Search found 83 matches

by nganju
Tue Oct 15, 2019 3:25 pm
Forum: Job Opportunities
Topic: USGS Mendenhall Postdoctoral opportunity
Replies: 0
Views: 239

USGS Mendenhall Postdoctoral opportunity

Apologies for cross-postings, the USGS is seeking a motivated postdoctoral researcher for a two-year Mendenhall position. The goal of this research opportunity is to investigate the influence of vegetation and geomorphic type on marsh edge dynamics and marsh resilience with numerical modeling. The s...
by nganju
Sun Mar 20, 2016 9:22 pm
Forum: Job Opportunities
Topic: USGS Mendenhall Postdoctoral Fellowship
Replies: 1
Views: 3588

USGS Mendenhall Postdoctoral Fellowship

The USGS Woods Hole Coastal and Marine Science Center is looking for creative scientists to explore connections between hydrodynamics, vegetation, and ecosystem services using numerical models. The complete announcement is here:
http://geology.usgs.gov/postdoc/opps/20 ... 0Ganju.htm
by nganju
Tue Jun 17, 2014 8:10 pm
Forum: ROMS Discussion
Topic: tidal analysis of large output files
Replies: 22
Views: 6477

Re: tidal analysis of large output files

ignore that...just reread Wilkin's post more carefully.
by nganju
Tue Jun 17, 2014 8:09 pm
Forum: ROMS Discussion
Topic: tidal analysis of large output files
Replies: 22
Views: 6477

Re: tidal analysis of large output files

I tried AVERAGES_DETIDE, and the averages file contained "zeta_detided" etc but none of the mentioned harmonic fit coefficients. Did I mess something up with the file writing specs (relevant ones below)? I can provide more info but assumed this is a straightforward error on my part. DT = 5.0 NTIMES ...
by nganju
Wed Jul 24, 2013 5:53 pm
Forum: Job Opportunities
Topic: USGS Mendenhall Postdoctoral Fellowship
Replies: 0
Views: 2658

USGS Mendenhall Postdoctoral Fellowship

Dear colleagues- The Sediment Transport Group of the U.S. Geological Survey Woods Hole Coastal and Marine Science Center is pleased to announce a new postdoctoral opportunity through the Mendenhall Research Fellowship Program. RO 14-44: Understanding estuarine geomorphic change under hurricane forci...
by nganju
Tue Jul 23, 2013 2:26 pm
Forum: Meetings/Workshops
Topic: Workshop: Linking hydro and eco models in estuaries
Replies: 0
Views: 1864

Workshop: Linking hydro and eco models in estuaries

Linking hydrodynamic and ecological models in estuaries: a workshop to discuss recent advances and approaches September 10-11, 2013 U.S. Geological Survey Woods Hole Science Center Woods Hole, MA We are convening a workshop to discuss advances in understanding estuarine ecology through coupled hydr...
by nganju
Mon Jul 01, 2013 2:16 pm
Forum: ROMS Trivia
Topic: What´s the difference between Modeling and Simulating
Replies: 10
Views: 4879

Re: What´s the difference between Modeling and Simulating

I think it's important for modelers to be able to defend their approaches, terminology, and philosophy to non-modelers. There are many disparaging comments made about models/modelers with little consideration for the value of model-derived information. There is substantial literature on the epistemo...
by nganju
Mon Oct 22, 2012 1:36 pm
Forum: ROMS Bugs
Topic: water depth in calculating wave orbital velocity
Replies: 3
Views: 2295

Re: water depth in calculating wave orbital velocity

I ran into this problem a few years ago and added in zeta...but to be consistent you should really be updating the wave field (height, period, dir) as water level (zeta+h) changes. Which is why a better option would be ROMS-SWAN coupling. If you don't have the computational power to do that, you cou...
by nganju
Wed Apr 25, 2012 12:43 pm
Forum: ROMS Discussion
Topic: The river question with dye and sediment
Replies: 3
Views: 1275

Re: The river question with dye and sediment

you probably want to define SUSPLOAD (suspended-sediment transport) in your header file.
As John pointed out, be careful about the indices also, that can cause problems if you are off by one...
by nganju
Tue Mar 20, 2012 7:56 pm
Forum: ROMS Discussion
Topic: blows up at 1st time step even after decreasing time step
Replies: 8
Views: 2544

