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Guidance on Running with LME datasets with CESM2.1.3 (CLM5)

wvsi3w

wvsi3w

wvsi3w
Member
oleson said:
I doubt there is a problem with the finidat file since that file would be interpolated to your new grid/domain at the beginning of the simulation and your simulation runs fine for a number of years.
One question I have is why do you have the anomaly forcing repeated in the file above, i.e.,

"datm.streams.txt.Anomaly.Forcing.Precip 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Temperature 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Pressure 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Humidity 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Uwind 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Vwind 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Shortwave 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Longwave 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Precip 2006 2006 2300",
"datm.streams.txt.Anomaly.Forcing.Temperature 2006 2006 2300",
"datm.streams.txt.Anomaly.Forcing.Pressure 2006 2006 2300",
"datm.streams.txt.Anomaly.Forcing.Humidity 2006 2006 2300",
"datm.streams.txt.Anomaly.Forcing.Uwind 2006 2006 2300",
"datm.streams.txt.Anomaly.Forcing.Vwind 2006 2006 2300",
"datm.streams.txt.Anomaly.Forcing.Shortwave 2006 2006 2300",
"datm.streams.txt.Anomaly.Forcing.Longwave 2006 2006 2300"

Also, I'd check the precipitation anomaly forcing file to make sure it has valid data throughout time, could it be corrupted from a bad download?
Click to expand...
Yes that was odd for me. At first, I thought this could be normal.

Also, this is my user_nl_datm file:

Code: 
anomaly_forcing = "Anomaly.Forcing.Precip","Anomaly.Forcing.Temperature","Anomaly.Forcing.Pressure","Anomaly.Forcing.Humidity","Anomaly.Forcing.Uwind","Anomal
y.Forcing.Vwind","Anomaly.Forcing.Shortwave","Anomaly.Forcing.Longwave"

fillalgo = "nn", "nn", "nn", "nn", "nn", "nn", "nn", "nn", "nn", "nn", "nn", "nn", "nn"

streams = "datm.streams.txt.CLMGSWP3v1.Solar 2000 2000 2014",
"datm.streams.txt.CLMGSWP3v1.Precip 2000 2000 2014",
"datm.streams.txt.CLMGSWP3v1.TPQW 2000 2000 2014",
"datm.streams.txt.presaero.SSP2-4.5 2015 2015 2101",
"datm.streams.txt.topo.observed 1 1 1",
"datm.streams.txt.co2tseries.SSP2-4.5 2015 2015 2500",
"datm.streams.txt.Anomaly.Forcing.Precip 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Temperature 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Pressure 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Humidity 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Uwind 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Vwind 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Shortwave 2015 2015 2100",
"datm.streams.txt.Anomaly.Forcing.Longwave 2015 2015 2100"

As you see, the anomaly list is not repeated in my namelist. I don't know why datm_in is showing a repeated list, also the repeated part is showing a different range (2006-2300) while my namelist was from 2015-2100!!!

Do you suggest removing these repeated lines manually and starting again from the beginning?

About the "precipitation anomaly forcing file" I checked the "pr" variable in both files (af.allvars.CESM.SSP1-2.6.2015-2100_c20220628.nc & af.allvars.CESM.SSP2-4.5.2015-2100_c20220628.nc), and they are valid.
 
O

oleson

Keith Oleson
CSEG and Liaisons
Staff member
I don't know why the repeated lines are being generated in your resolved datm_in. You are still usihg release-cesm2.1.3?
What domain file are you using for the anomaly forcing, e.g., in your datm.streams.txt.Anomaly.Forcing.Precip? It should be domain.b.e21.BHIST.f09_g17.CMIP6-historical.010.c200203.nc
 
wvsi3w

wvsi3w

wvsi3w
Member
oleson said:
I don't know why the repeated lines are being generated in your resolved datm_in. You are still usihg release-cesm2.1.3?
What domain file are you using for the anomaly forcing, e.g., in your datm.streams.txt.Anomaly.Forcing.Precip? It should be domain.b.e21.BHIST.f09_g17.CMIP6-historical.010.c200203.nc
Click to expand...
Yes I am still using 2.1.3 because my second objective hasn't yet finished.

