Search found 74 matches

by pmaccc
Sat Nov 18, 2023 3:39 pm
Forum: Ocean News
Topic: ROMS development cost according to the SCC program
Replies: 1
Views: 16426

Re: ROMS development cost according to the SCC program

Cheap at twice the price!
by pmaccc
Sun Oct 15, 2023 10:52 pm
Forum: ROMS Bugs
Topic: two solutions for sst with the same configuration
Replies: 4
Views: 6394

Re: two solutions for sst with the same configuration

The image on the right looks like it is having problems getting open boundary information into the domain. Are you using exactly the same open boundary conditions in the dot-in, and the same values in the boundary file? Also if you are using nudging to climatology, is the climatology the same, and i...
by pmaccc
Thu Oct 12, 2023 3:13 pm
Forum: Ocean News
Topic: John S. Allen (1937-2023)
Replies: 5
Views: 14489

Re: John S. Allen (1937-2023)

Indeed. So much of what we are able to do in our field has relied on the ideas, tools, and persistent encouragement that he provided. Let us all grab a chair in the front row in his honor.
by pmaccc
Thu Oct 12, 2023 3:10 pm
Forum: ROMS Discussion
Topic: diagnostics
Replies: 10
Views: 11875

Re: diagnostics

I think you can use: temp_rate = <d(temp*v)/dt>/<v> = <v>*<d(temp)/dt>/<v> + <temp>*<d(v)/dt>/<v> = <d(temp)/dt> + <temp>*<d(v)/dt>/<v> and then rearrange to find: <d(temp)/dt> = temp_rate - <temp>*<d(v)/dt>/<v> You can calculate the LHS using the difference of temp from two history files (the ones ...
by pmaccc
Tue May 16, 2023 2:06 pm
Forum: ROMS Discussion
Topic: Bottom Friction and How to Slow Down Currents in Shallow Regions
Replies: 11
Views: 7589

Re: Bottom Friction and How to Slow Down Currents in Shallow Regions

One hack we have used is to modify the nudgcoef.nc array, adding a non-zero inverse timescale to places we want to slow down. This is a 3-D array so you can have variation in the vertical as well as horizontal. Then we set u, and v to zero in the ocean_clm.nc in the same regions, and turn on momentu...
by pmaccc
Tue Apr 18, 2023 3:28 pm
Forum: ROMS Ecosystem
Topic: Biological Tracer from River
Replies: 6
Views: 10061

Re: Biological Tracer from River

Related to this, I found I had to make some edits to varinfo.yaml in order to get it to work with the fennel.h code. Specifically here is the diff between my edited version and the original version: (loenv) MacBook-Pro-6:varinfo pm8$ diff varinfo.yaml ORIG_varinfo.yaml 44c44 < #svn_repository: $URL:...
by pmaccc
Fri Mar 03, 2023 8:16 pm
Forum: ROMS Discussion
Topic: ROMS crashing when using LwSrc
Replies: 18
Views: 32705

Re: ROMS crashing when using LwSrc

Dear ROMS folks, we are still having the problem Aurora describes above when using LwScr. She has tried many things to fix this: -carefully checking the forcing files -injecting the source at all levels, or at the top level, instead of the bottom level -trying different advection schemes (A4 instead...
by pmaccc
Mon Jan 30, 2023 8:25 pm
Forum: ROMS Discussion
Topic: ROMS crashing when using LwSrc
Replies: 18
Views: 32705

Re: ROMS crashing when using LwSrc

John, Parker here - I am part of the project that Aurora is writing about. We have tried running versions of our model with HSIMT for salt + temp (instead of MPDATA) and it has given really poor results, essentially eroding most of the stratification in a model of Hood Canal. Hence I am not excited ...
by pmaccc
Sat Dec 17, 2022 6:06 pm
Forum: ROMS Discussion
Topic: How to calculate flux to one basin through strait
Replies: 2
Views: 2696

Re: How to calculate flux to one basin through strait

We generally calculate fluxes through sections using hourly saved output (for runs with tidal variability), and then calculating the transport at each time on the native u- or v-grid, interpolating h, zeta, salt, temp, etc. from neighboring rho-grid points onto the velocity grid. You can also do thi...
by pmaccc
Mon Nov 28, 2022 11:03 pm
Forum: ROMS Installation
Topic: US Supercomputers
Replies: 0
Views: 2727

US Supercomputers

Dear ROMS folk, does anyone have experience to share about running ROMS on any of the national supercomputers available through the NSF ACCESS (formerly XSEDE) system? The list of possible resources is here: https://allocations.access-ci.org/resources.

