January 2015 - firedrake - imperial.ac.uk

Re: [firedrake] Nullspace & VectorSpaceBasis
by Andrew McRae 29 Apr '15

29 Apr '15

Four comments: 1) If I understand correctly, PETSc insists that the diagonal entries of the sparse matrix are filled in. Usually, the LHS form will cause this to happen; however, that obviously isn't the case for your form! 2) It should be possible to build the nullspace you want, but I'm clueless on the actual syntax. This wouldn't get around (1) without further fixes from our end. 3) Could the equations given not be included in the weak form for the rest of the problem? 4) If not, there might be a hacky "add-a-weighted-mass-matrix-to-the-LHS" fix you could use?.... Andrew On 11 December 2014 at 12:46, Anna Kalogirou <a.kalogirou(a)leeds.ac.uk> wrote: > Dear all, > > I am trying to solve a simple problem (linear water wave equations), > where I have the Laplace equation in a square domain with Neumann > boundary conditions on the three sides and on the top boundary two > equations are satisfied. > > I have the following code: > -------------------------------------- > V = FunctionSpace(mesh,"CG",1) > > eta0 = Function(V).interpolate(Expression("cos(2*pi*x[0])")) > phi0 = Function(V) > eta1 = Function(V) > phi1 = Function(V) > eta = TrialFunction(V) > phi = TrialFunction(V) > v = TestFunction(V) > > aeta = v*eta*ds(4) > Leta = v*eta0*ds(4) + dt*inner(grad(v),grad(phi0))*dx > > eta_problem = LinearVariationalProblem(aeta,Leta,eta1) > eta_solver = LinearVariationalSolver(eta_problem) > > aphi = v*phi*ds(4) > Lphi = (v*phi0 - g*dt*v*eta1)*ds(4) > > phi_problem = LinearVariationalProblem(aphi,Lphi,phi1) > phi_solver = LinearVariationalSolver(phi_problem) > -------------------------------------- > > The error I get tells me that Object is in wrong state, and Matrix is > missing diagonal entry 39. > > I thought this had to do with the problem being singular, so I tried to > build the nullspace but I don't know how to define the VectorSpaceBasis. > Any help would be appreciated. > > Thank you very much. > > Regards, Anna. > > _______________________________________________ > firedrake mailing list > firedrake(a)imperial.ac.uk > https://mailman.ic.ac.uk/mailman/listinfo/firedrake >

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Re: [firedrake] Firedrake Installation
by Andrew McRae 06 Apr '15

