January 2016 - firedrake - imperial.ac.uk

Still error after COFFEE / petsc update
by Gregory, Alastair 29 Jan '16

29 Jan '16

Hi, My error is still occurring with this test case (attached) after the updates in COFFEE and petsc. Does anyone know what is going on? Does it run on anyone else's machine? The error is also attached. Many Thanks, Alastair Alastair Gregory ------------------------------------------------------------------------------------------ Numerical Analysis Research Postgraduate Imperial College London - Grantham Institute of Climate Change Room 759 Huxley Building, South Kensington (Tel: 07794 243913) | (Email: a.gregory14(a)imperial.ac.uk) -------------------------------------------------------------------------------------------

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Re: [firedrake] pip nadgered
by Colin Cotter 28 Jan '16

28 Jan '16

Oh yes, it does. Thanks --cjc On 28 January 2016 at 21:12, Homolya, Miklós <m.homolya14(a)imperial.ac.uk> wrote: > Not sure if it helps, but can you please cd out of the firedrake directory > and try again? > > > ------------------------------ > *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:* 28 January 2016 21:09 > *To:* firedrake > *Subject:* [firedrake] pip nadgered > > Dear Firedrakers, > My pip doesn't work on my workstation since trying to rebuild PETSc post > the recent change. I get: > > (firedrake)cjc1@ma-gauss:~/firedrake/src/firedrake/firedrake$ pip > > Traceback (most recent call last): > > File "/home/cjc1/firedrake/bin/pip", line 7, in <module> > > from pip import main > > File > "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pip/__init__.py", > line 13, in <module> > > from pip.utils import get_installed_distributions, get_prog > > File > "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pip/utils/__init__.py", > line 15, in <module> > > import zipfile > > File "/usr/lib/python2.7/zipfile.py", line 6, in <module> > > import io > > File "/home/cjc1/firedrake/src/firedrake/firedrake/io.py", line 9, in > <module> > > from pyop2.logger import warning, RED > > File > "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/__init__.py", > line 9, in <module> > > from op2 import * > > File > "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/op2.py", line > 38, in <module> > > import backends > > File > "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/backends.py", > line 41, in <module> > > from logger import warning > > File > "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/logger.py", > line 38, in <module> > > from mpi import MPI > > File > "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/mpi.py", line > 38, in <module> > > from utils import trim > > File > "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/utils.py", > line 46, in <module> > > from configuration import configuration > > File > "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/configuration.py", > line 42, in <module> > > class Configuration(dict): > > File > "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/configuration.py", > line 86, in Configuration > > os.path.join(gettempdir(), > > File "/usr/lib/python2.7/tempfile.py", line 269, in gettempdir > > tempdir = _get_default_tempdir() > > File "/usr/lib/python2.7/tempfile.py", line 200, in _get_default_tempdir > > with _io.open(fd, 'wb', closefd=False) as fp: > > AttributeError: 'module' object has no attribute 'open' > > > Does this make sense to anyone? > > > all the best > > --cjc > > -- > http://www.imperial.ac.uk/people/colin.cotter > <http://www.imperial.ac.uk/people/colin.cotter> > Home - Dr Colin Cotter <http://www.imperial.ac.uk/people/colin.cotter> > www.imperial.ac.uk > Summary. My research in numerical analysis and scientific computing > focusses on the design, analysis and implementation of numerical methods > for weather forecasting ... > > > www.cambridge.org/9781107663916 > > > -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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pip nadgered
by Colin Cotter 28 Jan '16

28 Jan '16

Dear Firedrakers, My pip doesn't work on my workstation since trying to rebuild PETSc post the recent change. I get: (firedrake)cjc1@ma-gauss:~/firedrake/src/firedrake/firedrake$ pip Traceback (most recent call last): File "/home/cjc1/firedrake/bin/pip", line 7, in <module> from pip import main File "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pip/__init__.py", line 13, in <module> from pip.utils import get_installed_distributions, get_prog File "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pip/utils/__init__.py", line 15, in <module> import zipfile File "/usr/lib/python2.7/zipfile.py", line 6, in <module> import io File "/home/cjc1/firedrake/src/firedrake/firedrake/io.py", line 9, in <module> from pyop2.logger import warning, RED File "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/__init__.py", line 9, in <module> from op2 import * File "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/op2.py", line 38, in <module> import backends File "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/backends.py", line 41, in <module> from logger import warning File "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/logger.py", line 38, in <module> from mpi import MPI File "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/mpi.py", line 38, in <module> from utils import trim File "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/utils.py", line 46, in <module> from configuration import configuration File "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/configuration.py", line 42, in <module> class Configuration(dict): File "/home/cjc1/firedrake/local/lib/python2.7/site-packages/pyop2/configuration.py", line 86, in Configuration os.path.join(gettempdir(), File "/usr/lib/python2.7/tempfile.py", line 269, in gettempdir tempdir = _get_default_tempdir() File "/usr/lib/python2.7/tempfile.py", line 200, in _get_default_tempdir with _io.open(fd, 'wb', closefd=False) as fp: AttributeError: 'module' object has no attribute 'open' Does this make sense to anyone? all the best --cjc -- http://www.imperial.ac.uk/people/colin.cotter www.cambridge.org/9781107663916

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Re: [firedrake] libpetsc.3.05.2.dylib error
by David Ham 28 Jan '16

