Search found 944 matches

by jcwarner
Tue Mar 02, 2021 7:05 pm
Forum: ROMS Problems
Topic: Blowing up problem when using sediment
Replies: 8
Views: 1569

Re: Blowing up problem when using sediment

with any blowup, you need to look at the rst file, his file, and stdout to see what information it is telling you. if you look at the rst file, where is the problem? at the boundary? at the wet/dry masking (for example). try to restart it before the solution occurred. you can typically restart from ...
by jcwarner
Sun Feb 28, 2021 10:05 pm
Forum: ROMS Discussion
Topic: Problem in getting started with SWAN+ROMS
Replies: 1
Views: 196

Re: Problem in getting started with SWAN+ROMS

Neel- It seems like you could use our COAWST model, it has the same ROMS version and we have added many updates to SWAN Coupling and other capabilities. If you want to get that code here: https://github.com/jcwarner-usgs/COAWST we have a user manual that describes how to setup some basic cases like ...
by jcwarner
Sun Feb 28, 2021 2:50 pm
Forum: ROMS Problems
Topic: Problem when I try to compile ROMS with "make" command
Replies: 1
Views: 79

Re: Problem when I try to compile ROMS with "make" command

i am not sure about that tutorial, but to build roms you need to use one of the build scripts.

go here
https://www.myroms.org/wiki/Getting_Started
and read that page.

also make sure you see the section about
https://www.myroms.org/wiki/build_Script

that should help a bit.
by jcwarner
Fri Feb 26, 2021 12:03 am
Forum: ROMS Discussion
Topic: problem with two-way nesting
Replies: 28
Views: 1990

Re: problem with two-way nesting

either way please let us know. would like to figure this one out.
by jcwarner
Thu Feb 25, 2021 2:49 pm
Forum: ROMS Discussion
Topic: problem with two-way nesting
Replies: 28
Views: 1990

Re: problem with two-way nesting

we have a 3 nest of USeast - Carolinas - Outer Banks and i am not seeing this behavior of the currents along the boundaries. can you put the grids and the contact files somewhere accessible?
by jcwarner
Wed Feb 24, 2021 6:22 pm
Forum: ROMS Discussion
Topic: problem with two-way nesting
Replies: 28
Views: 1990

Re: problem with two-way nesting

the exterior points of the child grid are replaced with information from the contact file during initialization, in get_grid. At those points, data is interpolated from the parent and the nesting needs characteristics of the parent at those locations. I have found some issues with this for the maski...
by jcwarner
Mon Feb 22, 2021 3:16 am
Forum: ROMS Discussion
Topic: Fatal error in MPI_Recv
Replies: 12
Views: 1078

Re: Fatal error in MPI_Recv

in your scrip file use (1) SWAN_COORD='../../Projects/Mangkhut/swan_coord.grd', SWAN_BATH='../../Projects/Mangkhut/swan_bathy.bot', SWAN_NUMX=524, SWAN_NUMY=350, CARTESIAN=0, SWAN_COORD(1)='../../Projects/Mangkhut/swan_coord.grd', SWAN_BATH(1)='../../Projects/Mangkhut/swan_bathy.bot', SWAN_NUMX(1)=5...
by jcwarner
Mon Feb 22, 2021 3:12 am
Forum: ROMS Discussion
Topic: Error to run script_coawst
Replies: 5
Views: 614

Re: Error to run script_coawst

i downloaded all of your files, compiled SCRIP, and I can duplicate your error. but there is more information: " Error in netWarning! ***HDF5 library version mismatched error*** The HDF5 header files used to compile this application do not match the version used by the HDF5 library to which this app...
by jcwarner
Sat Feb 20, 2021 3:23 pm
Forum: ROMS Discussion
Topic: Fatal error in MPI_Recv
Replies: 12
Views: 1078

Re: Fatal error in MPI_Recv

the sparse matrix calls are reading the scrip interpolation weights.
What do you have in the scrip.in to compute the interpolation weights?
-j
by jcwarner
Tue Feb 09, 2021 10:21 pm
Forum: ROMS Discussion
Topic: Error to run script_coawst
Replies: 5
Views: 614

Re: Error to run script_coawst

sorry for the late reply.
did you figure this out?
can you attach the scrip.in file?
by jcwarner
Tue Feb 09, 2021 9:48 pm
Forum: ROMS Installation
Topic: Compiling Error for COAWST
Replies: 6
Views: 681

Re: Compiling Error for COAWST

are you still having this problem?
can you send the full output of the std out.
-j
by jcwarner
Tue Feb 09, 2021 1:22 pm
Forum: ROMS Discussion
Topic: problem with two-way nesting
Replies: 28
Views: 1990

Re: problem with two-way nesting

I have been working on the nesting for a while now. There are some simple steps that i can take to check on a few things. Is your setup easy to share out?
what ts_advection are you using? time steps?
-j
by jcwarner
Mon Feb 08, 2021 2:51 pm
Forum: ROMS Discussion
Topic: Fatal error in MPI_Recv
Replies: 12
Views: 1078

Re: Fatal error in MPI_Recv

if your roms grid size(h) is 525 351

then, for the SWAN INPUT file, you need to have
INPGRID BOTTOM CURVILINEAR 0 0 524 350 EXC 9.999000e+003
by jcwarner
Thu Feb 04, 2021 9:14 pm
Forum: ROMS Installation
Topic: COAWST compilation error -- wec_vf.f90
Replies: 2
Views: 208

Re: COAWST compilation error -- wec_vf.f90

looks like a couple of issues.
a year ago or so i changed some parts of the makefile and coawst.bash files and the Compilers files.
are you using most recent versions of them?
which Compilers/ ? file are you using.
-j
by jcwarner
Wed Feb 03, 2021 1:36 pm
Forum: ROMS Discussion
Topic: Fatal error in MPI_Recv
Replies: 12
Views: 1078

Re: Fatal error in MPI_Recv

if you look in the output, you will see that you basically have the same error with different values MCT::m_SparseMatrixPlus::initFromRoot_:: FATAL--length of vector y different from row count of sMat.Length of y = 185152 Number of rows in sMat = 184275 031.MCT(MPEU)::die.: from MCT::m_SparseMatrixP...
by jcwarner
Tue Feb 02, 2021 7:39 pm
Forum: ROMS Discussion
Topic: Fatal error in MPI_Recv
Replies: 12
Views: 1078

Re: Fatal error in MPI_Recv

please read all of the Err* files. This is half way through: "MCT::m_SparseMatrixPlus::initFromRoot_:: FATAL--length of vector y different from row count of sMat.Length of y = 184275 Number of rows in sMat = 183400 010.MCT(MPEU)::die.: from MCT::m_SparseMatrixPlus::initFromRoot_()" so the MCT is rea...
by jcwarner
Tue Feb 02, 2021 3:16 pm
Forum: ROMS Discussion
Topic: Fatal error in MPI_Recv
Replies: 12
Views: 1078

Re: Fatal error in MPI_Recv

there is not enough information here to figure out what the issue is.
can you dig in a bit deeper?
by jcwarner
Tue Feb 02, 2021 3:13 pm
Forum: ROMS Installation
Topic: Compiling Error for COAWST
Replies: 6
Views: 681

Re: Compiling Error for COAWST

yes, the compiler flags might be set too strict, and reducing that can help. But fundamentally there is a potential issue that an integer is being broadcasted as a real. I did a search in distribute.F for "CALL mpi_bcast (A, Asize" and the only place that shows up is once near the bottom in the rout...
by jcwarner
Sat Jan 23, 2021 3:42 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 26
Views: 1353

Re: Error while executing ROMS for a self created grid region

those other errors were initiated by the first one, so get the init file method figured out then try again.
by jcwarner
Fri Jan 22, 2021 5:43 pm
Forum: ROMS Problems
Topic: Error while executing ROMS for a self created grid region
Replies: 26
Views: 1353

Re: Error while executing ROMS for a self created grid region

looks closely at the output text, and you will see INP_PAR:FIND_FILE - empty file name string for standard input script KeyWord: ININAME so the code is looking for a file listed in the ININAME field in the ocean.in If you use #define ANA_INITIAL then it will not look for the ininame and you can use ...
by jcwarner
Thu Jan 21, 2021 3:30 pm
Forum: ROMS Problems
Topic: Blowing up problem when using sediment
Replies: 8
Views: 1569

Re: Blowing up problem when using sediment

I am not really clear what you are trying to do but here are some thoughts. The estuary test case has grid cells on the order of 100m (or so, i dont remember exactly). So therefore it can not generate ripples that are on the order of 10's of cm. Instead, we have coded different methods to 'predict' ...
by jcwarner
Wed Jan 20, 2021 12:54 pm
Forum: ROMS Problems
Topic: netcdf output from SWAN
Replies: 3
Views: 2365

Re: netcdf output from SWAN

that is a known issue for me. Currently you can only have netcdf output for one of the grids when using my swan nesting. it is on my list to correct soon. sorry. also, for future reference, can you and others who read this please post non-roms issues on this other github site: https://github.com/jcw...
by jcwarner
Sat Jan 09, 2021 3:08 am
Forum: ROMS Discussion
Topic: forrtl: severe (194): Run-Time Check Failure
Replies: 3
Views: 509

Re: forrtl: severe (194): Run-Time Check Failure

this says "Run-Time Check Failure. "
so it could be that the compiler flags are set to check for certain issues. these issues may or may not affect the simulation.
I have not dug into SWAN lately, but maybe you could look at the compiler flags and see what is doing this.
by jcwarner
Fri Jan 08, 2021 9:42 pm
Forum: ROMS Sediment
Topic: Estuary_test: are sediment size units and output critical stress right?
Replies: 1
Views: 542

Re: Estuary_test: are sediment size units and output critical stress right?

sorry for the late reply. i looked into this and the values written to the his files are ok, but the units may not be. The stresses tau_ce tau_cd are /rho when read, so they are written out as m2/s2. so it should say m2/s2 in the his nc file. The Sd50 is read in and converted to m, so that should al...
by jcwarner
Wed Dec 30, 2020 9:40 pm
Forum: ROMS Discussion
Topic: forrtl: severe (194): Run-Time Check Failure
Replies: 3
Views: 509

Re: forrtl: severe (194): Run-Time Check Failure

this is really a SWAN question.
are you trying to run a swan grid driven by a nest output from a different run?
by jcwarner
Wed Dec 23, 2020 4:34 pm
Forum: ROMS Discussion
Topic: Error to run script_coawst
Replies: 5
Views: 614

Re: Error to run script_coawst

looks to me like a netcdf/hdf5 issue. make sure you have the correct paths for
NETCDF_INCDIR and NETCDF_LIBDIR.
if you cant figure it out. please post a ticket here:
https://github.com/jcwarner-usgs/COAWST
thanks,
j
by jcwarner
Wed Dec 23, 2020 3:15 am
Forum: ROMS Discussion
Topic: COMPUTE command in swan
Replies: 2
Views: 196

Re: COMPUTE command in swan

are you trying to do this with swan by itself or in a coupled mode?
it would not work in a coupled mode.
the coupled mode is setup to only work with swan running over a computational period that is the same as the other models.
by jcwarner
Sun Dec 20, 2020 6:03 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 1118

Re: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred

getting close, but it still looks like something is wrong with the ocean times. what is the ocean_time in the ocean ini netcdf file? and what are the attributes for that (ncdump and ncks the ocean_time in the ini file). these need to be consistent with the dstart and time_ref. try to figure it out. -j
by jcwarner
Fri Dec 18, 2020 9:08 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 1118

Re: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred

so the problem is that the forcing time is at 4983379200 days. that number is probably in seconds (not days), 4983379200/3600/24=57678 and that number is probably julian(2016,10,1)-2400000=57678 So you need to change the values of time in that forcings file from v2d_time[0]=4983379200 days v2d_time[...
by jcwarner
Fri Dec 18, 2020 2:38 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 1118

Re: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred

looks to me like something is wrong with "time". the error is: "MULTIFILE_INFO_S2D - Error while processing lateral boundary multi-files: data does not include initialization time = 2174-09-15 00:00:00.00 ****-**-** 00:00:00.00 ****-**-** 00:00:00.00 Projects/Sarika/merged_coawst_bdy.nc" Your input ...
by jcwarner
Thu Dec 17, 2020 6:24 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 1118

Re: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred

ok. so this is looking for the Quick output file writes.
Your ocean.in has
! NQCK == 0
! NDEFQCK == 0
lets try it with this:
NQCK == 0
NDEFQCK == 0
and see if that works.
by jcwarner
Thu Dec 17, 2020 5:14 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 1118

Re: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred

in the *.err file we have: mage PC Routine Line Source coawstM 0000000003C4696A Unknown Unknown Unknown libpthread-2.17.s 00002AAF329CD5D0 Unknown Unknown Unknown coawstM 000000000092471A edit_file_struct_ 212 edit_multifile.f90 coawstM 000000000090A307 read_phypar_ 2198 read_phypar.f90 coawstM 0000...
by jcwarner
Thu Dec 17, 2020 4:29 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 1118

