Low-level API Poisson equation #71

amartinhuertas · 2021-02-11T03:01:07Z

after some final touches (see issue #60 for more details), I think the Low-Level tutorial is ready to merge!

The only thing which is missing is the following observation:

https://github.com/gridap/Tutorials/blob/dev-tutorials/src/poisson_dev_fe.jl#L368

for which I do not have an answer yet. We can leave it there, remove it, or try to find the reason, answer and solve it if necessary.

What do you think?

* Added that HEX_AXIS will create n-cubes * Fixed minor typo

Dev tutorials

Minor changes

0.15 Documentation comments still pending to be adapted.

…p#master * Updated Manifest, among other, to point to Gridap#master

amartinhuertas · 2021-03-11T08:13:53Z

Hi @fverdugo ... I went over all your comments in regards to this PR. See #71 (comment) for more details.

I had the following issues:

I tried to put consecutive lines which I want in different code cells by putting a blank line among them, but it did not work. Do u know how to do this?
The usage of print_op_tree causes an error in the CI system. https://github.com/gridap/Tutorials/runs/2084255358?check_suite_focus=true#step:6:1 Have you ever seen this error?
I could not test whether Debugger works in JNs. My local installation is broken, and I do not want to fix it now because I am lecturing with JNs. Can you try this and comment at the begnining of the tutorial if this possibility exists?
The other points which are under the pending header are points which I did not actually know what you pretended I do with them.

fverdugo · 2021-03-11T09:14:16Z

Thanks! I'll take a look.

fverdugo · 2021-03-12T08:55:18Z

I tried to put consecutive lines which I want in different code cells by putting a blank line among them, but it did not work. Do u know how to do this?

Simply by adding an empty comment line between them. I.e.,

DomainStyle(Qₕ) == ReferenceDomain()
#
DomainStyle(Qₕ) == PhysicalDomain()

I could not test whether Debugger works in JNs. My local installation is broken, and I do not want to fix it now because I am lecturing with JNs. Can you try this and comment at the begnining of the tutorial if this possibility exists?

To simplify things (for us and for the reader), I would write the tutorial assuming that the reader will do it by executing the cells in the notebook (just like the other tutorials). If you need to show intermediate results, you can split the cells as commented above. I would recommend to use a debugger just as an optional step.

The usage of print_op_tree causes an error in the CI system. https://github.com/gridap/Tutorials/runs/2084255358?check_suite_focus=true#step:6:1 Have you ever seen this error?

I have never seen this error, but by looking at the implementation of print_op_tree in Gridap it seems that there is a bug:

https://github.com/gridap/Gridap.jl/blob/3e3b006b5046b628449c0053af4e5c82c5063111/src/Arrays/PrintOpTrees.jl#L34

It should be stdout instead of stdin, right?

The other points which are under the pending header are points which I did not actually know what you pretended I do with them.

The issue about spurious memory allocation still has to be further investigated...

fverdugo · 2021-03-12T08:56:31Z

Hi @amartinhuertas! please find my replay to your last questions above ☝️

fverdugo · 2021-03-12T09:22:41Z

Regarding the bug in print_op_tree gridap/Gridap.jl#563

trying to address without success

Rewrote the first passages taking into account the following remark " To simplify things (for us and for the reader), I would write the tutorial assuming that the reader will do it by executing the cells in the notebook (just like the other tutorials). "

corresponding to Gridap.jl git repo #master branch so that we have access to the following bug-fix: gridap/Gridap.jl#563

amartinhuertas · 2021-03-13T03:42:49Z

Simply by adding an empty comment line between them. I.e.,

Ok, I do not know why, but I though this was a dirty hack, and I was expecting a more sophisticated solution (e.g., an special markdown tag). I already followed this approach in 83f986d.

It should be stdout instead of stdin, right?

Yes. it should be stdout. I am now leveraging your bug-fix in this branch. Let us see whether this solves the problem.