That is odd because the anomaly forcing files initially had this domain (domain.permafrostRCN_P2.c2013.nc) written in them so I thought I shouldnt change it:

e.g. datm.streams.txt.Anomaly.Forcing.Precip :
Code: 
<?xml version="1.0"?>
<file id="stream" version="1.0">
<dataSource>
   GENERIC
</dataSource>
<domainInfo>
  <variableNames>
     time    time
        xc      lon
        yc      lat
        area    area
        mask    mask
  </variableNames>
  <filePath>
 /scratch/USER/cesm/inputdata/atm/datm7/anomaly
  </filePath>
  <fileNames>
     domain.permafrostRCN_P2.c2013.nc
  </fileNames>
</domainInfo>
<fieldInfo>
   <variableNames>
     pr  prec_af
   </variableNames>
   <filePath>
 /scratch/USER/cesm/inputdata/atm/datm7/anomaly
   </filePath>
   <fileNames>
    af.allvars.CESM.SSP1-2.6.2015-2100_c20220628.nc
   </fileNames>
   <offset>
      0
   </offset>
</fieldInfo>
</file>

I will change it to what you mentioned and let you know how it goes.
 
wvsi3w

wvsi3w

wvsi3w
Member
Dear Keith,
I have tried downloading the domain (domain.b.e21.BHIST.f09_g17.CMIP6-historical.010.c200203.nc), and it fails to find it:
Code: 
svn export failed with output:  and errput svn: E170000: URL 'https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/atm/datm7/anomaly_forcing/domain.b.e21.BHIST.f09_g17.CMIP6-historical.010.c200203.nc' doesn't exist

Checking server None with protocol None
Setting resource.RLIMIT_STACK to 300000000 from (300000000, -1)
Client protocol None not enabled
ERROR: Could not find all inputdata on any server

To get it manually with wget, I also couldn't find the domain file online (is not in this link either: - Revision 70792: /trunk/inputdata/share/domains )
 
O

oleson

Keith Oleson
CSEG and Liaisons
Staff member
Well, the domain file you are using should work as well, since it has a mask of 1 everywhere on the grid and there is precip anomaly forcing everywhere.
I guess I would check your atm log file and see what atmospheric (not anomaly) forcing is being read in and then check the precip field on that forcing file. Since the model is failing at the same point no matter what the SSP is, it seems like that might point to a problem with the forcing.
 
wvsi3w

wvsi3w

wvsi3w
Member
oleson said:
Well, the domain file you are using should work as well, since it has a mask of 1 everywhere on the grid and there is precip anomaly forcing everywhere.
I guess I would check your atm log file and see what atmospheric (not anomaly) forcing is being read in and then check the precip field on that forcing file. Since the model is failing at the same point no matter what the SSP is, it seems like that might point to a problem with the forcing.
Click to expand...
Thank you
It was indeed one of the files from Precip. I checked the atm log file, and it ended in these:
Code: 
/scratch/USER/cesm/inputdata/atm/datm7/atm_forcing.datm7.GSWP3.0.5d.v1.c170516/Precip/clmforc.GSWP3.c2011.0.5x0.5.Prec.2003-09.nc     169
(shr_dmodel_readstrm) file ub: /scratch/USER/cesm/inputdata/atm/datm7/atm_forcing.datm7.GSWP3.0.5d.v1.c170516/TPHWL/clmforc.GSWP3.c2011.0.5x0.5.TPQWL.2003-09.nc     169
(datm_comp_run) atm: model date 20330921   82800s
(datm_comp_run) atm: model date 20330921   84600s
(datm_comp_run) atm: model date 20330922       0s
(shr_dmodel_readstrm) file ub: /scratch/USER/cesm/inputdata/atm/datm7/atm_forcing.datm7.GSWP3.0.5d.v1.c170516/Solar/clmforc.GSWP3.c2011.0.5x0.5.Solr.2003-09.nc     170
(datm_comp_run) atm: model date 20330922    1800s

So I checked the 2003-09 Precip file with ncview, and it was indeed damaged in the middle. removed it and downloaded it again and continued the run, but again another file was broken (2004-01), so I did the same thing, and it is running now.