Re: blows up at 1st time step even after decreasing time ste

are you missing a boundary cell in the analytical forcing? plot the output for ubar/vbar/zeta along the boundary and see if one cell is being held at zero instead of varying with your function.
by nganju
Mon Mar 12, 2012 6:22 pm
Forum: ROMS Discussion
Topic: blows up at 1st time step even after decreasing time step
Replies: 8
Views: 2544

Re: blows up at 1st time step even after decreasing time ste

could you post an image of your grid, and perhaps a zoom-in of where the blow-up is happening?
by nganju
Wed Feb 15, 2012 1:43 pm
Forum: ROMS Discussion
Topic: blows up at 1st time step even after decreasing time step
Replies: 8
Views: 2544

Re: blows up at 1st time step even after decreasing time ste

you have a dx between 13 and 58 m, and a dy between 13 and 84 m, a timestep of 100 s, and a Courant number of 4.
I would try reducing the timestep. Also make sure you have no depth values less than zero, even if they are masked.
by nganju
Mon Feb 06, 2012 1:41 pm
Forum: ROMS Discussion
Topic: Problem with ROMS wetting/drying and turbulence model(s)
Replies: 8
Views: 3121

Re: Problem with ROMS wetting/drying and turbulence model(s)

what does your vertical stretching look like?
by nganju
Wed Aug 17, 2011 12:44 am
Forum: ROMS Problems
Topic: ROMS 3.4 Stalling
Replies: 4
Views: 1280

Re: ROMS 3.4 Stalling

Is it stalling on the first time step, at some random spot, or just before writing to a history file? I recall having a similar problem...
by nganju
Sun Jul 03, 2011 4:50 pm
Forum: ROMS Problems
Topic: model blowing up
Replies: 4
Views: 1673

Re: model blowing up

Yes, even with masking the minimum depth must be greater than zero, even in masked cells. With wetting and drying, you activate "WET_DRY", and specify your mask as cells which should never become wet. You then have the option of making any wet cell a negative depth. When zeta exceeds that depth+dcri...
by nganju
Sun Jul 03, 2011 12:45 am
Forum: ROMS Problems
Topic: model blowing up
Replies: 4
Views: 1673

Re: model blowing up

and your courant number is 0.8.
I would also reduce the timestep by half.
by nganju
Sun Jul 03, 2011 12:44 am
Forum: ROMS Problems
Topic: model blowing up
Replies: 4
Views: 1673

Re: model blowing up

If you look at the output for vertical stretching, it looks like your shallowest depth is zero in your grid file.
All cells must be greater than zero unless using wetting/drying.
by nganju
Fri Jul 01, 2011 2:21 am
Forum: ROMS Bugs
Topic: possible bug in inputing sediment parameters
Replies: 2
Views: 1671

Re: possible bug in inputing sediment parameters

I think you have a bad continutation of the line in your input file. It is probably repeating the last value on the first line and not seeing the remaining entries. Did you edit the file in Windows? If so try dos2unix on your sediment input file. In any case, 42 sediment classes is a lot. It actuall...
by nganju
Fri Jul 01, 2011 2:14 am
Forum: ROMS Discussion
Topic: Unexpected ROMS blow-up
Replies: 2
Views: 1967

Re: Unexpected ROMS blow-up

I've found the best way to diagnose a blow-up like the one you describe is to save restart output very frequently and look at the fields of zeta, u, v; and also the change in those fields between the last time step and the second-to-last time step. This usually shows you where problems may be.
by nganju
Thu Jun 30, 2011 2:30 am
Forum: ROMS Problems
Topic: Changing AKT_BAK values has no effect on model results
Replies: 8
Views: 3083

Re: Changing AKT_BAK values has no effect on model results

I think it's "GLS_Kmin", and in gls_corstep.h the tke is set to MAX(Tke,gls_kmin)...
You can try dropping this value to 1e-9 and see if changing AKt_bak now gives different results...
by nganju
Thu Jun 30, 2011 12:47 am
Forum: ROMS Problems
Topic: Changing AKT_BAK values has no effect on model results
Replies: 8
Views: 3083