Thanks,

Parker
by pmaccc
Tue Sep 13, 2022 4:20 pm
Forum: Job Opportunities
Topic: Postdoc: Victoria BC, Coastal Carbon Sequestration
Replies: 0
Views: 1993

Postdoc: Victoria BC, Coastal Carbon Sequestration

Come join our team investigating the carbon sequestration potential of Canada's coastal oceans! You'll need experience working with ROMS for coastal ocean downscaling, and enthusiasm for working in an interdisciplinary team. Please apply by September 30, 2022, though we will accept applications unti...
by pmaccc
Fri Jul 08, 2022 3:48 pm
Forum: ROMS Information
Topic: LIMIT_VVISC
Replies: 5
Views: 7175

LIMIT_VVISC

I see in this ticket from Hernan: https://www.myroms.org/projects/src/ticket/736 that the ability to limit the eddy viscosity and diffusivity was introduced about 5 years ago (e.g. if LIMIT_VVISC is defined in your .h then the code will use AKV_LIMIT from your .in, and the default in ocean.in is 10^...
by pmaccc
Fri Jun 10, 2022 3:33 pm
Forum: ROMS Problems
Topic: swrad in varinfo.yaml
Replies: 1
Views: 1753

Re: swrad in varinfo.yaml

Never mind this question - I figured out that I had inadvertently defined ANA_SRFLUX. Oops!
by pmaccc
Thu Jun 09, 2022 11:19 pm
Forum: ROMS Problems
Topic: swrad in varinfo.yaml
Replies: 1
Views: 1753

swrad in varinfo.yaml

I am using fairly up-to-date ROMS code, including the new varinfo.yaml. It does not seem to be reading my swrad.nc atmospheric forcing file. I wonder if this is a problem with how I am interacting with the SWRAD alias in varinfo.yaml. It reads all the other atm forcing files just fine. Thanks, Parker
by pmaccc
Mon Apr 25, 2022 4:37 pm
Forum: ROMS Installation
Topic: compile ROMS error
Replies: 12
Views: 16936

Re: compile ROMS error

Excellent suggestion. You are a genius! It turned out that in my ROMS source folder the makefile was old (rev. 968). Notably, I had created that folder using git clone, and for some reason when I did git pull it did not update the makefile. Weird. In any case I have gone back to getting the source u...
by pmaccc
Mon Apr 25, 2022 3:53 pm
Forum: ROMS Installation
Topic: compile ROMS error
Replies: 12
Views: 16936

Re: compile ROMS error

Thanks for the tip. Unfortunately it did not change things. Even compiling with an exact copy of the latest Linux-ifort.mk produces the same error message: [pmacc@n3263 test0]$ ./build_roms.sh rm -f -r core *.ipo /gscratch/macc/parker/LO_roms_user/test0/Build_roms /mmfs1/home/pmacc/make_macros.mk cp...
by pmaccc
Sun Apr 24, 2022 4:51 pm
Forum: ROMS Installation
Topic: compile ROMS error
Replies: 12
Views: 16936

Re: compile ROMS error

Dear all, I'm having trouble compiling after updating to the most recent version. I had been able to compile with a fairly recent version (after the introduction of the new varinfo.yaml file). Now when I run my build_roms.sh it fails quickly, with only this output: [pmacc@n3263 test0]$ ./build_roms....
by pmaccc
Fri Mar 04, 2022 7:27 pm
Forum: ROMS Bugs
Topic: Typos in roms.in and varinfo.dat
Replies: 2
Views: 4126

Re: Typos in roms.in and varinfo.dat

I think a couple of other river variables required by the Fennel code may also be missing from varinfo.dat. In fennel_var.h (release 1054) it asks for: CASE ('idRtrc(iPhyt)') idRtrc(iPhyt)=varid CASE ('idRtrc(iZoop)') idRtrc(iZoop)=varid but there are no phytoplankton or zooplankton river fields in ...
by pmaccc
Mon Jan 17, 2022 6:04 pm
Forum: ROMS Ecosystem
Topic: Light attenuation in Fasham
Replies: 4
Views: 8617

Re: Light attenuation in Fasham

I think that the units of AttChl are still given incorrectly in the latest version of ROMS/External/bio_Fennel.in:

! Light attenuation by chlorophyll [1/(mg_Chl m2)], {0.02486d0}.

