Trouble with Fenics docker notebook on Mac OSX after updating docker

matt.m...@gmail.com

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Jul 29, 2016, 1:25:14 PM7/29/16

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THANKS YOU! to all responsible for Fenics and most recently making the use of Jupyter notebooks possible.

I am a novice to Fenics, but an experienced user of Jupyter notebooks.

Using Fenics in the Jupyter notebook has been going well for about a month.

Wanting to take advantage of the new matplotlib plotting capabilities I updated using

fenicsproject pull stable

This went fine.

I then created and launched a notebook

fenicsproject notebook mycyl

fenicsproject start mycyl

I then opened web browser at the indicated URL, saw my usual list of files and opened a notebook that worked previously.

There were two problems.

1. The file was opened as “Read only” (see screenshot)

This is different behavior than previously.

2. The notebook gave an error.

I ran an example from the Tutorial:

from dolfin import *

#from mshr import *

import numpy as np

from matplotlib import cm

import matplotlib.pyplot as plt

%matplotlib inline

# Create mesh and define function space

mesh = UnitSquareMesh(20,20)

V = FunctionSpace(mesh, 'Lagrange', 1)

# Define boundary conditions

u0 = Expression('1 + x[0]*x[0] + 2*x[1]*x[1]')

def u0_boundary(x, on_boundary):

return on_boundary

bc = DirichletBC(V, u0, u0_boundary)

# Define variational problem

u = TrialFunction(V)

v = TestFunction(V)

f = Constant(-6.0)

a = inner(nabla_grad(u), nabla_grad(v))*dx

L = f*v*dx

# Compute solution

u = Function(V)

solve(a == L, u, bc)

# Plot solution and mesh

#plot(mesh)

plot(u)

# Dump solution to file in VTK format

# file = File("poisson.pvd")

# file << u

# Hold plot

#interactive()

and got the following error message:

RuntimeErrorTraceback (most recent call last)
<ipython-input-4-651fcf6b9953> in <module>()
     10 V = FunctionSpace(mesh, 'Lagrange', 1)
     11 # Define boundary conditions
---> 12 u0 = Expression('1 + x[0]*x[0] + 2*x[1]*x[1]')
     13 def u0_boundary(x, on_boundary):
     14     return on_boundary

/home/fenics/build/lib/python2.7/site-packages/dolfin/functions/expression.pyc in __new__(cls, cppcode, *args, **kwargs)
    651         cpp_base, members = compile_expressions([cppcode],
    652                                                 [generic_function_members],
--> 653                                                 mpi_comm=kwargs.get("mpi_comm"))
    654         cpp_base, members = cpp_base[0], members[0]
    655 

/home/fenics/build/lib/python2.7/site-packages/dolfin/compilemodules/expressions.pyc in compile_expressions(cppargs, generic_function_members, mpi_comm)
    216         code_snippets), classnames, additional_declarations="\n".join(\
    217                                                      additional_declarations),
--> 218                                                  mpi_comm=mpi_comm)
    219 
    220     return expression_classes, all_members

/home/fenics/build/lib/python2.7/site-packages/dolfin/compilemodules/expressions.pyc in compile_expression_code(code, classnames, module_name, additional_declarations, mpi_comm)
    144     compiled_module = compile_extension_module(\
    145         code, additional_declarations=additional_declarations, \
--> 146         mpi_comm=mpi_comm)
    147 
    148     # Get the compiled class

/home/fenics/build/lib/python2.7/site-packages/dolfin/compilemodules/jit.pyc in mpi_jit(*args, **kwargs)
     63         # Just call JIT compiler when running in serial
     64         if MPI.size(mpi_comm) == 1:
---> 65             return local_jit(*args, **kwargs)
     66 
     67         # Compile first on process 0