Re: Changing AKT_BAK values has no effect on model results

Malcolm Scully at ODU has nicely illustrated that the "Galperin correction" in the turbulence scheme effectively sets a minimum TKE value that overrides the change in Akt_bak. Hopefully he will see this and give the detailed explanation, but I think the solution is to change TKE_min in the input fil...
by nganju
Mon Jun 27, 2011 11:21 am
Forum: ROMS Ecosystem
Topic: respiration by phytoplankton
Replies: 0
Views: 2262

respiration by phytoplankton

Hi-
Is respiration by phytoplankton represented in the Fasham/Fennel code somewhere? I have a hard time finding it, but I've been assured it's in there. Thanks...
by nganju
Wed Jun 15, 2011 2:27 pm
Forum: ROMS Ecosystem
Topic: possible typo in Fennel.h?
Replies: 1
Views: 1917

Re: possible typo in Fennel.h?

sorry, ignore this....it makes complete sense as is.
by nganju
Wed Jun 15, 2011 2:21 pm
Forum: ROMS Ecosystem
Topic: possible typo in Fennel.h?
Replies: 1
Views: 1917

possible typo in Fennel.h?

In fennel.h, line 707 has: ! Phytoplankton grazing by zooplankton. ! cff1=fac1*Bio(i,k,iZoop)*Bio(i,k,iPhyt)/ & & (K_Phy(ng)+Bio(i,k,iPhyt)*Bio(i,k,iPhyt)) cff3=1.0_r8/(1.0_r8+cff1) Bio(i,k,iPhyt)=cff3*Bio(i,k,iPhyt) as the grazing rate; but Fennel (2006), Eq. 7 has Phytoplankton^2 in the numerator....
by nganju
Tue Jun 14, 2011 9:21 pm
Forum: ROMS Ecosystem
Topic: adding processes to fasham
Replies: 5
Views: 3905

Re: adding processes to fasham

I am still debating how to deal with it...I suppose macroalgae should have a vertical component, as it will grow vertically in response to light and nutrients. But I am not sure I want it advecting around, as in the areas I am working in, it is usually attached to the bottom substrate. Is there a si...
by nganju
Tue Jun 14, 2011 1:12 am
Forum: ROMS Ecosystem
Topic: adding processes to fasham
Replies: 5
Views: 3905

Re: adding processes to fasham

I am adding macroalgae dynamics to fennel.h. I plan on treating it not as a tracer but as a variable whose density changes as a function of nutrients, light, etc. If I add it as 2D (r2dvar) biological tracer will it automatically be advected around by step3d_t or is there an easy hack? Is there a be...
by nganju
Fri Mar 25, 2011 7:23 pm
Forum: ROMS Ecosystem
Topic: ROMS linkage to EPA WASP model
Replies: 0
Views: 2127

ROMS linkage to EPA WASP model

Has anyone attempted to pass ROMS-calculated mass fluxes and tracers to the EPA's water quality model, WASP? The WASP model is linked offline with other codes (e.g. EFDC), so I think this should be easy to do. Any information or advice is appreciated, thanks...
by nganju
Fri Feb 04, 2011 2:15 pm
Forum: ROMS FAQ
Topic: build.bash problem
Replies: 10
Views: 10930

Re: build.bash problem

the command "dos2unix" will convert the file, as in "dos2unix build.bash"
by nganju
Mon Dec 13, 2010 2:33 pm
Forum: ROMS Sediment
Topic: Can SWAN model used to simulate sediment transport on ocean
Replies: 1
Views: 2963

Re: Can SWAN model used to simulate sediment transport on oc

One option is to use the SSW_BBL option in ROMS, and directly specify wave height and period throughout the domain, thereby avoiding SWAN. You can use simple wave formulas, for a given wind speed, fetch, and water depth to calculate the wave characteristics, and put those in a netcdf forcing file. S...
by nganju
Fri Nov 19, 2010 3:05 pm
Forum: ROMS Bugs
Topic: WET_DRY and application of masks
Replies: 0
Views: 822

WET_DRY and application of masks

Should the wet/dry masks (e.g. rmask_wet, umask_wet) be used in step3d_t, step2d_lf_am3, etc? They are defined and read into those routines, but never actually used. I am having problems with anomalously high salinities and temperatures on the edges of wet/dry masks, and I wonder if fill values are ...
by nganju
Wed Aug 18, 2010 5:32 pm
Forum: ROMS Discussion
Topic: Determination of Bottom roughness Zob in Input file *. in
Replies: 1
Views: 1044

