installation using Docker #96

DavideBaroliUniLu · 2016-09-21T14:33:50Z

In this pull request, I create a docker container based on phusion image:0.9.19.
The docker-exec is use to launch the docker machine with X11 enable. For the structure of dockerfile separation I follow the FeNiCs one.
For any reference to docker, you can see "Containers for portable, productive and performant scientific computing" ([(http://arxiv.org/abs/1608.07573])

mtezzele

I am not used to docker. Can you provide a simple "how to use it", please?
Moreover we have to figure out why the linux tests are failing...

mtezzele · 2016-09-21T14:51:38Z

dockerfiles/dev-env-base/.bash_history

@@ -0,0 +1,2 @@
+ls


Is this file necessary?

No it is not necessary.
The only necessary is the Dockerfile in the two subfolder and the docker-exec.

mtezzele · 2016-09-21T14:53:10Z

dockerfiles/base/Dockerfile

+# experience, namely; creating the user PyGeM, setting up the users
+# environment and the default entry point and cmds.
+#
+# Authors:


Please remove the list of authors. We do not follow this style and github easily shows the author of each file.

mtezzele · 2016-09-21T14:53:41Z

dockerfiles/dev-env-base/Dockerfile

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+# Author Davide Baroli <davide.baroli@uni.lu>


Please remove the list of authors. We do not follow this style and github easily shows the author of each file.

For style ok.

DavideBaroliUniLu · 2016-09-21T19:36:23Z

The dockerfile allows you to install a container with the environment and PyGeM as a virtual machine. So it aim is devote to distribute the code to everyone independently from the operator system of the local machine. It can be also used for installation on cluster.
How to use:

build the container
go in base folder
docker build --tag=pygem-base:phusion .
It compiles and creates the container, then you can push for instance on quay or dockerhub. (with a docker push)
go to dev-env
(pay attention on the first line of the file, "FROM " should be in accordance with the name of the base container )
docker build --tag=pygem-dev-env:phusion .
Again you can push on open pubblic (quay or dockerhub)
Finally to run the image
I put the docker-exec file ( it allows to use X11 - so the gui )
./docker-exec pygem-dev-env:phusion
Then the user can easy use PyGeM without any "requirement" or difficulty in installation.
In addition if you want to shared document/code with the container you can run
docker run -v $pwd:/home/PyGeM/shared -ti pygem-dev-env:phusion

mtezzele · 2016-09-22T09:44:08Z

Ok thank you very much. It is a very useful PR. There is still the author in dockerfiles/base/Dockerfile file. When you are able to fix docker with travis I will merge. If you need help just ask.

mtezzele · 2016-09-22T09:45:19Z

It would be great if you could add the "how to use docker with pygem" in the readme file.

DavideBaroliUniLu · 2016-09-22T09:51:59Z

I am adding the docker build and run in .travis.ylm.
I am also pushing the image to
docker.io/pygemdocker/pygem--base:latest
docker.io/pygemdocker/pygem-env-base:latest
How to use docker with pygem with pre-compiled image?
docker run -ti --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix docker.io/pygemdocker/pygem-env-base:latest
To share a folder that contain the geometry files or your code:
docker run -ti --rm -e DISPLAY=$DISPLAY -v /tmp/.X11-unix:/tmp/.X11-unix -v $PWD:/home/PyGeM/shared pygemdocker/pygem-env-base:latest

…738 on travis-ci)

DavideBaroliUniLu · 2016-09-22T11:19:05Z

The travis compiles fine. But I am still pushing on docker.io the second container.
you can check the uploading in [https://cloud.docker.com/pygemdocker/repository/list]

mtezzele · 2016-09-22T11:46:19Z

What is the difference between the base container and the env-base?

Remember to remove the author in the base file.

In the travis file I think some code is replicated in the case of a linux machine. The docker image has everything we need to test the package right? So we do not have to install everything twice. Maybe an if statement for the osx case will fix it. Otherwise I just did not get docker entirely and I apologize :)

If you add the how to in the readme I will merge (I think the section Dependencies and installation will fit the purpose). Thanks!

DavideBaroliUniLu · 2016-09-22T14:25:06Z

Base container consists of : pulling phusion (light version of ubuntu 16.04) and set the permission to user PyGeM.
Dev-Env depend on Base container and consist of : dependency library + PyGeM.
Can we specify multiple travis file ? One for classical installation based on conda and one for docker ( just pulling from a repository hosting on cloud as in deal.ii or fenics)? I push the dockerfiles since a developer can adapt them to his personal requirement.
If the user has win/mac/linux and install docker, then thanks to docker potentiality one has a virtual enviroment with all correct dependency and same performance of full installation.
The only issue is that it is impossible now to test "via travis" the build of docker machine.

luca-heltai · 2016-09-22T14:28:46Z

Actually, it could be possible to simply let travis build the docker machine, use it to do the testing, and then once building the docker and testing have passed, deploy the newly built docker image to docker-hub.

mtezzele · 2016-10-10T09:19:07Z

@DavideBaroliUniLu are you able to implement the suggestion of Luca?