/home/fenics/build/lib/python2.7/site-packages/dolfin/compilemodules/compilemodule.pyc in compile_extension_module(code, module_name, additional_declarations, additional_system_headers, mpi_comm, **instant_kwargs)
    427         # Check that the swig version of the compiled module is the same as
    428         # dolfin was compiled with
--> 429         check_swig_version(compiled_module)
    430         return compiled_module
    431 

/home/fenics/build/lib/python2.7/site-packages/dolfin/compilemodules/compilemodule.pyc in check_swig_version(compiled_module)
    260                          "version is not the same as extension module swig "\
    261                          "version: '%s' != '%s' " % \
--> 262                          (cpp.__swigversion__, compiled_module.swigversion))
    263 
    264 @mpi_jit_decorator

/home/fenics/build/lib/python2.7/site-packages/dolfin/cpp/common.pyc in dolfin_error(location, task, reason)
   2897 
   2898     """
-> 2899     return _common.dolfin_error(location, task, reason)
   2900 
   2901 def deprecation(feature, version_deprecated, message):

RuntimeError: 

*** -------------------------------------------------------------------------
*** DOLFIN encountered an error. If you are not able to resolve this issue
*** using the information listed below, you can ask for help at
***
***     fenics-...@googlegroups.com
***
*** Remember to include the error message listed below and, if possible,
*** include a *minimal* running example to reproduce the error.
***
*** -------------------------------------------------------------------------
*** Error:   Unable to compiling extension module.
*** Reason:  Incompatible swig versions detected. DOLFIN swig version is not the same as extension module swig version: '3.0.10' != '3.0.8' .
*** Where:   This error was encountered inside compilemodule.py.
*** Process: 0
*** 
*** DOLFIN version: 2016.1.0
*** Git changeset:  f4e22e59622b42182d16059f0212ddb1c6aa8712
*** -------------------------------------------------------------------------

Screen Shot 2016-07-29 at 10.09.58 AM.png

Jack Hale

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Jul 29, 2016, 1:43:43 PM7/29/16

to fenics-support

Hi Matt,

No problem glad it's been useful for you.

Can you try two things:

1) Clean your instant cache using fenicsproject clean-cache stable. SWIG has been upgraded in the latest container. We hold a persistent cache of compiled objects shared between containers but that cache breaks when updating.
2) Upgrade to the latest version of the fenicsproject script by using the same copy and paste line from the website you used to install. This should fix your file permissions issue. The image and the script should work in tandem to get permissions right. The ins and outs of this are quite complicated so no space to explain this here.
3) You may need to recreate your container using fenicsproject notebook.

Post back if it doesn't work.

matt.m...@gmail.com

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Jul 29, 2016, 2:18:43 PM7/29/16

to fenics-support

After moving into the directory for my project I did each of the following and they seemed to go fine.

fenicsproject clean-cache stable

curl -s https://get.fenicsproject.org | bash

fenicsproject notebook cyl

fenicsproject start cyl

All went well and I went to URL in browser, saw my list of files and launched the notebook.

1. The notebook is still “readonly"

2. When I run the notebook I got this *different* error shown below. In the terminal window there are many lines regarding FCC, compiling, reusing, caching, etc.

Calling FFC just-in-time (JIT) compiler, this may take some time.


IOErrorTraceback (most recent call last)
<ipython-input-2-641831270709> in <module>()
      1 # Create mesh and define function space
      2 mesh = UnitSquareMesh(20,20)
----> 3 V = FunctionSpace(mesh, 'Lagrange', 1)
      4 # Define boundary conditions
      5 u0 = Expression('1 + x[0]*x[0] + 2*x[1]*x[1]')

/home/fenics/build/lib/python2.7/site-packages/dolfin/functions/functionspace.pyc in __init__(self, *args, **kwargs)
    204                 self._init_from_ufl(*args, **kwargs)
    205             else:
--> 206                 self._init_convenience(*args, **kwargs)
    207 
    208     def _init_from_ufl(self, mesh, element, constrained_domain=None):

