The help-desk from csdms

CSDMS JupyterHub account

Thank you for signing up to use the CSDMS JupyterHub. To complete the signup, please provide your CSDMS username, the first four characters of your username on the CSDMS JupyterHub, as well as a brief description of why you're signing up (a single sentence is fine).

CSDMS username:
fdedonck

First four characters of username:
fded

Describe why you're signing up for an account:
I'm an attendee of the 2020 ESP In Summer School

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CSDMS JupyterHub account

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First four characters of username:
rjle

Describe why you're signing up for an account:
Try out notebooks and think about adding some for GeoClaw.

Once you've completed these steps, you'll typically get an approval within one business day.

Local installation of Frost Number Model notebook?

hi there,

I opened the Frost Number model example from the pymt read the docs website, and launched it in Binder.
https://hub.gke.mybinder.org/user/csdms-pymtbd2npumi/notebooks/notebooks/frost_number.ipynb

However, I want a local installation of this notebook instead, so i follow the instructions in the first section of the notebook. The download of the notebook is stated to be here:
curl -O https://raw.githubusercontent.com/csdms/pymt/master/docs/demos/frost_number.ipynb

If I use that command in my terminal window, it returns the following error message.
[W 09:57:47.814 NotebookApp] 400 GET /api/contents/NOTEBOOKS/PERMAFROST/frost_number.ipynb?type=notebook&_=1578589067677 (::1): Unreadable Notebook: /Users/overeem/NOTEBOOKS/PERMAFROST/frost_number.ipynb NotJSONError("Notebook does not appear to be JSON: '404: Not Found\n'...")

Still a file image appears in my local directory, but it does not open as a jupyter notebook.

Is it better to tell users to do the conda install and export the binder notebook?

CSDMS JupyterHub account

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*CSDMS username: huxiaoni

*First four characters of username: huxi

*Describe why you're signing up for an account: a requirement for the ESPin summer school

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Pymt_Sedflux

Hi there,
Could i ask a help for my last questions. Why the maximum grain size for bed load the the sedflux model allows is only 0.005m which seems unreasonable？

bed_load_sediment_grain_size:
  description: Grain size of bed-load sediment
  value:
    default:  400.0
    range:
      max:  5000.0
      min:  0.1
    type:  float
    units:  um

And should we make the compaction process file stay open because there is a compaction cofficient in sediment file?
Does it possible to use sedflux2d under pymt environment? I did not find a manule about how to use it.

CSDMS JupyterHub account

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First four characters of username:
lhsu

Describe why you're signing up for an account:
To be able to be backup for a presentation doing a demo on CSDMS JupyterHub (by Rich McDonald.)

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About Sedflux software

Hello guys:
I am interested in Sedflux software. In the illustration document, there should have sedflux in the WMT(The CSDMS Web Modeling Tool Link：https://csdms.colorado.edu/wmt/）. But I didn't find the Sedflux module in it. So I am very confused. I wonder what happend with it? Is the Sedflux software deleted from the WMT or I just didn't find the right web link to get this service?

CSDMS JupyterHub account

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CSDMS username:
Hgudipati

First four characters of username:
Hgud

Describe why you're signing up for an account:
ESPIn participant

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CSDMS JupyterHub account

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CSDMS username: Eyalmarder

First four characters of username: Eyal

Describe why you're signing up for an account: ESPIN 2020 workshop

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Binder does not launch from the Pymt examples

hi there,
we are trying to start some of the examples of Pymt models, by trying to open Binder links.
They do not (always) open, and keep spinning for a really long time (more than 5 minutes).
We tried from a mac-using a chrome browser, and mac- using a firefox browser. There is no specific error message, only a warning that it 'takes longer than usual to start your instance'.

Specifically I tried to open:
https://pymt.readthedocs.io/en/latest/examples.html
Frost Number model
GIPL and ECsimplesnow

CSDMS 2019 Clinic Surveys

Link to CSDMS 2019 clinic surveys:

CSDMS JupyterHub account

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CSDMS username:
Yuvalshmilo

First four characters of username:
Yuva

Describe why you're signing up for an account:
ESPIn summer course 2020

Once you've completed this step, you'll typically get an approval within one business day.