06 Apr '15

Hi all, Suet [cc'd], one of Colin's project students, is encoutering the following error when using the PyOP2 'quick install' script. Can anyone help? IIRC, this is running in a (32-bit?) Ubuntu 14.04 virtual machine. (Last night, she was getting an mpi4py error, but I believe this <https://github.com/OP2/PyOP2/commit/e15b3ee8d72369f10c9a84d944a3ecbf06f7e927> fixed that). Cheers, Andrew On 16 November 2014 13:28, Lee, Suet <suet.lee11(a)imperial.ac.uk> wrote: > I ran the install mpi4py commange but I have a new error now: > > > mosh@ubuntu:~$ wget -O - > https://github.com/OP2/PyOP2/raw/master/install.sh | sudo bash > --2014-11-16 13:20:14-- > https://github.com/OP2/PyOP2/raw/master/install.sh > Resolving github.com (github.com) 192.30.252.131 > Connecting to github.com (github.com)|192.30.252.131|:443... connected. > HTTP request sent, awaiting response... 302 Found > Location: https://raw.githubusercontent.com/OP2/PyOP2/master/install.sh > [following] > --2014-11-16 13:20:16-- > https://raw.githubusercontent.com/OP2/PyOP2/master/install.sh > Resolving raw.githubusercontent.com (raw.githubusercontent.com) > 185.31.18.133 > Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.31.18.133|:443... > connected. > HTTP request sent, awaiting response... 200 OK > Length: 3667 (3.6K) [text/plain] > Saving to: ‘STDOUT’ > > 100%[======================================>] 3,667 --.-K/s in > 0s > > 2014-11-16 13:20:16 (40.6 MB/s) - written to stdout [3667/3667] > > PyOP2 installation started at Sun Nov 16 13:20:16 GMT 2014 > on Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC > 2014 i686 i686 i686 GNU/Linux > > *** Privileged installation *** > Running unprivileged commands as mosh > > *** Preparing system *** > > *** Installing dependencies *** > > *** Installing PETSc *** > > *** Installing PyOP2 *** > > [ubuntu:31603] *** Process received signal *** > [ubuntu:31603] Signal: Floating point exception (8) > [ubuntu:31603] Signal code: Integer divide-by-zero (1) > [ubuntu:31603] Failing at address: 0xb74d6da0 > [ubuntu:31603] [ 0] [0xb779a40c] > [ubuntu:31603] [ 1] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2cda0) > [0xb74d6da0] > [ubuntu:31603] [ 2] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2e71c) > [0xb74d871c] > [ubuntu:31603] [ 3] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x2ea8b) > [0xb74d8a8b] > [ubuntu:31603] [ 4] /usr/lib/i386-linux-gnu/libhwloc.so.5(+0x98f6) > [0xb74b38f6] > [ubuntu:31603] [ 5] > /usr/lib/i386-linux-gnu/libhwloc.so.5(hwloc_topology_load+0x1c6) > [0xb74b48ec] > [ubuntu:31603] [ 6] /usr/lib/libopen-rte.so.4(orte_odls_base_open+0x7b1) > [0xb76fa881] > [ubuntu:31603] [ 7] /usr/lib/openmpi/lib/openmpi/mca_ess_hnp.so(+0x2445) > [0xb7488445] > [ubuntu:31603] [ 8] /usr/lib/libopen-rte.so.4(orte_init+0x1cf) [0xb76cfb3f] > [ubuntu:31603] [ 9] /usr/lib/libopen-rte.so.4(orte_daemon+0x256) > [0xb76ec1c6] > [ubuntu:31603] [10] orted() [0x80485b3] > [ubuntu:31603] [11] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xf3) > [0xb7504a83] > [ubuntu:31603] [12] orted() [0x80485f8] > [ubuntu:31603] *** End of error message *** > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a > daemon on the local node in file ess_singleton_module.c at line 343 > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a > daemon on the local node in file ess_singleton_module.c at line 140 > [ubuntu:31601] [[INVALID],INVALID] ORTE_ERROR_LOG: Unable to start a > daemon on the local node in file runtime/orte_init.c at line 128 > -------------------------------------------------------------------------- > It looks like orte_init failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during orte_init; some of which are due to configuration or > environment problems. This failure appears to be an internal failure; > here's some additional information (which may only be relevant to an > Open MPI developer): > > orte_ess_set_name failed > --> Returned value Unable to start a daemon on the local node (-128) > instead of ORTE_SUCCESS > -------------------------------------------------------------------------- > -------------------------------------------------------------------------- > It looks like MPI_INIT failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during MPI_INIT; some of which are due to configuration or environment > problems. This failure appears to be an internal failure; here's some > additional information (which may only be relevant to an Open MPI > developer): > > ompi_mpi_init: orte_init failed > --> Returned "Unable to start a daemon on the local node" (-128) instead > of "Success" (0) > -------------------------------------------------------------------------- > [ubuntu:31601] *** An error occurred in MPI_Init_thread > [ubuntu:31601] *** on a NULL communicator > [ubuntu:31601] *** Unknown error > [ubuntu:31601] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort > -------------------------------------------------------------------------- > An MPI process is aborting at a time when it cannot guarantee that all > of its peer processes in the job will be killed properly. You should > double check that everything has shut down cleanly. > > Reason: Before MPI_INIT completed > Local host: ubuntu > PID: 31601 > -------------------------------------------------------------------------- > PyOP2 installation failed > See /home/mosh/PyOP2/pyop2_install.log for details > > > Any idea what's going on? > > > Suet >

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FInAT mailing list
by David Ham 31 Jan '15

31 Jan '15

Dear Firedrakers, Since FInAT involves people outside the Firedrake project who have no interest in our chatter, I have established a FInAT mailing list. Any of you who wish to follow FInAT development discussions are invited to subscribe to the list: https://mailman.ic.ac.uk/mailman/listinfo/finat Regards, David -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Locally installed FFC not found on ARCHER
by Eike Mueller 30 Jan '15

