Re: [firedrake] 1+1 dimensional hierarchical meshes and function spaces
On 15 December 2014 at 23:00, Eike Mueller <e.mueller@bath.ac.uk> wrote:
Hi Lawrence,
actually, it looks like that patch has already been integrated into the petsc branch you recommend below. Building petsc and petsc4py works fine with that branch. Which pyop2 branch do I want to use? Still local-par_loop? I guess I have to update ffc, ufl etc. at the moment I haven't got firedrake to work yet, it says the pyop2 and firedrake versions are not compatible.
Thanks,
Eike
PS: Are there actually any instructions on the web on obtaining and building coffee? I lost Fabio's email, I googled and figured it out myself now, but the repository is a bit hidden...
It's buried in the PyOP2 installation page <http://www.firedrakeproject.org/obtaining_pyop2.html>, on the Firedrake website. Quite obvious from the table of contents, somewhat less obvious once you scroll further down.
--
Dr Eike Hermann Mueller Research Associate (PostDoc)
Department of Mathematical Sciences University of Bath Bath BA2 7AY, United Kingdom
+44 1225 38 5633 <+44%201225%2038%205633> e.mueller@bath.ac.uk <http://people.bath.ac.uk/em459/>http://people.bath.ac.uk/em459/
On 9 Dec 2014, at 09:31, Lawrence Mitchell < lawrence.mitchell@imperial.ac.uk> wrote:
On 9 Dec 2014, at 09:13, Eike Mueller <e.mueller@bath.ac.uk> wrote:
hanks, I will give it a go. Just looking at my petsc, I'm currently using the master and have the applied the patch below (which you sent me on 11 Oct). Do I still need this, or has this been integrated into the petsc branch you mention?
Yes, I think so.
Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
Hi Andrew, ok, thanks! Sorry, I didn't spot it, but looking at it now confirms that I did the right thing to build it. Eike -- Dr Eike Hermann Mueller Research Associate (PostDoc) Department of Mathematical Sciences University of Bath Bath BA2 7AY, United Kingdom +44 1225 38 5633 e.mueller@bath.ac.uk http://people.bath.ac.uk/em459/
On 15 Dec 2014, at 23:03, Andrew McRae <a.mcrae12@imperial.ac.uk> wrote:
On 15 December 2014 at 23:00, Eike Mueller <e.mueller@bath.ac.uk> wrote: Hi Lawrence,
actually, it looks like that patch has already been integrated into the petsc branch you recommend below. Building petsc and petsc4py works fine with that branch. Which pyop2 branch do I want to use? Still local-par_loop? I guess I have to update ffc, ufl etc. at the moment I haven't got firedrake to work yet, it says the pyop2 and firedrake versions are not compatible.
Thanks,
Eike
PS: Are there actually any instructions on the web on obtaining and building coffee? I lost Fabio's email, I googled and figured it out myself now, but the repository is a bit hidden...
It's buried in the PyOP2 installation page, on the Firedrake website. Quite obvious from the table of contents, somewhat less obvious once you scroll further down.
--
Dr Eike Hermann Mueller Research Associate (PostDoc)
Department of Mathematical Sciences University of Bath Bath BA2 7AY, United Kingdom
+44 1225 38 5633 e.mueller@bath.ac.uk http://people.bath.ac.uk/em459/
On 9 Dec 2014, at 09:31, Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk> wrote:
On 9 Dec 2014, at 09:13, Eike Mueller <e.mueller@bath.ac.uk> wrote: hanks, I will give it a go. Just looking at my petsc, I'm currently using the master and have the applied the patch below (which you sent me on 11 Oct). Do I still need this, or has this been integrated into the petsc branch you mention?
Yes, I think so.