Re: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred

there is not enough information for me to determine what is going wrong.
You need to dig into the full output being written.
Did SWAN give Err* files? Maybe try to run the system with one model at a time, to see if each model can handle your new application. then slowly add each component.
by jcwarner
Thu Dec 17, 2020 3:25 pm
Forum: ROMS Discussion
Topic: Error to run coupling WRF+ROMS+SWAN
Replies: 5
Views: 538

Re: Error to run coupling WRF+ROMS+SWAN

SWAN uses the symbol & for a comment line, not ! Does this work: && KEYWORD TO CREATE WIND GRID && INPGRID WIND REGULAR 0 0 299 219 0.25 0.25 & NONSTATIONARY 20161016.000000 6 HR 20161018.000000 &READINP WIND 1 'Projects/Sarika_new/swan_GFS_Oct2012.dat' 4 0 FREE This is getting more into COAWST issu...
by jcwarner
Thu Dec 17, 2020 2:08 pm
Forum: ROMS Discussion
Topic: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 18
Views: 1118

Re: DYNAMICS OPTION: Eulerian Mass Coordinate forrtl: severe (174): SIGSEGV, segmentation fault occurred

ok. you have this NCLMFILES == 2 ! number of climate files CLMNAME == Projects/Sarika4/coawst_clm_20161016.nc | Projects/Sarika4/coawst_clm_20161017.nc NBCFILES == 2 ! number of boundary files ! BRYNAME == Projects/Sandy/Sarika_bdy.nc BRYNAME == Projects/Sarika4/coawst_bdy_20161016.nc | Projects/Sar...
by jcwarner
Wed Dec 16, 2020 2:04 pm
Forum: ROMS Discussion
Topic: Bottom flux for Fennel model
Replies: 3
Views: 419

Re: Bottom flux for Fennel model

are you sure it gets in that loop with the btflux variable? i dont see that variable in the code, it should be btflx.
do this:
grep -nir btflux ROMS/*
and
grep -nir btflx ROMS/*

do you see btflux as a variable anywhere else??
-j
by jcwarner
Sun Dec 13, 2020 3:06 am
Forum: ROMS Discussion
Topic: Error to run coupling WRF+ROMS+SWAN
Replies: 5
Views: 538

Re: Error to run coupling WRF+ROMS+SWAN

try this && KEYWORD TO CREATE WIND GRID && INPGRID WIND REGULAR -105 10 0 220 160 0.25 0.25 & NONSTATIONARY 20121028.000000 6 HR 20121031.000000 &READINP WIND 1 'Projects/Sandy/swan_GFS_Oct2012.dat' 4 0 FREE this sets the INPGRID for WIND, so then SWAN knows that it will get wind on a grid. Then com...
by jcwarner
Sat Dec 12, 2020 8:05 pm
Forum: ROMS Discussion
Topic: Error to run coupling WRF+ROMS+SWAN
Replies: 5
Views: 538

Re: Error to run coupling WRF+ROMS+SWAN

this is an error from SWAN. it is saying "Error : It is not recommended to use quadruplets Error : in combination with zero wind conditions." Also looks like you turned off the winds: !&& KEYWORD TO CREATE WIND GRID && !INPGRID WIND REGULAR -105 10 0 220 160 0.25 0.25 & ! NONSTATIONARY 20121028.0000...
by jcwarner
Fri Dec 11, 2020 12:44 am
Forum: ROMS Bugs
Topic: a potential bug: SWAN not receives or not processes the sea surface level from ROMS
Replies: 7
Views: 928

Re: a potential bug: SWAN not receives or not processes the sea surface level from ROMS

glad you figured it out!
SWAN needs those flags in the input file so that internally it create the input grids, etc. they are the same effect as roms cppdefs, but swan uses keywords not cpp options.
I will make this more clear in the documentation.
-j
by jcwarner
Fri Dec 11, 2020 12:40 am
Forum: ROMS Problems
Topic: Subscript error regarding BED array in stratified cohesive sediment application (with COAWST)
Replies: 12
Views: 943

Re: Subscript error regarding BED array in stratified cohesive sediment application (with COAWST)

ok. glad you are digging in.
What is a deep sea water fall? can you show a pcolor of the bottom stresses? how high do they get?
i am sure we can come up with something, but let me see what the domain looks like.
thanks,
j
by jcwarner
Fri Dec 11, 2020 12:36 am
Forum: ROMS Discussion
Topic: ROMS 3.7 nesting problems
Replies: 6
Views: 372

Re: ROMS 3.7 nesting problems

i am not familiar with this test case but maybe you should re-create the connectivity file. that error should not occur if the grids and connections are set up correctly. can you show a plot of the 3 grids, and the outline of grid 2 and grid 3? how much space is there between the perimeter of grid 3...
by jcwarner
Mon Dec 07, 2020 2:22 pm
Forum: ROMS Problems
Topic: Subscript error regarding BED array in stratified cohesive sediment application (with COAWST)
Replies: 12
Views: 943

Re: Subscript error regarding BED array in stratified cohesive sediment application (with COAWST)

i think this path your are on will help, and you have identified several issues that need to be addressed. However we are in hope that your statement: "Why the available sediments are being reduced so fast is another question but it could just be due to some spin up artefacts which would take up too...
by jcwarner
Fri Dec 04, 2020 1:49 pm
Forum: ROMS Discussion
Topic: forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 9
Views: 808

Re: forrtl: severe (174): SIGSEGV, segmentation fault occurred

you need to look more closely at the whole output. The coupled simulation ran for 0.5 hours: ....... 622479824 2174-09-15 00:29:52.00 5.370047E-03 2.261209E+04 2.261210E+04 4.180266E+16 (191,053,16) 1.041893E-05 2.883283E-04 1.864959E-01 1.586292E+00 622479825 2174-09-15 00:30:00.00 5.370267E-03 2.2...
by jcwarner
Thu Dec 03, 2020 1:41 pm
Forum: ROMS Bugs
Topic: a potential bug: SWAN not receives or not processes the sea surface level from ROMS
Replies: 7
Views: 928

Re: a potential bug: SWAN not receives or not processes the sea surface level from ROMS

i am not seeing much wrong here. need to keep looking. i went back to the original log file and searched for WLEV 42480 2015-07-18 11:48:00.00 6.631682E-03 1.852537E+03 1.852543E+03 7.089705E+10 (374,563,15) 1.241157E-02 2.806246E-04 3.950358E+00 9.911014E-01 ..... ** ROMS grid 1 sent data to SWAN g...
by jcwarner
Wed Dec 02, 2020 6:06 pm
Forum: ROMS Bugs
Topic: a potential bug: SWAN not receives or not processes the sea surface level from ROMS
Replies: 7
Views: 928

Re: a potential bug: SWAN not receives or not processes the sea surface level from ROMS

so i just ran the inlet test again and it is fine. so there is something wrong in your setup.
can we look at the PRINT* files? how did you set the swan depths?
what does your INPUT file have?
-j
by jcwarner
Wed Dec 02, 2020 4:18 pm
Forum: ROMS Discussion
Topic: forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 9
Views: 808

Re: forrtl: severe (174): SIGSEGV, segmentation fault occurred

ok. SWAN has some issues with the arrays, and depending on the debug flags, it will stop compiling. swan is not the problem, so lets not go down this road. the problem you were having is with roms. it stopped when it tried to close a file. how about you setup the application to only use roms. then c...
by jcwarner
Tue Dec 01, 2020 2:32 pm
Forum: ROMS Bugs
Topic: a potential bug: SWAN not receives or not processes the sea surface level from ROMS
Replies: 7
Views: 928

Re: a potential bug: SWAN not receives or not processes the sea surface level from ROMS

that looks strange.
What is the 2.25 from? do you have wet/dry on, so that 2.25 is on land and probably masked out in swan.
can you make a pcolor plot of swan water level and roms water level at 07/18/06?
you do not have define ZETA_CONST ?
-j
by jcwarner
Tue Dec 01, 2020 2:07 pm
Forum: ROMS Discussion
Topic: forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 9
Views: 808

Re: forrtl: severe (174): SIGSEGV, segmentation fault occurred

1. Yes, Kate is suggesting you edit the coawst.bash (or roms.bash) and set USE_DEBUG=on 2. can you post your cleaned ocean.in 3. the error was coawstM 000000000092471A edit_file_struct_ 212 edit_multifile.f90 coawstM 000000000090A307 read_phypar_ 2198 read_phypar.f90 so if you edit Build/read_phypar...
by jcwarner
Sat Nov 28, 2020 2:48 pm
Forum: ROMS Discussion
Topic: Problem and question about SWAN in COAWST
Replies: 1
Views: 381

Re: Problem and question about SWAN in COAWST

sorry for the late reply on this. Looks like the wind data to drive swan is not constructed correctly, or the swan grid file was not constructed correctly. That is why the lines look like that. Can you try to run swan by itself with just one grid? You could even do WIND 20. 45. (wind speed dir) in t...
by jcwarner
Sat Nov 28, 2020 2:23 pm
Forum: ROMS Discussion
Topic: forrtl: severe (174): SIGSEGV, segmentation fault occurred
Replies: 9
Views: 808

Re: forrtl: severe (174): SIGSEGV, segmentation fault occurred

i looked at your ocean.in and there are a lot of TABS in there. if dont know if this is exactly the problem, but i remember other people had trouble when there are tabs in the ocean.in. You need to clean up that file. there are editing tools to do this. then give it another try. for coawst related i...
by jcwarner
Tue Nov 24, 2020 1:51 pm
Forum: ROMS Discussion
Topic: Issues with tides in COAWST Estuary_Test2
Replies: 3
Views: 521

Re: Issues with tides in COAWST Estuary_Test2

Looks like you are digging in deep to the estuary test 2. I think Hans Burchard and I made up this case (mostly him) to have something different than the straight standard case we had before. To get the system to be the way you want, will require some tests. But here are some suggestions. the easter...
by jcwarner
Mon Nov 09, 2020 12:56 am
Forum: ROMS Discussion
Topic: Adding Sediment to the Latte Example
Replies: 3
Views: 638

Re: Adding Sediment to the Latte Example

there are many other test cases to choose from. if you want to grab our version of the COAWST system, we distribute a rip current test, inlet test, etc. Most of them have sediment so there are several examples to choose from.
https://github.com/jcwarner-usgs/COAWST
-j
by jcwarner
Mon Nov 02, 2020 11:33 pm
Forum: ROMS Discussion
Topic: Problem with ssh response to uniform winds.
Replies: 4
Views: 387

Re: Problem with ssh response to uniform winds.

is there a reason you dont use NS periodic? also there is an upwelling test case distributed with the code that you might want to try first, just to get an idea of what that case can do.
-j
by jcwarner
Sun Nov 01, 2020 12:32 am
Forum: ROMS Discussion
Topic: run error when applying forcing file
Replies: 7
Views: 526

Re: run error when applying forcing file

check your ocean.in file make sure you dont have nffiles twice
NFFILES ==
...
NFFILES ==

the FRC array is allocated in read_phypar
CASE ('NFFILES')
...
allocate ( FRC(max_Ffiles,Ngrids) )

so it seems to be doing that call twice.
-j
by jcwarner
Wed Oct 21, 2020 1:46 pm
Forum: ROMS Discussion
Topic: Bathymetry differences in nested simulations
Replies: 5
Views: 752

Re: Bathymetry differences in nested simulations

i am not sure why a 3 would have an issue but a 5 factor would work. If it blew up right away, that is the best type of problem. Look at the std out and make sure there are no nans, look at the rst file to see where it had troubles. You have to be a detective some times.
by jcwarner
Tue Oct 20, 2020 5:40 pm
Forum: ROMS Discussion
Topic: Bathymetry differences in nested simulations
Replies: 5
Views: 752

Re: Bathymetry differences in nested simulations

nice animation! For your bathy question, i am not sure there is an exact answer. It could depend on the grid sizes, bathy itself, wet/dry if that is active, etc. IF what you have is working well, then i would suggest you can modify the bathy in most of the child, but dont adjust the child bathy alon...
by jcwarner
Wed Oct 07, 2020 3:03 pm
Forum: ROMS Sediment
Topic: Diffusion of sediment tracers in the water column
Replies: 1
Views: 427

Re: Diffusion of sediment tracers in the water column

sorry i did not get to this earlier. for now, the horiz diffusion of sediment is treated like any other tracer. so you would need to add a horiz mix (like your ts_dif2 and mix_geo_ts). the coeffs will be the TNU2 set in the ocean .in file. Also, you may want to update your code and use the new featu...
by jcwarner
Thu Sep 17, 2020 12:36 pm
Forum: ROMS Problems
Topic: segmentation fault occurred when read initial condition
Replies: 3
Views: 676

Re: segmentation fault occurred when read initial condition

suggest you do this.
recompile with DEBUG=on, that will give a coawstG
run it with just 1 proc, this will make the error more easy to see.
by jcwarner
Wed Sep 16, 2020 11:10 pm
Forum: ROMS Discussion
Topic: SWAN+WRF coupling problem using COAWST
Replies: 2
Views: 477

Re: SWAN+WRF coupling problem using COAWST

can you try an update to the code and make sure you have the most recent version? i think that was an issue we corrected.
If you still have troubles, can you make an issue here:
https://github.com/jcwarner-usgs/COAWST
thanks,
j
by jcwarner
Wed Sep 16, 2020 1:02 pm
Forum: ROMS Problems
Topic: segmentation fault occurred when read initial condition
Replies: 3
Views: 676