30 Jan '15

Dear firedrakers, I need to install my own version of FFC, since the one already installed in /work/y07/y07/fdrake appears not to be compatible with the firedrake version I use: RuntimeError: Incompatible Firedrake version 0.12.0 and FFC version unknown. So I installed FFC locally and added it to PYTHONPATH: /work/n02/n02/eike//git_workspace//firedrake-helmholtzsolver/source:/work/n02/n02/eike//git_workspace//firedrake-bench:/work/n02/n02/eike//git_workspace//pybench:/work/n02/n02/eike//git_workspace//firedrake:/work/n02/n02/eike//git_workspace//PyOP2:/work/n02/n02/eike//git_workspace//petsc4py/cray-gnu-shared/lib/python2.7/site-packages/:/work/n02/n02/eike//git_workspace//COFFEE/build/lib:/work/n02/n02/eike//git_workspace//ffc/build/lib.linux-x86_64-2.7/:/work/n02/n02/eike//Library:/work/y07/y07/fdrake/ufl/lib/python2.7/site-packages:/work/y07/y07/fdrake/scientificpython/lib/python2.7/site-packages:/work/y07/y07/fdrake/psutil/lib/python2.7/site-packages:/work/y07/y07/fdrake/mpi4py/lib/python2.7/site-packages:/work/y07/y07/fdrake/instant/lib/python2.7/site-packages:/work/y07/y07/fdrake/fiat/lib/python2.7/site-packages:/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages:/work/y07/y07/fdrake/decorator-3.4.0/lib/python2.7/site-packages:/work/y07/y07/fdrake/petsc/arch-linux2-cxx-opt/lib/pyth on2.7/site-packages:/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages:/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7:/usr/local/packages/cse/bolt/0.6/modules However, in python, the /work/y07/y07/fdrake version comes *first*, so it always picked up when I import ffc and I keep getting the error message above: eike@eslogin008 $ python Python 2.7.6 |Anaconda 1.9.2 (64-bit)| (default, Jan 17 2014, 10:13:17) [GCC 4.1.2 20080704 (Red Hat 4.1.2-54)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import sys >>> print sys.path ['', '/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages/FFC-1.4.0_-py2.7-linux-x86_64.egg', '/work/y07/y07/fdrake/decorator-3.4.0/lib/python2.7/site-packages/decorator-3.4.0-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/python_hostlist-1.14-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/GridDataFormats-0.2.4-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/setuptools-2.2-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/extasy.coco-0.1-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/MDAnalysis-0.8.1-py2.7-linux-x86_64.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/python_hostlist-1.14-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/GridDataFormats-0.2.4-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/apache_libcloud-0.15.1-py2.7.egg', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/setuptools-2.2-py2.7.egg', '/work/n02/n02/eike/git_workspace/firedrake-helmholtzsolver/source', '/work/n02/n02/eike/git_workspace/firedrake-bench', '/work/n02/n02/eike/git_workspace/pybench', '/work/n02/n02/eike/git_workspace/firedrake', '/work/n02/n02/eike/git_workspace/PyOP2', '/work/n02/n02/eike/git_workspace/petsc4py/cray-gnu-shared/lib/python2.7/site-packages', '/work/n02/n02/eike/git_workspace/COFFEE/build/lib', '/work/n02/n02/eike/git_workspace/ffc/build/lib.linux-x86_64-2.7', '/work/n02/n02/eike/Library', '/work/y07/y07/fdrake/ufl/lib/python2.7/site-packages', '/work/y07/y07/fdrake/scientificpython/lib/python2.7/site-packages', '/work/y07/y07/fdrake/psutil/lib/python2.7/site-packages', '/work/y07/y07/fdrake/mpi4py/lib/python2.7/site-packages', '/work/y07/y07/fdrake/instant/lib/python2.7/site-packages', '/work/y07/y07/fdrake/fiat/lib/python2.7/site-packages', '/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages', '/work/y07/y07/fdrake/decorator-3.4.0/lib/python2.7/site-packages', '/work/y07/y07/fdrake/petsc/arch-linux2-cxx-opt/lib/python2.7/site-packages', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7', '/usr/local/packages/cse/bolt/0.6/modules', '/work/y07/y07/cse/anaconda/1.9.2/lib/python27.zip', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/plat-linux2', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/lib-tk', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/lib-old', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/lib-dynload', '/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/PIL'] Any idea what is going on here? I can of course remove the unwanted FFC path, but there must be a more obvious solution. Thanks a lot, Eike