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
Hi, I just tried it again, when I attempt to pull the local-par_loop branch I get: eikemueller@138-38-166-201 $ git pull Your configuration specifies to merge with the ref 'local-par_loop' from the remote, but no such ref was fetched. so maybe the remote branch has been deleted? I would also like to add the changes re. linking to additional libraries (LAPACK, BLAS) during the JIT compilation to PyOP2 (so far only a local patch). Can I go ahead and create a branch based on master and then put in a pull request? I now use the PyOP2 master. However, I get the following error when loading firedrake: Python 2.7.8 (default, Jul 13 2014, 17:11:32) [GCC 4.2.1 Compatible Apple LLVM 5.1 (clang-503.0.40)] on darwin Type "help", "copyright", "credits" or "license" for more information.
import firedrake Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/eikemueller/PostDocBath/EllipticSolvers/firedrake/firedrake/__init__.py", line 25, in <module> from pyop2.logger import set_log_level, info_red, info_green, info_blue, log # noqa File "/Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/__init__.py", line 9, in <module> from op2 import * File "/Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/op2.py", line 39, in <module> import base File "/Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/base.py", line 57, in <module> from coffee.base import Node ImportError: No module named base
If I try to import the problematic module, I get:
import base Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/base.py", line 45, in <module> from configuration import configuration File "/Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/configuration.py", line 40, in <module> from exceptions import ConfigurationError ImportError: cannot import name ConfigurationError
Thanks, 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@bath.ac.uk http://people.bath.ac.uk/em459/
On 15 Dec 2014, at 23:03, Andrew McRae <a.mcrae12@imperial.ac.uk> wrote:
On 15 December 2014 at 23:00, Eike Mueller <e.mueller@bath.ac.uk <mailto:e.mueller@bath.ac.uk>> wrote: Hi Lawrence,
actually, it looks like that patch has already been integrated into the petsc branch you recommend below. Building petsc and petsc4py works fine with that branch. Which pyop2 branch do I want to use? Still local-par_loop? I guess I have to update ffc, ufl etc. at the moment I haven't got firedrake to work yet, it says the pyop2 and firedrake versions are not compatible.
Thanks,
Eike
PS: Are there actually any instructions on the web on obtaining and building coffee? I lost Fabio's email, I googled and figured it out myself now, but the repository is a bit hidden...
It's buried in the PyOP2 installation page <http://www.firedrakeproject.org/obtaining_pyop2.html>, on the Firedrake website. Quite obvious from the table of contents, somewhat less obvious once you scroll further down.
--
Dr Eike Hermann Mueller Research Associate (PostDoc)
Department of Mathematical Sciences University of Bath Bath BA2 7AY, United Kingdom
+44 1225 38 5633 <tel:+44%201225%2038%205633> e.mueller@bath.ac.uk <mailto:e.mueller@bath.ac.uk> <http://people.bath.ac.uk/em459/>http://people.bath.ac.uk/em459/ <http://people.bath.ac.uk/em459/>
On 9 Dec 2014, at 09:31, Lawrence Mitchell <lawrence.mitchell@imperial.ac.uk <mailto:lawrence.mitchell@imperial.ac.uk>> wrote:
On 9 Dec 2014, at 09:13, Eike Mueller <e.mueller@bath.ac.uk <mailto:e.mueller@bath.ac.uk>> wrote:
hanks, I will give it a go. Just looking at my petsc, I'm currently using the master and have the applied the patch below (which you sent me on 11 Oct). Do I still need this, or has this been integrated into the petsc branch you mention?
Yes, I think so.
Lawrence _______________________________________________ firedrake mailing list firedrake@imperial.ac.uk <mailto:firedrake@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/firedrake <https://mailman.ic.ac.uk/mailman/listinfo/firedrake>
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi Eike, On 16/12/14 08:57, Eike Mueller wrote:
Hi,
I just tried it again, when I attempt to pull the local-par_loop branch I get:
eikemueller@138-38-166-201 $ git pull Your configuration specifies to merge with the ref 'local-par_loop' from the remote, but no such ref was fetched.
so maybe the remote branch has been deleted?
I would also like to add the changes re. linking to additional libraries (LAPACK, BLAS) during the JIT compilation to PyOP2 (so far only a local patch). Can I go ahead and create a branch based on master and then put in a pull request?
Please base your changes on the columnwise_kernels branch (which adds support for iterating over the base set of an extruded set: you need this for your columnwise inverses, I think), and then propose it as a pull request.