AttChl == 0.02486d0

Should be [m2 / (mg Chl)] right?
by pmaccc
Mon Dec 06, 2021 10:37 pm
Forum: ROMS Problems
Topic: zero_phase_date
Replies: 1
Views: 3475

zero_phase_date

I am updating my system to use the most recent version of ROMS (my current version is from 2016, oops!). I am able to run the upwelling example on my cluster, but when I try to run using my realistic forcing ROMS appears to halt right after successfully reading the initial state from a history file,...
by pmaccc
Thu Dec 02, 2021 5:30 pm
Forum: ROMS Installation
Topic: How to organize custom bio code
Replies: 3
Views: 6647

Re: How to organize custom bio code

Hernan and John, thanks so much for your answers - very helpful!
by pmaccc
Wed Dec 01, 2021 8:52 pm
Forum: ROMS Installation
Topic: How to organize custom bio code
Replies: 3
Views: 6647

How to organize custom bio code

Dear ROMS-ulans, I have some custom bio code based on fennel. In the past I have kept it all in ROMS/Nonlinear/Biology next to all the other bio code. However, I am updating everything to the latest ROMS revision, and would like to keep my edits out of the svn repo as much as possible. I have found ...
by pmaccc
Sun Nov 14, 2021 6:34 pm
Forum: ROMS Problems
Topic: Boundary forcing error (t3dbc_im)
Replies: 8
Views: 15041

Re: Boundary forcing error (t3dbc_im)

Sam,

I'm having a very similar problem to the one you describe, I think. When ROMS reads my boundary forcing for SSH the min values are zero (in the log) even though I can find no zeros in the bry.nc file. What was it you did to solve your problem?

Thanks,

Parker
by pmaccc
Mon Nov 08, 2021 10:16 pm
Forum: Job Opportunities
Topic: Two Postdocs at University of Victoria
Replies: 0
Views: 1946

Two Postdocs at University of Victoria

Great opportunity to work on climate effects on coastal waters:

https://hansialice.github.io/posts/2021 ... rtunities/
by pmaccc
Tue Nov 02, 2021 4:46 pm
Forum: ROMS Bugs
Topic: tiling and divide by zero error
Replies: 10
Views: 18198

Re: tiling and divide by zero error

I'll look into updating the version. What always holds my group back on this topic is that we have a custom NPZD model - mostly is it separate programs, but it requires a few edits to the ROMS source code as well. I'd like to design my system to absorb ROMS updates more easily. We are not using nest...
by pmaccc
Tue Nov 02, 2021 4:16 pm
Forum: ROMS Bugs
Topic: tiling and divide by zero error
Replies: 10
Views: 18198

Re: tiling and divide by zero error

Hernan, the grid size is (30, 1302, 663) (s_rho, eta_rho, xi_rho). ROMS version is revision 823, from 2016. I suppose I should try with a newer version! I don't know where to look for the I/O library but if you give me a clue I will find it. I am writing to NetCDF4 with compression: #define DEFLATE,...
by pmaccc
Tue Nov 02, 2021 3:48 pm
Forum: ROMS Bugs
Topic: tiling and divide by zero error
Replies: 10
Views: 18198

Re: tiling and divide by zero error

Thanks, John. I did adjust NtileI and NtileJ accordingly, and did not change wrt_his. I'll see if I can find any more info.
by pmaccc
Mon Nov 01, 2021 10:58 pm
Forum: ROMS Bugs
Topic: tiling and divide by zero error
Replies: 10
Views: 18198

tiling and divide by zero error

I am having a curious problem on a cluster I use to run ROMS. I have 10 nodes with 40 cores each, and have routinely been running ROMS using mpi job on all 400 cores. However, when I try to run the same job with 200 or 40 cores I get an error like this: [pmacc@klone1 driver]$ cat slurm-1501920.out (...
by pmaccc
Mon Sep 27, 2021 5:14 pm
Forum: Job Opportunities
Topic: Postdoc with Parker MacCready at University of Washington
Replies: 0
Views: 2064