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Re: [firedrake] Locally installed FFC not found on ARCHER
by David Ham 29 Jan '15

29 Jan '15

Can we change the way FFC uses setuptools so this doesn't happen? I mean the easy_install faff doesn't occur for all python packages, right? On 29 January 2015 at 11:43, Rathgeber, Florian < florian.rathgeber(a)imperial.ac.uk> wrote: > Eike, I have fixed this, so you should be able to remove your hack. > > For reference: the problem is the following file: > /work/y07/y07/fdrake/ffc/lib/python2.7/site-packages/easy-install.pth > > This file is (re)created *every time* the FFC installation is updated > since FFC uses the setuptools egg installation. Due to a setuptools > "feature" all the eggs contained in this file are *prepended* to > sys.path and end up *before* anything in PYTHONPATH and there is > *nothing* you can do to prevent this. The only fix is to edit this .pth > file and remove or comment the offending lines (first and last). > > What we might be able to do is not actually install FFC but point the > module at the source try and build the extension modules in place. > Thoughts? > > On 29/01/15 11:25, Eike Mueller wrote: > > Hi Lawrence, > > > > ok, adding > > > > import sys > > > sys.path.remove('/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages/FFC-1.4.0_-py2.7-linux-x86_64.egg') > > > > > > at the top of firedrake/__init__.py seems to fix it for me. > > > > Thanks, > > > > Eike > > > > > > On 29/01/15 10:37, Lawrence Mitchell wrote: > > On 29/01/15 10:23, Eike Mueller wrote: > >>>> Dear firedrakers, > >>>> > >>>> I need to install my own version of FFC, since the one already > >>>> installed in /work/y07/y07/fdrake appears not to be compatible with > >>>> the firedrake version I use: > >>>> > >>>> RuntimeError: Incompatible Firedrake version 0.12.0 and FFC > >>>> version unknown. > >>>> > >>>> So I installed FFC locally and added it to PYTHONPATH: > >>>> > >>>> > /work/n02/n02/eike//git_workspace//firedrake-helmholtzsolver/source:/work/n02/n02/eike//git_workspace//firedrake-bench:/work/n02/n02/eike//git_workspace//pybench:/work/n02/n02/eike//git_workspace//firedrake:/work/n02/n02/eike//git_workspace//PyOP2:/work/n02/n02/eike//git_workspace//petsc4py/cray-gnu-shared/lib/python2.7/site-packages/:/work/n02/n02/eike//git_workspace//COFFEE/build/lib:/work/n02/n02/eike//git_workspace//ffc/build/lib.linux-x86_64-2.7/:/work/n02/n02/eike//Library:/work/y07/y07/fdrake/ufl/lib/python2.7/site-packages:/work/y07/y07/fdrake/scientificpython/lib/python2.7/site-packages:/work/y07/y07/fdrake/psutil/lib/python2.7/site-packages:/work/y07/y07/fdrake/mpi4py/lib/python2.7/site-packages:/work/y07/y07/fdrake/instant/lib/python2.7/site-packages:/work/y07/y07/fdrake/fiat/lib/python2.7/site-packages:/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages:/work/y07/y07/fdrake/decorator-3.4.0/lib/python2.7/site-packages:/work/y07/y07/fdrake/petsc/arch-linux2-cxx-opt/lib > /p > >>>> > >> y > > th > >>>> > >>>> > >>>> > on2.7/site-packages:/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages:/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7:/usr/local/packages/cse/bolt/0.6/modules > >>>> > >>>> > >>>> > >>>> > >>>> However, in python, the /work/y07/y07/fdrake version comes *first*, > >>>> so it always picked up when I import ffc and I keep getting the > >>>> error message above: > > > > This looks like the standard easy_install disaster. I never know how > > to fix this unfortunately. > > > > Lawrence > > -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Re: [firedrake] Locally installed FFC not found on ARCHER
by David Ham 29 Jan '15