Pymt_Sedflux—What's the maximum and minimum value of all the variables in sedflux model?

Hi there,

I wonder if there is range for the maximum and minimum value of the bed-load grain size and other variables? For example, because i saw there is a file named parameters.yaml in the template input files for sedflux 3d as seen below, there is a maximum and minimum value defined and i just always thought that means a range for the bed-load grain size value. Does this thought correct? What's the real meaning of them?
bed_load_sediment_grain_size:
description: Grain size of bed-load sediment
value:
default: 400.0
range:
max: 5000.0
min: 0.1
type: float
units: um
I also want to know is there an upper limit for the number of sediment grain types, seasons for river and epoches?
And there are some other input variables which are not mentioned in sedflux documentation, for example the variable 'channel_exit_x-section_mean_of_depth'. Because there are also the variable 'depth' in river file, i just don't know what's the relationship of them. If the delta morphology is more controled by the 'channel_exit_x-section_mean_of_depth' than 'depth' which is defined in river file ? And also what's the maximum and minimum value for these 'other input variables'?

Except the questions above, i also have my last two questions. I feel confused by the plum process file. I saw there is a description for it in the sedflux documents as seen below. Does that mean if i want to run plum model alone, i need to download the two files? And if i just run the sedflux3d model, Does i also need to download them ?
To run the plume model you will need two input files. I’ve create an example of each to get you started:
plume_config.kvf: describes some physical and numerical constants used by the model.
plume_flood.kvf: describes input conditions to the model.
And there is a function named model.parameters. I wonder what it works for? Because it seems that it's output is the variables and their values of the template input files, not the new input files which we created by setup functions and have changed the values and variables for them by manule.

CSDMS JupyterHub account

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CSDMS username:
Josiearcuri

First four characters of username:
josi

Describe why you're signing up for an account:
I'm signing up in preparation for ESPIn 2020

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CSDMS JupyterHub account

Thank you for signing up to use the CSDMS JupyterHub. To complete the signup, please provide your CSDMS username, the first four characters of your username on the CSDMS JupyterHub, as well as a brief description of why you're signing up (a single sentence is fine).

CSDMS username:
BenjaminC

First four characters of username:
Benj

Describe why you're signing up for an account:
ESPIn

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CSDMS JupyterHub account

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First four characters of username:
mpip

Describe why you're signing up for an account:
I’m going to science the isht out of this.

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Using GeoClaw on Jupyterhub

Nice that you have a Jupyterhub set up!

I'm trying it out and have a couple questions. I see from this page that if I submit a lab I could ask to have this software available, but I wonder if there are instructions somewhere for doing these things for a user who wants to use GeoClaw on the JupyterHub without using an existing lab?

I found I could install Clawpack fine by opening a terminal and using git clone, etc., and then in a notebook I can import clawpack.geoclaw fine, and also refer to the CLAW environment variable (used when running the fortran parts of GeoClaw) if I first do this:
```
import sys, os
CLAW = '/home/jupyter-rjleveque/clawpack'
sys.path.insert(0, CLAW)
os.environ['CLAW'] = CLAW
```
I am wondering if there's a way to set things up so when I come back to my JupyterHub account, my PYTHONPATH and CLAW environment variables are set like this, or will I need to always set these from within a notebook?

Note: I tried adding these environment variables to /home/jupyter-rjleveque/.bashrc but that didn't affect the environment in a notebook when I restarted the server.
It didn't find gfortran when I tried running this notebook locally, so it died in the compile step. Is there something that needs to be added to the path for this?

CSDMS JupyterHub account

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CSDMS username: Fclapuyt

First four characters of username: fclapuyt

Describe why you're signing up for an account: I am participating to ESPIn 2020

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CSDMS JupyterHub account

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CSDMS username:
AdeyemiOlusola

First four characters of username:
ao.ol

Describe why you're signing up for an account:
To learn more and become a solid researcher

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Are these files needed for BMI 2.0? Can you help explain the purpose of these files?