28 Jan '16

Hi Anna, You appear to be running a firedrake you have installed globally. (It's in /usr/local). Are you sure the virtualenv was active when you typed this? I suspect you have a very old firedrake with a broken PETSc installed globally which you usually don't hit. Regards, David On Wed, 27 Jan 2016 at 14:14 Anna Kalogirou <A.Kalogirou(a)leeds.ac.uk> wrote: > Dear all, > > I was getting the error below, but it went away after a Firedrake update. > However, now my code is running and the burgers tutorial is not, returning > the same error I was getting earlier. > > Anna. > > > Traceback (most recent call last): > File "burgers.py", line 36, in <module> > from firedrake import * > File "/usr/local/lib/python2.7/site-packages/firedrake/__init__.py", > line 30, in <module> > from assemble import * > File "/usr/local/lib/python2.7/site-packages/firedrake/assemble.py", > line 8, in <module> > import assembly_cache > File > "/usr/local/lib/python2.7/site-packages/firedrake/assembly_cache.py", line > 40, in <module> > import function > File "/usr/local/lib/python2.7/site-packages/firedrake/function.py", > line 9, in <module> > import assemble_expressions > File > "/usr/local/lib/python2.7/site-packages/firedrake/assemble_expressions.py", > line 15, in <module> > import functionspace > File > "/usr/local/lib/python2.7/site-packages/firedrake/functionspace.py", line > 10, in <module> > import dmplex > ImportError: > dlopen(/usr/local/lib/python2.7/site-packages/firedrake/dmplex.so, 2): > Library not loaded: > /usr/local/lib/python2.7/site-packages/petsc/lib/libpetsc.3.05.2.dylib > Referenced from: > /usr/local/lib/python2.7/site-packages/firedrake/dmplex.so > Reason: image not found >

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libpetsc.3.05.2.dylib error
by Anna Kalogirou 27 Jan '16

27 Jan '16

Dear all, I was getting the error below, but it went away after a Firedrake update. However, now my code is running and the burgers tutorial is not, returning the same error I was getting earlier. Anna. Traceback (most recent call last): File "burgers.py", line 36, in <module> from firedrake import * File "/usr/local/lib/python2.7/site-packages/firedrake/__init__.py", line 30, in <module> from assemble import * File "/usr/local/lib/python2.7/site-packages/firedrake/assemble.py", line 8, in <module> import assembly_cache File "/usr/local/lib/python2.7/site-packages/firedrake/assembly_cache.py", line 40, in <module> import function File "/usr/local/lib/python2.7/site-packages/firedrake/function.py", line 9, in <module> import assemble_expressions File "/usr/local/lib/python2.7/site-packages/firedrake/assemble_expressions.py", line 15, in <module> import functionspace File "/usr/local/lib/python2.7/site-packages/firedrake/functionspace.py", line 10, in <module> import dmplex ImportError: dlopen(/usr/local/lib/python2.7/site-packages/firedrake/dmplex.so, 2): Library not loaded: /usr/local/lib/python2.7/site-packages/petsc/lib/libpetsc.3.05.2.dylib Referenced from: /usr/local/lib/python2.7/site-packages/firedrake/dmplex.so Reason: image not found

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Indexing
by Angwenyi David 18 Jan '16

18 Jan '16

Hi all, I wanted to extend the solution to the linear wave equation to a non-linear one. Could someone look at the attached script. I get the following error: IndexError: tuple index out of range How can I resolve the issue? Any reading material to that effect? Thanks. Angwenyi

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Re: [firedrake] Error Log Unknown
by Fabio Luporini 14 Jan '16

14 Jan '16

Hi, More precisely, this has to do with coffee. You could actually file the issue here: https://github.com/coneoproject/COFFEE/issues Thanks -- Fabio 2016-01-14 10:42 GMT+00:00 Mitchell, Lawrence < lawrence.mitchell(a)imperial.ac.uk>: > > > On 14/01/16 10:37, Gregory, Alastair wrote: > > Hi, > > > > > > I have an error log and err file for a persistent error that appears > > for any Firedrake code I'm running currently. It's only occurred > > recently and I think it's to do with a PyOP2 update. > > > > > > The c file that the log refers to is attached also. > > > > > > Does anyone know what this means? > > Yes, that looks like a bug. Please report it as (with a python code > for us to reproduce the problem) on the firedrake issues page > (github.com/firedrakeproject/firedrake/issues) > > Thanks, > > Lawrence > >

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Error Log Unknown
by Gregory, Alastair 14 Jan '16

14 Jan '16

Hi, I have an error log and err file for a persistent error that appears for any Firedrake code I'm running currently. It's only occurred recently and I think it's to do with a PyOP2 update. The c file that the log refers to is attached also. Does anyone know what this means? Many Thanks, Alastair Gregory

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Monolithic matrices
by Justin Chang 14 Jan '16

14 Jan '16

Hi all, Say if I had this mixed function space: parameters["matnest"] = False Q = FunctionSpace(mesh,"CG",1) W = Q*Q*Q u1,u2,u3 = TrialFunctions(W) v1,v2,v3 = TestFunctions(W) What will the corresponding global matrix format be? Will it be of type MATMPIBAIJ of block size 3? Or will it simply be a monolithic MATMPIAIJ matrix? Thanks, Justin

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Time loop
by Angwenyi David 12 Jan '16

12 Jan '16

Hi all, I have a system of discretised equations attached resulting from non-linear wave equation. I am defeated on coding the time loop. How can I go about it? Thanks in advance. David

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