29 Jan '15

> > > On 29 January 2015 at 11:51, Rathgeber, Florian < florian.rathgeber(a)imperial.ac.uk> wrote: > On another note: I *really* don't have time to continue maintaining the > fdrake modules on ARCHER and appreciate if someone else (Michael? > Lawrence?) could take on this task. I also don't have time to sort out > this current issue, sorry about that. > > I totally understand. This is in a very literal sense not your job. We will explicitly reallocate this task. David > Florian > > -- Dr David Ham Departments of Mathematics and Computing Imperial College London http://www.imperial.ac.uk/people/david.ham

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Re: [firedrake] Locally installed FFC not found on ARCHER
by Andrew McRae 29 Jan '15

29 Jan '15

Why are we installing FFC in the first place? Is it just because there are some C files (which we don't use) that need compiling? On 29 Jan 2015 11:43, "Rathgeber, Florian" <florian.rathgeber(a)imperial.ac.uk> wrote: > Eike, I have fixed this, so you should be able to remove your hack. > > For reference: the problem is the following file: > /work/y07/y07/fdrake/ffc/lib/python2.7/site-packages/easy-install.pth > > This file is (re)created *every time* the FFC installation is updated > since FFC uses the setuptools egg installation. Due to a setuptools > "feature" all the eggs contained in this file are *prepended* to > sys.path and end up *before* anything in PYTHONPATH and there is > *nothing* you can do to prevent this. The only fix is to edit this .pth > file and remove or comment the offending lines (first and last). > > What we might be able to do is not actually install FFC but point the > module at the source try and build the extension modules in place. > Thoughts? > > On 29/01/15 11:25, Eike Mueller wrote: > > Hi Lawrence, > > > > ok, adding > > > > import sys > > > sys.path.remove('/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages/FFC-1.4.0_-py2.7-linux-x86_64.egg') > > > > > > at the top of firedrake/__init__.py seems to fix it for me. > > > > Thanks, > > > > Eike > > > > > > On 29/01/15 10:37, Lawrence Mitchell wrote: > > On 29/01/15 10:23, Eike Mueller wrote: > >>>> Dear firedrakers, > >>>> > >>>> I need to install my own version of FFC, since the one already > >>>> installed in /work/y07/y07/fdrake appears not to be compatible with > >>>> the firedrake version I use: > >>>> > >>>> RuntimeError: Incompatible Firedrake version 0.12.0 and FFC > >>>> version unknown. > >>>> > >>>> So I installed FFC locally and added it to PYTHONPATH: > >>>> > >>>> > /work/n02/n02/eike//git_workspace//firedrake-helmholtzsolver/source:/work/n02/n02/eike//git_workspace//firedrake-bench:/work/n02/n02/eike//git_workspace//pybench:/work/n02/n02/eike//git_workspace//firedrake:/work/n02/n02/eike//git_workspace//PyOP2:/work/n02/n02/eike//git_workspace//petsc4py/cray-gnu-shared/lib/python2.7/site-packages/:/work/n02/n02/eike//git_workspace//COFFEE/build/lib:/work/n02/n02/eike//git_workspace//ffc/build/lib.linux-x86_64-2.7/:/work/n02/n02/eike//Library:/work/y07/y07/fdrake/ufl/lib/python2.7/site-packages:/work/y07/y07/fdrake/scientificpython/lib/python2.7/site-packages:/work/y07/y07/fdrake/psutil/lib/python2.7/site-packages:/work/y07/y07/fdrake/mpi4py/lib/python2.7/site-packages:/work/y07/y07/fdrake/instant/lib/python2.7/site-packages:/work/y07/y07/fdrake/fiat/lib/python2.7/site-packages:/work/y07/y07/fdrake/ffc/lib/python2.7/site-packages:/work/y07/y07/fdrake/decorator-3.4.0/lib/python2.7/site-packages:/work/y07/y07/fdrake/petsc/arch-linux2-cxx-opt/lib > /p > >>>> > >> y > > th > >>>> > >>>> > >>>> > on2.7/site-packages:/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages:/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7:/usr/local/packages/cse/bolt/0.6/modules > >>>> > >>>> > >>>> > >>>> > >>>> However, in python, the /work/y07/y07/fdrake version comes *first*, > >>>> so it always picked up when I import ffc and I keep getting the > >>>> error message above: > > > > This looks like the standard easy_install disaster. I never know how > > to fix this unfortunately. > > > > Lawrence > >