Hi, a few of us are in the process of updating and improving the pyDeltaRCM numerical model.

This model was compliant with BMI 1.0 at some point, but was not maintained. We would like to continue to support the BMI, and have chosen to split out the BMI as a wrapper around the core model in a separate repository. I've gotten most of the BMI 2.0 setup worked out, I think. Check it out and let me know if you have suggestions!

The question I have though, is what is the purpose of these files? The files were last touched by @mdpiper 4 yrs ago. I didn't find anything in the 2.0 specs about these files.

Are these files templates of some kind for the BMI? Can the replaced by adequate documentation? Are they required to be BMI 2.0 compliant? Is there documentation you can point me to for how to update these files? Any information you can provide will be helpful, thanks!

Relates to #2 in that repo (respond there if you prefer!).

CSDMS JupyterHub account

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CSDMS username: HunjHunj

*First four characters of username:*hunj

*Describe why you're signing up for an account:*ESPIn

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CSDMS JupyterHub account

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CSDMS username:
mohittunwal

First four characters of username:
mohi

Describe why you're signing up for an account:
ESPIn 2020

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Scrub outdated page from website

There are pages on the CSDMS wiki that are outdated, and which may provide misleading information to the CSDMS community. One example is https://csdms.colorado.edu/wiki/CMT_Tutorial_Marssim. This page should be removed, or at least marked as obsolete.

Issues for testing Pymt demo Jupyter Notebooks

I tried to test all the Pymt example Jupyter Notebooks (https://github.com/csdms/pymt/tree/master/docs/demos) on HydroShare Jupyterhub and had the following issues. Thanks!

subside:
issue 1: import "plugin" error
Sedflux3D:
issue 1: import "plugin" error
issue 2: no "get_current_time", "get_time_step" attribute (But most of the other cells seem to work well)
child:
issue 1: import "plugin" error
issue 2: no "child" model
Sedflux3D_and_child:
issue 1: import "plugin" error
issue 2: no "child" model
Example_01_Basic_User_GIPL/ Example_02_GIPL_ECSimpleSnow: (may not be an issue)
A user needs to run the following command in the HydroShare Jupyterhub terminal before running the code:
conda install pymt_gipl pymt_ecsimplesnow seaborn -c conda-forge

CSDMS JupyterHub account

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CSDMS username:
Cjroland

First four characters of username:
Cjro

Describe why you're signing up for an account:
ESPIn summer school participant

Once you've completed this step, you'll typically get an approval within one business day.

Running MARSSIM

@alimaye writes:

Hi Mark,
I'm writing with a question about running a model through CSDMS. I came across some of the helpful tutorials you authored on the website. I'd like to run the model MARSSIM, along the lines described in this tutorial:
https://csdms.colorado.edu/wiki/CMT_Tutorial_Marssim
In the last few weeks Lynn McCready and colleagues have set me up with CU login credentials and HPC account on blanca. I'm writing to check which interface I should use to run MARSSIM (i.e., CMT vs. WMT). I successfully logged into WMT but did not see a way to select the MARSSIM model. With CMT, the updated version of the GUI showed beach as the only login option, and the login failed (despite a VPN connection to colorado.edu).
Thanks for your help. I'm excited to get started with these great modeling tools!
Ajay

Access GPU nodes on CSDMS HPC

@SwiftHickory writes:

For my clinic, I'd like to show a demo of our GPU version code. I'd like to ask if there is any available GPU cluster that we can access during the clinic. We have figured out other way to do it but if there is any available one, it will be much easier for us.

Coupling DeltaRCM with CEM

Have done some preliminary work to couple the CEM model with DeltaRCM through the use of the pymt framework. Mariela Perignon converted the original DeltaRCM model to Python, making it WMT/BMI compliant in the process. Using the BMI variables, this model coupling is achieved with relative ease.

Currently however, the coastline reshaping by the CEM model is not working as we expected. When the models are coupled from initialization in an empty basin, the CEM forces wash away any deposition generated by DeltaRCM. When the CEM model is run on a pre-developed DeltaRCM topography we are seeing 'spotty' reworking along the channels that does not seem realistic. An example of this behavior is attached.