Postdoc with Parker MacCready at University of Washington

The Coastal Modeling Group in the School of Oceanography at the University of Washington seeks a postdoctoral researcher to work on a new project “LiveOcean Model Enhancement and Transition to Operations,” funded through the NOAA Coastal and Ocean Modeling Testbed. If you are inspired to use regiona...
by pmaccc
Thu Sep 16, 2021 9:32 pm
Forum: Job Opportunities
Topic: Postdoc at University of Victoria
Replies: 0
Views: 2024

Postdoc at University of Victoria

This is a great opportunity to get involved with ROMS-based climate downscaling:

https://hansialice.github.io/posts/2021 ... rtunities/
by pmaccc
Fri Aug 20, 2021 3:56 pm
Forum: Job Opportunities
Topic: Postdoc at UW Applied Physics Lab
Replies: 0
Views: 1991

Postdoc at UW Applied Physics Lab

There is a postdoc available to work with and expand an ongoing ROMS modeling project:
https://ap.washington.edu/ahr/position- ... b_id=78220
Cheers, Parker
by pmaccc
Wed Jul 07, 2021 4:54 pm
Forum: ROMS Discussion
Topic: How to compute the energy dissipation in the model
Replies: 8
Views: 3765

Re: How to compute the energy dissipation in the model

Siva, Budgets can be surprisingly difficult to calculate, and are easy to make coding errors in. When you make a budget term from the diagnostics, try to make the same budget term from scratch using the history files, and then plot the two on the same graph vs. time. In most cases they should be rea...
by pmaccc
Wed Jul 07, 2021 4:24 pm
Forum: ROMS Discussion
Topic: How to compute the energy dissipation in the model
Replies: 8
Views: 3765

Re: How to compute the energy dissipation in the model

Siva - that is a perplexing result. How do you know that KE decreases with time?
by pmaccc
Fri Jun 25, 2021 4:52 pm
Forum: ROMS Discussion
Topic: How to compute the energy dissipation in the model
Replies: 8
Views: 3765

Re: How to compute the energy dissipation in the model

We give some details about using the ROMS diagnostics to calculate terms in energy budgets in this paper. Email me if you want a copy. pmacc@uw.edu MacCready, P., and S. N. Giddings, 2016: The Mechanical Energy Budget of a Regional Ocean Model. J. Phys. Oceanogr., 46, JPO-D-16-0086.1, doi:10.1175/JP...
by pmaccc
Mon Dec 07, 2020 4:32 pm
Forum: ROMS Discussion
Topic: Energetics
Replies: 5
Views: 4430

Re: Energetics

Peida,

The shared folder just had things like mexcdf and the seawater routines, which are publicly available. However, I am not supporting that code at all any more and I strongly urge you to write your own from scratch.

Cheers,

Parker
by pmaccc
Fri Sep 27, 2019 9:51 pm
Forum: ROMS Problems
Topic: Problem reading input files
Replies: 1
Views: 1802

Problem reading input files

I have an idealized simulation in which I am adding a complex river source condition. The goal is to make a boundary source/sink pattern that is like the mouth of an estuary with the usual tidally averaged two layer exchange flow. I am using preprocessing tools and a recent version or ROMS that I ha...
by pmaccc
Wed Sep 11, 2019 6:16 pm
Forum: ROMS Discussion
Topic: if I can set hc=Tcline>hmin?
Replies: 7
Views: 4539

Re: if I can set hc=Tcline>hmin?

Thanks very much for the clarification, Kate. It was unclear to me in the wiki which restriction was removed. And now I see in ROMS/Utility/set_scoord.F where this is implemented (lines 176-178 in the version I have):

ELSE IF (Vtransform(ng).eq.2) THEN
hc(ng)=Tcline(ng)
END IF
by pmaccc
Wed Sep 11, 2019 4:01 pm
Forum: ROMS Discussion
Topic: if I can set hc=Tcline>hmin?
Replies: 7
Views: 4539

Re: if I can set hc=Tcline>hmin?