/home/fenics/build/lib/python2.7/site-packages/dolfin/functions/functionspace.pyc in _init_convenience(self, mesh, family, degree, form_degree, constrained_domain, restriction)
    256 
    257         self._init_from_ufl(mesh, element,
--> 258                             constrained_domain=constrained_domain)
    259 
    260     def _init_from_cpp(self, cppV, **kwargs):

/home/fenics/build/lib/python2.7/site-packages/dolfin/functions/functionspace.pyc in _init_from_ufl(self, mesh, element, constrained_domain)
    222         #if dolfin_element is None or dolfin_dofmap is None:
    223         #    assert dolfin_element is None and dolfin_dofmap is None, "Expecting both or none of these."
--> 224         dolfin_element, dolfin_dofmap = _compile_dolfin_element(element, mesh, constrained_domain=constrained_domain)
    225 
    226         # Initialize the cpp.FunctionSpace

/home/fenics/build/lib/python2.7/site-packages/dolfin/functions/functionspace.pyc in _compile_dolfin_element(element, mesh, constrained_domain)
     87 
     88     # JIT-compile element to get ufc_element and ufc_dofmap
---> 89     ufc_element, ufc_dofmap = jit(element, mpi_comm=mesh.mpi_comm())
     90 
     91     dolfin_element = cpp.FiniteElement(ufc_element)

/home/fenics/build/lib/python2.7/site-packages/dolfin/compilemodules/jit.pyc in mpi_jit(*args, **kwargs)


     63         # Just call JIT compiler when running in serial
     64         if MPI.size(mpi_comm) == 1:

---> 65             return local_jit(*args, **kwargs)


     66 
     67         # Compile first on process 0

/home/fenics/build/lib/python2.7/site-packages/dolfin/compilemodules/jit.pyc in jit(ufl_object, form_compiler_parameters, mpi_comm)
    122 
    123     # Execute!
--> 124     result = ffc.jit(ufl_object, parameters=p)
    125     if isinstance(ufl_object, ufl.Form):
    126         compiled_form, module, prefix = result

/home/fenics/build/lib/python2.7/site-packages/ffc/jitcompiler.pyc in jit(ufl_object, parameters)
    199     use_ctypes = os.environ.get("FFC_USE_CTYPES")
    200     if not use_ctypes:
--> 201         module = jit_build_with_instant(ufl_object, module_name, parameters)
    202     else:
    203         module = jit_build_with_dijitso(ufl_object, module_name, parameters)

/home/fenics/build/lib/python2.7/site-packages/ffc/jitcompiler.pyc in jit_build_with_instant(ufl_object, module_name, parameters)
     99 
    100         # Write to file
--> 101         write_code(code_h, code_c, module_name, parameters)
    102 
    103         # Build module using Instant

/home/fenics/build/lib/python2.7/site-packages/ffc/formatting.pyc in write_code(code_h, code_c, prefix, parameters)
    134 def write_code(code_h, code_c, prefix, parameters):
    135     # Write file(s)
--> 136     _write_file(code_h, prefix, ".h", parameters)
    137     if code_c:
    138         _write_file(code_c, prefix, ".cpp", parameters)

/home/fenics/build/lib/python2.7/site-packages/ffc/formatting.pyc in _write_file(output, prefix, postfix, parameters)
    159     "Write generated code to file."
    160     filename = os.path.join(parameters["output_dir"], prefix + postfix)
--> 161     with open(filename, "w") as hfile:
    162         hfile.write(output)
    163     info("Output written to " + filename + ".")

IOError: [Errno 13] Permission denied: './ffc_element_6f207fe7cb7a4724787b60b35d278be111fc5980.h'

Jack Hale

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Jul 29, 2016, 3:30:49 PM7/29/16

to fenics-support

It's a permissions issue now... Make sure you have the very latest image:

fenicsproject pull stable

If that doesn't work:

Which host OS do you have? Could you post the output of the fenicsproject script commands so I can see how the container is being setup? What are the permissions of the file in the container (open a terminal in Jupyter and run stat on a file in /home/fenics). And in the project directory?

