I think that it would be nice to have links to the appropriate github pages from CMIP6 Control vocabulary minimum requirements.

e.g. replace institutions_ids with

"institutions_ids [ raw ]"

Hello,

I'm trying to use CMOR3 to write satellite climate data records in obs4MIPs format, but I can't access several of the web pages on https://cmor.llnl.gov/.

I can access the Getting Started (https://cmor.llnl.gov/) and API pages (https://cmor.llnl.gov/mydoc_cmor3_api/), but none of the rest, such as Installation (https://cmor.llnl.gov/mydoc_cmor3_conda/) and Python Examples (https://cmor.llnl.gov/mydoc_cmor3_python/), nor even the Contact Us page (https://cmor.llnl.gov/mydoc_contacts/)

For these I get a 403 Forbidden error.

Thanks for any help.
Cheers
Simon

I wonder if Appendix would not be a more logical place for Control Vocabulary (CMIP6)

I even wonder if this and all the CMIP6 sections of Appendix should be in a CMOR and CMIP (or CMOR and CMIP6) new section between Examples and Appendix

You may also want to add PCMDI/cmor#255 and similar information to a Creating new tables (for a new MIP?) cookbook in the Appendix

@dnadeau4 The acknowledgements (https://cmor.llnl.gov/acknowledgements/ ) mentions lots of folks, but doesn't mention that CMOR was conceived and originally designed by me, and CMOR1 was largely coded by me, with substantial contributions from Charles.
I also think it would be appropriate to include our names somewhere on https://cmor.llnl.gov/ since I wrote most of that text. (We should update it in several places to reflect application to CMIP6)

The PrePARE documentation at https://cmor.llnl.gov/mydoc_cmip6_validator/ is for a previous version and doesn't reflect the usage in the current versions (3.3.2 or 3.4.0).

Hi

On https://cmor.llnl.gov/mydoc_contacts/ its written to subscribe to the cmor mailing list you need to send a mail with the content subscribe cmor to [email protected]. However, if I do this, I receive a mail with the following content:

> |subscribe cmor|
Unknown command - "|SUBSCRIBE". Try HELP.

We need to make sure that all the documentation is correct and up-to-date.

I don't think it is clear for CMIP6 where one should obtain the example input file and in general what CMOR needs. Please review and correct the following text for accuracy and then modify the documentation.

1. I think we should move https://github.com/PCMDI/cmor/blob/master/Test/CMOR_input_example.json to https://github.com/PCMDI/cmip6-cmor-tables/tree/master/Tables .

2. In its description of "Arguments", the function cmor_dataset_json(), documented in https://cmor.llnl.gov/mydoc_cmor3_api/ , currently points to https://raw.githubusercontent.com/PCMDI/cmor/master/Test/test2.json i . It should point to: https://github.com/PCMDI/cmip6-cmor-tables/tree/master/Tables .

3. Address the following issues 58, 55, 38, and 36 in https://github.com/PCMDI/cmor3_documentation/issues.
   Please insert the following text just before the paragraph that begins "Converting data with CMOR typically involves the following steps ...".

4. Most importantly, In the documentation on the "getting started overview page" at https://cmor.llnl.gov/ , please insert the following text just before the paragraph that begins "Converting data with CMOR typically involves the following steps ...". (First carefully check for correctness.)

The following input files are typically needed by CMOR:

• the "User Input File" (e.g., CMOR_input_example.json), which provides user-supplied metadata and configuration directives.
• A "controlled vocabulary file" (e.g., "CMIP6_CV.json), which concatenates into a single file most of the CMIP6 controlled vocabularies archived at https://github.com/WCRP-CMIP/CMIP6_CVs . This file is updated frequently as additional models and institutions register to participate in CMIP6.
• a "CMOR Table" (e.g., CMIP6_amon.json), which provides for each variable that might be written by CMOR much of the required metatdata. It also provides additional information that CMOR uses to correctly write the data and to enable certain QC checks.
• a "Vertical Coordinate Formula Terms Table" (e.g., CMIP6_formula_terms.json)
• a "Coordinates Table" (e.g., CMIP6_coordinate.json) CMIP6
• CMIP6_grids.json supplements the Coordinates Table with axis information that is sometimes needed in the treatment of unstructured grids.