Re: segmentation fault occurred when read initial condition

not sure. but both inlet test and upwelling use ana_initial. So how about you try something that needs an initial netcdf file. You could try our Sandy case, set it up to just use roms only (undef swan and undef wrf). That case uses a netcdf initial file. lets see if that works.
-j
by jcwarner
Tue Sep 15, 2020 12:05 am
Forum: ROMS Problems
Topic: ROMS<kshedstrom version> blow at the fist timestep
Replies: 2
Views: 433

Re: ROMS<kshedstrom version> blow at the fist timestep

are you using the newest version of the input scrip? you need to have the tracer advection schemes selected, such as ! Set horizontal and vertical advection schemes for active and inert ! tracers. A different advection scheme is allowed for each tracer. ! For example, a positive-definite (monotonic)...
by jcwarner
Mon Sep 14, 2020 12:09 am
Forum: ROMS Bugs
Topic: Error to run roms_clm_roms_master_climatology_coawst_mw
Replies: 1
Views: 343

Re: Error to run roms_clm_roms_master_climatology_coawst_mw

this is a tough one. the netcdf variable must be interpolated incorrectly, or something like that. try a different time period just to try and get it to work.
by jcwarner
Mon Aug 24, 2020 1:16 pm
Forum: ROMS Sediment
Topic: Lake_jersey test case error at first time steps
Replies: 4
Views: 693

Re: Lake_jersey test case error at first time steps

can you look through the entire stdout and see if there are any nans above that? maybe there is something wrong with the forcings??
by jcwarner
Mon Aug 24, 2020 1:14 pm
Forum: ROMS Installation
Topic: COAWST V3.6 Compiling error
Replies: 1
Views: 365

Re: COAWST V3.6 Compiling error

can you please re=post this message here:
https://github.com/jcwarner-usgs/COAWST/issues
by jcwarner
Mon Aug 24, 2020 1:13 pm
Forum: ROMS Bugs
Topic: Error to run netcdf_load command on Matlab
Replies: 1
Views: 431

Re: Error to run netcdf_load command on Matlab

this is a matlab issue. You need to include the path(s) to all the mfiles so that matlab knows where those scripts are.
-j
by jcwarner
Tue Aug 04, 2020 12:57 pm
Forum: ROMS Installation
Topic: Compiling COAWST_v3.6 errror
Replies: 9
Views: 1205

Re: Compiling COAWST_v3.6 errror

lets move this conversation over here. put a post here:
https://github.com/jcwarner-usgs/COAWST/issues
by jcwarner
Mon Aug 03, 2020 1:44 pm
Forum: ROMS Installation
Topic: Compiling COAWST_v3.6 errror
Replies: 9
Views: 1205

Re: Compiling COAWST_v3.6 errror

looks like a WRF/ WPS issue. I am not sure this is the correct forum for a question like that. try the WRF forum
https://forum.wrfforum.com/
by jcwarner
Fri Jul 31, 2020 12:27 pm
Forum: ROMS Installation
Topic: Compiling COAWST_v3.6 errror
Replies: 9
Views: 1205

Re: Compiling COAWST_v3.6 errror

your build.log shows a coawstM. So you are good to go.
the ls command display is messy, but i see a coawstM in there.
As i said earlier, it will not create a wrf.exe, I make it create a libwrf.a and then i link with that file.
-j
by jcwarner
Thu Jul 30, 2020 5:27 pm
Forum: ROMS Installation
Topic: Compiling COAWST_v3.6 errror
Replies: 9
Views: 1205

Re: Compiling COAWST_v3.6 errror

Thanks David.
dont worry about the wrf.error. I do not let the system build a wrf.exe, i do not let swan build a swan.exe, nor a ww3.exe etc. I just make libraries, pull them all together as a coawstM.

i agree with your netcdf analysis. thanks,
-j
by jcwarner
Thu Jul 30, 2020 12:20 pm
Forum: ROMS Installation
Topic: Compiling COAWST_v3.6 errror
Replies: 9
Views: 1205

Re: Compiling COAWST_v3.6 errror

i think your problem is a general roms issue, and i think it has to do with the final link at the end. it is having trouble with the netcdf f90 libs. i see: -L/work/apps/gnu_4.8.5/netcdf/4.3.3.1/lib -lnetcdff -L/work/apps/gnu_4.8.5/netcdf/4.3.3.1/lib -lnetcdf -lnetcdf try to clean this up, remove th...
by jcwarner
Tue Jul 21, 2020 7:41 pm
Forum: ROMS Discussion
Topic: Profiling COAWST with 2-way coupled ROMS/SWAN
Replies: 2
Views: 448

Re: Profiling COAWST with 2-way coupled ROMS/SWAN

not sure what Unused 03 is. But for the coupling, if you see something like this: 97 2020-07-21 04:51:00.00 3.755311E-02 2.266493E+04 2.266496E+04 2.088627E+16 (762,292,16) 3.718707E-02 5.124825E-02 4.006800E-01 3.243301E+00 98 2020-07-21 04:54:00.00 3.755672E-02 2.266491E+04 2.266495E+04 2.088623E+...
by jcwarner
Sun Jul 19, 2020 11:16 pm
Forum: ROMS Discussion
Topic: time-dependent bottom fluxes in roms?
Replies: 3
Views: 815

Re: time-dependent bottom fluxes in roms?

how about using Wilkin's new LwSrc? This is a vertical point source at a rho point and can have tracers with it. (as opposed to LuvSrc which is a lateral point source at a u- or v- point). You need to set the correct flags (now in the ocean.in) but it could be a viable option. The LwSrc is in get_da...
by jcwarner
Mon Jul 13, 2020 2:25 pm
Forum: ROMS Discussion
Topic: error compiling ana_lrflux
Replies: 2
Views: 380

Re: error compiling ana_lrflux

here is what's happening. You defined solar_source, and in globaldefs there is : #if defined LMD_SKPP || defined SOLAR_SOURCE || \ defined BULK_FLUXES || defined BIOLOGY # define SHORTWAVE #endif so with shortwave now automatically defined, we go to mod_forces we have # ifdef SHORTWAVE real(r8), poi...
by jcwarner
Thu Jul 02, 2020 2:09 pm
Forum: ROMS Discussion
Topic: Running error: unable to open existing NetCDF file
Replies: 6
Views: 891

Re: Running error: unable to open existing NetCDF file

i am wondering if your ocean.in files are older. because all the ocean.in were renamed to roms_ini.nc a while ago.
by jcwarner
Tue Jun 23, 2020 9:23 pm
Forum: ROMS Discussion
Topic: Roms with ice module in Coawst
Replies: 13
Views: 1356

Re: Roms with ice module in Coawst

rhoAir(i)=PairM*100.0_r8/(blk_Rgas*TairK(i)* & & (1.0_r8+0.61_r8*Q(i))) can you also check Q(i)? #if defined CORE_FORCING || defined SPECIFIC_HUMIDITY ! Incoming humidity is specific humidity in (kg/kg) Q(i)=RH #else IF (RH.lt.2.0_r8) THEN !RH fraction cff=cff*RH !Vapor pres (mb) Q(i)=0.62197_r8*(cf...
by jcwarner
Tue Jun 23, 2020 7:07 pm
Forum: ROMS Bugs
Topic: Sandy case in Coawst with WW3 only
Replies: 1
Views: 474

Re: Sandy case in Coawst with WW3 only

can you post this as an issue here:

https://github.com/jcwarner-usgs/COAWST
by jcwarner
Tue Jun 23, 2020 4:57 pm
Forum: ROMS Discussion
Topic: Roms with ice module in Coawst
Replies: 13
Views: 1356

Re: Roms with ice module in Coawst

well, my guess is the '/' sign, it probably has a zero on the bottom. .../(rhoAir(i)*blk_Cpa) so now we start to go backwards. -blk_Cpa is a constant, so no issue there. -rhoAir(i) is computed in bulk flux as rhoAir(i)=PairM*100.0_r8/(blk_Rgas*TairK(i)* & & (1.0_r8+0.61_r8*Q(i))) PairM = Pair(i,j) :...
by jcwarner
Sat Jun 20, 2020 8:10 pm
Forum: ROMS Discussion
Topic: Roms with ice module in Coawst
Replies: 13
Views: 1356

Re: Roms with ice module in Coawst

can you try and run without ICE_MODEL and see if the T and S are ok?
that may help identify the issue.
-j
by jcwarner
Tue Jun 16, 2020 7:28 pm
Forum: ROMS Discussion
Topic: units of omega
Replies: 6
Views: 714

Re: units of omega

i think omega is written to the his file as m/s. here is what i see: in omega.F, W (omega) is computed as W(i,j,k)=W(i,j,k-1)- & & (Huon(i+1,j,k)-Huon(i,j,k)+ & & Hvom(i,j+1,k)-Hvom(i,j,k)) so it has units of m3/s in wrt his, we have ! ! Write out S-coordinate omega vertical velocity (m/s). ! CALL s...
by jcwarner
Thu Jun 11, 2020 10:37 pm
Forum: ROMS Discussion
Topic: Compiling problem of inlet_test
Replies: 7
Views: 867

Re: Compiling problem of inlet_test

can you create an issue here
https://github.com/jcwarner-usgs/COAWST/issues
and post output of the full build.
it has a problem earlier than what you showed.
by jcwarner
Thu Jun 11, 2020 1:13 pm
Forum: ROMS Discussion
Topic: Compiling problem of inlet_test
Replies: 7
Views: 867

Re: Compiling problem of inlet_test

i am not sure. it looks like you have -DMPI in the cpp. If you want to use the Inlet_test and run wave -current interaction, i suggest you use our COAWST code. we have this on github now:
https://github.com/jcwarner-usgs/COAWST
the setups are very similar.
-j
by jcwarner
Tue Jun 09, 2020 8:33 pm
Forum: ROMS Discussion
Topic: Compiling problem of inlet_test
Replies: 7
Views: 867

Re: Compiling problem of inlet_test

the file ROMS/Utility/mp_exchange.F for tile_neighbors has .. USE mod_parallel ... # if defined MPI Null_Value=MPI_PROC_NULL # else Null_Value=-1 # endif and then the MODULE mod_parallel ... #ifdef MPI include 'mpif.h' #endif so the mpif.h should be passed to the mp_exchange routines. mpif.h should ...
by jcwarner
Tue Jun 09, 2020 8:18 pm
Forum: ROMS Problems
Topic: forcing interpolation not working
Replies: 7
Views: 1313

Re: forcing interpolation not working

i just checked my forcing for the Sandy test case and the atm forcing is on a separate grid that is not identical to either of the roms grids. I remember changing this a while ago to make the test case forcing files a lot smaller, it is just a test case. So for the Sandy case, ROMS does read correct...
by jcwarner
Mon Jun 08, 2020 11:47 pm
Forum: ROMS Discussion
Topic: grid generation for idealized geometry
Replies: 4
Views: 878

Re: grid generation for idealized geometry

For the ROMS distribution we have the classic estuary test grid from our 2005 OM paper, that was rectangular. In COAWST we have an estuary_test 2 "This application tests the ROMS for a prismatic shaped estuary that is 110 km long with the ocean end being 60 kms wide. The width of the estuary decreas...
by jcwarner
Thu Jun 04, 2020 8:19 pm
Forum: ROMS Problems
Topic: forcing interpolation not working
Replies: 7
Views: 1313

Re: forcing interpolation not working

i just ran the Sandy test case with grid refinement 2 grids roms +swan and it worked fine. it reads in met data for both roms grids. The output you show: Min = 1.00000000E+35 Max = -1.00000000E+35) is a pure report from roms of what it reads from your netcdf forcing file. do an ncview of that forcin...
by jcwarner
Thu Jun 04, 2020 8:14 pm
Forum: ROMS Usage
Topic: How do I input my own netCDF grid file for the ROMS Upwelling test case?
Replies: 10
Views: 1463

Re: How do I input my own netCDF grid file for the ROMS Upwelling test case?

probably something to do with the bathy Minimum Z-grid spacing, DZmin = -5.58178863E+04 m Maximum Z-grid spacing, DZmax = 6.41893191E+04 m at 1 km grid spacing, you probably should not have any negative depths (these would be elevations on land above the sea level). suggest you set a min depth = 1 m...
by jcwarner
Tue May 26, 2020 2:46 pm
Forum: ROMS Discussion
Topic: Unread or missing keyword 'NBCFILES' from input script
Replies: 1
Views: 383

Re: Unread or missing keyword 'NBCFILES' from input script

looks like you need to update your ocean.in to a more recent version.