Jack

matt.m...@gmail.com

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Jul 29, 2016, 5:39:10 PM7/29/16

to fenics-support

Jack,

Thanks very much for all of your ongoing help. I am a bit embarrassed by all this as I’m quite inexperienced with all the terminal level stuff, so it’s possible that I’ve made a mess of things somewhere deep inside along the way. For example, I’ve not always been paying attention to which directory I am in when I do the “pull stable” or other fenicsproject commands. As far as I recall I’ve always done “fenicsproject notebook myname” in the directory where all my notebook files are.

If it would be easier, I am happy to delete all relevant fenics/docker related files and start completely from scratch (being sure to backup all my notebooks).

== HOST: OSX 10.9.5 (this is my laptop)

===TERMINAL LOG

## .

## ## ## ==

## ## ## ## ## ===

/"""""""""""""""""\___/ ===

~~~ {~~ ~~~~ ~~~ ~~~~ ~~~ ~ / ===- ~~~

\______ o __/

\ \ __/

\____\_______/

docker is configured to use the default machine with IP 192.168.99.100

For help getting started, check out the docs at https://docs.docker.com

csm-mmoelter-m1:~ mmoelter$ cd Documents/LiquidCrystal/Cylinder/DockFenics

csm-mmoelter-m1:DockFenics mmoelter$ fenicsproject pull stable

[docker pull quay.io/fenicsproject/stable]

Using default tag: latest

latest: Pulling from fenicsproject/stable

f069f1d21059: Already exists

ecbeec5633cf: Already exists

ea6f18256d63: Already exists

54bde7b02897: Already exists

a3ed95caeb02: Already exists

ce9e695a6234: Already exists

a3ed95caeb02: Already exists

7d53475230cf: Already exists

f9cc7fcaeb59: Already exists

cbae41b257a8: Already exists

f4361ee97fe4: Already exists

53463f9bb986: Already exists

2ffec7e531d5: Already exists

d6bf654ed4cf: Already exists

a38171602c8b: Already exists

e791c109926c: Already exists

de3d7f52fcd5: Already exists

ed28c46b1d60: Already exists

ba84cf3736dd: Already exists

2116c2c0d3e4: Already exists

0898d930a5da: Already exists

995a7d028595: Already exists

c7787c280973: Already exists

f30f67ee1f43: Already exists

4b89d500bc3e: Already exists

b00844b71e72: Already exists

67ad95401144: Already exists

0e43b3c67087: Already exists

9515ec6258fd: Already exists

Digest: sha256:dcf00216e6424974469244fb394496d4bc70d1a839bc7d4737d84b43f4453918

Status: Image is up to date for quay.io/fenicsproject/stable:latest

csm-mmoelter-m1:DockFenics mmoelter$ docker images

REPOSITORY TAG IMAGE ID CREATED SIZE

quay.io/fenicsproject/stable latest 96603218bc91 8 days ago 1.435 GB

csm-mmoelter-m1:DockFenics mmoelter$ docker ps

CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES

csm-mmoelter-m1:DockFenics mmoelter$ fenicsproject notebook permtest

Creating new FEniCS Project notebook project permtest.

[docker volume create --name instant-cache-quay.iofenicsprojectstable]

instant-cache-quay.iofenicsprojectstable

[docker create -p 192.168.99.100:3000-4000:8888 --env HOST_UID=2018471 --env HOST_GID=9999 -v instant-cache-quay.iofenicsprojectstable:/home/fenics/.instant -v '/Users/mmoelter/Documents/LiquidCrystal/Cylinder/DockFenics':/home/fenics/shared -w /home/fenics/shared --label org.fenicsproject.created_by_script=true --label org.fenicsproject.project_type='notebook' --name permtest quay.io/fenicsproject/stable 'jupyter-notebook --ip=0.0.0.0']

ffdc06f59060cc588b194ce9c111855d0ef213e8aa7c7e7b63c69faeb7ecf02e

To start the session, type the following command:

fenicsproject start permtest

You will find the current working directory '/Users/mmoelter/Documents/LiquidCrystal/Cylinder/DockFenics' under ~/shared.

csm-mmoelter-m1:DockFenics mmoelter$ fenicsproject start permtest

Starting project named permtest.

[docker start permtest]

permtest

You can access the Jupyter notebook at http://192.168.99.100:3024

[docker attach permtest]

