Search found 54 matches

by pmaccc
Thu Dec 02, 2021 5:30 pm
Forum: ROMS Installation
Topic: How to organize custom bio code
Replies: 3
Views: 209

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: 209

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: 1036

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: 307

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: 390

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: 390

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: 390

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: 390

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: 457

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: 378

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: 420

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: 1257

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: 1257

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: 1257

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: 2203

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: 914

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: 1763

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: 1763

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: 1763

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: 2214

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: 1389

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: 1389

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: 1389

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: 3091

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: 3091

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: 2350

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: 3715

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: 1532

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: 4582

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: 16
Views: 7897

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: 16
Views: 7897

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: 16
Views: 7897

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: 16
Views: 7897

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: 2203

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: 9280

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: 9280

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: 9280

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: 9280

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: 9280

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: 3845

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: 7
Views: 3917

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: 6075

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: 7
Views: 3917

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: 7
Views: 3917

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: 7
Views: 3917

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: 1514

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: 3830

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: 5882

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: 2239

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: 2514

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: 3727

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: 1895

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: 2015

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: 21325

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...