-j
by jcwarner
Sat May 23, 2020 12:51 am
Forum: ROMS Discussion
Topic: Graphite loop optimizations cannot be used (isl is not available)
Replies: 4
Views: 994

Re: Graphite loop optimizations cannot be used (isl is not available)

it does not relate to MCT. It has to do with your compiler, maybe the gcc, ?? , maybe the optimizations?
i did a little googling
https://gcc.gnu.org/gcc-4.8/changes.html
that page has some info. i am really not sure, have not seen this one before. looks like a compiler issue, not the code.
by jcwarner
Thu May 21, 2020 3:57 pm
Forum: ROMS Discussion
Topic: Graphite loop optimizations cannot be used (isl is not available)
Replies: 4
Views: 994

Re: Graphite loop optimizations cannot be used (isl is not available)

you need to edit a file in your Compilers dir. most likely:
Compilers/Linux-gfortran.mk
but i did a search and dont see any graphite flags in there. maybe post more of the build.
where is that flag coming from??
by jcwarner
Thu May 21, 2020 1:18 pm
Forum: ROMS Usage
Topic: How do I input my own netCDF grid file for the ROMS Upwelling test case?
Replies: 10
Views: 1463

Re: How do I input my own netCDF grid file for the ROMS Upwelling test case?

for the upwelling case you would need to edit
ROMS/Include/upwelling.h and change
#define ANA_GRID
to
#undef ANA_GRID

recompile,

and change ROMS/External/roms_upwelling.in from
GRDNAME == roms_grd.nc
to
GRDNAME == YOUR GRID NAME here

-j
by jcwarner
Tue May 19, 2020 5:23 pm
Forum: ROMS Discussion
Topic: Blow up problem in ROMS 3.9
Replies: 2
Views: 657

Re: Blow up problem in ROMS 3.9

a new feature in the latest ROMS is the ability to choose different advection schemes for each tracer. But you need to be careful to use the new ocean.in format. from your output is see: Tracer Advection Scheme: NLM ======================== Variable Grid Horizontal Vertical --------- ---- ----------...
by jcwarner
Mon May 18, 2020 4:16 pm
Forum: ROMS Discussion
Topic: using MPI for nested simulations
Replies: 1
Views: 411

Re: using MPI for nested simulations

currently you need to use the same number of tiles for each grid. So if you have 12 tiles, then grid 1 could be NtileI=3 and NtileJ = 4; grid 2 could be NtileI=12 NtileJ=1; etc. but the total has to be 12 (or whatever you use) for each grid. I am looking into changing this, but it takes a redistribu...
by jcwarner
Sun May 17, 2020 1:06 am
Forum: ROMS Discussion
Topic: Blow up problem
Replies: 3
Views: 809

Re: Blow up problem

these values seem odd: GET_GRID - mask on RHO-points: mask_rho (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc) (Min = 0.00000000E+00 Max = 1.15000000E+02) GET_GRID - mask on U-points: mask_u (Grid = 01, File: /gpfs/projects/WilsonGroup/ROMS/OIB/ROMS_Grid1_msk02.nc) (Min = ...
by jcwarner
Fri May 15, 2020 3:06 pm
Forum: ROMS Discussion
Topic: Instabilities in LF-AM3 caused by wetting/drying?
Replies: 4
Views: 634

Re: Instabilities in LF-AM3 caused by wetting/drying?

i am not sure the exact horiz resolution to start using wet-dry, but i would think on the order of 100m and less, more like 10 m or less ?? really depends on the application. think of the beach, and the tide (or surge) coming in and out. what is the horizontal distance from the high tide line to the...
by jcwarner
Fri May 15, 2020 2:29 pm
Forum: ROMS Discussion
Topic: Instabilities in LF-AM3 caused by wetting/drying?
Replies: 4
Views: 634

Re: Instabilities in LF-AM3 caused by wetting/drying?

the wet-dry scheme is a very sensitive approach and we spent a large effort to get this into roms. It is not solving an exact equation, instead wet-dry prevent flow out of a cell if the total water depth is less than Dcrit. that is all. but it is complicated due to the multiple time levels. In pract...
by jcwarner
Thu Apr 30, 2020 2:29 pm
Forum: ROMS Discussion
Topic: Could I repeat the simulation forced by bulk flux by using its output?
Replies: 3
Views: 708

Re: Could I repeat the simulation forced by bulk flux by using its output?

there was someone else who asked this, but i cant find that set of posts. I dont think it worked for them. some reasons might be that the swrad penetrates below the ocean surface, this effects the mixing and shear etc. and that affects the computed su/vstr. Then if you drive the model with the pre-c...
by jcwarner
Mon Apr 27, 2020 9:05 pm
Forum: ROMS Bugs
Topic: FORTRAN error - Probably related to January changes
Replies: 4
Views: 613

Re: FORTRAN error - Probably related to January changes

this just got added in the last src ticket 850. Think it could just be commented out for now:

CASE ('Ltracing')
Npts=load_l(Nval, Cval, 1, Lvalue)
! Ltracing=Lvalue(1) <---line 895

Slide1.PNG
by jcwarner
Mon Apr 27, 2020 8:39 pm
Forum: ROMS Benchmarks
Topic: output of ROMS memory usage
Replies: 1
Views: 672

Re: output of ROMS memory usage

it may not have been in my version a while ago. there is not a cpp def for it. However I just pushed out a new version with all of Rutgers updates. Ran the Sandy test case and it shows mem usage (see below). So you should be all set. thanks, john >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>...
by jcwarner
Wed Apr 22, 2020 4:19 pm
Forum: ROMS Bugs
Topic: Possible bug in wetdry.F for nested apps
Replies: 14
Views: 2015

Re: Possible bug in wetdry.F for nested apps

this looks cool! i looked at your paper:
https://sriha.net/articles/storm-surge- ... ing-drying
and you are really digging into the fine details. dont think many people have cascaded down from km to m scales. nice to see.
by jcwarner
Tue Apr 21, 2020 8:15 pm
Forum: ROMS Discussion
Topic: Issue with the vertical mixing
Replies: 3
Views: 722

Re: Issue with the vertical mixing

this is a power point i gave in 2002: surface_mix.png the text is here: Warner, J.C., Sherwood, C., Arango, H., and Signell, R. (2005). “Performance of Four Turbulence Closure Models Implemented Using a Generic Length Scale Method.” Ocean Modelling, v. 8/1-2, p. 81-113. check your surface stress. we...
by jcwarner
Mon Apr 20, 2020 10:11 pm
Forum: ROMS Discussion
Topic: Inlet_test with SWAN only under constant wind speed
Replies: 1
Views: 519

Re: Inlet_test with SWAN only under constant wind speed

just got back around to trying this. sorry for the delay. I get an error, but it says more Errfile01 Error : Quadruplets should be activated when SWAN so if i turn quads back on by commenting this line : &OFF QUAD then it works. also make sure you have correct paths to the input files. i see you hav...
by jcwarner
Thu Apr 16, 2020 1:54 pm
Forum: ROMS Discussion
Topic: Test of open boundary conditions
Replies: 12
Views: 1669

Re: Test of open boundary conditions

earlier you had said "My [new] test case features a geostrophic surface eddy that moves into the domain from one open boundary and leaves at another." This is reminiscent of the soliton test case, distributed. we also modified it at some point for a nesting test case, to show that you need 2-way to ...
by jcwarner
Sun Apr 12, 2020 11:53 pm
Forum: ROMS Discussion
Topic: Test of open boundary conditions
Replies: 12
Views: 1669

Re: Test of open boundary conditions

these look really cool! there has been a good bit of work on roms open BC's. i have not looked into the details in a while. here are some thoughts: -if you go here: https://www.myroms.org/wiki/Boundary_Conditions you can get a good paper : Marchesiello, P., J. C. McWilliams, A. F. Shchepetkin, 2001:...
by jcwarner
Fri Apr 03, 2020 1:22 pm
Forum: ROMS Discussion
Topic: Question about the tidal forcing file
Replies: 3
Views: 1137

Re: Question about the tidal forcing file

and then in set tides you have stuff like: omega=cff/Tperiod(itide) DO j=MIN(JstrR,Jstr-1),JendR DO i=MIN(IstrR,Istr-1),IendR angle=UV_Tangle(i,j,itide)-angler(i,j) <--------- here it corrects for the grid angle Cangle=COS(angle) Sangle=SIN(angle) phase=omega-UV_Tphase(i,j,itide) Cphase=COS(phase) S...
by jcwarner
Fri Apr 03, 2020 1:19 pm
Forum: ROMS Discussion
Topic: Question about the tidal forcing file
Replies: 3
Views: 1137

Re: Question about the tidal forcing file

i have not looked at the tides files in a long time, but in our tides tools m file we have: cangleID = netcdf.defVar(nc_init,'tide_Cangle','double',[xrhodimID erhodimID ntidedimID]); netcdf.putAtt(nc_init,cangleID,'long_name','tidal current inclination angle'); netcdf.putAtt(nc_init,cangleID,'units'...
by jcwarner
Thu Apr 02, 2020 7:58 pm
Forum: ROMS Problems
Topic: ROMS requires history file from the first run
Replies: 4
Views: 680

Re: ROMS requires history file from the first run

if it is a new run, why is time step 163080? what is dstart?
not sure.
by jcwarner
Thu Apr 02, 2020 7:04 pm
Forum: ROMS Problems
Topic: ROMS requires history file from the first run
Replies: 4
Views: 680

Re: ROMS requires history file from the first run

if it is a new run, then you should set nrrec = 0 (? right) so then it would not look for his11, instead it would create a new his1. ?
-j
by jcwarner
Sun Mar 29, 2020 7:28 pm
Forum: ROMS Bugs
Topic: Limited cores can be used for SWAN in the COAWST package
Replies: 3
Views: 757

Re: Limited cores can be used for SWAN in the COAWST package

SWAN tiles its domain by dividing the longest edge into the number of cores. So your longest edge is 542 and that happpens to be in the x-dir, divide by 30 gives around 18. so each tile is 18x437. for coawst i need to have the tiles be square, so that we can combine them with roms grid to determine ...
by jcwarner
Thu Mar 26, 2020 1:17 pm
Forum: ROMS Installation
Topic: ERROR COMPILING FOR THE FIRST TIME
Replies: 15
Views: 1724

Re: ERROR COMPILING FOR THE FIRST TIME

"initially editing any file with Wordpad"
WordPad is just as bad. That is not a good alternative.
I use emacs, or TextPad.
-j
by jcwarner
Tue Mar 24, 2020 10:37 pm
Forum: ROMS Installation
Topic: ERROR COMPILING FOR THE FIRST TIME
Replies: 15
Views: 1724

Re: ERROR COMPILING FOR THE FIRST TIME

really not sure what is going on with that. if this is holding you up, you could just edit the *.f90 and put the closing quote, then do ./roms.bash -noclean or (not recommended) you could edit the *.F and just replace to my_fort = "gfortran" but then it will not be correct if you change the compiler...
by jcwarner
Tue Mar 24, 2020 4:58 pm
Forum: ROMS Installation
Topic: ERROR COMPILING FOR THE FIRST TIME
Replies: 15
Views: 1724

Re: ERROR COMPILING FOR THE FIRST TIME

longshot but .... where do you specify gfortran. in the roms.bash or something, right. make sure there are no characters after the gfortran, like a horrible tab or space or any weird unseen character.
can you post your roms.bash??
-j
by jcwarner
Tue Mar 24, 2020 1:26 pm
Forum: ROMS Installation
Topic: ERROR COMPILING FOR THE FIRST TIME
Replies: 15
Views: 1724

Re: ERROR COMPILING FOR THE FIRST TIME

in your build.bash, you set FORT=gfortran then in the makefile, it reads that $FORT from the environment and makes it -DMY_FORT='"$(FORT)"' so now the var MY_FORT is "gfortran" then in mod_strings it compiles character (len=80) :: my_fort = MY_FORT to become character (len=80) :: my_fort = "gfortran...
by jcwarner
Tue Mar 24, 2020 1:02 pm
Forum: ROMS Results
Topic: strange velocity results (need some ideas to correct them)
Replies: 5
Views: 1193

Re: strange velocity results (need some ideas to correct them)

do the temp and salt fields looks blocky?
by jcwarner
Tue Mar 24, 2020 12:55 pm
Forum: ROMS Bugs
Topic: ROMS Code failing in between when it is creating new NetCDF file to write the output
Replies: 1
Views: 448

Re: ROMS Code failing in between when it is creating new NetCDF file to write the output

looks like it is failing while trying to write a variable into the quick files. what is on line 4393 of Build/mod_netcdf.f90? ceanM 00000000008EBB0D mod_netcdf_mp_net 4393 mod_netcdf.f90 look at that section of code and see what it is trying to write. try to comile with debug=on and that will give o...
by jcwarner
Mon Mar 23, 2020 6:12 pm
Forum: ROMS Results
Topic: strange velocity results (need some ideas to correct them)
Replies: 5
Views: 1193

Re: strange velocity results (need some ideas to correct them)

not sure it is a BC issue.
what are you using for TS advection? turb closures?
do you N2S2_HORAVG on??
-j
by jcwarner
Tue Mar 17, 2020 2:19 pm
Forum: ROMS Sediment
Topic: sediment settling flux
Replies: 3
Views: 778

Re: sediment settling flux

the tracer nnew time level is the "tracer * Hz". the tracer nstp time level is just the tracer value.
so yes, be careful.
by jcwarner
Tue Mar 17, 2020 1:56 pm
Forum: ROMS Discussion
Topic: Problem with setting up inlet_test
Replies: 28
Views: 2783

