error saving salinity

[Veronica Tamsitt]

Hi all,

I'm running CMS with my own MOM5 output. I've been running it successfully with u,v,w for a while but would like to also save temperature and salinity along trajectories.

I am running into the following error:

 Error: You set outputsaln to true but there are no salinity files

If I make outputsaln=.false. in ibm.list, then it runs fine and saves temperature, but for some reason isn't working with salinity as well. I am generating separate nest files for T and S in the same way, and as far as I can tell I am using consistent naming conventions for the T and S variables.

I've looked into the code a bit and see where the error is occurring in getphysicaldata.f90, and it looks like it can't find the salinity files, which points to a problem with the salnname. I may be missing something obvious, but I haven't been able to figure it out.

I've copied my nest_1.nml file below as well as output from ncdump for both a T and S nest file.

Thanks in advance!

Veronica

&nest_input

 axorderX=4

 axorderY=3

 axorderZ=2

 axorderT=1

 xstart= 80.1

 xend= 80.0

 ystart=-90

 yend=-57

 zstart= 0.541281

 zend= 5709.44

 zaxis_positive_direction= "down"

 tstart_yy=80

 tstart_mm=1

 tstart_dd=1

 tend_yy=84

 tend_mm=12

 tend_dd=31

 time_step=86400

 time_units= "days"

 lon_nameU= "xu_ocean"

 lat_nameU= "yu_ocean"

 lon_nameV= "xu_ocean"

 lat_nameV= "yu_ocean"

 lon_nameW= "xt_ocean"

 lat_nameW= "yt_ocean"

 lon_nameT= "xt_ocean"

 lat_nameT= "yt_ocean"

 dep_nameU= "st_ocean"

 dep_nameV= "st_ocean"

 dep_nameW= "sw_ocean"

 dep_nameT= "st_ocean"

 time_name= "time"

 uvel_name= "u"

 vvel_name= "v"

 wvel_name= "wt"

 wvel_positive_direction = "upward"

 velocity_conversion_factor=1

 temp_name="t"

 saln_name="s"

 fill_value=1.2676506E30

 agrid=.false.

 orthogrid=.true.

$end

e

netcdf nest_1_00800101000000s {

dimensions:

        time = UNLIMITED ; // (1 currently)

        st_ocean = 75 ;

        yt_ocean = 548 ;

        xt_ocean = 3600 ;

variables:

        float time(time) ;

                time:units = "days since 0001-01-01 00:00:00" ;

                time:calender_type = "JULIAN" ;

                time:calender = "JULIAN" ;

        float st_ocean(st_ocean) ;

                st_ocean:units = "metres" ;

                st_ocean:long_name = "tcell zstar depth" ;

                st_ocean:positive = "down" ;

        float yt_ocean(yt_ocean) ;

                yt_ocean:units = "degrees_N" ;

                yt_ocean:long_name = "tcell latitude" ;

        float xt_ocean(xt_ocean) ;

                xt_ocean:units = "degrees_E" ;

                xt_ocean:long_name = "tcell longitude" ;

        float s(time, st_ocean, yt_ocean, xt_ocean) ;

                s:_FillValue = 1.267651e+30f ;

                s:units = "PSU" ;

                s:long_name = "salinity" ;

// global attributes:

                :description = "KDS75" ;

netcdf nest_1_00800101000000t {

dimensions:

        time = UNLIMITED ; // (1 currently)

        st_ocean = 75 ;

        yt_ocean = 548 ;

        xt_ocean = 3600 ;

variables:

        float time(time) ;

                time:units = "days since 0001-01-01 00:00:00" ;

                time:calender_type = "JULIAN" ;

                time:calender = "JULIAN" ;

        float st_ocean(st_ocean) ;

                st_ocean:units = "metres" ;

                st_ocean:long_name = "tcell zstar depth" ;

                st_ocean:positive = "down" ;

        float yt_ocean(yt_ocean) ;

                yt_ocean:units = "degrees_N" ;

                yt_ocean:long_name = "tcell latitude" ;

        float xt_ocean(xt_ocean) ;

                xt_ocean:units = "degrees_E" ;

                xt_ocean:long_name = "tcell longitude" ;

        float t(time, st_ocean, yt_ocean, xt_ocean) ;

                t:_FillValue = 1.267651e+30f ;

                t:units = "degrees C" ;

                t:long_name = "temperature" ;

// global attributes:

                :description = "KDS75" ;

[Veronica Tamsitt]

This issue has been resolved.

It turns out the documentation says that when using your own nest files you need to create individual nest files for each variable, but actually the code reads temperature, salinity, sea surface height etc all as different variables from within a single file, named *t.nc (e.g. nest_1_yyyymmddhhmmsst.nc)

From the documentation:

'You can also add vertical velocity (w), temperature (t), and salinity (s) files as needed. So for each time

step for which oceanographic files are available, you will need at least two and up to 5 different files. Each

file will store only one field (u, v, w, t or s).'

I will flag this issue on the Github page.

Thanks,

Veronica

[Robin F]

Hi Veronica,

Thank you for debugging this issue and for flagging it on Github, it’s probably going to help other users in the future.

Best,

> Le 24 mars 2019 à 22:43, Veronica Tamsitt <veronica...@gmail.com> a écrit :
>
> This issue has been resolved.
>
> It turns out the documentation says that when using your own nest files you need to create individual nest files for each variable, but actually the code reads temperature, salinity, sea surface height etc all as different variables from within a single file, named *t.nc (e.g. nest_1_yyyymmddhhmmsst.nc)
>
> From the documentation:
> 'You can also add vertical velocity (w), temperature (t), and salinity (s) files as needed. So for each time
> step for which oceanographic files are available, you will need at least two and up to 5 different files. Each
> file will store only one field (u, v, w, t or s).'
>
> I will flag this issue on the Github page.
>
> Thanks,
>
> Veronica
>

--

Robin Faillettaz, Ph.D
——————————————————————

Postdoctoral Research Fellow
RECOVER2 project
University of Miami
Rosenstiel School of Marine & Atmospheric Science
4600 Rickenbacker Causeway, Miami, FL 33149-1098, USA
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Robin.Fa...@gmail.com
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