Kate, thanks for your helpful response. I agree that what I want to use for hc is the Tcline I specify in the .in file. What is still unclear to me is if "hmin" is used anywhere in the calculation of z. From the "warning" paragraph here: https://www.myroms.org/wiki/Vertical_S-coo...
by pmaccc
Tue Sep 10, 2019 11:11 pm
Forum: ROMS Discussion
Topic: if I can set hc=Tcline>hmin?
Replies: 7
Views: 4539

Re: if I can set hc=Tcline>hmin?

I have a related question. I have a grid where the min value of h is 4 m, and I specify Tcline = 10 m in the .in file. So if I am understanding things right ROMS should use hc = 4 m when calculating the z coordinates (I use Transform function 2 and Stretching function 4). Yet in my history files the...
by pmaccc
Sun Aug 04, 2019 3:42 pm
Forum: ROMS Problems
Topic: Error climatology file: not include initialization time
Replies: 6
Views: 3823

Re: Error climatology file: not include initialization time

I am having a related problem. I have a daily model run I do, which has worked fine the past 2 weeks. This morning it did not work because for some reason ROMS was looking for a bry file starting 1 second earlier than the one I made. This is the error message in the log file: CHECK_MULTIFILE - Error...
by pmaccc
Mon May 13, 2019 7:22 pm
Forum: ROMS Problems
Topic: Tide Phase Problem
Replies: 4
Views: 3130

Re: Tide Phase Problem

Thanks for the suggestions. I stopped using ramp_tides because (1) it seemed to handle the "rude awakening" without blowing up, and (2) it meant that I always had to make 2 versions of the executable. If I were always doing long "cold start" runs I could just have the ramp_tides ...
by pmaccc
Mon May 13, 2019 6:31 pm
Forum: ROMS Problems
Topic: Tide Phase Problem
Replies: 4
Views: 3130

Re: Tide Phase Problem

I am adding to all 8 tidal frequencies, and doing so in degrees in my "tides.nc" forcing file. My varinfo.dat implies to me that the input should be in degrees and that ROMS (rev. 823) converts it internally to radians: 'tide_Ephase' ! Input 'tidal elevation phase angle' 'degrees' ! [radia...
by pmaccc
Mon May 13, 2019 5:18 pm
Forum: ROMS Problems
Topic: Tide Phase Problem
Replies: 4
Views: 3130

Tide Phase Problem

I have a realistic run that uses tidal forcing from TPXO7.2 at the boundaries, both SSH and UV. The tidal forcing runs perfectly in general. I make some hand adjustments the the tidal amplitude when I make the forcing, to better match observations. This also works fine. However when I try to make ad...
by pmaccc
Tue Jan 22, 2019 10:19 pm
Forum: ROMS Discussion
Topic: Weights in VSHAPE and layers thickness?
Replies: 6
Views: 4934

Re: Weights in VSHAPE and layers thickness?

Kate - thanks for the tip. I realize that our choices about the vertical coordinate transform and stretching have not been updated for some time. I tried experimenting with VTRANSFORM = 2 and VSTRETCHING = 4, and can see that the results might be smoother than what I am using, but they won't be fund...
by pmaccc
Mon Jan 21, 2019 12:27 am
Forum: ROMS Discussion
Topic: Weights in VSHAPE and layers thickness?
Replies: 6
Views: 4934

Re: Weights in VSHAPE and layers thickness?

I am using what I think are fairly common vertical stretching parameters: THETA_S,4 THETA_B,0.8 TCLINE,0 N,30 VTRANSFORM,1 VSTRETCHING,1 and when I have a river source with 10 m depth the upper layer is rather thin, like 5 cm. So when I have very high river flow, and a Vshape that varied linearly fr...
by pmaccc
Fri Dec 07, 2018 5:10 pm
Forum: ROMS Discussion
Topic: Virtual salt flux sea surface boundary condition
Replies: 4
Views: 3676

Re: Virtual salt flux sea surface boundary condition

John, I like all the ideas you mention to solve this problem. I favor the more physical solution (add of subtract freshwater) but understand that this will need modifications to the volume conservation. My reason for replying is more basic. I use bulk fluxes and provide a rain field in my forcing, b...
by pmaccc
Wed Jul 11, 2018 11:36 pm
Forum: ROMS Sediment
Topic: Wave-current BBL drag coefficient as output
Replies: 4
Views: 5909