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Fwd: Re: [PRISM] PRISM Research Data and Software Management
by Lawrence Mitchell 29 Jan '15

29 Jan '15

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Imperial firedrakers, for those of you not on the PRISM list, note there is a talk on research data management *today* at 11am in Aeronautics (see below for more info). You may wish to come along. Cheers, Lawrence - -------- Forwarded Message -------- Subject: Re: [PRISM] PRISM Research Data and Software Management Date: Wed, 28 Jan 2015 12:44:32 +0000 From: Chris Cantwell <c.cantwell(a)imperial.ac.uk> Organization: Imperial College London To: prism(a)imperial.ac.uk Dear all, Just to reminder you, we have the PRISM RDM meeting tomorrow at 11am in RH266 (Aeronautics). Cheers, Chris On 18/01/15 20:06, Chris Cantwell wrote: > Dear all, > > Due to the coincidental scheduling of a College-wide RDM review > meeting in this slot, the PRISM RDM micro-workshop has been pushed > back to allow us to hear about the outcome of this meeting. The new > time is: > > *Thursday 29th January, 11am - 1pm* > > The room remains the same. > > Cheers, Chris > > > On 09/01/15 17:05, Chris Cantwell wrote: >> Dear all, >> >> The next PRISM technical seminar will be an micro-workshop on >> research data and software management. >> >> Time: Wednesday 28th January, 2-4pm Place: Roderic Hill >> RH266 (Aeronautics) >> >> There will be a talk from Christian Jacobs on research data >> management using PyRDM and Gerard Gorman will provide a brief >> update on the College's current thinking. There will also be time >> for discussion as to how the PRISM partners can best capitalise >> on this topic. >> >> Cheers, Chris >> >> > - -- Chris Cantwell Imperial College London South Kensington Campus London SW7 2AZ Email: c.cantwell(a)imperial.ac.uk www.imperial.ac.uk/people/c.cantwell _______________________________________________ prism mailing list prism(a)imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/prism -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQEcBAEBAgAGBQJUygNlAAoJECOc1kQ8PEYvSiAIAMUp7VFAEkylIyGqny96r9Ms DMrFsLUZSOHw3Br0RwQrEzfTziZ+kDTwPSotsE+vV24m7n7ecT3wjd6sRB3jVc4E Yc1BFDXeZEXMRdKATgjTvvfLQwcmEm4v05Z0MzPG/E9DE8kWvQUdIELXPH7YbGdr oW902HGbIxHzS7qcuL6oXisXenZdBcnh9kRCLgNwlRt0Ph4h0MKSqCrd6K/M0n3E 7UeiPUAf4nu5FzG0SNIFtXcv7Tc4PHKgE+kEZ8TgsIYhnUXn+MDMLZCMb2OUfriC ZTRHURc9cehEBznUhUnoPhi3wpcmGeTLkkCckJ6TKPXm/oHXa0cjV3DUveL7QIg= =Z9rP -----END PGP SIGNATURE-----

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petsc4py installation on ARCHER: directory lib/petsc-conf not found
by Eike Mueller 28 Jan '15