[I 21:18:45.087 NotebookApp] Writing notebook server cookie secret to /home/fenics/.local/share/jupyter/runtime/notebook_cookie_secret

[I 21:18:45.109 NotebookApp] Serving notebooks from local directory: /home/fenics/shared

[I 21:18:45.110 NotebookApp] 0 active kernels

[I 21:18:45.110 NotebookApp] The Jupyter Notebook is running at: http://0.0.0.0:8888/

[I 21:18:45.110 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).

[W 21:18:45.111 NotebookApp] No web browser found: could not locate runnable browser.

[I 21:19:02.158 NotebookApp] 302 GET / (192.168.99.1) 0.59ms

[I 21:19:18.085 NotebookApp] Writing notebook-signing key to /home/fenics/.local/share/jupyter/notebook_secret

[W 21:19:18.088 NotebookApp] Notebook FenicsTutorialTest.ipynb is not trusted

[W 21:19:18.116 NotebookApp] 404 GET /nbextensions/widgets/notebook/js/extension.js?v=20160729211845 (192.168.99.1) 10.44ms referer=http://192.168.99.100:3024/notebooks/FenicsTutorialTest.ipynb

[I 21:19:18.298 NotebookApp] Kernel started: aad5e88d-99e5-49a9-9ff8-465d1385246b

[I 21:19:37.569 NotebookApp] New terminal with automatic name: 1

I went to the URL listed (http://192.168.99.100:3024) and the notebook started as usual. I opened a file and it is still “read only”.

If I try to run it I get the permission error from before.

== FILE PROPERTIES

1. The output from the Terminal within the notebook is shown in the screenshot.

(I couldn’t figure out how to copy/paste from in the terminal...)

2. After shutting down the notebook I got this for the same file in the terminal:

csm-mmoelter-m1:DockFenics mmoelter$ stat FenicsTutorialTest.ipynb

16777218 15259949 -rw-r--r-- 1 mmoelter domain^users 0 74117 "Jul 29 14:19:18 2016" "Jul 25 13:08:34 2016" "Jul 25 13:08:34 2016" "Apr 13 16:50:21 2016" 4096 152 0 FenicsTutorialTest.ipynb

csm-mmoelter-m1:DockFenics mmoelter$

Appreciate all the help. Matt

Screen Shot 2016-07-29 at 2.36.02 PM.png

Jack Hale

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Jul 30, 2016, 7:03:43 AM7/30/16

to Matt Moelter, fenics-support

Hi Matt,

Inside the <container, Jupyter> shell session, could you run:

bash
sudo chown -R $HOST_UID:$HOST_GID /home/fenics/shared

You should then have the correct permissions.

Technical explanation:

I moved to a more conservative approach for getting file permissions
right between the container and the host, although, I didn't expect
there to be any issues on Mac OS X so its a bit of a surprise. Linux
is more problematic. Especially with clashing UIDs and GIDs... I'm
playing around on my OS X machine here and it's jack/staff outside the
container and fenics/fenics inside the container, with UID/GID of
fenics user and group in the container matching the UID/GID of
jack/staff outside.

Does it work correctly if you start with a totally fresh directory, a
new project and new files?

Jack Hale

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matt.m...@gmail.com

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Jul 31, 2016, 3:45:38 PM7/31/16

to fenics-support

Jack,

Thanks for your heroic efforts to help me figure this out.

Perhaps I should just start completely over from scratch.

Remove and reinstall the fenicsproject script and then pull stable.

The only problem is that I don’t know where all the fenics/docker files have been put.

I did

fenicsproject start cal

and then opened the URL in the browser.

The file “FenicsTutorialTest.ipynb” opened as read-only as before

In addition, I noticed that from within Jupyter Notebook main page I could not open a new Python filed.

(see screenshot)

Inside the Jupyter notebook I opened a terminal and did this:

$ stat FenicsTutorialTest.ipynb

File: 'FenicsTutorialTest.ipynb'

Size: 74117 Blocks: 152 IO Block: 4096 regular file

Device: 1fh/31d Inode: 106 Links: 1

Access: (0644/-rw-r--r--) Uid: ( 1000/ UNKNOWN) Gid: ( 50/ staff)

Access: 2016-07-30 21:38:46.000000000 +0000