Do you know what we should do if this happens a lot? I mean, is there a way to check the forcing files when we download them with some command or some script to see if they are all ok and not damaged?
 
O

oleson

Keith Oleson
CSEG and Liaisons
Staff member
I'm not sure, maybe something like: ./check_input_data --download --debug, or ./check_input_data --download --chksum?
 
wvsi3w

wvsi3w

wvsi3w
Member
oleson said:
I'm not sure, maybe something like: ./check_input_data --download --debug, or ./check_input_data --download --chksum?
Click to expand...
Thanks for your help.
I have found another issue which is weird:

Code: 
 (shr_strdata_advance) ERROR: for stream           15
 (shr_strdata_advance) ERROR: dt limit1    76316.0000000000
   28.0000000000000        1.50000000000000
 (shr_strdata_advance) ERROR: dt limit2     20150116           0    20150213
           0
 ERROR: (shr_strdata_advance) ERROR dt limit for stream

If you remember last time, I had an error regarding the dtlimit (Guidance on Running with LME datasets with CESM2.1.3 (CLM5)), and you suggested using 1.e36 to get around it.

This time, instead of starting from 2020, I was trying to start my SSP run from 2015, and I faced the same error! This didn't happen when I started with 2020 restart file.

I am using the restart file from that simulation where dtlimit in its user_nl_datm was set to 1.e36 (from 2000-2015).

Prior to this, I was starting from 2020-01-01, and the restart file from 2020-01-01 is from a simulation in which the dtlimit was also set to 1.e36 in the datm user namelist file, but my SSP run (from 2020 onwards) didn't have any problem and is running now.

I only see this error when I am starting from earlier (like 2015).

Do you think this occurs because the 2015-2020 simulation was forced with a SSP and the 2000-2015 simulation was not? (In both, I did set dtlimit to 1.e36, I don't know what is wrong here)

I think I should set dtlimit to 1.e36 if I want to run from 2015-2100 using the restart file from 2015 (?)
 
wvsi3w

wvsi3w

wvsi3w
Member
wvsi3w said:
Thanks for your help.
I have found another issue which is weird:

Code: 
 (shr_strdata_advance) ERROR: for stream           15
 (shr_strdata_advance) ERROR: dt limit1    76316.0000000000
   28.0000000000000        1.50000000000000
 (shr_strdata_advance) ERROR: dt limit2     20150116           0    20150213
           0
 ERROR: (shr_strdata_advance) ERROR dt limit for stream

If you remember last time, I had an error regarding the dtlimit (Guidance on Running with LME datasets with CESM2.1.3 (CLM5)), and you suggested using 1.e36 to get around it.

This time, instead of starting from 2020, I was trying to start my SSP run from 2015, and I faced the same error! This didn't happen when I started with 2020 restart file.

I am using the restart file from that simulation where dtlimit in its user_nl_datm was set to 1.e36 (from 2000-2015).

Prior to this, I was starting from 2020-01-01, and the restart file from 2020-01-01 is from a simulation in which the dtlimit was also set to 1.e36 in the datm user namelist file, but my SSP run (from 2020 onwards) didn't have any problem and is running now.

I only see this error when I am starting from earlier (like 2015).

Do you think this occurs because the 2015-2020 simulation was forced with a SSP and the 2000-2015 simulation was not? (In both, I did set dtlimit to 1.e36, I don't know what is wrong here)

I think I should set dtlimit to 1.e36 if I want to run from 2015-2100 using the restart file from 2015 (?)
Click to expand...
I did set the dtlimit in user_nl_datm to 1.e36 for a case that starts from 2015 (for all of the 13 streams), and it failed with the same error!

I guess I have to start from 2020 :(
 
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