The files used by CMOR for CMIP6 are archived in https://github.com/PCMDI/cmip6-cmor-tables/tree/master/Tables, and all but the CMOR_input_example.json file must not be modifed by the user. The CMOR_input_example.json file must be edited to accurately reflect the output being written by the user (but do not modify the lines of text appearing after the comment line, "#note": " **** The following will be obtained from the CV and do not need to be defined here"). Note that the CMIP6_CV.json file found in https://github.com/PCMDI/cmip6-cmor-tables/tree/master/Tables are updated whenever new models and institutions are registered to participate in CMIP6.

@dnadeau4 I think you should replace control with controlled in several places of https://cmor.llnl.gov/mydoc_cmor3_CV/ and possibly other pages, in order to be consistent with the way @durack1 is using it on https://github.com/WCRP-CMIP/CMIP6_CVs

@dnadeau4 @mattben it seems that the certificate for the https://cmor.llnl.gov site isn't correct, as below:

I am not an experienced user, so I just followed the instructions. Everything went ok until "make" phase. The computer complains about the absence of several mathematical functions (e.g., atan, log10, and so on) in the one of c-written code. The community advised to add -lm flag at the link phase, but I cannot understand where exactly it should be done. Any advice on how to change Makefile or something else?

E. Rozanov

Hi, i have every step of your installation guide (using the github source) but i was facing some issues:

1. i also had to install zlibrary form http://zlib.net/
2. i also had to install the m4 package (sudo apt-get install m4)
3. i also had to install python pip (sudo apt-get install python-pip)
4. using pip i needed to install numpy (sudo pip install numpy)
5. after compiling all the libraries i tried to import cmor and got following error:
_Traceback (most recent call last):
File "", line 1, in
File "/usr/local/lib/python2.7/dist-packages/CMOR-3.2-py2.7-linux-x86_64.egg/cmor/init.py", line 7, in
from cmor_const import *
File "/usr/local/lib/python2.7/dist-packages/CMOR-3.2-py2.7-linux-x86_64.egg/cmor/cmor_const.py", line 1, in
import cmor
ImportError: libnetcdf.so.11: cannot open shared object file: No such file or directory

To solve this issue i had to add the path to die shared lib to LD_LIBRARY_PATH! (in my case: export LD_LIBRARY_PATH=$HOME/build/lib)

maybe this could be mentioned in the installation guide!

Also most links to the dependencies are broken!
HDF5: https://www.hdfgroup.org/downloads/hdf5/source-code/
UDUNITS2: ftp://ftp.unidata.ucar.edu/pub/udunits/udunits-2.2.25.tar.gz

i used a Ubuntu 16.04 LTS VM for compiling CMOR

best regards,
Florian

Hi *,
first, thanks for your great work. I hope this is the right place for my questions.
With CMOR3, the cmor_write call changes in the C-version. Now, no file_suffix can be transferred as a parameter. How does CMOR then find the chunk file in append-mode in CMOR3? Could you please update the doc for cmor_write? It would be a great help, thanks a lot.

Another problem concerning the append-mode happens in CMOR-2.9.2 and some earlier versions, however I could not test it in CMOR3 yet: An error occurred with variables having a hybrid vertical axis. The auxiliary variable ps0 needs to be written with the parameter store_with in this case. However, the time axis is at least wrong or an error occurs when applying CMOR in append mode for these variables with hybrid vertical axes.
Are you aware of or can you reproduce the problem i tried to describe? ^^

The append mode is really helpful in the operational work and we would like to use it also for these kind of variables. So i am grateful for your help.

I work at the DKRZ and develop a CDO operator which uses the CMOR library.
So best regards from Germany,
Fabian Wachsmann

cmor_set_cur_dataset_attribute() is missing from the API documentation.