The issue about spurious memory allocation still has to be further investigated...

Yes, but apart from this, there are still two additional comments without solution yet.

amartinhuertas · 2021-03-13T04:01:33Z

Regarding the bug in print_op_tree gridap/Gridap.jl#563

This solves the issue in the tutorials CI ! Great!

fverdugo · 2021-03-15T09:18:22Z

export FEBasis, BasisStyle, TestBasis and TrialBasis from FESpaces (but not from Gridap)

The definition of FEBasis will change in Gridap v0.16. FEBasis will be an abstract type, with SingleFieldFEBasis and MultiFieldFEBasis specializations. I expect to register Gridap v0.16 during this week. They will be exported from the corresponding modules.

The actual purpose of Broadcasting is allowing to write lazy_map(Broadcasting(*),a,b) instead of lazy_map((ai,bi)->ai.*bi,a,b). The main reason is syntactic sugar (even though there are a number of dispatches specialized for Broadcasting for performance reasons.)

This is just a minor comment.

amartinhuertas · 2021-03-16T04:47:37Z

Ok ... so the pull request can be accepted, right?

fverdugo · 2021-03-16T06:47:07Z

Ok ... so the pull request can be accepted, right?

By looking at the Manifest, it seems that this PR relies on an unregistered version of Gridap. I'd wait until we release Gridap 0.15.3 with the patch related to the print_op_tree and change the Manifest here accordingly.

amartinhuertas · 2021-03-16T07:00:51Z

By looking at the Manifest, it seems that this PR relies on an unregistered version of Gridap.

Yeah, true. I should remove the Manifest.toml from the github repo.

I'd wait until we release Gridap 0.15.3 with the patch related to the print_op_tree and change the Manifest here accordingly.

Ok. Let us wait until then. Are we waiting for a particular event in order to release Gridap 0.15.3? If not, I can help to prepare this new release.

fverdugo · 2021-03-16T07:08:22Z

Ok. Let us wait until then. Are we waiting for a particular event in order to release Gridap 0.15.3? If not, I can help to prepare this new release.

Perfect if you can release this!

The only part missing is to add a couple of entries in the NEWS.md related with the last PRs, move to 0.15.3 in the Project.toml, check that all tests pass and release. See also https://github.com/gridap/Gridap.jl/wiki/How-to-register-a-julia-package#specific-steps-to-registering-gridap

amartinhuertas · 2021-03-16T08:39:29Z

The only part missing is to add a couple of entries in the NEWS.md related with the last PRs

Looking at the PRs accepted since the last release (0.15.2), I see (ordered by PR id, not chronologically): #553, #555, #556, #559, #563, #564. If this is the case, we should add 6 entries to the NEWS.md file (not actually a couple), right? On the other hand ... are all these minor release patches?

fverdugo · 2021-03-16T08:45:47Z

Yes, sorry. We usually only include the most relevant changes in NEWS.md, it is not needed to include all PRs.

In this case, I would mention that 1) we have fixed a bug in print_op_tree and 2) that the cell map in meshes of linear simplices is now an array of affine maps, which allows one to compute laplacians of the shape functions among other things.

amartinhuertas · 2021-03-16T09:10:24Z

Ok, thanks! PR requested in gridap/Gridap.jl#566

amartinhuertas · 2021-03-16T12:10:48Z

@fverdugo ... all tests passed with Gridap 0.15.3 (new release). I think the PR is ready to merge.

fverdugo

A couple of minor comments and we are ready to go!

fverdugo · 2021-03-16T14:44:50Z

.vscode/launch.json

@@ -0,0 +1,17 @@
+{


Perhaps we can add this file to .gitignore

It was already in .gitignore. Possible added accidentally into the repository before was in gitignore. I have removed the file.

fverdugo · 2021-03-16T14:45:47Z

Project.toml

@@ -15,7 +16,6 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"

 [compat]
-Gridap = "0.15"


Please, do not remove Gridap from the compat section. Use Gridap 0.15.3 since this is the version that has the bugfix we need.