Modify: 2016-07-25 20:08:34.000000000 +0000

Change: 2016-07-25 20:08:34.000000000 +0000

Birth: -

$ bash

# FEniCS stable version image

Welcome to FEniCS/stable!

This image provides a full-featured and optimized build of the stable

release of FEniCS.

To help you get started this image contains a number of demo

programs. Explore the demos by entering the 'demo' directory, for

example

cd ~/demo/documented/poisson/python/

python demo_poisson.py

fenics@cf4b6b4a79b7:~/shared$ sudo chown -R $HOST_UID:$HOST_GID /home/fenics/shared

fenics@cf4b6b4a79b7:~/shared$ stat FenicsTutorialTest.ipynb

File: 'FenicsTutorialTest.ipynb'

Size: 74117 Blocks: 152 IO Block: 4096 regular file

Device: 1fh/31d Inode: 106 Links: 1

Access: (0644/-rw-r--r--) Uid: ( 1000/ UNKNOWN) Gid: ( 50/ staff)

Access: 2016-07-30 21:38:46.000000000 +0000

Modify: 2016-07-25 20:08:34.000000000 +0000

Change: 2016-07-25 20:08:34.000000000 +0000

Birth: -

fenics@cf4b6b4a79b7:~/shared$

The file is still “read-only”.

== Another issue

There is one other confusing thing (related?). In trying to see what was what I found some docker command to see what existed.

“docker images” shows an existing image.

But when I do “docker ps” there are no containers listed.

However, if I then do “fenicsproject start cal” and it starts and gives a URL to use for the notebook.

Does this mean a container exists somewhere that docker can’t see...I am way out of my depth here.

csm-mmoelter-m1:~ mmoelter$ docker images

REPOSITORY TAG IMAGE ID CREATED SIZE

quay.io/fenicsproject/stable latest 96603218bc91 10 days ago 1.435 GB

csm-mmoelter-m1:~ mmoelter$ docker ps

CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES

csm-mmoelter-m1:~ mmoelter$ pwd

/Users/mmoelter

csm-mmoelter-m1:~ mmoelter$ cd Documents/LiquidCrystal/Cylinder/DockFenics

csm-mmoelter-m1:DockFenics mmoelter$ pwd

/Users/mmoelter/Documents/LiquidCrystal/Cylinder/DockFenics

csm-mmoelter-m1:DockFenics mmoelter$ docker images

REPOSITORY TAG IMAGE ID CREATED SIZE

quay.io/fenicsproject/stable latest 96603218bc91 10 days ago 1.435 GB

csm-mmoelter-m1:DockFenics mmoelter$ docker ps

CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES

csm-mmoelter-m1:DockFenics mmoelter$ fenicsproject start cyl

Starting project named cyl.

[docker start cyl]

cyl

You can access the Jupyter notebook at http://192.168.99.100:3031

[docker attach cyl]

Thanks again...Matt

Screen Shot 2016-07-31 at 12.26.49 PM.png

Jack Hale

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Aug 1, 2016, 4:50:09 AM8/1/16

to fenics-support

Hi Matt,

Let me deal with your two requests separately.

Docker questions:

By default, `docker ps` only shows running containers. `docker ps -a` will show all running and stopped containers. To clarify, an image and a container are seperate things; an image contains an immutable description of an environment and how to start it (e.g. quay.io/fenicsproject/stable), a container is an instantiation of an image (e.g. cyl). You can have many containers, all created from the same image.

Your permissions problem:

I can see the issue now. Even though HOST_UID and HOST_GID are being passed at the `docker create` command by the script, HOST_UID still seems to be 1000.

Compare the behaviour on my machine:

fenics@fd0be8ec974b:~/shared$ echo $HOST_GID

1429829944

fenics@fd0be8ec974b:~/shared$ echo $HOST_UID

1451946547

fenics@fd0be8ec974b:~/shared$ stat untitled.txt

File: 'untitled.txt'

Size: 4 Blocks: 1 IO Block: 512 regular file

Device: 27h/39d Inode: 64053250 Links: 1

Access: (0644/-rw-r--r--) Uid: (1451946547/ fenics) Gid: (1429829944/ fenics)

Access: 2016-07-29 19:35:57.000000000 +0000

Modify: 2016-07-29 19:35:57.000000000 +0000

Change: 2016-08-01 08:41:43.000000000 +0000

Birth: -

Could you do `echo $HOST_UID` and `echo $HOST_GID` to confirm the issue? I simply cannot recreate the problem on any of my machines, very perplexing.