Re: Problem with setting up inlet_test

looks like it cant find a file, maybe the wind file or the setup file.?? can you send to me /home/henry/coawst/COAWST/WW3/model/tmp/w3iogomd.F90 /home/henry/coawst/COAWST/WW3/model/tmp/ww3_shel.F90 i can look on those line numbers and see what file it is trying to find. WW3 does a lot of soft links ...
by jcwarner
Mon Mar 16, 2020 3:11 pm
Forum: ROMS Sediment
Topic: sediment settling flux
Replies: 3
Views: 778

Re: sediment settling flux

be careful in here. a quick look i can see the bottom of the bio routine has: ... DO i=Istr,Iend cff=Bio(i,k,ibio)-Bio_old(i,k,ibio) t(i,j,k,nnew,ibio)=t(i,j,k,nnew,ibio)+cff*Hz(i,j,k) so to put the Bio back into the tracer array, the Bio gets multiplied by Hz. so that is probably where the units ge...
by jcwarner
Tue Feb 18, 2020 1:29 am
Forum: ROMS Discussion
Topic: Problem with setting up inlet_test
Replies: 28
Views: 2783

Re: Problem with setting up inlet_test

yes we have roms wrf ww3 swan coupling in the coawst system. if you send me an email, i can add you to that distribution.
jcwarner@usgs.gov
-j
by jcwarner
Fri Feb 07, 2020 5:37 pm
Forum: ROMS Bugs
Topic: Possible bug in wetdry.F for nested apps
Replies: 14
Views: 2015

Re: Possible bug in wetdry.F for nested apps

we made some updates in those exchanges as well, but it had to deal with the masking that was used. Either Dave or I will send you the changes in a bit. we have some applications that we are working on first to test this out.
-j
by jcwarner
Thu Jan 16, 2020 12:05 am
Forum: ROMS Bugs
Topic: WET_DRY and Gridbuilder Problem
Replies: 21
Views: 3175

Re: WET_DRY and Gridbuilder Problem

(4)I use Dcrit=0.1m. You mean I should refine my grid? Now horiziontal resolution is 100m. this is clear that you are not fully aware of how to use wet dry. it is simple. can you get our paper in Comp and Geosci? https://darchive.mblwhoilibrary.org/bitstream/handle/1912/6207/1-s2.0-S0098300413001362...
by jcwarner
Tue Jan 14, 2020 2:50 pm
Forum: ROMS Bugs
Topic: WET_DRY and Gridbuilder Problem
Replies: 21
Views: 3175

Re: WET_DRY and Gridbuilder Problem

-changing hmin to zero is basically removing all the 'land' parts of your grid, so that removed your wet dry problem. - an hmin of -100 means that you have a small hill about 100 m above sea level. that might be troubles for roms. so maybe you could set landmask=0 for cells that are above, lets say,...
by jcwarner
Mon Dec 30, 2019 2:06 pm
Forum: ROMS Discussion
Topic: Add a in ROMS
Replies: 2
Views: 678

Re: Add acceleration in ROMS equations

a suggestion would be to impose a BODY_FORCE. do a search for "body_force" in the discussion threads. you can have the body force act over a portion or the entire water column.
-j
by jcwarner
Fri Dec 20, 2019 1:27 pm
Forum: ROMS Sediment
Topic: Migrating Trench Test Case
Replies: 2
Views: 621

Re: Migrating Trench Test Case

yes i saw your other email. it is on my list. i have not run this case in a while. give me a little time to try it out.
-j
by jcwarner
Wed Dec 18, 2019 12:58 am
Forum: ROMS Discussion
Topic: Question about ROMS-SWAN coupling
Replies: 2
Views: 599

Re: Question about ROMS-SWAN coupling

roms and swan can have different grids. yes that test Inlet_test/DiffGrid is an example of that. there is more information for that test case in the coawst manual.
-j
by jcwarner
Fri Dec 06, 2019 2:06 pm
Forum: ROMS Discussion
Topic: converting roms grid to swan grid
Replies: 4
Views: 816

Re: converting roms grid to swan grid

please read the swan manual.
the 999.. values tell swan those are land mask locations.
those 999.. values need to be the same as the Exception value you list in your swan.input file.
-j
by jcwarner
Tue Dec 03, 2019 1:40 pm
Forum: ROMS Discussion
Topic: Generating initial file
Replies: 7
Views: 1024

Re: Generating initial file

well, if the get_ijrg m file exists, and your matlab can not find it,
then maybe it has to deal with the paths for matlab. maybe you need to set all the Tools/ folder to be in your matlab path??
-j
by jcwarner
Tue Nov 26, 2019 1:59 pm
Forum: ROMS Discussion
Topic: restart file error
Replies: 4
Views: 706

Re: restart file error

well, the cpp options says Activated C-preprocessing Options: .... SANDY Hurricane Sandy .... AVERAGES Writing out time-averaged nonlinear model fields so it is looking to do the averages, and since it is a restart, it is looking to add to the existing avg restart. If you dont want averages, then un...
by jcwarner
Wed Nov 20, 2019 7:32 pm
Forum: ROMS Benchmarks
Topic: Speed-up advice?
Replies: 2
Views: 973

Re: Speed-up advice?

we have been using TS_HSIMT in COAWST. it is a pos def scheme, faster than mpdata. would be nice to know how the tracer advection compares between the 2 schemes. Have you tried different tiling? how many cores / node does it have?
by jcwarner
Tue Nov 12, 2019 3:10 am
Forum: ROMS Discussion
Topic: COAWST grid script help
Replies: 2
Views: 705

Re: COAWST grid script help

in create_roms_xygrid it should have projection='mercator'; and then it saves a file (i just called it temp_jcw33.mat) then mat2roms_mw loads that file into a structure s. as s = load(theMatFile); so in the mat2roms_mw there should be a s.projection, and it should = mercator. do you know how to chec...
by jcwarner
Thu Nov 07, 2019 1:56 pm
Forum: ROMS Sediment
Topic: unable to find variable: sand in input NetCDF
Replies: 5
Views: 1304

Re: unable to find variable: sand in input NetCDF

not sure. if you ncview the ini file, does bed thick look ok? do you have bed_thick defined with the correct dimensions
bed_thickness(1:xi_rho,1:eta_rho,1:Nbed,1:length(init_time))
-j
by jcwarner
Tue Nov 05, 2019 12:59 pm
Forum: ROMS Installation
Topic: ROMS-WRF compiling problem
Replies: 5
Views: 3568

Re: ROMS-WRF compiling problem

"***************************************************************************** No environment variable NETCDF set. Stopping ***************************************************************************** " Please go through the log file closely. WRF needs to have the locations of the netcdf libs. Of c...
by jcwarner
Sun Nov 03, 2019 1:44 am
Forum: ROMS Discussion
Topic: error in comile a file
Replies: 2
Views: 531

Re: error in comile a file

probably sounds like you did not set the correct compiler in the build.bash script.
need to set
export FORT=ifort
or
export FORT=gfortran
or
export FORT=pgi
by jcwarner
Thu Oct 31, 2019 6:15 pm
Forum: ROMS Discussion
Topic: Problem with setting up inlet_test
Replies: 28
Views: 2783

Re: Problem with setting up inlet_test

this is the Rutgers way of specifying the coupling:
Ocean Export: bath:SSH:Ubar:Vbar:ZO
Waves Export: Wdir:Wamp:Wlen:Wptop:Wpbot:Wubot

i will send you the coawst way in a minute.
-j
by jcwarner
Wed Oct 30, 2019 5:29 pm
Forum: ROMS Discussion
Topic: Problem with setting up inlet_test
Replies: 28
Views: 2783

Re: Problem with setting up inlet_test

we have been advancing the coupling to swan a lot more, it will be a more recent version of swan, we also added more wave current interactions, more sediment algorithms, vegetation/marsh, wave watch 3 coupling, wrf coupling, infragravity wave model, new wave-current asymmetry bedload, ... bunch of s...
by jcwarner
Wed Oct 30, 2019 5:07 pm
Forum: ROMS Discussion
Topic: Problem with setting up inlet_test
Replies: 28
Views: 2783

Re: Problem with setting up inlet_test

i suggest that you should be using COAWST for roms + swan coupling. We distribute a manual that has explanations of the inlet test and many other test cases. also how to compile and install mct. we dont use arpack. if you need coawst, send me an email to jcwarner@usgs.gov the same swan issue will be...
by jcwarner
Wed Oct 30, 2019 12:45 pm
Forum: ROMS Discussion
Topic: Problem with setting up inlet_test
Replies: 28
Views: 2783

Re: Problem with setting up inlet_test

ok i can see the problem now. for some reason, when your code does the cpp preprocessing it changes line 14 from ! equal to REAL2 ) 30.72 to 30.72 the pre-processor tries to clean up the code a bit, and for some reason it is messing this up. It looks like the rest of the Do me a favor and edit SWAN/...
by jcwarner
Wed Oct 30, 2019 3:01 am
Forum: ROMS Discussion
Topic: Problem with setting up inlet_test
Replies: 28
Views: 2783

Re: Problem with setting up inlet_test

no i need to see the .f90
i need to see what the compiler is seeing on that line.
by jcwarner
Wed Oct 30, 2019 1:57 am
Forum: ROMS Discussion
Topic: Problem with setting up inlet_test
Replies: 28
Views: 2783

Re: Problem with setting up inlet_test

ok the search continues. it has cd /Users/venuscheung/ocean_model/inlet_test_romsG/Build_roms; /usr/local/Cellar/open-mpi/4.0.2/bin/mpif90 -c -frepack-arrays -O3 -I/usr/local/MCT/include -ffixed-form ocpmix.f90 ocpmix.f90:14:9: 14 | 30.72 | 1 Error: Invalid character in name at (1) can you send to m...
by jcwarner
Tue Oct 29, 2019 5:29 pm
Forum: ROMS Discussion
Topic: Problem with setting up inlet_test
Replies: 28
Views: 2783

Re: Problem with setting up inlet_test

ok so you need to edit
Compilers/Darwin-gfortran.mk

can you send the whole build.log? so i can see what flags are being issued? Look at the FFLAGS and make sure it is sending the Fixed format options.
by jcwarner
Mon Oct 28, 2019 7:37 pm
Forum: ROMS Discussion
Topic: Readings for different CPP options
Replies: 1
Views: 515

Re: Readings for different CPP options

we have a coupled system call COAWST that has coupled roms + wrf +swan + ww3 and a few other submodules. If you want access to that code, you can send me an email at
jcwarner@usgs.gov
we have a manual with a lot of information and lists about 50 pubs that have used the system.
-john
by jcwarner
Mon Oct 28, 2019 7:32 pm
Forum: ROMS Discussion
Topic: Problem with setting up inlet_test
Replies: 28
Views: 2783

Re: Problem with setting up inlet_test

if you type
uname -s
what comes back?
can you send the whole build log?
-j
by jcwarner
Mon Oct 28, 2019 4:08 pm
Forum: ROMS Discussion
Topic: Problem with setting up inlet_test
Replies: 28
Views: 2783

Re: Problem with setting up inlet_test

the problem here is that SWAN has characters after column 72 that list when the code was updated. for example, the offending line in ocpmix.F is ! logical function EQREAL ( Checks whether REAL1 is appr. 30.72 and as you can see, the 30.72 is actually swan jargon for the version update. To fix this y...
by jcwarner
Sun Sep 29, 2019 11:14 pm
Forum: ROMS Discussion
Topic: SWAN can't use more than one CPU
Replies: 16
Views: 6340

Re: SWAN can't use more than one CPU

not sure. are you writing to multiple netcdf files? this part is where swan opens files for each processor for writing. comment out swan writing of output just to see if that makes is work.
by jcwarner
Mon Sep 23, 2019 1:30 pm
Forum: ROMS Installation
Topic: Asking for cpp and control files
Replies: 3
Views: 722

Re: Asking for cpp and control files

if you are just trying to run roms, then stick with applications that just use roms. Upwelling is great. Once you get that to work, then start building your own application. There is no need to keep running test cases. If you can find a test case that is close to what you want to do, then run that c...
by jcwarner
Mon Sep 23, 2019 12:38 pm
Forum: ROMS Installation
Topic: Asking for cpp and control files
Replies: 3
Views: 722

Re: Asking for cpp and control files

what is your long term goal? do you want to run a coupled application? or are you just trying to compile the differnt test cases. if you are running a coupled application of roms+swan, then i suggest you use COAWST. you can send me an email at jcwarner@usgs.gov. If you are just running that test to ...
by jcwarner
Mon Sep 16, 2019 5:28 pm
Forum: ROMS Tools and Techniques
Topic: restart error with nested grid
Replies: 4
Views: 840

Re: restart error with nested grid

notice the "\"
by jcwarner
Mon Sep 16, 2019 3:51 pm
Forum: ROMS Tools and Techniques
Topic: restart error with nested grid
Replies: 4
Views: 840

Re: restart error with nested grid

the mud and sand LBC's are in the sediment.in file, such as for Projects/Inlet_test/Refined

LBC(isTvar) == Gra Clo Gra Gra \ ! idsed(:), compact
Nes Nes Nes Nes

Yours would be different on the first line, but the 2nd line should be Nes.
by jcwarner
Mon Sep 16, 2019 3:17 pm
Forum: ROMS Discussion
Topic: NGCname
Replies: 2
Views: 586