Re: Determination of Bottom roughness Zob in Input file *. in

Hi- If you are using the the logarithmic formulation, then ROMS will only use the defined ZoB to calculate ustar and bottom stress. If you use SSW_BBL for the bottom boundary calculations, you can then use SSW_CALC_ZNOT, which will sum the roughness contributions from grain roughness (ZoN), sediment...
by nganju
Fri May 28, 2010 5:56 pm
Forum: ROMS Information
Topic: Specifying velocities within your domain
Replies: 1
Views: 1611

Re: Specifying velocities within your domain

Hi Rebecca- (1) If you break the surface (i.e. negative h), mask_rho needs to have a value of 0 instead of 1. If you are using ana_grid, you can specify the masked areas easily enough using ana_mask.h. For this domain, you should probably have the seamount break the surface. (2) I don't know if you ...
by nganju
Tue May 11, 2010 4:53 pm
Forum: ROMS Ecosystem
Topic: adding processes to fasham
Replies: 5
Views: 3905

adding processes to fasham

Hello- I am boldly straying into new territory with a very crude sense of biology, so any help is appreciated. We plan to simulate nutrient dynamics in a shallow estuary, where the following processes are most important: 1. nitrification/denitrification in the sediments; 2. uptake of nitrate and amm...
by nganju
Thu Mar 04, 2010 5:22 pm
Forum: ROMS Discussion
Topic: literature on grid resolution
Replies: 0
Views: 604

literature on grid resolution

Can anyone recommend seminal or recent papers on the effect of horizontal resolution on simulated flows in the nearshore? I have found several papers dealing with oceanic circulation and resolution, but nothing for inner shelf or nearshore regions. Thanks...
by nganju
Mon Feb 01, 2010 1:53 am
Forum: ROMS Problems
Topic: How to set Hmin (<0m), Tcline, Hc in WET_DRY
Replies: 3
Views: 1592

Re: How to set Hmin (<0m), Tcline, Hc in WET_DRY

the values of hc and Tcline in your *.in file need to match the values in the initialization file.
negative depths are allowed with WET_DRY.
by nganju
Fri Jan 15, 2010 4:15 pm
Forum: ROMS Source
Topic: Adding variables to history and averages files
Replies: 15
Views: 8982

Re: Adding variables to history and averages files

I'm fairly certain my problem is not related to tabs, since I've added variables before with no problems. But I am now trying to split the ubar_hadv diagnostic into the u*du/dx and v*du/dy terms, add them as idDu2d variables, and having the same problem reported above. I'm sure it's a silly error, b...
by nganju
Fri Jan 08, 2010 2:19 pm
Forum: ROMS Discussion
Topic: ROMS Swan coupling
Replies: 35
Views: 5300

Re: ROMS Swan coupling

Did you try changing the max file number to something larger than 200?
by nganju
Thu Jan 07, 2010 3:23 pm
Forum: ROMS Discussion
Topic: ROMS Swan coupling
Replies: 35
Views: 5300

Re: ROMS Swan coupling

The ROMS run is instructed to run for 86400 time steps at 360 s per time step = 360 days The SWAN run is instructed to run from 1/1/04 to 12/10/04 = 344 days This will cause SWAN to stop coupling and ROMS to sit and wait. These times need to match, for both coupling and the length of your SWAN input...
by nganju
Tue Jan 05, 2010 1:32 pm
Forum: ROMS Discussion
Topic: ROMS Swan coupling
Replies: 35
Views: 5300

Re: ROMS Swan coupling

I also think the first error may be fixed by changing the "highest file ref. number" in the SWAN configuration file (swaninit)
by nganju
Tue Jan 05, 2010 1:29 pm
Forum: ROMS Discussion
Topic: ROMS Swan coupling
Replies: 35
Views: 5300

Re: ROMS Swan coupling

I think the problem is the time step and duration of the ROMS and SWAN runs not matching. Can you show us the number and size of the ROMS time steps?
by nganju
Tue Dec 22, 2009 2:08 pm
Forum: ROMS Sediment
Topic: About the morphological changes in sea floor
Replies: 4
Views: 3587

Re: About the morphological changes in sea floor

if SED_MORPH is turned on, the new variable that is reported in the history files is "bath", which is the new updated water depth. The change in depth is the difference in "bath" from each successive time step. The change in bed thickness is the difference in "bed_thickness". Bed thickness is report...
by nganju
Mon Dec 21, 2009 1:59 am
Forum: ROMS Sediment
Topic: About the morphological changes in sea floor
Replies: 4
Views: 3587

