various small issues after git-clone, compile, run tests

[knbknb]

After the Dep.6.4 seminar talk (awesome but overwhelming) I've installed Moose and Golem on my PC. Didn't know anything about Moose and Golem until then. I did the following because I just like to try things out. Maybe you like to get feedback from first-time users.

Now I have a working Moose installation on my Linux PC, ubuntu 16.04 with 4 CPUs and 24 GB RAM, kernel 4.4.0-137-generic #163-Ubuntu SMP Mon Sep 24 13:14:43 UTC 2018 x86_64

Moose master branch, commit 56178d8, from 2018-10-16

test/run_tests
Ran 1735 tests in 258.1 seconds.
1735 passed, 73 skipped, 0 pending, 0 failed

Various issues

1. From Golem's test suite all tests passed but 1 test failed:

test:TH.2D_transient ............................................................. [FINISHED] FAILED (EXODIFF)
--------------------------------------------------------------------------------------------------------------
Ran 44 tests in 160.8 seconds.
43 passed, 0 skipped, 0 pending, 1 FAILED

Details:

test:TH.2D_transient: ERROR: 
test:TH.2D_transient:    *****************************************************************
test:TH.2D_transient:               EXODIFF	(Version: 2.90) Modified: 2018-02-15
test:TH.2D_transient:               Authors:  Richard Drake, rrdrake@sandia.gov           
test:TH.2D_transient:                         Greg Sjaardema, gdsjaar@sandia.gov          
test:TH.2D_transient:               Run on    2018/10/18   13:13:24 CEST
test:TH.2D_transient:    *****************************************************************
test:TH.2D_transient: 
test:TH.2D_transient: Reading first file ... 
test:TH.2D_transient: Reading second file ... 
test:TH.2D_transient:   FILE 1: /home/knb/code/git/projects/Golem/test/tests/TH/gold/TH_2D_transient_out.e
test:TH.2D_transient:    Title: TH_2D_transient_out.e
test:TH.2D_transient:           Dim = 3, Blocks = 1, Nodes = 9882, Elements = 4800, Nodesets = 6, Sidesets = 6
test:TH.2D_transient:           Vars: Global = 0, Nodal = 2, Element = 3, Nodeset = 0, Sideset = 0, Times = 3
test:TH.2D_transient: 
test:TH.2D_transient:   FILE 2: /home/knb/code/git/projects/Golem/test/tests/TH/TH_2D_transient_out.e
test:TH.2D_transient:    Title: TH_2D_transient_out.e
test:TH.2D_transient:           Dim = 3, Blocks = 1, Nodes = 9882, Elements = 4800, Nodesets = 6, Sidesets = 6
test:TH.2D_transient:           Vars: Global = 0, Nodal = 2, Element = 3, Nodeset = 0, Sideset = 0, Times = 3
test:TH.2D_transient: 
test:TH.2D_transient: exodiff: INFO .. Map option is not needed.
test:TH.2D_transient: 
test:TH.2D_transient: Nodal coordinates will be compared .. tol:    1e-06 (absolute), floor:        0
test:TH.2D_transient: Time step values will be compared .. tol:  5.5e-06 (relative), floor:    1e-10
test:TH.2D_transient: No Global variables on either file.
test:TH.2D_transient: Nodal variables to be compared:
test:TH.2D_transient: 	pore_pressure                    tol:  5.5e-06 (relative), floor:    1e-10
test:TH.2D_transient: 	temperature                            5.5e-06 (relative),           1e-10
test:TH.2D_transient: Element variables to be compared:
test:TH.2D_transient: 	vx                               tol:  5.5e-06 (relative), floor:    1e-10
test:TH.2D_transient: 	vy                                     5.5e-06 (relative),           1e-10
test:TH.2D_transient: 	vz                                     5.5e-06 (relative),           1e-10
test:TH.2D_transient: No Element Attribute variables on either file.
test:TH.2D_transient: No Nodeset variables on either file.
test:TH.2D_transient: No Sideset variables on either file.
test:TH.2D_transient: Sideset Distribution Factors will be compared .. tol:    1e-06 (relative), floor:        0
test:TH.2D_transient: 
test:TH.2D_transient:   ==============================================================
test:TH.2D_transient:   NOTE: All node and element ids are reported as global ids.
test:TH.2D_transient: 
test:TH.2D_transient: Sideset Distribution Factors:
test:TH.2D_transient:   --------- Time step 1, 0.0000000e+00 ~ 0.0000000e+00, rel diff:  0.00000e+00 ---------
test:TH.2D_transient: Nodal variables:
test:TH.2D_transient: Element variables:
test:TH.2D_transient:   --------- Time step 2, 3.5000000e+03 ~ 3.5000000e+03, rel diff:  0.00000e+00 ---------
test:TH.2D_transient: Nodal variables:
test:TH.2D_transient:    temperature    rel diff: -1.6335222e-03 ~ -1.6334518e-03 = 4.31226e-05 (node 9882)
test:TH.2D_transient: Element variables:
test:TH.2D_transient:   --------- Time step 3, 7.0000000e+03 ~ 7.0000000e+03, rel diff:  0.00000e+00 ---------
test:TH.2D_transient: Nodal variables:
test:TH.2D_transient:    temperature    rel diff: -4.8462806e-03 ~ -4.8462504e-03 = 6.23805e-06 (node 9882)
test:TH.2D_transient: Element variables:
test:TH.2D_transient: 
test:TH.2D_transient: exodiff: Files are different
test:TH.2D_transient: 
test:TH.2D_transient:  
test:TH.2D_transient: ################################################################################
test:TH.2D_transient: Tester failed, reason: EXODIFF
test:TH.2D_transient: 