I now use the PyOP2 master. However, I get the following error when loading firedrake:
Python 2.7.8 (default, Jul 13 2014, 17:11:32) [GCC 4.2.1 Compatible Apple LLVM 5.1 (clang-503.0.40)] on darwin Type "help", "copyright", "credits" or "license" for more information.
import firedrake Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/eikemueller/PostDocBath/EllipticSolvers/firedrake/firedrake/__init__.py",
line 25, in <module>
from pyop2.logger import set_log_level, info_red, info_green, info_blue, log # noqa File "/Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/__init__.py",
line 9, in <module> from op2 import * File
"/Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/op2.py",
line 39, in <module>
import base File "/Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/base.py",
line 57, in <module>
from coffee.base import Node ImportError: No module named base
Please remove the directory /Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/coffee and things should work again, I hope. Cheers, Lawrence -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with undefined - http://www.enigmail.net/ iQEcBAEBAgAGBQJUj/zVAAoJECOc1kQ8PEYv6+UH/14O1WZpHjT22B7Fvino5KBS gtBq5QhKlq4RYIe7qhAuJJE8s29AsDWfXw/ii+PyUclH5FfP5OAHNQBtsWydjGGc Vrg5oIonmDY8fczhwdRo/hR7H+ociyaS0Ru4YSc9FUR8Qph/EJ3GIA8Gx3s9v3K4 Funykrz4OBUFwgK9oWtB+QMx+YEGy7XPwbsdAKZm7je0Ln8N+avD1h1OS5jbUQfl q9j0aUFbiwaudmNVPq3zGj1lx6KIOBrOhLIGurRemX9OBcImabBf723Qiiq2YCl+ zAGffGGlIiH/mXpOV2waO9NjL/FI9Jv/sxJ1xXXRm+d7DjSluy0VryuPIS4wsCU= =Q8ej -----END PGP SIGNATURE-----
Hi Lawrence,
Please base your changes on the columnwise_kernels branch (which adds support for iterating over the base set of an extruded set: you need this for your columnwise inverses, I think), and then propose it as a pull request.
I created a new branch with the fix, but don’t have permissions to push it: eikemueller@138-38-166-201 $ git push -u origin link_libraries_in_kernels remote: Permission to OP2/PyOP2.git denied to eikehmueller. fatal: unable to access 'https://github.com/OP2/PyOP2.git/': The requested URL returned error: 403
Please remove the directory
/Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/coffee
and things should work again, I hope.
yes, that fixes it. Many thanks, Eike
On 16/12/14 10:23, Eike Mueller wrote:
Hi Lawrence,
Please base your changes on the columnwise_kernels branch (which adds support for iterating over the base set of an extruded set: you need this for your columnwise inverses, I think), and then propose it as a pull request.
I created a new branch with the fix, but don’t have permissions to push it:
eikemueller@138-38-166-201 $ git push -u origin link_libraries_in_kernels remote: Permission to OP2/PyOP2.git denied to eikehmueller. fatal: unable to access 'https://github.com/OP2/PyOP2.git/': The requested URL returned error: 403
I've given you access, accept the invite and you should be able to push. Florian
Please remove the directory
/Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/coffee
and things should work again, I hope.
yes, that fixes it.
Many thanks,
Eike
Hi Florian and Lawrence, thanks for adding me! I now pushed my changes directly to the columnwise_kernel branch, hope that was ok. But the changes I made still do not work, in particular I can’t access the variable self._kernel._libs in host.py (line 714), even though I added it in the same way as _cpp in base.by (line 3630). I have to put in the hack just following line 715 if I want it to work in my case. This is very odd, since I checked that self._kernel is of type pyop2.host.Kernel (Pdb) print type(self._kernel) <class 'pyop2.host.Kernel’> which is derived from pyop2.base.Kernel Thanks, 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@bath.ac.uk http://people.bath.ac.uk/em459/
On 16 Dec 2014, at 10:33, Florian Rathgeber <florian.rathgeber@imperial.ac.uk> wrote:
On 16/12/14 10:23, Eike Mueller wrote:
Hi Lawrence,
Please base your changes on the columnwise_kernels branch (which adds support for iterating over the base set of an extruded set: you need this for your columnwise inverses, I think), and then propose it as a pull request.
I created a new branch with the fix, but don’t have permissions to push it:
eikemueller@138-38-166-201 $ git push -u origin link_libraries_in_kernels remote: Permission to OP2/PyOP2.git denied to eikehmueller. fatal: unable to access 'https://github.com/OP2/PyOP2.git/': The requested URL returned error: 403
I've given you access, accept the invite and you should be able to push.
Florian
Please remove the directory
/Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/coffee
and things should work again, I hope.
yes, that fixes it.