Re: Wave-current BBL drag coefficient as output

Related to this thread, I have a model run which uses quadratic bottom drag. Since there is a wide range of bathymetric depth over the domain, the height above the bottom of the deepest velocity varies from a few cm (shallow water) to tens of meters (deep water). I would like to estimate the velocit...
by pmaccc
Fri May 04, 2018 7:51 pm
Forum: ROMS Tools and Techniques
Topic: wind work
Replies: 2
Views: 2577

Re: wind work

In this paper: MacCready, P., and S. N. Giddings, 2016: The Mechanical Energy Budget of a Regional Ocean Model. J. Phys. Oceanogr., 46, JPO-D-16-0086.1, doi:10.1175/JPO-D-16-0086.1 (available by open access) we calculated the "geostrophic wind work" in Fig 10, and the method of calculation...
by pmaccc
Sat Feb 24, 2018 5:44 pm
Forum: ROMS Problems
Topic: excess mixing in k-epsilon GLS mixing; bug or misconfigured?
Replies: 8
Views: 8323

Re: excess mixing in k-epsilon GLS mixing; bug or misconfigu

Very interesting. What was AKT_BAK for your simulations?
by pmaccc
Tue Dec 12, 2017 6:31 pm
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 18
Views: 20005

Re: CPU time and MPI issues with nested grids

John, Here are the time reports from the log file. What stands out is that most of the total time is devoted to message passing between the two grids (I'm not sure why the numbers don't all add up to 100%). Nonlinear model elapsed time profile, Grid: 01 Allocation and array initialization .............
by pmaccc
Mon Dec 11, 2017 9:08 pm
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 18
Views: 20005

Re: CPU time and MPI issues with nested grids

Thanks to everyone for your help. I did succeed in getting my realistic run to work with 2-way nesting. The problem is that the performance is poor. I'm running on 144 cores using the Intel compiler and mpi. The parent grid alone runs at faster than 1 minute per hour, and the child grid alone in 3 m...
by pmaccc
Fri Dec 08, 2017 10:35 pm
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 18
Views: 20005

Re: CPU time and MPI issues with nested grids

When I create a new grid using coarse2fine.m what is the correct number of rows and columns to put in the .in file for the refined grid? For a regular grid I just look at the size of a field on the rho-grid and subtract 2 from both dimensions to get the right number. Is it the same for the refinemen...
by pmaccc
Fri Dec 01, 2017 9:07 pm
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 18
Views: 20005

Re: CPU time and MPI issues with nested grids

I'm trying 2-way nesting in an existing run. I made the refined grid and contacts files using the matlab tools. Then I recompiled the executable using the NESTING flag. When I try to run it with mpirun I get a segmentation fault right away. I'm running on 144 cores across 6 nodes. One question is ab...
by pmaccc
Fri Jul 07, 2017 3:23 pm
Forum: ROMS Discussion
Topic: Energetics
Replies: 5
Views: 4430

Re: Energetics

Reiner, We recently published a paper which gives a method for complete energy budgets in ROMS: MacCready, P., and S. N. Giddings (2016) The Mechanical Energy Budget of a Regional Ocean Model. J. Phys. Oceanogr., 46, 2719–2733, doi:10.1175/JPO-D-16-0086.1. http://journals.ametsoc.org/doi/10.1175/JPO...
by pmaccc
Sat Apr 22, 2017 12:03 am
Forum: ROMS Ecosystem
Topic: Climatology and nudging in ecosystem models
Replies: 17
Views: 16471

Re: Climatology and nudging in ecosystem models

Kate and John,

I added the time attribute to the bio climatology variables in their NetCDF file and this appears to have fixed the problem. Hooray and thanks so much for your help!!