I tried this twice. I don't know what's wrong here, and I won't investigate. This is not my expertise.
Maybe you should write a small paragraph telling the user how serious this is if 1 test fails. Maybe it's just a false alarm here (tiny temperature differences) and you can change some tolerance value(s) or acceptance criteria here ?

2. Moreover your paper says:

The source code and the input files of
the five numerical examples presented in this paper, plus a suite
of specific benchmark cases, are available for downloading from a
GitHub repository (https://github.com/ajacquey/Golem).

but there seems to be no such folder /examples/ (or similar) in the github repo. I haveb't really looked, and I don't care, and I don't need the examples, but maybe someone else will notice. I think a dummy paragraph /"coming soon" will suffice

3. Maybe this is a moose issue, but still:
   I think it is appropriate to inform the user that the Moose installer alters the PATH variable. Moose brings its own python (Python 2.7.15 :: Anaconda, Inc. in /opt/moose/miniconda/bin), so many Python scripts or Python-based binaries (e.g. "diffuse" editor) that rely on the system's Python will cease to work when called from a bash shell. I had to change the PATH back to the old value by removing /opt/moose/miniconda/bin.

[ajacquey]

First of all, thanks for your feedback Knut!
Glad to hear that "most" of the installation went smooth for you and I appreciate that you took the time to go through all the installation process.

1. Concerning your first point, the error that you get is not that bad.
   During the run_test script, we run a suite of simple simulations with the local installation and then compare the results produced with some "gold" results which are stored in the repository. The error that you get is meaning that the simulations ran fine but that there are some differences between the results produced by your installation and the gold results (EXODIFF error).
   I noticed that this test was leading to this error last week on my installation as well after I updated my MOOSE environment. I will try to investigate the issue and fix it.

2. Indeed, the input files from the paper are not in the repository yet. We are finalizing an online documentation (which can be built on the fly) which contains additional information about the input files and will push everything to the repository together. I hope to have it done by the end of the year...

3. You are definitively right. MOOSE is installing its own python environment and it can mess with an existing Python environment. I had problems myself some time ago. I will add a note concerning this in the README file.

Thanks again for your feedback and your time, I really appreciate it.
Cheers,

Antoine

[knbknb]

Yes that one test had only a tiny error; and I have commented out the modifications of the .bashrc files.

One more idea, or rather a suggestion, I had was: Maybe it would be convenient to offer Moose and your app packaged together, as a Docker container. But then you need a download site (a registry) and documentation for that....

MOOSE seems to be a really powerful software. unfortunately I don't have the time to dive deeper into this subject matter, so I'll close this issue here.