Re: About the morphological changes in sea floor

The variable "bath" tracks changes in depth, assuming you are using the "SED_MORPH" option to actively update the bathymetry. If you are not using SED_MORPH, but just want to track erosion and deposition, the variable "bed_thickness" tracks the net erosion or deposition.
by nganju
Thu Sep 24, 2009 1:41 pm
Forum: ROMS Tools and Techniques
Topic: Offline nesting
Replies: 3
Views: 1206

Re: Offline nesting

I used Mathieu's toolbox for interpolation, but found a few bugs where the main function (e.g. NEST_CreateNestingTotalArray) calls other routines (e.g. InterpolGetSpMat...) with a different set of arguments than the routine is expecting. I think there were about 5 of these I had to correct. Once the...
by nganju
Tue Mar 03, 2009 8:29 pm
Forum: ROMS Discussion
Topic: zeta and set_scoord, set_depth
Replies: 1
Views: 876

Re: zeta and set_scoord, set_depth

sorry, we see Zt_avg1 is calculated in set_zeta...
by nganju
Tue Mar 03, 2009 8:14 pm
Forum: ROMS Discussion
Topic: zeta and set_scoord, set_depth
Replies: 1
Views: 876

zeta and set_scoord, set_depth

Hopefully this is a stupid question...which routine is responsible for adding zeta to bathymetry (h) in the computation of time-evolving vertical stretching/layer thicknesses? We don't see any reference to zeta in either set_depth or set_scoord, only references to the initial bathymetry. Thanks in a...
by nganju
Thu Jul 31, 2008 5:50 pm
Forum: ROMS Information
Topic: coupling_*.in file and Wubot
Replies: 0
Views: 1329

coupling_*.in file and Wubot

To hopefully save someone else a little time... In the supplied examples of Externals/coupling_*.in files, SWAN does not provide bottom orbital velocites or wave dissipation to ROMS. If you want this field passed, you need to add the Wubot (or Wdiss) field to Export(waves) and Import(ocean). If you ...
by nganju
Thu Jul 24, 2008 12:17 pm
Forum: ROMS Problems
Topic: SWAN coupling, with output
Replies: 6
Views: 2078

Re: SWAN coupling, with output

SWAN spec2d files are about 1MB, ROMS output looks fine, I can try with one processor and report back. I will also update if necessary...
by nganju
Thu Jul 24, 2008 12:19 am
Forum: ROMS Problems
Topic: SWAN coupling, with output
Replies: 6
Views: 2078

Re: SWAN coupling, with output

The offending output command in the SWAN input file is SPECOUT (output 2D spectra); the TABLE command (output parameters in ascii format) has also caused the same problem. The ROMS output file stops after writing a typical line (time, kinetic energy, etc). The most recently written-to SWAN PRINT fil...
by nganju
Wed Jul 23, 2008 8:33 pm
Forum: ROMS Problems
Topic: SWAN coupling, with output
Replies: 6
Views: 2078

SWAN coupling, with output

On separate occassions, at different times during the same simulation, ROMS/SWAN coupled runs halt in the middle of the run. There is no error in the ROMS output file, the SWAN PRINT file is usually in the middle of processing an output request, and the cluster issues an error file with the phrase "...
by nganju
Wed Jul 16, 2008 2:25 pm
Forum: ROMS Sediment
Topic: SSW_LOGINT: z1 goes negative
Replies: 3
Views: 2840

Re: SSW_LOGINT: z1 goes negative

Another resolved problem to report for this one...in set_scoord.F # if defined WET_DRY hc(ng)=MIN(MAX(hmin(ng),0.0_r8),Tcline(ng)) # else hc(ng)=MIN(hmin(ng),Tcline(ng)) # endif If you are using SED_MORPH, hmin should technically be variable, but it looks like it is pulled once, at the beginning of ...
by nganju
Mon Jul 14, 2008 8:53 pm
Forum: ROMS Usage
Topic: CBLAST with SWAN_COUPLING
Replies: 6
Views: 1813

Re: CBLAST with SWAN_COUPLING

Just to update, my problem (for both versions of the code) was that I had commented out the matlab file output commands (BLOCK) in the SWAN input file. Apparently those output commands must be specified for SWAN to pass information to ROMS. One additional note: SWAN's begin time is not considered wh...
by nganju
Tue Apr 29, 2008 10:20 pm
Forum: ROMS Usage
Topic: CBLAST with SWAN_COUPLING
Replies: 6
Views: 1813

