(firedrake)alsgregory@alsgregory-HP-Z420-Workstation:~/Documents/PhD/Firedrake/firedrake/src/COFFEE$ git describe --tags 0.1.0-3-gb98154a (firedrake)alsgregory@alsgregory-HP-Z420-Workstation:~/Documents/PhD/Firedrake/firedrake/src/COFFEE$ git rev-parse HEAD b98154a7f07a6f094fd2d821474b28af7c096197 Many Thanks, Alastair ________________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> Sent: 29 January 2016 10:06 To: firedrake Subject: Re: [firedrake] Still error after COFFEE / petsc update Hi Alastair,

On 29 Jan 2016, at 09:30, Gregory, Alastair <a.gregory14@imperial.ac.uk> wrote:

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?

This works for me on up-to-date everything. Can you change into the COFFEE source directory: /path/to/firedrake-virtualenv/src/COFFEE And show the output of: git describe --tags and git rev-parse HEAD Cheers, Lawrence

Thanks, unfortunately same error. Many Thanks, Alastair ________________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> Sent: 29 January 2016 10:16 To: firedrake Subject: Re: [firedrake] Still error after COFFEE / petsc update

On 29 Jan 2016, at 10:10, Gregory, Alastair <a.gregory14@imperial.ac.uk> wrote:

(firedrake)alsgregory@alsgregory-HP-Z420-Workstation:~/Documents/PhD/Firedrake/firedrake/src/COFFEE$ git describe --tags 0.1.0-3-gb98154a (firedrake)alsgregory@alsgregory-HP-Z420-Workstation:~/Documents/PhD/Firedrake/firedrake/src/COFFEE$ git rev-parse HEAD b98154a7f07a6f094fd2d821474b28af7c096197

OK, that looks good, can you run "firedrake-clean" and then try again. Lawrence

I get /home/alsgregory/Documents/PhD/Firedrake/firedrake/local/lib/python2.7/site-packages/coffee/__init__.pyc to the initial query. Then, when I try firedrake-update again (to my recollection I've done that post coffee update) I now get, ---> 20 from firedrake import * 21 parameters["pyop2_options"]["log_level"] = "WARNING" /home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/firedrake/__init__.py in <module>() 29 from pyop2 import op2 # noqa 30 ---> 31 from firedrake.assemble import * 32 from firedrake.bcs import * 33 from firedrake.checkpointing import * /home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/firedrake/assemble.py in <module>() 7 from pyop2.profiling import timed_region, profile 8 ----> 9 from firedrake import assembly_cache 10 from firedrake import assemble_expressions 11 from firedrake import ffc_interface /home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/firedrake/assembly_cache.py in <module>() 39 from pyop2.mpi import MPI, _MPI 40 ---> 41 from firedrake.parameters import parameters 42 from firedrake.petsc import PETSc 43 /home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/firedrake/parameters.py in <module>() 4 from ffc import default_parameters 5 from pyop2.configuration import configuration ----> 6 from firedrake.citations import Citations 7 8 /home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/firedrake/citations.py in <module>() 86 87 # Register the firedrake paper for citations ---> 88 Citations().register("Rathgeber2015") 89 90 # The rest are all registered only when using appropriate functionality. /home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/firedrake/citations.py in register(self, key) 60 if cite is None: 61 raise KeyError("Did not find a citation for '%s', did you forget to add it?" % key) ---> 62 PETSc.Sys.registerCitation(cite) 63 64 @classmethod AttributeError: type object 'petsc4py.PETSc.Sys' has no attribute 'registerCitation' many Thanks, Alastair ________________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> Sent: 29 January 2016 10:27 To: firedrake Subject: Re: [firedrake] Still error after COFFEE / petsc update

On 29 Jan 2016, at 10:21, Gregory, Alastair <a.gregory14@imperial.ac.uk> wrote:

Thanks, unfortunately same error.