Ok, Added. But I was not aware that I had removed it ... perhaps it was the package manager automatically or something like that?

fverdugo · 2021-03-17T06:45:15Z

Hi @amartinhuertas. Thanks for the changes.

Just a question, what is dev/Gridap for? Do we need it?

amartinhuertas · 2021-03-17T07:19:29Z

Just a question, what is dev/Gridap for? Do we need it?

I dont think so. Removed. You have 100 eyes!

santiagobadia and others added 30 commits August 12, 2020 16:07

Poisson for devs

1b0a2c0

Added FillArrays

60ea66e

Added comments to poisson_dev_fe

a276fd7

Added new version of dev-tutorial w/ Francesc comments

f759c55

Merge branch 'master' of github.com:gridap/Tutorials into dev-tutorials

c665fa9

changed build

5ae9643

Minor changes

e7978c4

* Added that HEX_AXIS will create n-cubes * Fixed minor typo

fix typo

3807b7e

.gitignore change

b48e48e

passed aspell to poisson_dev_fe

709e3a2

poisson_dev_fe fixed more typos and a couple of line breaks

5bb5746

poisson_dev_fe added a couple of clarifying comments and links

2bcf256

Update poisson_dev_fe.jl

d02290a

Update poisson_dev_fe.jl

3837445

Merge pull request #42 from ericneiva/dev-tutorials

456e514

Dev tutorials

Merge branch 'dev-tutorials' into minor_changes_to_tutorials_dev

f1a94a9

Merge pull request #39 from gridap/minor_changes_to_tutorials_dev

cc9ae38

Minor changes

Minor changes to poisson dev tutorial

b51c67f

Updating Project toml to Gridap 0.14

3aec7ea

Some (partial) changes to let poisson_dev_fe work with Gridap 0.14.X

e8bd33c

Major steps towards a Poisson driver for developers adapted to Gridap

49d7516

0.15 Documentation comments still pending to be adapted.

First working version of Poisson tutorial for developers

ffe3949

Commented out Manifest.toml in .gitignore temporarily

4347336

Added Manifest.toml temporarily

7f596c9

More work into poisson dev fe

feca728

* Adapted Poisson tutorial for developers to latest renaming in Grida…

1427da1

…p#master * Updated Manifest, among other, to point to Gridap#master

More work into Poisson driver for developers

0d1c731

More work into Poisson tutorial for developers

1914943

More work into poisson_dev_fe.jl

ff70681

More work into poisson_dev_fe.jl

57bf8ef

amartinhuertas added 3 commits March 13, 2021 14:15

Actually addressed what d3d1658 was

83f986d

trying to address without success

[poisson_dev_fe]

847ea7c

Rewrote the first passages taking into account the following remark " To simplify things (for us and for the reader), I would write the tutorial assuming that the reader will do it by executing the cells in the notebook (just like the other tutorials). "

Temporarily replaced JuliaRegistries Gridap version by the one

3bab6f5

corresponding to Gridap.jl git repo #master branch so that we have access to the following bug-fix: gridap/Gridap.jl#563

amartinhuertas added 2 commits March 16, 2021 22:13

Deleted Manifest.toml

c8a43d7

Re-ignoring Manifest.toml

54b761f

fverdugo requested changes Mar 16, 2021

View reviewed changes

amartinhuertas added 2 commits March 17, 2021 14:54

Removed .vscode/launch.json

1e4c8af

Added Gridap 0.15.3 in the compat section

94508a9

Removed dev/Gridap

441b719

fverdugo approved these changes Mar 17, 2021

View reviewed changes

fverdugo merged commit 388a329 into master Mar 17, 2021

fverdugo deleted the dev-tutorials branch March 17, 2021 07:37

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Low-level API Poisson equation #71

Low-level API Poisson equation #71

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Low-level API Poisson equation #71

Low-level API Poisson equation #71

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