Hello Hernan- Thanks for the information; I try my best to troubleshoot before posting to the board. I don't expect to have my problems solved by others, I only want to share the information in case others duplicate the problem. In the original post, what is odd is that TEST_HEAD and INLET_TEST run ...
by nganju
Tue Apr 29, 2008 8:44 pm
Forum: ROMS Usage
Topic: CBLAST with SWAN_COUPLING
Replies: 6
Views: 1813

I updated to release 177, and now compilation fails... cd Build; ifort -c -O2 /align /G7 /MD /Ox -I/cygdrive/c/ROMS/MPICH2/include init ial.f90 /object:initial.o Intel(R) Fortran Compiler for 32-bit applications, Version 9.0 Build 20050430 Z Package ID: W_FC_P_9.0.018 Copyright (C) 1985-2005 Intel C...
by nganju
Tue Apr 29, 2008 6:53 pm
Forum: ROMS Usage
Topic: CBLAST with SWAN_COUPLING
Replies: 6
Views: 1813

CBLAST with SWAN_COUPLING

I successfully compiled and ran TEST_HEAD and INLET_TEST with waves-ocean coupling. I also successfully compiled and ran the CBLAST application, without coupling. I also ran CBLAST with SWAN alone, no problems. I compiled CBLAST successfully with SWAN_COUPLING activated, but when I try to run the ap...
by nganju
Fri Apr 25, 2008 11:53 pm
Forum: ROMS Problems
Topic: Compiling TEST_HEAD: IPO errors
Replies: 4
Views: 1271

found it... mpiexec -localonly....
it's running now...
by nganju
Fri Apr 25, 2008 11:51 pm
Forum: ROMS Problems
Topic: Compiling TEST_HEAD: IPO errors
Replies: 4
Views: 1271

After using the untouched-CSTM branch I created a few weeks back, and reinstalling MCT outside of the branch, I compiled with no problems. When I try to execute mpiexec -np 2 ./oceanM.exe ROMS/External/coupling_inlet_test.in I get a uniquely USGS-type error... Credentials for nganju-pr rejected conn...
by nganju
Fri Apr 25, 2008 5:46 pm
Forum: ROMS Problems
Topic: Compiling TEST_HEAD: IPO errors
Replies: 4
Views: 1271

The MCT libraries were built with fmpich2.lib, and my makefile flag also uses fmpich2.lib. I have a feeling it may be a path issue: when I added the /usr/local/lib and /usr/local/include paths (where libmpeu.a and libmct.a are located), all unresolved externals went away except for the MPI-related o...
by nganju
Thu Apr 24, 2008 8:10 pm
Forum: ROMS Problems
Topic: Compiling TEST_HEAD: IPO errors
Replies: 4
Views: 1271

Compiling TEST_HEAD: IPO errors

I installed MPICH2, and built the MCT libraries successfully (CYGWIN-ifort dual-core Windows computer). I used the same flags in my ROMS makefile as the MCT makefile. Compilation for TEST_HEAD goes smoothly until very near the end, where I get a plethora of "IPO errors". Previous postings on this su...
by nganju
Sat Mar 29, 2008 1:15 am
Forum: ROMS Usage
Topic: Application setup. Please help!
Replies: 36
Views: 16694

sorry, i was late to the dance
by nganju
Sat Mar 29, 2008 1:14 am
Forum: ROMS Usage
Topic: Application setup. Please help!
Replies: 36
Views: 16694

From the output file: your barotropic courant number (>5) seems high, i think <1 is more appropriate...perhaps your grid resolution is too fine (dx = 3.8 e -5 km = 0.038 m ???????). something is wrong with your grid spacing, i assume?
by nganju
Wed Jan 30, 2008 2:04 am
Forum: ROMS Installation
Topic: netCDF 3.6.2, Ubuntu 7.10, 32bit, Intel Fortran
Replies: 12
Views: 5179

In my case, those errors arose when the netcdf libraries are built with a different compiler than the one you are using to compile ROMS. Perhaps you can check the netcdf website for successful build output for your system, and make sure the libraries were built correctly. other than that, i have no ...
by nganju
Wed Dec 19, 2007 11:31 pm
Forum: ROMS Installation
Topic: problem building netcdf-90 interface with ifort under cygwin
Replies: 3
Views: 3276