PM
by pmaccc
Fri Apr 21, 2017 8:10 pm
Forum: ROMS Ecosystem
Topic: Climatology and nudging in ecosystem models
Replies: 17
Views: 16471

Re: Climatology and nudging in ecosystem models

Kate, related to your comment about the time variable, in our _clm input file here are what salt (whose climatology is read) and NO3 (whose climatology is not read) look like: In [8]: print(ds['salt']) <class 'netCDF4._netCDF4.Variable'> float64 salt(salt_time, s_rho, eta_rho, xi_rho) long_name: sal...
by pmaccc
Fri Apr 21, 2017 7:47 pm
Forum: ROMS Ecosystem
Topic: Climatology and nudging in ecosystem models
Replies: 17
Views: 16471

Re: Climatology and nudging in ecosystem models

Kate, Here is the complete debugging error message (actually one of many identical ones, presumably because I am running on 72 cores): forrtl: severe (408): fort: (3): Subscript #1 of the array TVAL has value 0 which is less than the lower bound of 1 Image PC Routine Line Source oceanG 0000000001CD5...
by pmaccc
Fri Apr 21, 2017 7:06 pm
Forum: ROMS Ecosystem
Topic: Climatology and nudging in ecosystem models
Replies: 17
Views: 16471

Re: Climatology and nudging in ecosystem models

Thanks very much, John and Kate. Running with USE_DEBUG=on I get errors like: forrtl: severe (408): fort: (3): Subscript #1 of the array TVAL has value 0 which is less than the lower bound of 1 I have turned on the flags for processing of bio tracer climatology in my bio.in file, as well as the nudg...
by pmaccc
Fri Apr 21, 2017 6:10 pm
Forum: ROMS Ecosystem
Topic: Climatology and nudging in ecosystem models
Replies: 17
Views: 16471

Re: Climatology and nudging in ecosystem models

I am having a similar problem to John's. I am trying to read climatology fields (in this case from a NetCDF file instead of specifying them analytically) and use them for nudging to climatology in a strip near the open boundaries. This works fine for the velocities, and for salt and temp, but the ru...
by pmaccc
Fri Aug 28, 2015 9:48 pm
Forum: Job Opportunities
Topic: Coastal Modeling Postdoc at University of Washington
Replies: 0
Views: 4597

Coastal Modeling Postdoc at University of Washington

A Post-doctoral research position in ocean modeling is available in the School of Oceanography at the University of Washington. The successful candidate will join the UW Coastal Modeling Group to work on development and testing of a daily forecast model of coastal-estuarine circulation and biogeoche...
by pmaccc
Thu May 02, 2013 6:22 pm
Forum: ROMS Discussion
Topic: diagnostics
Replies: 10
Views: 11875

Re: diagnostics

I figured out the problem with my salt_rate test. salt_rate is NOT <ds/dt>, where <> denotes averaging over the time period for which diagnostics are collected. Instead (I think) salt_rate = <d(s*v)/dt>/<v> where v is the (changing) volume of a given grid cell. When I use this interpretation to chec...
by pmaccc
Mon Apr 29, 2013 7:24 pm
Forum: ROMS Problems
Topic: Diagnostics don't add up!
Replies: 10
Views: 10604

Re: Diagnostics don't add up!

I just tried adding up the momentum diagnostics in one of my runs and couldn't find any obvious error, or any difference between u and v momentum budgets. Are you using "nudging to climatology" in your domain? I believe this would add an extra term to the momentum budgets that would not be...
by pmaccc
Fri Apr 12, 2013 9:51 pm
Forum: ROMS Discussion
Topic: diagnostics
Replies: 10
Views: 11875

Re: diagnostics

I wonder if the problem might arise in the two different versions of the calculation of DiaTwrk(i,j,k,itrc,iTrate) taken from step3d_t.F. I assume the first, active, version forces the salt_rate diagnostic to equal the sum of all the other terms. Then the second, commented out, version appears to ca...
by pmaccc
Fri Mar 29, 2013 6:43 pm
Forum: ROMS Discussion
Topic: diagnostics
Replies: 10
Views: 11875

Re: diagnostics

I did some more analysis on the problem of the salt_rate diagnostic. The plot shows the evolution of temperature and salt at a surface model location, both from history and average files. They look very similar. Then I calculate the time derivative of both and plot it on the bottom row, comparing it...
by pmaccc
Fri Mar 29, 2013 12:39 am
Forum: ROMS Discussion
Topic: diagnostics
Replies: 10
Views: 11875

Re: diagnostics

I'm using the diagnostic feature for some budgets. In the course of some error checking I compared the field from salt_rate to the difference between salt fields from the history files saved at the beginning and end of the diagnostic averaging period. The shapes and magnitudes, e.g. of a vertical pr...
by pmaccc
Fri Sep 07, 2012 12:09 am
Forum: ROMS Discussion
Topic: ZCLM_NUDGING
Replies: 1
Views: 2298

ZCLM_NUDGING

It appears to me that the flag ZCLM_NUDGING is missing from ROMS/Include/cppdefs.h, yet it still seems to have an active role to play in parts of the code, e.g. ana_nudgcoef.h and mod_clima.F (I am using version number 629 of the code). Any thoughts?