Many thanks,
Eike
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
On 16/12/14 10:52, Eike Mueller wrote:
Hi Florian and Lawrence,
thanks for adding me! I now pushed my changes directly to the columnwise_kernel branch, hope that was ok. But the changes I made still do not work, in particular I can’t access the variable
self._kernel._libs
in host.py (line 714), even though I added it in the same way as _cpp in base.by (line 3630). I have to put in the hack just following line 715 if I want it to work in my case. This is very odd, since I checked that self._kernel is of type pyop2.host.Kernel
(Pdb) print type(self._kernel) <class 'pyop2.host.Kernel’>
which is derived from pyop2.base.Kernel
By "cannot access", do you mean you get an AttributeError? Or not the value you expect? Have you cleared relevant caches? Florian
Thanks,
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@bath.ac.uk <mailto:e.mueller@bath.ac.uk> http://people.bath.ac.uk/em459/
On 16 Dec 2014, at 10:33, Florian Rathgeber <florian.rathgeber@imperial.ac.uk <mailto:florian.rathgeber@imperial.ac.uk>> wrote:
On 16/12/14 10:23, Eike Mueller wrote:
Hi Lawrence,
Please base your changes on the columnwise_kernels branch (which adds support for iterating over the base set of an extruded set: you need this for your columnwise inverses, I think), and then propose it as a pull request.
I created a new branch with the fix, but don’t have permissions to push it:
eikemueller@138-38-166-201 $ git push -u origin link_libraries_in_kernels remote: Permission to OP2/PyOP2.git denied to eikehmueller. fatal: unable to access 'https://github.com/OP2/PyOP2.git/': The requested URL returned error: 403
I've given you access, accept the invite and you should be able to push.
Florian
Please remove the directory
/Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/coffee
and things should work again, I hope.
yes, that fixes it.
Many thanks,
Eike
Hi Florian, arrgh! It was the caches again... After running scripts/firedrake-clean it did work. Thanks, 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@bath.ac.uk http://people.bath.ac.uk/em459/
On 16 Dec 2014, at 10:58, Florian Rathgeber <florian.rathgeber@imperial.ac.uk> wrote:
On 16/12/14 10:52, Eike Mueller wrote:
Hi Florian and Lawrence,
thanks for adding me! I now pushed my changes directly to the columnwise_kernel branch, hope that was ok. But the changes I made still do not work, in particular I can’t access the variable
self._kernel._libs
in host.py (line 714), even though I added it in the same way as _cpp in base.by (line 3630). I have to put in the hack just following line 715 if I want it to work in my case. This is very odd, since I checked that self._kernel is of type pyop2.host.Kernel
(Pdb) print type(self._kernel) <class 'pyop2.host.Kernel’>
which is derived from pyop2.base.Kernel
By "cannot access", do you mean you get an AttributeError? Or not the value you expect? Have you cleared relevant caches?
Florian
Thanks,
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@bath.ac.uk <mailto:e.mueller@bath.ac.uk> http://people.bath.ac.uk/em459/
On 16 Dec 2014, at 10:33, Florian Rathgeber <florian.rathgeber@imperial.ac.uk <mailto:florian.rathgeber@imperial.ac.uk>> wrote:
On 16/12/14 10:23, Eike Mueller wrote:
Hi Lawrence,
Please base your changes on the columnwise_kernels branch (which adds support for iterating over the base set of an extruded set: you need this for your columnwise inverses, I think), and then propose it as a pull request.
I created a new branch with the fix, but don’t have permissions to push it:
eikemueller@138-38-166-201 $ git push -u origin link_libraries_in_kernels remote: Permission to OP2/PyOP2.git denied to eikehmueller. fatal: unable to access 'https://github.com/OP2/PyOP2.git/': The requested URL returned error: 403
I've given you access, accept the invite and you should be able to push.
Florian
Please remove the directory
/Users/eikemueller/PostDocBath/EllipticSolvers/PyOP2/pyop2/coffee
and things should work again, I hope.
yes, that fixes it.
Many thanks,
Eike
_______________________________________________ firedrake mailing list firedrake@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/firedrake
participants (4)
-
Andrew McRae
-
Eike Mueller
-
Florian Rathgeber
-
Lawrence Mitchell