Did this work in the end? I am trying to install ROMS 3.0 and netcdf 3.6.2 on my cygwin machine/ifort and having the same problem.
by nganju
Thu Dec 13, 2007 9:55 pm
Forum: ROMS Discussion
Topic: ROMS with MATLAB..!
Replies: 22
Views: 8615

ROMS and MATLAB

Many people use Matlab to create and modify the *.nc (netcdf) files that are used for grid, forcing, and output files. To do this, you need to install the mexcdf interface for Matlab. I think there are other postings on the board that explain how to do this. good luck...
by nganju
Mon Nov 26, 2007 4:24 pm
Forum: ROMS Tools and Techniques
Topic: Problem plotting with Rslice
Replies: 6
Views: 4021

it looks like you need to edit snc_roms_get_grid to set hmin=0 instead of hmin=min(min(h)), since h does not exist when SED_MORPH is on
by nganju
Mon Sep 17, 2007 3:39 pm
Forum: ROMS Discussion
Topic: ROMS coupling to groundwater model
Replies: 1
Views: 1048

ROMS coupling to groundwater model

Are there any known attempts to couple ROMS with groundwater models, e.g. for studies of coastal saltwater intrusion, submarine groundwater discharge, etc.? Is this something that could be handled by the Model Coupling Toolkit? Just curious...
by nganju
Thu May 31, 2007 3:55 pm
Forum: ROMS Problems
Topic: Segmentation fault with WET_DRY
Replies: 4
Views: 2509

Hello Shih-Nan-
I haven't figured it out yet, and I am first trying to get a complete run with sed_morph before i try switching wet_dry on again. When I do get to that point, I will probably just run it in serial, and do two runs at once on my machine...
by nganju
Tue May 29, 2007 9:41 pm
Forum: ROMS Sediment
Topic: SSW_LOGINT: z1 goes negative
Replies: 3
Views: 2840

Wetting and drying is off right now... I put in a catch and the restarted model went for another few days before a different problem emerged (rapid bed deposition in the same spot, with large negative sediment concentrations?). Back to the first crash: bustrc and buvstrc were Nan's in the time step ...
by nganju
Tue May 29, 2007 8:26 pm
Forum: ROMS Sediment
Topic: SSW_LOGINT: z1 goes negative
Replies: 3
Views: 2840

SSW_LOGINT: z1 goes negative

I have been having problems with shallow cells, especially when using SED_MORPH to accelerate bed change. The domain is a relatively shallow subembayment of SF Bay, with tides and freshwater input. Larger SED_MORPH causes an earlier crash, in the same cell. After some troubleshooting, I determined t...
by nganju
Tue Apr 17, 2007 11:39 pm
Forum: ROMS Problems
Topic: Segmentation fault with WET_DRY
Replies: 4
Views: 2509

Segmentation fault with WET_DRY

Hello- I have two computers: a dual-processor Linux with Intel 9, and a dual-core windowsXP/Cygwin with Intel 8. The configuration that I have been running on the Linux machine for some time has been with WET_DRY off. When I turn WET_DRY on, I get a segmentation fault after the first time step (stac...
by nganju
Thu Apr 12, 2007 8:59 pm
Forum: ROMS Problems
Topic: automated process
Replies: 2
Views: 1262

thanks for the advice, that is exactly what i needed...
by nganju
Wed Apr 11, 2007 11:43 pm
Forum: ROMS Problems
Topic: automated process
Replies: 2
Views: 1262

automated process

Hello-
I am running on a dual-processor Linux desktop, and I want to have a simple shell script command that recognizes when the oceanO process ends, and invokes a command to start another run. I am not very familiar with linux-type commands, so any help is appreciated, thanks in advance...
by nganju
Mon Apr 09, 2007 6:06 pm
Forum: ROMS Usage
Topic: Coupling of m3-m2 initial conditions
Replies: 8
Views: 3522

i ran a similar configuration, instead of clamping the inflow at the north and gradient for the outflow in the south, I clamped the outflow in the south, and gradient for the inflow at the north. This worked well for me, and gave me the correct inflow at the north once it reached steady-state...
by nganju
Thu Mar 08, 2007 7:49 pm
Forum: ROMS Installation
Topic: CYGWIN permissions
Replies: 0
Views: 1222