…rsion of sip since the default version selected by conda has incompatible api with qt4

DavideBaroliUniLu · 2016-10-10T14:04:41Z

I am running the deployment with dockerhub at "[https://hub.docker.com/r/pygemdocker/pygem/]".
I add 2 modification to the travis.ylm file:

specification of library version
substitution of the docker building in travis.ylm by running one hosted on dockerhub.org.

mtezzele · 2016-10-10T14:08:02Z

I fixed 5 minutes ago the compatibility with the new version of python-occ. A rebase should fix it.

* # This is a combination of 4 commits. # The first commit's message is: tests added for gui init # The 2nd commit message will be skipped: # tests added for gui init # The 3rd commit message will be skipped: # test for the main part of gui code # The 4th commit message will be skipped: # test for the main part of gui code * trying to solve conflicts * removed pillow from packages * removed pillow from travis installation

… it more general and fast

mathLab#87) changed the order of the points in the plot of bounding box

* More tests for radial and doc * one more test for beckert

* improved performance in freeform (~25%) * fixed bug and improved flexibility in unvhandler * new write comparison in unv tests

…/PyGeM into dbaroli/docker

DavideBaroliUniLu · 2016-10-11T12:58:49Z

I perform both rebase with squash. Now it is pretty better.

mtezzele · 2016-10-11T13:41:54Z

I don't think you did. See here. You have to rebase with respect to the upstream/master. Ideally the rebase should has the following output: your branch (the yellow one) has to start from my last commit merged. Something like this should work: git rebase -i mathlab/master. See here for more details.

DavideBaroliUniLu · 2016-10-11T14:46:52Z

You have right. I get your point.
I have only clean my branch history. But I have this error in rebase operation with respect to the master.
Could not apply 6640a29... write method in the RBFParameters class and tests.
I have also fetch it.
What i notice is : the log with pick is back with respect to one on matlab/master during the rebase opereation. Do you know how to solve it ?

mtezzele · 2016-10-11T16:26:05Z

The problem is that you have merged this branch with another one that is much older than yours. The rebase now produces conflicts. The ugly but effective way is to close this PR, then you have to open another PR with only one commit of the new files you added/edited in this PR. After this I will links the two PR in order to have some history.

add dockerfiles

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DavideBaroliUniLu changed the title ~~installation using Docker vm~~ installation using Docker Sep 21, 2016

mtezzele reviewed Sep 21, 2016

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DavideBaroliUniLu added 6 commits September 21, 2016 21:43

remove .bash_history

9908cfd

add testing of dockerfile in travis

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adding docker sudo permission

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requirement for docker services

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root permission move to run

81cc562

small bug

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spelling error

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DavideBaroliUniLu closed this Sep 22, 2016

DavideBaroliUniLu reopened this Sep 22, 2016

DavideBaroliUniLu added 2 commits September 22, 2016 12:09

move docker-run for README purpose, pulling from docker.io

a105884

update travis, docker command in travis work only on linux ( issue #5…

daf2b36

…738 on travis-ci)

fullfill the request;clean unused file

66cfc12

DavideBaroliUniLu added 3 commits October 10, 2016 15:48

make one Dockerfile

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pushing the Dockerfile

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update travis.yml pulling from dockerhub autobuild-deployment; add ve…

0b570ef

…rsion of sip since the default version selected by conda has incompatible api with qt4

specify the tag

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fsalmoir and others added 23 commits October 11, 2016 14:52

readme updated with rbf and gui

845fa1b

removed the repeated gui paragraph

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now we can plot iges, vtk and stl on the gui during the execution

5fb2c36

some documentation and tests added for the gui new features

8011b67

some documentation and tests added for the gui new features

df51043

changed picture and caption of gui in readme

ecdd9ad

now matplotlib figures are centered on the geometry

7e91fba

changed some lines of code in plot method of vtkhandler class to make…

cb05388

… it more general and fast

RBF class and documentation

210ff58

minor fixes

12f939b

test rbf

84e1593

changed the order of the points in the plot of bounding box cause it … (

29925af

mathLab#87) changed the order of the points in the plot of bounding box

More tests for radial and doc (mathLab#88)

dd90813

* More tests for radial and doc * one more test for beckert

pylint fixes and workaround for mac users

39bdcea

utility to plot rbf control points

2ac1b4d

unvhandler fixes and freeform performances improved (mathLab#91)

61fdaa6

* improved performance in freeform (~25%) * fixed bug and improved flexibility in unvhandler * new write comparison in unv tests

tutorial for rbf and documentation

1c6f850

added link to youtube video tutorial

bdf5788

nautical example added

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add dockerfiles

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update travis.yml with docker running; update README.md

ba79d92

Merge branch 'dbaroli/docker' of https://github.com/DavideBaroliUniLu…

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…/PyGeM into dbaroli/docker

DavideBaroliUniLu closed this Oct 11, 2016

DavideBaroliUniLu reopened this Oct 11, 2016

DavideBaroliUniLu closed this Oct 11, 2016

		@@ -0,0 +1,50 @@
		# Author Davide Baroli <davide.baroli@uni.lu>

installation using Docker #96

installation using Docker #96

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