Any suggestions, tips, or pieces of advice are greatly appreciated. As far as I know, this model coupling has not been done before, and it could be a nice combination of reduced-complexity models. If there is someone else I should be contacting about this please let me know.

CouplingDemo.pdf

Jay

CSDMS JupyterHub account

Thank you for signing up to use the CSDMS JupyterHub. To complete the signup, please provide your CSDMS username, the first four characters of your username on the CSDMS JupyterHub, as well as a brief description of why you're signing up (a single sentence is fine).

CSDMS username: esaavedrac

First four characters of username: edsa

Describe why you're signing up for an account: ESPIn 2020

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CSDMS JupyterHub account

Thank you for signing up to use the CSDMS JupyterHub. To complete the signup, please provide your CSDMS username, the first four characters of your username on the CSDMS JupyterHub, as well as a brief description of why you're signing up (a single sentence is fine).

CSDMS username: Jhariharan

First four characters of username: Jhar

Describe why you're signing up for an account: ESPIn2020

Once you've completed this step, you'll typically get an approval within one business day.

Example for coupling models with different time and spatial scales

Jongmin Byun wrote:

Could you show me a good example of the coupling models which have different time and spatial scales?
In addition to that, it would be very helpful to know the documentation or literature for the strategy to couple those models.

About models installation

Hi guys,
I came across a confused problem when I was trying to install models from pymt. That is the solving environment was always failed to set. All models have such a problem for me. As shown below:

(pymt) C:\Users\张明杰>conda install -c conda-forge pymt pymt_sedflux
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Collecting package metadata (repodata.json): failed

CondaHTTPError: HTTP 000 CONNECTION FAILED for url https://conda.anaconda.org/conda-forge/win-64/repodata.json
Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.
'https://conda.anaconda.org/conda-forge/win-64'

Hope to get your reply as soon as possible. Very thanks!

setting up/running pynetlogo tutorial

Hi - I'm trying to work my way through the pynetlogo tutorials (https://pynetlogo.readthedocs.io/en/latest/) - Two issues - I think unrelated. Likely because I'm still new to installing these type of packages as well as setting things up in the correct directories.

The easiest 'issue' is I don't see example 1 in the github repository I downloaded. So can't run it -but this is not a CSDMS problem

Unrelated? though i expect the problem would pop up if I tried to run the missing tutorial - I think Ive installed everything I need (through Anaconda) but when I try to copy and paste the example code into a new jupyter notebook I get errors on the very first cell - I'm in the folder where the files are so I think I'm in the right place. I've installed pynetlogo, Jpype but I have not done anything with the Python extension for NetLogo (I didn't understand how to use it)

if you have time it would be great to chat by phone/share my screen with you - Jill

TypeError                                 Traceback (most recent call last)
<ipython-input-1-14aac9fcc9d1> in <module>
      9 import pyNetLogo
     10 
---> 11 netlogo = pyNetLogo.NetLogoLink(gui=True)
     12 
     13 netlogo.load_model('./models/Wolf Sheep Predation_v6.nlogo')

~\anaconda3\lib\site-packages\pyNetLogo\core.py in __init__(self, gui, thd, netlogo_home, netlogo_version, jvm_home, jvmargs)
    219             netlogo_home = get_netlogo_home()
    220         if not netlogo_version:
--> 221             netlogo_version = establish_netlogoversion(netlogo_home)
    222         if not jvm_home:
    223             jvm_home = jpype.getDefaultJVMPath()

~\anaconda3\lib\site-packages\pyNetLogo\core.py in establish_netlogoversion(path)
    104     pattern = re.compile(r'(?:(\d+)\.)?(?:(\d+)\.)?(\*|\d+)$')
    105 
--> 106     netlogo = os.path.basename(os.path.normpath(path))
    107     match = pattern.search(netlogo)
    108     version = match.group()

~\anaconda3\lib\ntpath.py in normpath(path)
    450 def normpath(path):
    451     """Normalize path, eliminating double slashes, etc."""
--> 452     path = os.fspath(path)
    453     if isinstance(path, bytes):
    454         sep = b'\\'

TypeError: expected str, bytes or os.PathLike object, not NoneType

https://github.com/permamodel/permamodel/pull/68

hi there,

We have a component that is fully wrapped with a Basic Model Interface BMI posted here: permamodel/permamodel#68

Can we add this component to the Python Modeling Tool? pymt?
How can we assign someone on the CSDMS team to help with this?
How do we know when this component is added to pymt?