28 Jan '15

Dear firedrakers, I'm trying to update my firedrake installation on ARCHER, and I came across an issue with petsc4py. I'm using the dmplex-1d-refinement branch of PETSc (latest version from mapdes), which I can build without problems. When I then try to install petsc4py (branch firedrake, also from mapdes) I get: eike@eslogin006 $ python setup.py install --prefix=`pwd`/$PETSC_ARCH running install running build running build_src running build_py running build_ext error: /work/n02/n02/eike/git_workspace/petsc/cray-gnu-shared/lib/petsc-conf/variables: No such file or directory This directory is not created during the PETSc installation, so it's odd that petsc4py is looking for it. There seem to have been some recent changes to the configuration, see e.g. here: commit 76e91a3c243d089c5102cc8e68a0881b5d48a885 Author: Barry Smith <bsmith(a)mcs.anl.gov> Date: Tue Jan 13 10:11:20 2015 -0600 location of PETSc configuration files was changed to lib/petsc-conf from the previous directory conf I rolled back to petsc4py commit 99a07fb395949e1c03fb0af8954d784f5c3b18fe, but if I try to build then I get the error message below. I suspect that the dmplex-1d-refinement PETSc branch is missing the relevant changes in the master? Should I use a different PETSc branch? Thanks a lot, Eike eike@eslogin006 $ git log -1 commit 99a07fb395949e1c03fb0af8954d784f5c3b18fe Merge: bcfcbe4 02ee487 Author: Lisandro Dalcin <dalcinl(a)gmail.com> Date: Tue Jan 13 17:46:49 2015 +0300 Merge branch 'maint' eike@eslogin006 $ python setup.py install --prefix=`pwd`/$PETSC_ARCH running install running build running build_src running build_py running build_ext PETSC_DIR: /work/n02/n02/eike/git_workspace/petsc PETSC_ARCH: cray-gnu-shared version: 3.5.2 development scalar-type: real precision: double language: CONLY compiler: cc linker: cc building 'PETSc' extension creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/cray-gnu-shared creating build/temp.linux-x86_64-2.7/cray-gnu-shared/src cc -pthread -fPIC -fPIC -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall -DPETSC_DIR=/work/n02/n02/eike/git_workspace/petsc -I/fs2/n02/n02/eike/git_workspace/petsc/cray-gnu-shared/include -I/work/n02/n02/eike/git_workspace/petsc/cray-gnu-shared/include -I/work/n02/n02/eike/git_workspace/petsc/include -Isrc/include -I/work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/numpy/core/include -I/work/y07/y07/cse/anaconda/1.9.2/include/python2.7 -c src/PETSc.c -o build/temp.linux-x86_64-2.7/cray-gnu-shared/src/PETSc.o In file included from /work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1760:0, from /work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:17, from /work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/numpy/core/include/numpy/arrayobject.h:4, from src/include/petsc4py/numpy.h:11, from src/petsc4py.PETSc.c:240, from src/PETSc.c:3: /work/y07/y07/cse/anaconda/1.9.2/lib/python2.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:15:2: warning: #warning "Using deprecated NumPy API, disable it by " "#defining NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it by " \ ^ In file included from src/PETSc.c:3:0: src/petsc4py.PETSc.c: In function '__pyx_pf_8petsc4py_5PETSc_4SNES_56hasNPC': src/petsc4py.PETSc.c:150802:3: warning: implicit declaration of function 'SNESHasNPC' [-Wimplicit-function-declaration] __pyx_t_1 = __pyx_f_8petsc4py_5PETSc_CHKERR(SNESHasNPC(__pyx_v_self->snes, (&__pyx_v_has_npc))); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[35]; __pyx_lineno = 238; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^ src/petsc4py.PETSc.c: In function '__pyx_pf_8petsc4py_5PETSc_4SNES_188getCompositeNumber': src/petsc4py.PETSc.c:159512:3: warning: implicit declaration of function 'SNESCompositeGetNumber' [-Wimplicit-function-declaration] __pyx_t_1 = __pyx_f_8petsc4py_5PETSc_CHKERR(SNESCompositeGetNumber(__pyx_v_self->snes, (&__pyx_v_cn))); if (unlikely(__pyx_t_1 == -1)) {__pyx_filename = __pyx_f[35]; __pyx_lineno = 686; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^ src/petsc4py.PETSc.c: In function '__pyx_pf_8petsc4py_5PETSc_6DMPlex_120distributeOverlap': src/petsc4py.PETSc.c:211458:47: warning: passing argument 3 of 'DMPlexDistributeOverlap' from incompatible pointer type __pyx_t_3 = __pyx_f_8petsc4py_5PETSc_CHKERR(DMPlexDistributeOverlap(__pyx_v_self->__pyx_base.dm, __pyx_v_coverlap, (&__pyx_v_sf->sf), (&__pyx_v_dmOverlap))); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[41]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^ In file included from /work/n02/n02/eike/git_workspace/petsc/include/petsc.h:16:0, from src/petsc4py.PETSc.c:236, from src/PETSc.c:3: /work/n02/n02/eike/git_workspace/petsc/include/petscdmplex.h:186:29: note: expected 'ISLocalToGlobalMapping' but argument is of type 'struct _p_PetscSF **' PETSC_EXTERN PetscErrorCode DMPlexDistributeOverlap(DM, PetscInt, ISLocalToGlobalMapping, PetscSF *, DM *); ^ In file included from src/PETSc.c:3:0: src/petsc4py.PETSc.c:211458:47: warning: passing argument 4 of 'DMPlexDistributeOverlap' from incompatible pointer type __pyx_t_3 = __pyx_f_8petsc4py_5PETSc_CHKERR(DMPlexDistributeOverlap(__pyx_v_self->__pyx_base.dm, __pyx_v_coverlap, (&__pyx_v_sf->sf), (&__pyx_v_dmOverlap))); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[41]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^ In file included from /work/n02/n02/eike/git_workspace/petsc/include/petsc.h:16:0, from src/petsc4py.PETSc.c:236, from src/PETSc.c:3: /work/n02/n02/eike/git_workspace/petsc/include/petscdmplex.h:186:29: note: expected 'struct _p_PetscSF **' but argument is of type 'struct _p_DM **' PETSC_EXTERN PetscErrorCode DMPlexDistributeOverlap(DM, PetscInt, ISLocalToGlobalMapping, PetscSF *, DM *); ^ In file included from src/PETSc.c:3:0: src/petsc4py.PETSc.c:211458:47: error: too few arguments to function 'DMPlexDistributeOverlap' __pyx_t_3 = __pyx_f_8petsc4py_5PETSc_CHKERR(DMPlexDistributeOverlap(__pyx_v_self->__pyx_base.dm, __pyx_v_coverlap, (&__pyx_v_sf->sf), (&__pyx_v_dmOverlap))); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[41]; __pyx_lineno = 509; __pyx_clineno = __LINE__; goto __pyx_L1_error;} ^ In file included from /work/n02/n02/eike/git_workspace/petsc/include/petsc.h:16:0, from src/petsc4py.PETSc.c:236, from src/PETSc.c:3: /work/n02/n02/eike/git_workspace/petsc/include/petscdmplex.h:186:29: note: declared here PETSC_EXTERN PetscErrorCode DMPlexDistributeOverlap(DM, PetscInt, ISLocalToGlobalMapping, PetscSF *, DM *); ^ error: command 'cc' failed with exit status 1