Parker
by pmaccc
Thu Jun 07, 2012 8:59 pm
Forum: ROMS Installation
Topic: SVN problem
Replies: 4
Views: 7161

Re: SVN problem

I am trying to get the latest ROMS using svn onto a linux machine. This has worked many times in the past but today it chokes halfway through with the error message: svn: Can't read file 'ROMS_620/Lib/ARPACK/LAPACK/.svn/log': Permission denied A possible clue is that today for the first time I got t...
by pmaccc
Tue Dec 13, 2011 4:04 pm
Forum: ROMS Discussion
Topic: river salinity overshoot
Replies: 11
Views: 10516

Re: river salinity overshoot

In my experience you can help with this problem by making your rivers longer, so that non-zero salinity doesn't penetrate up to the river source cells. This naturally avoids the problem of having very sharp gradients which can lead to numerical inaccuracy.
by pmaccc
Fri Oct 28, 2011 3:32 pm
Forum: Job Opportunities
Topic: Postdoc: Modeling coastal-global climate interactions
Replies: 0
Views: 2900

Postdoc: Modeling coastal-global climate interactions

We seek applications for a postdoctoral research associate at the University of Washington School of Oceanography.  The postdoc will work in new Department of Energy-funded team exploring how circulation and mixing in estuaries and on the continental shelf might change under future climate scenarios...
by pmaccc
Thu Mar 04, 2010 5:43 pm
Forum: Job Opportunities
Topic: Postdoc: Harmful Algal Blooms & the Columbia River Plume
Replies: 0
Views: 3234

Postdoc: Harmful Algal Blooms & the Columbia River Plume

Postdoctoral Position: Harmful Algal Blooms & the Columbia River Plume The interdisciplinary PNWTOX project, jointly funded by NOAA and NSF, will use existing data in parallel with state of the art physical and bio-physical models to advance our understanding of HAB development/dissipation and ...
by pmaccc
Fri Oct 03, 2008 8:54 pm
Forum: ROMS Installation
Topic: ROMS3, g95, OS X 10.5.4, netcdf-3.6.3
Replies: 4
Views: 5278

Re: ROMS3, g95, OS X 10.5.4, netcdf-3.6.3

Following the suggestions of Andreas and Rob, I got ROMS3.# running on my relatively new MacBook Pro. For reference I have written up the exact steps I used, at:
http://www.ocean.washington.edu/people/ ... notes.html

Cheers, Parker
by pmaccc
Wed Jun 04, 2008 4:05 pm
Forum: Job Opportunities
Topic: Estuary Modeling Postdoctoral Position
Replies: 0
Views: 2560

Estuary Modeling Postdoctoral Position

The University of Washington, School of Oceanography invites applications for a postdoctoral position. The position requires a PhD in Physical Oceanography, or related field, and expertise in numerical circulation modeling. The successful applicant will work closely with a Physical Oceanographer, Dr...
by pmaccc
Fri Jun 23, 2006 8:41 pm
Forum: Job Opportunities
Topic: Postdoctoral Research Associate, Coastal Ecosystem Modeling
Replies: 0
Views: 2767

Postdoctoral Research Associate, Coastal Ecosystem Modeling

The University of Washington, School of Oceanography invites applications for a postdoctoral position. The position requires a PhD in Biological or Physical Oceanography, or related field, and expertise in numerical ecosystem modeling. The successful applicant will work on the Columbia River Plume N...
by pmaccc
Mon Apr 19, 2004 3:52 pm
Forum: ROMS Discussion
Topic: Treatment of rivers
Replies: 20
Views: 28726

Estuarine Boundary Condition Notes

I would like to amplify some of Bob Chant's thoughts. Estuaries take a little bit of river flow, pull in a LOT of ocean water, mix the two, and spit out the mixture, which is usually only slightly fresher than oceanic. Two points then are worth noticing when formulating a "river" BC: (i) t...