Thank you for explaining the workflow.

Batch job submission failed: Invalid account or account/partition combination specified

Hi @mdpiper, I'm trying to run the job with sbatch. Here is my job script

#!/bin/bash

#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --time=00:10:00
#SBATCH --partition=shas
#SBATCH --qos=normal
#SBATCH --output=cc2dcpu-%j.out
#SBATCH --error=cc2dcpu-%j.err

module load intel/17.0.0
module load tbb/17.0.0
module load impi/2017.0.098
module load boost/1.64.0

export OMP_NUM_THREADS=8

../../dynearthsol2d_cpu core-complex.cfg

When I submit the job, it says:
sbatch: error: Batch job submission failed: Invalid account or account/partition combination specified

Did I miss something? Thanks.

Error in conda install of Dakota

@mdpiper I am working on setting up the conda environment.yml for my upcoming CSDMS clinic. I plan to use Dakota in this clinic. I was planning to use the Dakota package distributed through conda.

I created a new conda environment and made sure that my prior Dakota install was no longer present.

$ conda create -n dakota python=3.6
$ conda activate Dakota
$ conda install -c csdms-stack dakota
Collecting package metadata: done
Solving environment: failed

PackagesNotFoundError: The following packages are not available from current channels:

  - dakota -> lapack

Current channels:

  - https://conda.anaconda.org/csdms-stack/osx-64
  - https://conda.anaconda.org/csdms-stack/noarch
  - https://repo.anaconda.com/pkgs/main/osx-64
  - https://repo.anaconda.com/pkgs/main/noarch
  - https://repo.anaconda.com/pkgs/free/osx-64
  - https://repo.anaconda.com/pkgs/free/noarch
  - https://repo.anaconda.com/pkgs/r/osx-64
  - https://repo.anaconda.com/pkgs/r/noarch

To search for alternate channels that may provide the conda package you're
looking for, navigate to

    https://anaconda.org

and use the search bar at the top of the page.

please let me know how to fix this.
Thanks!

About pymt_sedflux 3D

Hi there,
I want to know if anyone knows what's the effects of 'bbl' files in process file of sedflux3D. Why there is no 'debris flow' file in the process file of sedflux3D?
[ bbl ]
active: yes
logging: no
repeat interval: always
algorithm (none|muds): none
external sediment source file: none

And how can I close the process of isostany? Should I just delete the'{{ isostasy_process_is_on }}' and change it with the word 'no'?
[ isostasy ]
active: {{ isostasy_process_is_on }}
logging: no
repeat interval: 25y
effective elastic thickness (m): {{ isostasy_effective_elastic_thickness }}
Youngs modulus (Pa): {{ isostasy_youngs_modulus }}
relaxation time (years): {{ isostasy_relaxation_time }}

kernel crashes on a csdms teaching jupyter pymt notebook

On behalf of one of the students using the CSDMS jupyter notebook hub.

trying to use the model Hydrotrend for a final project. Simply trying to initialize the model keeps causing the kernel to die. I'm not sure if the dataset I'm trying to run is too large or if the problem is something else. Can you help with this?

Question about PyPI packaging: wheel includes non-any

@mcflugen and @mdpiper I'm currently working on packaging terrainbento to distribute via PyPI. I had a question about CI and thought it best to ask it here. Context first, and the actually question is at the very bottom of the page.

I'm copying the approach that @mcflugen has done for Landlab.

