MPAS SST update file

[zmenzo]

Hello,

I have successfully run the MPAS-Atmosphere model without SST update files. I have successfully created the necessary srf_update file and made the appropriate changes to the streams list and name list files as instructed in the user's guide. However, when I run the atmosphere executable it instantly creates a log.atmosphere.0000.out file. (tail of the log.atmo file):

*** unable to open input file restart.2016-01-16_00.00.00.nc for stream 'restart'

*** unable to open input file x1.40962.AmB.2016-01-16_00.00.00.nc for stream 'iau'

*** unable to open input file lbc.2016-01-16_00.00.00.nc for stream 'lbc_in'

----- reading dimensions from stream 'surface' using file x4.535554.enso.sfc_update.nc
nCells = 535554

----- done reading dimensions from input streams -----


Processing decomposed dimensions ...

----- done processing decomposed dimensions -----


Assigning remaining dimensions from definitions in Registry.xml ...
THREE = 3
TWENTYONE = 21
nLags = 140 (input_soil_temperature_lag)
nOznLevels = 59 (noznlev)
nAerLevels = 29 (naerlev)
cam_dim1 = 4 (camdim1)
nVertLevelsP2 = 57
nIsoLevelsT = 5
nIsoLevelsZ = 13

----- done assigning dimensions from Registry.xml -----


WARNING: Variable qi not in input file.
WARNING: Variable qs not in input file.
WARNING: Variable qg not in input file.


It does not create an error log file which is making troubleshooting difficult. I have attached a copy of the namelist and streamslist files in addition to my working directory. Any suggestions would be greatly appreciated.

Zach

 

[mgduda]

There's nothing that I can see in your namelist or streams file that looks incorrect. If you're running on Cheyenne, do you see any error codes or signal numbers in the output produced by PBS (i.e., in your job's stdout/stderr file) that would indicate any reason for the failure? How many nodes, and in which queue are you running?

 

[zmenzo]

I figured it out! I downloaded a mesh file that was read-only. While I turned the gird file into a writable format, I also needed to do this for the decomposition and graph.info files. Thanks.

 

[mgduda]

It's good to hear you've been able to get SST updates working. I'm a bit surprised that simply changing the permissions of the grid and decomposition files had any effect -- the model only reads these files, and so having write permissions shouldn't make any difference. For what it's worth, it has been our experience that jobs can mysteriously fail on Cheyenne, and simply resubmitting the same job allows it to run the second time around.

 

[EMMANUEL]

I would like to know whether this way has resolved the issue?

 

[mgduda]

I would like to know whether this way has resolved the issue?

It's not clear in my mind what exactly was needed to resolve this, as I'm not convinced that making input files writable was necessary. Are you encountering a similar issue?

 

[EMMANUEL]

Yes I am facing the same issue. Can you kindly suggest me on this

 

[mgduda]

Yes I am facing the same issue. Can you kindly suggest me on this

Can you verify that the model runs correctly if you do not try to read a surface update file? In your namelist.atmosphere file, you'll need to set config_sst_update = false, and in your streams.atmosphere file, you'll need to set input_interval = "none" for the "surface" stream.

Also, which mesh are you using, and how many nodes or MPI tasks are you running with?

 

[EMMANUEL]

I tried config_sst_update = false (namelist)
config_sst_update = false (streams)
The error remain same

Is there anything to be changed here coz as per the error it is indicated that restart file is not available
<immutable_stream name="restart"
type="input;output"
filename_template="restart.$Y-$M-$D_$h.$m.$s.nc"
input_interval="initial_only"
output_interval="6_00:00:00" />


I'm using 240km uniform mesh (x1.10242.graph.info.part.64) and (ppn=36 nodes=2)

 

[mgduda]

If you've turned off SST updates and you're still seeing an error, then it sounds like the issue may not be the same as the one described by the original post in this thread. Just to confirm, you've set input_interval = "none" in the "surface" stream in your streams.atmosphere file (and not "config_sst_update = false (streams)" as you mentioned above), right?

With 2 nodes and 36 processors per node, it may be that you need a x1.10242.graph.info.part.72 file in your run directory rather than a x1.10242.graph.info.part.64 file. Are you using 64 or 72 MPI tasks?

Can you attach any log files that are created in your run directory?

 

[EMMANUEL]

If you've turned off SST updates and you're still seeing an error, then it sounds like the issue may not be the same as the one described by the original post in this thread. Just to confirm, you've set input_interval = "none" in the "surface" stream in your streams.atmosphere file (and not "config_sst_update = false (streams)" as you mentioned above), right?

With 2 nodes and 36 processors per node, it may be that you need a x1.10242.graph.info.part.72 file in your run directory rather than a x1.10242.graph.info.part.64 file. Are you using 64 or 72 MPI tasks?

Can you attach any log files that are created in your run directory?

Thank you Mr. mgduda for your support
I could find the problem in the model run. The problem was generated from the static file, regeneration of it has solved the issue and it works now without an error.