You can also try the manual approach here for now:

https://fenics-containers.readthedocs.io/en/latest/jupyter.html

I would also recommend moving from the Docker Toolbox to the new native Docker for Mac. No more Virtualbox.

Jack

matt.m...@gmail.com

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Aug 1, 2016, 12:34:05 PM8/1/16

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Jack,

1. Upon reviewing my workflow it might be possible that I (inadvertently) invoked “fenicsproject” commands from a regular terminal, not from within the Docker Quickstart terminal. Could this make a difference?

2. I created a new notebook container and started it, went to the URL.

Still having permission issues when trying to create a new Python2 notebook.

From a terminal in the Jupyter notebook I got:

$ pwd                                                                                                       

/home/fenics/shared                                                                                         

$ bash                                                                                                      

# FEniCS stable version image                                                                               

Welcome to FEniCS/stable!                                                                                   

This image provides a full-featured and optimized build of the stable                                       

release of FEniCS.                                                                                          

To help you get started this image contains a number of demo                                                

programs. Explore the demos by entering the 'demo' directory, for                                           

example                                                                                                     

    cd ~/demo/documented/poisson/python/                                                                    

    python demo_poisson.py                                                                                  

fenics@739b375ddf92:~/shared$ stat FenicsTutorialTest.ipynb                                                 

  File: 'FenicsTutorialTest.ipynb'                                                                          

  Size: 74117           Blocks: 152        IO Block: 4096   regular file                                    

Device: 1fh/31d Inode: 106         Links: 1                                                                 

Access: (0644/-rw-r--r--)  Uid: ( 1000/ UNKNOWN)   Gid: (   50/   staff)                                    

Access: 2016-07-31 19:36:06.000000000 +0000                                                                 

Modify: 2016-07-25 20:08:34.000000000 +0000                                                                 

Change: 2016-07-25 20:08:34.000000000 +0000                                                                 

 Birth: -                                                                                                   

fenics@739b375ddf92:~/shared$ echo $HOST_UID                                                                

2018471

fenics@739b375ddf92:~/shared$ echo $HOST_GID                                                                

9999

fenics@739b375ddf92:~/shared$                                                                               

I very much appreciate your continued support.

Matt

matt.m...@gmail.com

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Aug 5, 2016, 2:05:57 PM8/5/16

to fenics-support

Again, I appreciate all your help.

It works just fine following the manual instructions as you suggested.

(For other reasons I’m not currently able to upgrade to Docker for Mac.

Thanks...Matt

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