I've gotten to the point where I have successfully upload a wheel to PyPI 🎉

However, only one of my Travis build succeeded, and the others failed with an error like:

1.00s$ twine upload -u katybarnhart -p$TWINE_PASSWORD --verbose dist/*terrainbento*
Uploading distributions to https://upload.pypi.org/legacy/
Uploading terrainbento-1.1b2-py3-none-any.whl
100%|██████████| 257k/257k [00:00<00:00, 291kB/s] 
Content received from server:
<html>
 <head>
  <title>400 File already exists. See https://pypi.org/help/#file-name-reuse</title>
 </head>
 <body>
  <h1>400 File already exists. See https://pypi.org/help/#file-name-reuse</h1>
  The server could not comply with the request since it is either malformed or otherwise incorrect.<br/><br/>
File already exists. See https://pypi.org/help/#file-name-reuse
 </body>
</html>
HTTPError: 400 Client Error: File already exists. See https://pypi.org/help/#file-name-reuse for url: https://upload.pypi.org/legacy/

link to travis build

I think that this error has something to do with the name of the wheel, terrainbento-1.1b2-py3-none-any.whl. I expected that the none-any section would have included some information about the OS. I found information on PyPI indicating that none-any means that my wheel is cross platform.

I think this makes sense as terrainbento (unlike Landlab) doesn't require any compilation.

Am I correct in thinking that its OK that I just make one wheel. I can thus change my CI to just make one wheel and move forward?

installed pymt but hydrotrend is missing?

hi, I installed pymt on a windows machine today and hydrotrend is missing. We are running this at IWM in collaboration with Dr. Overeem.
Upon installation we receive the following error:

What would we need to do to fix this issue? thank you

download pymt model notebooks?

hi there,

Where can I download pymt model notebook examples? I can see the list and open each individually in binder. But it takes really long for binder to open up. Could there be a repository or a directl downoad from the same page in the readthedocs?

CSDMS JupyterHub account

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ale3

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I am teaching geomorphology this semester and want to use these scripts in my class to help teach geomorph + python

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update seed input on Rafem

Hi,

I am using the coupled CEM-RAFEM model and updates seed number in the run_model.py file as the screen shot below:

However, the rand_seed number in the input.yaml from the output of the experiment was not updated (as the figure below):

Would you like to look into it? Thank you for your help!

Checking function inputs (landlab/landlab#1223)

I want to change the callback function in the GroundwaterDupuitPercolator to have the form: callback_function(grid, recharge_rate, substep_dt, **kwargs). Presently it has the form callback_function(grid, substep_dt, **kwargs). @kbarnhart suggested that the pr should include testing the number of arguments in the user-provided function. This seems tricky given that the user will likely provide additional keyword arguments (e.g. the folder and file location to write an output) that confuse most of the methods I've seen that count the number of arguments a function takes. Is there a simple solution to this that can correctly ensure three (or two, giving a depricated warning) non-keyword arguments are supplied?

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CSDMS username: Bbovy

First four characters of username: bbov

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Thanks!

Linking Python to Fortran

Is there the capability in BMI in PyMT to link Python and Fortran code? I've heard that it can be done, but I haven't found any documentation about it.

Specifically, I have an existing Fortran 90 code that defines a bunch of different sediment transport capacity functions. I'd like to be able to call these functions using Python to compute sediment transport from hydraulic model results that are stored in ArcMap shapefiles. I have spent several days trying to use numpy.f2py, with no success.

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CSDMS username: gpolesen

First four characters of username: gpol

Describe why you're signing up for an account: ESPIn summer school

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Data for PyMT permafrost models

I need information on permafrost regions in North America. Therefore, the PyMT models for permafrost were recommended to me by @mdpiper.
Does the CSDMS offer data (esp. comprehensive time series of temperature) which can be used by the models? And if yes, how can I get access to them and incude them into the models?

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CSDMS username: Rachelallen

First four characters of username: rmal

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First four characters of username:
ChristinaB

Describe why you're signing up for an account:
@mcflugen @mdpiper Do I need a new account if I signed up at AGU 2019? I don't have this password. Could you reset for me? How long is this access valid for? Can I send students here? What about using for Waterhackweek

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