Re: NGCname

for non-nesting make sure you have
Ngrids = 1
NestLayers = 1
GridsInLayer = 1
What is the actual error?
by jcwarner
Tue Sep 10, 2019 12:02 pm
Forum: ROMS Bugs
Topic: DIAG speed trouble
Replies: 4
Views: 1120

Re: DIAG speed trouble

you have several options activated. suggest you try a more simple first approach and then add complexity. Try it without the river forcings and maybe without the volcons stuff and see if that works to start.
-j
by jcwarner
Mon Sep 09, 2019 2:44 pm
Forum: ROMS Discussion
Topic: Lat_u in ROMs output
Replies: 2
Views: 489

Re: Lat_u in ROMs output

sounds strange. check to see if you can get other variables, it might just be the server is not getting the data to you. if you can get lon_rho and lat_rho, or even better lon_psi and lat_psi, then you can compute the lon_u and lat_u and lon_v and lat_v to a reasonable degree of accuracy as compared...
by jcwarner
Wed Sep 04, 2019 11:44 pm
Forum: ROMS Results
Topic: ROMS + SWAN with nesting : obvious error in the results
Replies: 4
Views: 969

Re: ROMS + SWAN with nesting : obvious error in the results

BLOCK 'COMPGRID' NOHEADER 'NorthSea_wind.mat' LAY 4 WIND 1. OUTPUT 20110101.000000 1 HR
BLOCK 'COMPGRID' NOHEADER 'NorthSea_nest_wind.mat' LAY 4 WIND 1. OUTPUT 20110101.000000 1 HR

how about pcolor or quiver of the winds?
-j
by jcwarner
Wed Sep 04, 2019 12:13 pm
Forum: ROMS Results
Topic: ROMS + SWAN with nesting : obvious error in the results
Replies: 4
Views: 969

Re: ROMS + SWAN with nesting : obvious error in the results

ok. i think i understand what the issue is. If you just run SWAN by itself with NESTING (swan with 2 grids) you are getting an Hsig that is very large compared to SWAN by itself and other similar tests. Here are some suggestions: - do a pcolor of Hsig from the parent, hold on, pcolor hsig from child...
by jcwarner
Thu Aug 01, 2019 12:36 pm
Forum: ROMS Installation
Topic: Error with upwelling case
Replies: 2
Views: 646

Re: Error with upwelling case

did you build this with MPI=on ?? if so, then you need to run it with something like mpirun -np X ./romsG roms_upwelling.in where X is the number of total compute cores X = NtileI * NtileJ , as set in roms_upwelling.in if you did not use MPI=on, then it would be something like ./romsG < roms_upwelli...
by jcwarner
Tue Jul 30, 2019 2:51 am
Forum: ROMS Problems
Topic: variable not properly initialized in ROMS svn978 ?
Replies: 1
Views: 671

Re: variable not properly initialized in ROMS svn978 ?

if you are using roms+swan, you should use our coawst system. We also do not use the Mellor option anymore, we use vortex force.
if you need access to coawst you can send me an email.
jcwarner@usgs.gov

-j
by jcwarner
Mon Jul 01, 2019 1:54 pm
Forum: ROMS Usage
Topic: Could I only couple the parent domains ROMS and WRF?
Replies: 1
Views: 1060

Re: Could I only couple the parent domains ROMS and WRF?

When COAWST runs it will look to see that you have 2 WRF grids selected and then it will try to get data from both wrf grids to roms. So i suggest you do the weights. You can try it without the weights but i dont think it will work.
-j
by jcwarner
Wed Jun 19, 2019 2:19 am
Forum: ROMS Sediment
Topic: implement the point source of sediment in the ocean
Replies: 4
Views: 947

Re: implement the point source of sediment in the ocean

i think it works without adding the river. give it a try.
by jcwarner
Tue Jun 18, 2019 8:42 pm
Forum: ROMS Sediment
Topic: implement the point source of sediment in the ocean
Replies: 4
Views: 947

Re: implement the point source of sediment in the ocean

I have not used this in a while, but there is a LtracerSrc option. Can you look in the ocean.in for this? There is a description at the bottom of the file.
-j
by jcwarner
Mon Jun 17, 2019 1:01 pm
Forum: ROMS Discussion
Topic: Unstable with MY25_MIXING, but GLS works
Replies: 2
Views: 890

Re: Unstable with MY25_MIXING, but GLS works

it has been a while since I was in this part of the code, but one quick thought is that we have surface flux bc's for the gls term that is not included in the my25 method. # if defined CHARNOK Zos_eff(i)=MAX(charnok_alpha(ng)/g*0.5_r8* & & SQRT((sustr(i,j)+sustr(i+1,j))**2+ & & (svstr(i,j)+svstr(i,j...
by jcwarner
Fri Jun 07, 2019 5:28 pm
Forum: ROMS Information
Topic: error in compiling scrip_coawst
Replies: 6
Views: 1548

Re: error in compiling scrip_coawst

let just see if you can create a file in that directory. try this command

touch help.txt

and then do
ls -ltr
do you see that file?
by jcwarner
Thu May 30, 2019 2:52 pm
Forum: ROMS Problems
Topic: Stokes velocity fills dry cell uphill
Replies: 3
Views: 910

Re: Stokes velocity fills dry cell uphill

Thank you for the post. A couple of things: - looks like you are compiling for just a 2D application? because the error was in main2d. I have not tried to run a 2d application in a long time. i really suggest that you do SOLVE3D. Many of the physics we have added are for 3D applications, like turbul...
by jcwarner
Tue May 28, 2019 2:52 pm
Forum: ROMS Problems
Topic: Noisy SST
Replies: 9
Views: 1575

Re: Noisy SST

do the atm forcing fields look smooth ?
you could try mixing from my25 or gls and then activate N2S2_HORAVG.

-j
by jcwarner
Thu May 23, 2019 1:51 am
Forum: ROMS Bugs
Topic: typos in radiation_stress.F
Replies: 8
Views: 3717

Re: typos in radiation_stress.F

we dont really use the Mellor approach any more. suggest that you use the vortex force method (based on wave energy dissipation instead of wave energy gradients). if you want to use the WEC method, we have that in our coawst system. send me an email and i can add you to the distribution. jcwarner@us...
by jcwarner
Fri May 17, 2019 3:09 am
Forum: ROMS Problems
Topic: Performance issues using floats
Replies: 4
Views: 931

Re: Performance issues using floats

as you increase the number of procs for the job, then the tile size decreases. 300x300 tiled 8x14 gives a tile 38 x 20 cells. that is not very big. the job is spending more time exchanging information than performing computations. here are some previous posts in this issue https://www.myroms.org/for...
by jcwarner
Wed May 15, 2019 1:08 pm
Forum: ROMS Sediment
Topic: unable to find variable: sand in input NetCDF
Replies: 5
Views: 1304

Re: unable to find variable: sand in input NetCDF

have you been able to work on this? If you activate SEDIMENT, then the model needs some initial fields of bed thickness, porosity, etc. you can provide this information in ANA_SEDIMENT, or you need to include that information in the roms init nc file. we have some m files to create roms init with se...
by jcwarner
Mon May 13, 2019 6:42 pm
Forum: ROMS Problems
Topic: Tide Phase Problem
Replies: 4
Views: 1019

Re: Tide Phase Problem

ok. i forgot how the input went. mine does the same: tide_Ephase in degress in netcdf, varinfo converts to rads.
Do you use ramp_tides? What if you adjust tide_start in the ocean.in.
-j
by jcwarner
Mon May 13, 2019 6:21 pm
Forum: ROMS Problems
Topic: Tide Phase Problem
Replies: 4
Views: 1019

Re: Tide Phase Problem

basic Q: but are you adding the phase in radians? Ephase would have the most impact. are you adding to all the freqs or just some?
by jcwarner
Tue Apr 23, 2019 1:09 am
Forum: ROMS Usage
Topic: generating nested grid contacts
Replies: 2
Views: 1035

Re: generating nested grid contacts

so i know that we tested all this stuff before the workshop in Feb, but maybe we missed something. I dont do the exact procedure you show, i dont use the F=grid_extract.. command. so i am not sure if that is the problem. but here is what worked for our H Sandy test case. after you make the parent gr...
by jcwarner
Fri Apr 19, 2019 5:02 pm
Forum: ROMS Problems
Topic: Segmentation Fault when executing oceanM
Replies: 11
Views: 5831

Re: Segmentation Fault when executing oceanM

- i have not used pgi in awhile, so i did a Google on "Error: no such instruction: `vinserti128 $1,%xmm0,%ymm0,%ymm1'" and found this: https://www.pgroup.com/userforum/viewtopic.php?t=4904&sid=b1ec7d574c2f357163260c5965caa1f6 looks like a pgi issue. - Another thought is that you would not need paral...
by jcwarner
Thu Apr 18, 2019 2:50 pm
Forum: ROMS Discussion
Topic: Coastal flood risk assessment with ROMS?
Replies: 2
Views: 946

Re: Coastal flood risk assessment with ROMS?

ROMS has a wetting/drying capability and we use many roms+swan coupled simulations regularly. I know others have looked at inundations during storms, for example: Beudin, A., Ganju, N. K., Defne, Z., & Aretxabaleta, A. L. (2017). Physical response of a back-barrier estuary to a post-tropical cyclone...
by jcwarner
Wed Apr 17, 2019 5:50 pm
Forum: ROMS Problems
Topic: Segmentation Fault when executing oceanM
Replies: 11
Views: 5831

Re: Segmentation Fault when executing oceanM

i am not sure what you mean by a similar problem. How about we start over, and you explain the issue with as much information as you can. the last few lines of stdout saying "#0 0xFFFFFFFFFFFFFFFF" dont really tell me anything. so if you have something similar i would need to see the whole std out. ...
by jcwarner
Fri Apr 12, 2019 7:43 pm
Forum: ROMS Usage
Topic: tide time corrections
Replies: 1
Views: 745

Re: tide time corrections

set_tides.F cff=2.0_r8*pi*(time(ng)-tide_start*day2sec) DO itide=1,NTC ... omega=cff/Tperiod(itide) DO, .. DO ... Etide(i,j)=Etide(i,j)+ & & ramp*SSH_Tamp(i,j,itide)* & & COS(omega-SSH_Tphase(i,j,itide)) so it takes ocean_time-tide_start to get omega. if you have dstart and tide_start but start at 0...
by jcwarner
Wed Apr 10, 2019 1:10 pm
Forum: ROMS Installation
Topic: compiling upwelling
Replies: 10
Views: 1965

Re: compiling upwelling

well that looks worse.
can you attach the build.bash. want to make sure you set the compiler.
by jcwarner
Wed Apr 10, 2019 11:58 am
Forum: ROMS Installation
Topic: compiling upwelling
Replies: 10
Views: 1965

Re: compiling upwelling

so when i build i get something like this: [jwarner@poseidon-l1 breach338]$ ./coawst.bash rm -f -r core *.ipo ./Build /vortexfs1/usgs/jwarner/make_macros.mk makefile:248: INCLUDING FILE /vortexfs1/usgs/jwarner/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS cp -f /vortexfs1/apps...
by jcwarner
Mon Apr 08, 2019 12:26 pm
Forum: ROMS Discussion
Topic: blow up after first time step
Replies: 1
Views: 750

Re: blow up after first time step

so if you look at the history file using ncview (or similar), what do the fields look like? you are going to have to dig into the output to see what is happening. Is it having trouble at the open boundary, along the coast, etc. i see you have theta_s = 7 and that might be high. not sure. does it run...
by jcwarner
Mon Apr 08, 2019 11:32 am
Forum: ROMS Installation
Topic: compiling upwelling
Replies: 10
Views: 1965

Re: compiling upwelling

you might get to a problem with netcdf, and perhaps the -lnetcdff flag is needed, but right now your problem is: "cp -f /home/kzf/softwares/packman.active/include/netcdf.mod /home/kzf/myroms/projects/upwelling/Build_romsG cp -f /home/kzf/softwares/packman.active/include/typesizes.mod /home/kzf/myrom...
by jcwarner
Fri Mar 29, 2019 12:32 pm
Forum: ROMS Adjoint
Topic: ad passive tracer!
Replies: 1
Views: 779

Re: ad passive tracer!