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Question on mixed solves: RHS is not defined in product function space
by Eike Mueller 22 Jan '15

22 Jan '15

Dear firedrakers, assume I want to do the following solve of a mixed system: V1 = FunctionSpace(mesh, 'RT', 1) V2 = FunctionSpace(mesh, 'DG', 0) W = V1 * V2 lmbda = 1 u, p = TrialFunctions(W) v, q = TestFunctions(W) f = Function(V1) g = Function(V2) a = (p*q - q*div(u) + lmbda*inner(v, u) + div(v)*p)*dx L = (dot(u,f)+p*g)*dx u = Function(W) solve(a == L, u, solver_parameters=...) But now I take out the line L = (dot(u,f)+p*g)*dx and assume that somewhere I calculate instead: L1 = dot(TestFunction(V1),f)*dx L2 = TestFunction(V2)*g*dx L1 and L2 taken together contain the same information as L, but I can’t write L=L1+L2, because L1 and L2 were not defined using the mixed function spaces (assume that I calculated L1 and L2 somewhere else in the code, and I only use the mixed function spaces in this subroutine). So given L1 and L2, how can I build L, which can be used in the solve? What I currently do is this: m_u = dot(TestFunction(V1),TrialFunction(V1))*dx m_p = TestFunction(V2)*TrialFunction(V2)*dx f_u = Function(V1) f_p = Function(V2) solve(m_u=L1,f_u) solve(m_p=L2,f_p) L = (dot(u,f_u)+p*f_g)*dx which I believe does the right thing, but it involves mass solves. Is there a better way? Can I copy the data over directly? Thanks a lot, Eike -- Dr Eike Hermann Mueller Research Associate (PostDoc) Department of Mathematical Sciences University of Bath Bath BA2 7AY, United Kingdom +44 1225 38 5803 e.mueller(a)bath.ac.uk http://people.bath.ac.uk/em459/

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