CYGWIN permissions

Hello- My windows/cygwin computer was recently replaced, and after reinstalling cygwin, I find that access and permissions to compiled files are modified. For example, when I execute "make clean", cygwin reports that some of the files are protected (mostly SWAN-related files like waves_coupler.o"). ...
by nganju
Wed Feb 07, 2007 6:05 pm
Forum: ROMS Sediment
Topic: SEDMORPH parameters
Replies: 16
Views: 7598

SEDMORPH parameters

When using the SEDMORPH option, what is an appropriate "mud_morph_fac"? Does a value of 10, for example, mean the bed changes are scaled up by 10 at every time-step? Thanks in advance...
by nganju
Tue Jan 16, 2007 7:46 pm
Forum: ROMS Sediment
Topic: WET_DRY specifications
Replies: 2
Views: 2456

WET_DRY specifications

Hello-
Other than modifying "dcrit" in the *.in file, is there any modification needed in the grid file to use wetting and drying? If a certain cell should be available for wetting/drying, is it identified as a "1" in the masks? Thanks in advance...
by nganju
Mon Nov 20, 2006 7:38 pm
Forum: ROMS Discussion
Topic: River point source direction
Replies: 2
Views: 1796

River point source direction

Hello everyone- I have a river point source that runs into the domain in a diagonal fashion (does not run parallel to eta or xi directions). I am looking at effects close to this point source so I need the direction to be realistic near the source. Do I need to split up the total discharge (Qbar in ...
by nganju
Wed Nov 01, 2006 5:42 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34369

matlab's fault?

Thanks for the offer Rich- I was getting the files ready for you, and I tried something different: I created the grid, opened it in Matlab, and recomputed the depths using: zi=griddata(xbathy,ybathy,zbathy,lon_rho,lat_rho); I got the same strange result as seagrid gave. Then I remembered a problem I...
by nganju
Wed Nov 01, 2006 12:11 am
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 34369

seagrid funkiness

I was going to stay quiet, since seagrid has always worked ok for me, but i have always had the same quirks mentioned by sandro (except for the presto path issue). I get more orthogonal results with mex off, and the cell density is always changed when i convert to a roms file using seagrid2roms. i u...
by nganju
Tue Dec 06, 2005 7:57 pm
Forum: ROMS Installation
Topic: ifort 9.0 with Red Hat Linux EM64T
Replies: 11
Views: 7526

thanks for everyone's suggestions, all is running now. on a side note, I am getting a slight speed-up (~1-2%) when hyperthreading is turned off. I tried various tilings and in all cases it was faster with HT off. any reason to leave HT on?
by nganju
Wed Nov 02, 2005 10:09 pm
Forum: ROMS Installation
Topic: ifort 9.0 with Red Hat Linux EM64T
Replies: 11
Views: 7526

netcdf with ifort9.0

It looks like at least one person has had success building netcdf with ifort 9.0. what flags might you have used and what adjustments did you have to make for env. variables? I am still getting an error "skipping incompatible /lib*.* when searching for -lm", and I have tried adding all sorts of path...
by nganju
Mon Oct 03, 2005 7:05 pm
Forum: ROMS Installation
Topic: ifort 9.0 with Red Hat Linux EM64T
Replies: 11
Views: 7526

ifort 32 and 64 installed ok on the system (i had to install it to my user and not the root--i lack access still). I am not trying to install netcdf with the 64 bit until i can get 32 bit running.
by nganju
Mon Oct 03, 2005 4:20 pm
Forum: ROMS Installation
Topic: ifort 9.0 with Red Hat Linux EM64T
Replies: 11
Views: 7526

I am still working on installing the netcdf libraries. there is a file needed by the ./configure called "crt1.o" that is supposed to be in usr/bin/lib, on my machine it is in the folder usr/bin/lib64. So I simply need to copy the file, but alas the systems administrator did not give me full rights o...
by nganju
Mon Aug 22, 2005 6:40 pm
Forum: ROMS Installation
Topic: ifort 9.0 with Red Hat Linux EM64T
Replies: 11
Views: 7526

ifort 9.0 with Red Hat Linux EM64T

Hello, I just purchased a dual-processor 3.6Ghz Xeon machine (Dell Precision 670n) with "Red Hat Enterprise Linux WS v4Intel EM64T 64 bit" operating system. I plan on installing the recent Intel compiler (9.0) which claims to "support" 64bit Intel processors. Dell's website says "All XEON Processors...