1. you have ! Logical switches (TRUE/FALSE) to activate tracers point Sources/Sinks ! (like river runoff) and to specify which tracer variables to consider: ! [1:NAT+NPT,Ngrids]. See glossary below for details. LtracerSrc == F F F ! temperature, salinity, inert maybe this needs to be F F T 2. also s...
by jcwarner
Wed Mar 27, 2019 2:11 pm
Forum: ROMS Problems
Topic: Blowing up problem when using sediment
Replies: 8
Views: 1569

Re: Blowing up problem when using sediment

How about you look at the history file for these 600000 steps and see what is happening. is the model blowing up at the boundary (upstream or downstream), somewhere in the domain, what does the flow look like, etc. you may have to dig in and see how the solution looks to help figure out what is goin...
by jcwarner
Mon Mar 11, 2019 11:56 am
Forum: ROMS Problems
Topic: Run error
Replies: 1
Views: 746

Re: Run error

this looks like a problem with the paths of your system. Your work environment cannot find some shared objects (.so) for netcdf. This might be due to the PATH, LD_LIBRARY_PATH, or other environment variable. You should ask your computer administrator for some help. maybe something like this: https:/...
by jcwarner
Fri Mar 08, 2019 2:23 pm
Forum: ROMS Bugs
Topic: Pair and MPI version has problem with regridding
Replies: 10
Views: 2058

Re: Pair and MPI version has problem with regridding

what happens if you do MPI with one processor?
i can look at the press compensate, we want to use that for our hurricane simulations.
-j
by jcwarner
Thu Mar 07, 2019 2:24 pm
Forum: ROMS Problems
Topic: Test Case
Replies: 1
Views: 896

Re: Test Case

whatever test case you are running, the code can not find the grid
"READ_PHYPAR - Grid 01, could not find input file: roms_grd.nc"

i am not sure the application, but the code can not find that file.
-john
by jcwarner
Thu Mar 07, 2019 2:21 pm
Forum: ROMS Usage
Topic: BLOWING UP during nesting
Replies: 11
Views: 2436

Re: BLOWING UP during nesting

are you using wet/dry for the nest? how shallow do the water depths get?
-j
by jcwarner
Wed Feb 13, 2019 1:20 pm
Forum: ROMS Sediment
Topic: Negative suspended load concentrations near river runoff
Replies: 17
Views: 2834

Re: Negative suspended load concentrations near river runoff

think i found it! in sediment_inp.h there is a section of code CASE ('Qout(iMmass)') Npts=load_l(Nval, Cval, NCS, Ngrids, Lmud) DO ng=1,Ngrids DO itrc=1,NCS i=idBmas(itrc) Hout(i,ng)=Lmud(itrc,ng) END DO END DO but that 6th line should be Qout(i,ng)=Lmud(itrc,ng) So the Hout was being overwritten. C...
by jcwarner
Tue Feb 12, 2019 7:45 pm
Forum: ROMS Sediment
Topic: Negative suspended load concentrations near river runoff
Replies: 17
Views: 2834

Re: Negative suspended load concentrations near river runoff

does it report in the std out at the top with all the other zob, tcline, etc etc stuff, then it gets to sediment, it should report the sed classes, then does it say it will Hout().... and write out the sediment mass??
by jcwarner
Tue Feb 12, 2019 7:09 pm
Forum: ROMS Sediment
Topic: Negative suspended load concentrations near river runoff
Replies: 17
Views: 2834

Re: Negative suspended load concentrations near river runoff

are you doing mud or sand?
NNS =
NCS =
by jcwarner
Tue Feb 12, 2019 4:38 pm
Forum: ROMS Sediment
Topic: Negative suspended load concentrations near river runoff
Replies: 17
Views: 2834

Re: Negative suspended load concentrations near river runoff

i get bed mass written out.
make sure you set it for sand or mud, whichever you have activated.
by jcwarner
Tue Feb 12, 2019 2:32 am
Forum: ROMS Discussion
Topic: How to get boundary condition from new data Hycom for COAWST
Replies: 3
Views: 1424

Re: How to get boundary condition from new data Hycom for CO

we have updated all of our m files in the latest coawst distribution (feb 11, 2018). so you can give them a try. As ptimko said, look here http://tds.hycom.org/thredds/catalog.html -=-=-=-=-=-=-=-=-=-=-=-ACTIVE-=-=-=-=-=-=-=-=-=-=-=- -- Folder GLBy0.08/latest (Present + FORECASTS)/ -- Folder GLBy0.0...
by jcwarner
Tue Feb 12, 2019 1:32 am
Forum: ROMS Installation
Topic: test case
Replies: 4
Views: 1778

Re: test case

sorry i did not get back to you on this earlier. i am using coawst, which i just updated to the latest roms into our system, and this test case works. The i saw what you were doing: ./oceanS < ROMS/External/sediment_test_chan.in Sorry but you need to point to the ocean.in! well, now it is called rom...
by jcwarner
Tue Feb 12, 2019 1:03 am
Forum: ROMS Sediment
Topic: sediment initial conditions for median grain diameter
Replies: 2
Views: 974

Re: sediment initial conditions for median grain diameter

if you are serious about using the sediment capabilities, i suggest you use our coawst system. we have added more capabilities such as a more advanced bed load formulation, a floc model, and a faster positive definite advection scheme. we distribute m files for init conditions. you can send me an em...
by jcwarner
Mon Feb 11, 2019 4:31 pm
Forum: ROMS Sediment
Topic: Negative suspended load concentrations near river runoff
Replies: 17
Views: 2834

Re: Negative suspended load concentrations near river runoff

so a suggestion would be to change define TS_U3HADVECTION to define TS_MPDATA and see how that looks. Also, just a question: are the river sources all putting flow into the domain? some people use tidal river forcing that oscillates +/- to simulate a tidal flow. when you say negative sediment next t...
by jcwarner
Mon Feb 11, 2019 3:38 pm
Forum: ROMS Sediment
Topic: Negative suspended load concentrations near river runoff
Replies: 17
Views: 2834

Re: Negative suspended load concentrations near river runoff

There are many reasons why there can be negative concentration values, but most likely it may be from the advection scheme. Suggest you use TS_MPDATA, that should remain positive. Also, we have added a new scheme called TS_HSIMT into COAWST that is also positive definite, it is based on some flux li...
by jcwarner
Tue Feb 05, 2019 2:30 pm
Forum: ROMS Problems
Topic: RIP currents
Replies: 1
Views: 748

Re: RIP currents

our COAWST system has swan + roms coupled and we have a rip_current test case as shown in: Kumar, N., Voulgaris, G., Warner, J.C., and M., Olabarrieta (2012). Implementation of a vortex force formalism in the coupled ocean-atmosphere-wave-sediment transport (COAWST) modeling system for inner-shelf a...
by jcwarner
Sat Feb 02, 2019 3:38 pm
Forum: ROMS Usage
Topic: units of variable 'Dwave'
Replies: 6
Views: 1573

Re: units of variable 'Dwave'

Well, for some reason SWAN uses the word 'Cartesian' for 2 separate things. SET NAUTICAL = winds/waves dir from or SET CARTESIAN = winds/waves dir towards and now for something completely different COORDINATES CARTESIAN = uses x-y in meters or COORDINATES SPHERICAL = uses lat + lon more info in the ...
by jcwarner
Fri Feb 01, 2019 12:49 pm
Forum: ROMS Usage
Topic: units of variable 'Dwave'
Replies: 6
Views: 1573

Re: units of variable 'Dwave'

Lawrence- if you are using roms + swan, i recommend that you use COAWST instead, we have been updating swan there, adding new wave physics, etc. You can send me an email at jcwarner@usgs.gov to get that code. In short, Dwave output is in degrees, direction that the waves are from. (because we set NA...
by jcwarner
Thu Jan 31, 2019 1:10 pm
Forum: ROMS Results
Topic: ROMS Granular model result in all variables
Replies: 8
Views: 2545

Re: ROMS Granular model result in all variables

yes and try
#define N2S2_HORAVG
by jcwarner
Wed Jan 30, 2019 9:14 pm
Forum: ROMS Results
Topic: ROMS Granular model result in all variables
Replies: 8
Views: 2545

Re: ROMS Granular model result in all variables

does it start out like that or evolve to that? check the fields in your grid file like dmde dndx. check angle.
are you using N2S2_HORAVG?

-j
by jcwarner
Tue Jan 29, 2019 1:11 pm
Forum: ROMS Discussion
Topic: Correct CPP options to use ANA_WWAVE?
Replies: 4
Views: 1263

Re: Correct CPP options to use ANA_WWAVE?

The ana_wwave is for hwave, dwave, pwave_bot _top, etc = from wind waves, ie periods from ~ 2 to 20 seconds. Is this the wave band that you are interested in? when i hear 'gravity waves' i usually think of longer periods, but just wanted to make sure you knew what we intended for the names.
-john
by jcwarner
Wed Dec 19, 2018 1:22 pm
Forum: ROMS Discussion
Topic: High water speed values in hisfile
Replies: 4
Views: 1283

Re: High water speed values in hisfile

the error at the end of the output log is 132000 0001-02-25 00:00:00.00 1.203129E-02 7.265249E+03 7.265261E+03 5.839635E+14 (075,001,15) 7.890818E-04 3.869123E-03 2.404095E-02 1.595520E+00 NETCDF_PUT_FVAR_1D - error while writing variable: ocean_time in input file: /media/STORAGE/prueba_forc_build/o...
by jcwarner
Sat Dec 15, 2018 8:30 pm
Forum: ROMS Discussion
Topic: High water speed values in hisfile
Replies: 4
Views: 1283

Re: High water speed values in hisfile

how about looking at some forcing variables near those locations. what does sustr svstr zeta rho look like?? something is making the water move.
-j
by jcwarner
Sat Dec 15, 2018 8:27 pm
Forum: ROMS Bugs
Topic: Equation error in GLS model coded into gls_corstep.F
Replies: 5
Views: 1722

Re: Equation error in GLS model coded into gls_corstep.F

Hey Hernan. Before you update the code, how about you let me take a look at it and get back to you next week. I spent a good bit of time to code this in, and in a separate email chain Hans is looking at this as well. Give the people who coded it a chance to look it over first.

thanks,
john
by jcwarner
Fri Dec 07, 2018 1:54 pm
Forum: ROMS Usage
Topic: Operational Coupled Forecast Systems?
Replies: 3
Views: 1410

Re: Operational Coupled Forecast Systems?

Forecast systems: Hydro and Agro Informatics Institute http://www.thaiwater.net/v3/wrfroms/rain_forecast_pre/tab1/image1 USGS Woods Hole http://woodshole.er.usgs.gov/project-pages/cccp/public/COAWST.htm North Carolina State University http://omgsrv1.meas.ncsu.edu:8080/ocean-circulation-useast2/ Made...
by jcwarner
Tue Dec 04, 2018 1:09 pm
Forum: ROMS Sediment
Topic: Initial sediment layers
Replies: 3
Views: 1072

Re: Initial sediment layers

The sediment part in roms can be run with just roms. The swan coupling provides wave information that can be used by the ocean model to: - compute enhanced surface mixing due to tke wave breaking - computed wave driven flow using vortex force approach - compute enhanced bottom stresses due to combin...
by jcwarner
Tue Dec 04, 2018 12:42 am
Forum: ROMS Usage
Topic: Accessing forcing data from NCEP NOMADS
Replies: 1
Views: 1012

Re: Accessing forcing data from NCEP NOMADS

Thanks John. Yes we did take some steps earlier to take into account the http to https issue from NCEI etc. We got hit with that earlier when matlab failed, but Christie and Steve & others spent some time to update some m files, here is a post on that https://www.myroms.org/forum/viewtopic.php?f=23&...
by jcwarner
Sun Dec 02, 2018 3:39 pm
Forum: ROMS Results
Topic: ROMS + SWAN with nesting : error on the child grid
Replies: 21
Views: 4130

Re: ROMS + SWAN with nesting : error on the child grid

can send to me the scrip file you used to create the scrip weights?
and are the grids the same size for the parent roms/swan and the child roms/swan?
you need to make sure you enter the swan grid sizes correctly.
-j
by jcwarner
Sat Dec 01, 2018 2:16 am
Forum: ROMS Problems
Topic: Inlet_test and MCT coupler
Replies: 1
Views: 714

Re: Inlet_test and MCT coupler

looks like the compiler can not find your mct libraries. I have some explanation to build MCT in the coawst manual. Then you need to set MCT_INCDIR and MCT_LIBDIR, as described in the manual. give that a try and see if it helps.
-j
by jcwarner
Sat Dec 01, 2018 2:09 am
Forum: ROMS Results
Topic: ROMS + SWAN with nesting : error on the child grid
Replies: 21
Views: 4130

Re: ROMS + SWAN with nesting : error on the child grid

if i had to guess, i would ask what the time steps are being used for roms.
by jcwarner
Fri Nov 30, 2018 3:24 am
Forum: ROMS Results
Topic: ROMS + SWAN with nesting : error on the child grid
Replies: 21
Views: 4130

Re: ROMS + SWAN with nesting : error on the child grid

So i can get this to work. The grid files seem to be ok (2xbathy.bot and 2x coord.grd). They are ok. Here are some changes i did to the INPUT files: 1) I did not have your wind file, so i commented out the wind commands and added WIND 10. 0. this puts a 10 m/s wind from north on both grids. 2) You h...
by jcwarner
Thu Nov 29, 2018 1:11 pm
Forum: ROMS Results
Topic: ROMS + SWAN with nesting : error on the child grid
Replies: 21
Views: 4130

Re: ROMS + SWAN with nesting : error on the child grid

swan with nesting by itself (no roms) does not need the scrip weights, so there is an issue with the swan child grid. Can you send to me the 2 *.bot and the 2 *.grd swan files (4 files)
jcwarner@usgs.gov
thanks
-j
by jcwarner
Wed Nov 28, 2018 1:42 pm
Forum: ROMS Tools and Techniques
Topic: River input problem forrtl: severe (174): SIGSEGV,
Replies: 9
Views: 2355