Hmmm, to assuage my worries, can you do: python -c "import coffee; print coffee.__file__" To ensure you're getting the correct coffee in the virtualenv. I presume, also, that you've run firedrake-update appropriately. Lawrence

Thanks, I've done that, and it has gone back to it's original error... CompilationError: Command "['mpicc', '-std=c99', '-fPIC', '-Wall', '-march=native', '-O3', '-fno-ivopts', '-I/home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/petsc/include', '-I/home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/firedrake', '-I/home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/pyop2', '-msse', '-o', '/tmp/pyop2-cache-uid1000/af4e249f9c37fca833cbc5212bf91fd0_p7072.so.tmp', '/tmp/pyop2-cache-uid1000/af4e249f9c37fca833cbc5212bf91fd0_p7072.c', '-shared', '-L/home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/petsc/lib', '-Wl,-rpath,/home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/petsc/lib', '-lpetsc', '-lm']" return error status 1. Unable to compile code Compile log in /tmp/pyop2-cache-uid1000/af4e249f9c37fca833cbc5212bf91fd0_p7072.log Compile errors in /tmp/pyop2-cache-uid1000/af4e249f9c37fca833cbc5212bf91fd0_p7072.err Many Thanks, Alastair ________________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> Sent: 29 January 2016 11:11 To: firedrake Subject: Re: [firedrake] Still error after COFFEE / petsc update

On 29 Jan 2016, at 10:39, Gregory, Alastair <a.gregory14@imperial.ac.uk> wrote:

I get /home/alsgregory/Documents/PhD/Firedrake/firedrake/local/lib/python2.7/site-packages/coffee/__init__.pyc to the initial query.

AttributeError: type object 'petsc4py.PETSc.Sys' has no attribute 'registerCitation'

Can you try doing: firedrake-update --rebuild (Passing any PETSc options you previously did when using firedrake-install) Lawrence

Sure ________________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Homolya, Miklós <m.homolya14@imperial.ac.uk> Sent: 29 January 2016 11:48 To: firedrake Subject: Re: [firedrake] Still error after COFFEE / petsc update Can we see the .log and .err files? ________________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Gregory, Alastair <a.gregory14@imperial.ac.uk> Sent: 29 January 2016 11:30 To: firedrake Subject: Re: [firedrake] Still error after COFFEE / petsc update Thanks, I've done that, and it has gone back to it's original error... CompilationError: Command "['mpicc', '-std=c99', '-fPIC', '-Wall', '-march=native', '-O3', '-fno-ivopts', '-I/home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/petsc/include', '-I/home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/firedrake', '-I/home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/pyop2', '-msse', '-o', '/tmp/pyop2-cache-uid1000/af4e249f9c37fca833cbc5212bf91fd0_p7072.so.tmp', '/tmp/pyop2-cache-uid1000/af4e249f9c37fca833cbc5212bf91fd0_p7072.c', '-shared', '-L/home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/petsc/lib', '-Wl,-rpath,/home/alsgregory/Documents/PhD/Firedrake/firedrake/lib/python2.7/site-packages/petsc/lib', '-lpetsc', '-lm']" return error status 1. Unable to compile code Compile log in /tmp/pyop2-cache-uid1000/af4e249f9c37fca833cbc5212bf91fd0_p7072.log Compile errors in /tmp/pyop2-cache-uid1000/af4e249f9c37fca833cbc5212bf91fd0_p7072.err Many Thanks, Alastair ________________________________________ From: firedrake-bounces@imperial.ac.uk <firedrake-bounces@imperial.ac.uk> on behalf of Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> Sent: 29 January 2016 11:11 To: firedrake Subject: Re: [firedrake] Still error after COFFEE / petsc update

On 29 Jan 2016, at 10:39, Gregory, Alastair <a.gregory14@imperial.ac.uk> wrote:

I get /home/alsgregory/Documents/PhD/Firedrake/firedrake/local/lib/python2.7/site-packages/coffee/__init__.pyc to the initial query.

AttributeError: type object 'petsc4py.PETSc.Sys' has no attribute 'registerCitation'

Can you try doing: firedrake-update --rebuild (Passing any PETSc options you previously did when using firedrake-install) Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake