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CDO CMOR help

Added by SUMAN MAITY over 4 years ago

Dear all
This is Dr. Suman from IIT Bombay. Recently I was applying cdo cmor for my model output. Unfortunately, I couldn't get successful. I used:
cdo -v cmor,CMIP6_Amon.json ECHAM_Temp_2007.nc

OpenMP: num_procs=12 max_threads=1 num_devices=0
cdo cmor: 1. Start to read configuration files.
cdo cmor: 1.1. No info file was passed to the operator.
cdo cmor: 1.2. Try to parse default file: '/home/suman/CMIP6_work/kk/.cdocmorinfo'.
cdo cmor: 1.2. Successfully parsed default file: '/home/suman/CMIP6_work/kk/.cdocmorinfo'.
cdo cmor: 1. Successfully read configuration files.
cdo cmor: 2. Start to find a MIP table and to deduce a frequency from MIP table file.
cdo cmor: 2.1. Start to check whether 'project_id' or 'mip_era' is denoted.
cdo cmor: You have not provided 'mip_era' but only 'project_id'. If you try to produce CMIP5 standard,
It is recommended to use CMOR2 for this job instead.
cdo cmor: 2.1. Successfully found project_id / mip_era: 'Test'.
cdo cmor: 2.2. Start to find a MIP table file.
cdo cmor: 2.2. MIP table file 'CMIP6_Amon.json' exists in MIP table directory '/home/suman/CMIP6_work/kk'.
cdo cmor: 2. Successfully found a MIP table 'CMIP6_Amon' and deduced a MIP table frequency 'Amon'.
cdo cmor: 3. Start to open infile 'ECHAM_Temp_2007.nc'.
cdo cmor: 3. Successfully opened infile 'ECHAM_Temp_2007.nc'.
cdo cmor: 4. Start to check attributes.
cdo cmor: 4.1. Start to check attribute 'required_time_units'.
cdo cmor (Warning): Required Attribute 'required_time_units' from configuration is invalid!
Continue with infile time units instead.
cdo cmor: 4.1. Successfully checked attribute 'required_time_units'.

cdo cmor (Abort): , rtu

I couldn't understand where is the problem. Please help as soon as possible how to solve it out.

Best
Suman


Replies (6)

RE: CDO CMOR help - Added by Fabian Wachsmann over 4 years ago

Dear Dr. Suman,
do you use a configuration table (/home/suman/CMIP6_work/kk/.cdocmorinfo) to specify the global attributes and control keywords?
Could you add it here?

Note that 'Test' in

cdo cmor: 2.1. Successfully found project_id / mip_era: 'Test'.

stops 'cdo cmor' from checking whether your attribute configuration from the info file is O.K for CMIP5/CMIP6.

However, the time units seem to be O.K. so I am trying to figure out what happened.

Best regards,
Fabi

RE: CDO CMOR help - Added by SUMAN MAITY over 4 years ago

Dear Fabi
Yah I am using the default configuration table ( to specify the global attributes and control keywords) .cdocmorinfo which is attached here.
It may happen that I am doing something wrong unknowingly.
Therefore it will be helpful for me if you provide some standard examples with my data file. I went through the hands-on ppt but couldn't find the solution.
I installed cdo cmor through anaconda (as mentioned in cdo cmor userguide).
Expecting reply from you.

Best
Suman

cdocmorinfo (176 Bytes) cdocmorinfo

RE: CDO CMOR help - Added by Fabian Wachsmann over 4 years ago

If I ran cdo cmor the way you did, I receive:

cdo cmor (Abort): Attribute 'institution' is required. Either it is missing or notSet.
          Make sure that you have configured all following attributes:
          institution, source, experiment_id, rtu

which might be a bit more helpful. Are these lines before ', rtu' not printed on your screen?

It means that your configuration table is incomplete.

Yah I am using the default configuration table

Where did you get this one? I am not aware of this as a default.
If you want to create a complete info table, I recommend to use this GUI:
https://c6dreq.dkrz.de/cdocmorinfo/index.html
at least for the creation of one complete table. The GUI allows you to create a setting with all CMIP6-required attributes.
For attributes which are part of the Controlled Vocabulary you can only specify allowed values.

If you register on that GUI, you will be able to save your configuration table on the c6dreq server from the DKRZ.

One addition:
The variable 'ta' (what is probably the one in your input) is requested in CMIP for different pressure levels:

grep '"ta":' CMIP6_* -A 10 | grep plev
CMIP6_6hrPlevPt.json-            "dimensions": "longitude latitude plev3 time1", 
CMIP6_AERmonZ.json-            "dimensions": "latitude plev39 time", 
CMIP6_Amon.json-            "dimensions": "longitude latitude plev19 time", 
CMIP6_day.json-            "dimensions": "longitude latitude plev8 time", 
CMIP6_E1hr.json-            "dimensions": "longitude latitude plev3 time1", 
CMIP6_Eday.json-            "dimensions": "longitude latitude plev19 time", 
CMIP6_EdayZ.json-            "dimensions": "latitude plev19 time",


These numbers in the respective name of the plevs define the least number of levels that is requested. You are allowed to publish more but at least exactly the levels defined for that plev* axis.

The specific levels that are requested in each plev* are defined in the MIP-Table CMIP6_coordinate.json
Check that you provide ta on these levels.

Because different plev* axes might be requested in one MIP-Table, you also have to specify for example

z_axis=plev19

in the cmdline (or mapping table) - plev19 in the case of ta in CMIP6_Amon.json

Best regards,
Fabi

RE: CDO CMOR help - Added by SUMAN MAITY over 4 years ago

Dear Fabi
Thank you very much for your elaborated reply.But unfortunately, I am not clear and that's why couldn't proceed further.

1) For your kind information, the message you mentioned earlier (cdo cmor (Abort): Attribute 'institution' is required......), I am not getting in my screen. Which version are you using? I am using cdo-1.9.6 which comes with conda install (mentioned in cdo cmor user guide). I don't know what is the reason for that?
2) That configuration file I prepared for testing as I didn't know how to create that. As you told, I explored https://c6dreq.dkrz.de/cdocmorinfo/index.html but couldn't understand how to prepare the .cdocmorinfo file. Will you help me in step by step procedure? I couldn't understand where to go ("All attributes", "Source file", "Experiment file", "User file") in the website?
3) How to get registered with https://c6dreq.dkrz.de/cdocmorinfo/index.html? I saw there is no option to get registered.
4) I would like to request you to reply with step by step guide for a successful application of cdo cmor (command, files etc.). It will be very useful for me if you share a test data file and other required files along with various command used for different steps.
Please help me.

Best
Suman

RE: CDO CMOR help - Added by SUMAN MAITY over 4 years ago

Dear Fabi
I registered on that GUI (DKRZ) but couldn't understand how to proceed. Please help me by replying.

Best
Suman

RE: CDO CMOR help - Added by SUMAN MAITY over 4 years ago

Dear Fabi
This is a gentle reminder of my earlier email. Please reply. It will help me a lot.
Expecting a response from you,

Best
Suman

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