Hello,
Just a remark not very important : I see in fortran section "C source code" and not fortran source code
for fortran example in pdf file

• Add documentation for CMIP6Validator and cmip6_cv module
• Create Quicklook page with cmor API

1. The ncdump file for example 2 at https://cmor.llnl.gov/mydoc_cmor3_python/ has been corrupted: all of the upper-case letters have been made lower case.
2. In most (all?) of the examples, the time coordinates are incorrect. The calendar is set to "360-day", so January should be centered at 15 and February at 45; the bounds should be 0, 30, 60.
3. The "branch_method", "branch_time_in_parent", and "branch_time_in_child" attributes should all be omitted. If this is not possible, set branch_time_in_child = 0.0. Both branch times must be double precision, not float.

Hello,
I don't see cmor_axis in CMOR API documentation ??

There is a typo (charachter) at the beginning of https://cmor.llnl.gov/mydoc_cmip6_user_input/

Keys beginning with charachter # can be used as comment

In the file index.md there is a brief description of grid_mapping_name, in which a link to the CF conventions' grid mapping list in included. The link is dead. The (currently) correct URL is provided below

current bad url: http://cf-pcmdi.llnl.gov/documents/cf-conventions/1.1/cf-conventions.html#grid-mappings-and-projections

currently correct url: http://cfconventions.org/Data/cf-conventions/cf-conventions-1.7/cf-conventions.html#appendix-grid-mappings

The US Department of Energy wants public-facing DOE webpages to have following text and link as part of their footer.

Learn about the Department of Energy’s Vulnerability Disclosure Program

More on VDP:

VDP (Vulnerability Disclosure Program) is a centralized channel for the public to responsibly disclose vulnerabilities found in good faith and a centralized process and set of resources dedicated to vulnerability disclosure validation, triage, and routing for the enterprise.

• Having learned that installing cmor with Anaconda will install cdms2 and its dependencies, I think it would be interesting to make a note about that, and maybe mention UV-CDAT on the CMOR Anaconda installation page. PrePARE mentions CDMS (should it be CDMS2?) and links to the installation page that does not mention cdms... Well, I have just seen that the Installation page does not mention PrePARE either! Maybe you want to add a note about PrePARE in the installation :-)

• I wonder if there should be some introduction to the Installation section. I'm not sure following the Anaconda steps or the Github steps will get you the same thing in the end. I guess that with Anaconda you get a functioning python, the python wrapper of cmor and all the required dependencies, and PrePARE, but you don't get the fortran and C versions of CMOR (maybe there are there, but not easy to locate). And if you follow the Github steps, you get the fortran and C libraries, but maybe the python wrapper can't be used as is (because cdms2 is missing) and you don't get PrePARE?

cmor.llnl.gov uses an invalid security certificate. The certificate is only valid for the following names: pcmdi6.llnl.gov, aims.llnl.gov, cdp.llnl.gov, cf-pcmdi.llnl.gov, cf-trac.llnl.gov, icnwg.llnl.gov, esgf.llnl.gov, uvcdat.llnl.gov, uv-cdat.llnl.gov Error code: SSL_ERROR_BAD_CERT_DOMAIN

http://cmor.llnl.gov/ is redirecting to https://cmor.llnl.gov/ which is not a valid name for the certificate so it is impossible to visit the website without adding a security exception.

A possible problem with the documentation of the "units" argument of the cmor_variable and cmor_time_varying_grid_coordinate functions was raised: The documentation implies that if the unit is a (dimensionless) percentage, the user should pass units="percent", but I think it needs to pass "%". This is being checked and should be confirmed before making any change to the documentation.

The current contact page for the CMOR documentation contains outdated info. The last link under "CMIP6 table issues" is broken, and the mailing list info is for the defunct listserv email. I will remove the broken link, and replace the mailing list email with [email protected].

@durack1 @taylor13 Do you have other suggestsions?

In the anaconda installation documentation, '-c uvcdat' needs to be added to the conda create call:
conda create -n [YOUR_ENV_NAME_HERE] -c pcmdi -c uvcdat cmor

Is there any documentation to help in moving cmor2 code to cmor3 ?

Hello,
Page numbers are missing in table of contents in pdf file

Thanks

I'm following the instructions at

https://cmor.llnl.gov/mydoc_cmor3_conda/

and the process fails with the error

[...]
fatal: destination path 'cmor' already exists and is not an empty directory.
Traceback (most recent call last):
File "run_tests.py", line 3, in
from testsrunner import TestRunnerBase
ImportError: No module named testsrunner