualenv install (probably with --developer) is strongly recommended. Regards, David On Sun, 10 Apr 2016 at 11:06 Shipton, Jemma <j.shipton(a)imperial.ac.uk> wrote: > Hi All, > > > I'm finally moving with the times and have upgraded my macbook to El > Capitan with the intention of installing firedrake. I have got as far as > running firedrake-install --global but it has stopped with the error: > > > Traceback (most recent call last): > > File "firedrake-install", line 842, in <module> > > build_and_install_h5py() > > File "firedrake-install", line 565, in build_and_install_h5py > > raise InstallError("Unable to find installed PETSc when building h5py") > > __main__.InstallError: Unable to find installed PETSc when building h5py > > > Any idea what's gone wrong? > > > Thanks, > > Jemma >

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new firedrake install on El Capitan
by Shipton, Jemma 10 Apr '16

10 Apr '16

Hi All, I'm finally moving with the times and have upgraded my macbook to El Capitan with the intention of installing firedrake. I have got as far as running firedrake-install --global but it has stopped with the error: Traceback (most recent call last): File "firedrake-install", line 842, in <module> build_and_install_h5py() File "firedrake-install", line 565, in build_and_install_h5py raise InstallError("Unable to find installed PETSc when building h5py") __main__.InstallError: Unable to find installed PETSc when building h5py Any idea what's gone wrong? Thanks, Jemma

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Re: [firedrake] problems on my mac os x
by David Ham 09 Apr '16

09 Apr '16

Hi Francis, First, you only need to follow Miklos' instructions if you haven't updated since 4 Feb (those instructions are to get over a particular fix we had to apply to the install script. They are not usually needed). This is slightly hacky, but you can open up firedrake-update in an editor. Starting at around line 123 (depending slightly on which version you have), you can see a list of boolean assignments which record your original configuration flags. Regards, David On Sat, 9 Apr 2016 at 18:59 Francis Poulin <fpoulin(a)uwaterloo.ca> wrote: > Thanks for the responses. > > I did firedrake-install on my mac. I am redoing the firedrake-update > with PYTHONPATH clear and suspect that will do the trick. Thanks David. > > On my ubuntu machine I tried firedrake-update and that seemed much easier > (will do that in the future). I followed instructions from the Feb 4 email > (by Miklos) > > *cd to the top directory of the firedrake virtualenv* > *. ./bin/activate* > *cd src/firedrake/* > *git pull* > *./scripts/firedrake-install --rebuild-script --your-install-options* > > *Replace --your-install-options with the options you used to install > Firedrake. Then run:* > > *firedrake-update --clean* > > > This is clear but one problem is that I don't remember what options I > installed. Is there a way of figuring that out? I know that someone > recommended something involving petsc but have not been able to track down > the options. > > Thanks again. > Francis >

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