Re: River input problem forrtl: severe (174): SIGSEGV,

this section of mod_netcdf is newly modified. which one of these is line 852: DO i=1,MIN(Matts,n_gatt) att_id=i status=nf90_inq_attname(ncid, nf90_global, att_id, & & att_name(i)) IF (status.eq.nf90_noerr) THEN status=nf90_inquire_attribute(ncid, nf90_global, & & TRIM(att_name(i)), & & xtype = att_k...
by jcwarner
Wed Nov 28, 2018 1:21 am
Forum: ROMS Results
Topic: ROMS + SWAN with nesting : error on the child grid
Replies: 21
Views: 4130

Re: ROMS + SWAN with nesting : error on the child grid

i cant see the images. can you upload png files?
-j
by jcwarner
Tue Nov 27, 2018 7:33 pm
Forum: ROMS Results
Topic: ROMS + SWAN with nesting : error on the child grid
Replies: 21
Views: 4130

Re: ROMS + SWAN with nesting : error on the child grid

I am not really clear on these results, and perhaps i was not very clear either. 1) if you just run swan by itself, do you get results on both the parent and child that are consistent and look correct? 2) currents continuous = good, roms refinement works. 3) roms+swan coupled: you say that with it c...
by jcwarner
Tue Nov 27, 2018 1:10 pm
Forum: ROMS Tools and Techniques
Topic: River input problem forrtl: severe (174): SIGSEGV,
Replies: 9
Views: 2355

Re: River input problem forrtl: severe (174): SIGSEGV,

a few things: - does it work with just LuvSrc == T ! horizontal momentum transport and the rest == F ? that way we know it is just for river info, and not the tracers. - the mod sources has MyVarName = TRIM(Vname(1,idRxpo)), & so it is trying to read idRxpo, and trying to read attributes of that var...
by jcwarner
Tue Nov 27, 2018 12:54 am
Forum: ROMS Tools and Techniques
Topic: River input problem forrtl: severe (174): SIGSEGV,
Replies: 9
Views: 2355

Re: River input problem forrtl: severe (174): SIGSEGV,

so this is telling you something: oceanG 0000000002469367 mod_netcdf_mp_net 852 mod_netcdf.f90 oceanG 000000000253DC6C mod_sources_mp_al 109 mod_sources.f90 look in Build/mod_sources.f90 line 109 and it is probably calling mod_netcdf with some information. Look in Build/mod_netcdf.f90 line 852 and s...
by jcwarner
Thu Nov 22, 2018 11:56 pm
Forum: ROMS Results
Topic: ROMS + SWAN with nesting : error on the child grid
Replies: 21
Views: 4130

Re: ROMS + SWAN with nesting : error on the child grid

some things to try: - run it with just swan with 2 grids, not coupled. - do the currents in both grids look continuous? - try to run the swan files with INIT in both of them. this will help the child grid to have some init conditions. if you run the swan without any init commands, it can take a long...
by jcwarner
Thu Nov 22, 2018 10:51 pm
Forum: ROMS Results
Topic: ROMS + SWAN with nesting : error on the child grid
Replies: 21
Views: 4130

Re: ROMS + SWAN with nesting : error on the child grid

the winds should be important for the child.
can you send to me both of your swan input files?
jcwarner@usgs.gov
by jcwarner
Thu Nov 22, 2018 9:58 pm
Forum: ROMS Results
Topic: ROMS + SWAN with nesting : error on the child grid
Replies: 21
Views: 4130

Re: ROMS + SWAN with nesting : error on the child grid

how long into the model run is this? it may take some time for information to propagate into the child.
this depends on the initial conditions. Also, do you have the same winds on both swan grids? you can use copy the parent wind grid to put on the child.
-john
by jcwarner
Tue Nov 20, 2018 12:57 pm
Forum: ROMS Discussion
Topic: Dye boundary doesn't work when using passive tracer
Replies: 4
Views: 1231

Re: Dye boundary doesn't work when using passive tracer

i have not added a dye BC in a while, but I think you are missing a few things. - i assume you have something like NPT = 2 ! Number of inactive passive tracers - i think you need to add: ! Each tracer variable requires [1:4,1:NAT+NPT,Ngrids] values. Otherwise, ... LBC(isTvar) == Clo Per Gra Per \ ! ...
by jcwarner
Thu Nov 15, 2018 2:50 pm
Forum: ROMS Information
Topic: TPAR wave directions: correct or not on the ROMS grid angle
Replies: 2
Views: 1095

Re: TPAR wave directions: correct or not on the ROMS grid an

no.
The TPAR files go to SWAN, and SWAN knows how to deal with them on a curvilinear grid.
Then Dwave comes from SWAN to ROMS, and the coupler knows how to deal with the grid.
So in summary, just put the data in the TPAR files as you would normally.
-john
by jcwarner
Wed Nov 14, 2018 4:23 pm
Forum: ROMS Bugs
Topic: tiny little bug in get_state.F for time evolving bathymetry
Replies: 2
Views: 1065

Re: tiny little bug in get_state.F for time evolving bathyme

yes ROMS/Utility/get_state.F line 496 should be
WRITE (stdout,80) string, TRIM(Vname(1,idbath)), &
you can put that as a src ticket for Hernan to update.
thanks,
-john
by jcwarner
Tue Nov 13, 2018 1:41 pm
Forum: ROMS Sediment
Topic: tracer surface flux
Replies: 2
Views: 1085

Re: tracer surface flux

try using this in the project.h file

# define ANA_SMFLUX
# define ANA_BPFLUX
# define ANA_BSFLUX
# define ANA_BTFLUX
# define ANA_SPFLUX
# define ANA_SRFLUX
# define ANA_SSFLUX
# define ANA_STFLUX
by jcwarner
Mon Nov 12, 2018 12:23 am
Forum: ROMS Discussion
Topic: Temperature significantly near land areas
Replies: 4
Views: 1526

Re: Temperature significantly near land areas

a couple of things jump out here. - first it is best to put temp scales the same so we can see the differences. - second it seems a lot of cooling on east side, looks like a BC issue. - for the temp spikes near land: how is wrf data interpolated to roms grid? we had issues with the coupling at first...
by jcwarner
Wed Nov 07, 2018 2:26 pm
Forum: Meetings/Workshops
Topic: COAWST modeling system Training 2019
Replies: 0
Views: 1661

COAWST modeling system Training 2019

We are announcing a COAWST Training workshop to be held Mon – Thurs Feb 25-28, 2019 on the campus of the North Carolina State University, in Raleigh, NC. If you would like to attend the Training, please send an email to jcwarner@usgs.gov with a full list the people that would like to attend (Name, a...
by jcwarner
Wed Nov 07, 2018 1:27 am
Forum: ROMS Discussion
Topic: NetCDF: Start+count exceeds dimension bound
Replies: 2
Views: 985

Re: NetCDF: Start+count exceeds dimension bound

yes the dimensions are strictly enforced.
If you are new, i would recommend to use m files from someone/somewhere that already work. It will save you a lot of time.
-john
by jcwarner
Tue Nov 06, 2018 1:27 pm
Forum: ROMS Problems
Topic: Transport adjustment on the boundary
Replies: 6
Views: 1800

Re: Transport adjustment on the boundary

if you use flather boundary conditions (Fla), it does not guarantee that the mass flux imposed by the ubar on the boundary will be imposed at the boundary. For example one of the choices ends up with : ! ! Western edge, Flather boundary condition. ! .... bry_val=BOUNDARY(ng)%ubar_west(j) cff=1.0_r8/...
by jcwarner
Tue Nov 06, 2018 1:19 pm
Forum: ROMS Installation
Topic: compling build.bash
Replies: 2
Views: 1151

Re: compling build.bash

the compilation is using some ana* files (looks like ana_grid.h and ana_vmix.h) I suggest you: - copy those 2 files from ROMS/Functionals and place them in the directory with your project.h file - edit those files and provide the necessary information (they have examples in them). - make sure your b...
by jcwarner
Tue Nov 06, 2018 2:55 am
Forum: ROMS Problems
Topic: Transport adjustment on the boundary
Replies: 6
Views: 1800

Re: Transport adjustment on the boundary

i am not really clear what the full story is. I dont use obc_volcons, that is to conserve volume in the domain. but it seems you are not using that. other than that, there is no guarantee that the volume flux across all open boundaries will balance. For example, if you had an estuary with only one o...
by jcwarner
Mon Nov 05, 2018 3:14 pm
Forum: Job Opportunities
Topic: USGS Mendenhall postdoc
Replies: 0
Views: 818

USGS Mendenhall postdoc

We are pleased to announce opportunities for the USGS Mendenhall post doctoral positions. The main web site is here: https://geology.usgs.gov/postdoc/ with specific attention to Research Opportunity Number 17-19 "Hydrodynamics-based numerical modeling for predicting coastal change" where we are seek...
by jcwarner
Fri Nov 02, 2018 12:51 pm
Forum: ROMS Problems
Topic: Growing oscillations when using TS_MPDATA
Replies: 4
Views: 1440

Re: Growing oscillations when using TS_MPDATA

are the files for this mostly ana*?
can you send them to me? i could try it here quick.
-j
by jcwarner
Wed Oct 31, 2018 7:33 pm
Forum: ROMS Usage
Topic: How to generate contact netcdf?
Replies: 7
Views: 2150

Re: How to generate contact netcdf?

what exactly is the problem? do you get an error message? the commands would be something like this: ref_ratio=3; roms_child_grid='Sandy_roms_grid_ref3.nc'; F=coarse2fine('Sandy_roms_grid.nc','Sandy_roms_grid_ref3.nc', ... ref_ratio,Istr,Iend,Jstr,Jend); Gnames={'Sandy_roms_grid.nc','Sandy_roms_grid...
by jcwarner
Mon Oct 29, 2018 11:33 pm
Forum: ROMS Problems
Topic: Growing oscillations when using TS_MPDATA
Replies: 4
Views: 1440

Re: Growing oscillations when using TS_MPDATA

i cant open the ps file. how about a png?
how many grid cells is the domain. mpdata has a big footprint. needs at least 5 cells.
-j
by jcwarner
Tue Oct 16, 2018 12:57 pm
Forum: ROMS Problems
Topic: Cannot define variable, h when creating restart file
Replies: 1
Views: 899

Re: Cannot define variable, h when creating restart file

not sure what is going on here. Can you try it without the changes that you added?
-john
by jcwarner
Thu Oct 04, 2018 8:44 pm
Forum: ROMS Usage
Topic: What would happen if LMD_BKPP is undefined in LMD scheme?
Replies: 5
Views: 1618

Re: What would happen if LMD_BKPP is undefined in LMD scheme

Here is another paper that i remembered- https://marine.rutgers.edu/po/Papers/Durski_JGR04.pdf See what Scott did in that paper. I think he undefined the bottom bbl. The code looks to me like lmd_bkpp computes the eddy diffusivity and viscosity, and will replace those values where "! Compute boundar...
by jcwarner
Thu Oct 04, 2018 7:52 pm
Forum: ROMS Usage
Topic: What would happen if LMD_BKPP is undefined in LMD scheme?
Replies: 5
Views: 1618

Re: What would happen if LMD_BKPP is undefined in LMD scheme

here is a place to start:
https://www.myroms.org/wiki/Vertical_Mi ... erizations
suggest you also dig into the code a bit. you can grep for those options and they are mostly in Nonlinear/lmd_...

-j
by jcwarner
Wed Sep 26, 2018 1:51 pm
Forum: ROMS Discussion
Topic: ROMS history file has suddenly included restart record
Replies: 7
Views: 1806

Re: ROMS history file has suddenly included restart record

i am glad you found this out. I was looking around at all the recent updates and could not see any reason for that change in behavior. if you want to stop the addition of _0001, you could look in Nonlinear/output.F for the code: ifile=(iic(ng)-1)/ndefHIS(ng)+1 IF (Master) THEN WRITE (HIS(ng)%name,10...
by jcwarner
Tue Sep 11, 2018 1:04 pm
Forum: ROMS Usage
Topic: Compiling ROMS error
Replies: 2
Views: 1338

Re: Compiling ROMS error

if you set export USE_MPI=on # distributed-memory parallelism export USE_MPIF90= # compile with mpif90 script export USE_OpenMP= # shared-memory parallelism or export USE_MPI=on # distributed-memory parallelism export USE_MPIF90=on # compile with mpif90 script export USE_OpenMP= # shared-memory para...
by jcwarner
Tue Sep 04, 2018 2:37 pm
Forum: ROMS Bugs
Topic: MPI Tiling - Dumb Question
Replies: 5
Views: 1705

Re: MPI Tiling - Dumb Question

what does your mpirun command line look like? maybe your cluster also needs some slurm info like
#SBATCH --ntasks=108 # Number of MPI ranks
#SBATCH --nodes=3
#SBATCH --ntasks-per-node=36
or something ????
-j
by jcwarner
Wed Aug 22, 2018 2:09 pm
Forum: ROMS Problems
Topic: forrtl: severe (151): allocatable array is already allocated
Replies: 17
Views: 5074

Re: forrtl: severe (151): allocatable array is already alloc

yeah that is what i was going to look for. TABS = bad.
sometimes an errant character can get stuck in the file and cause an issue.
by jcwarner
Wed Aug 22, 2018 12:06 pm
Forum: ROMS Problems
Topic: forrtl: severe (151): allocatable array is already allocated
Replies: 17
Views: 5074

Re: forrtl: severe (151): allocatable array is already alloc

can you post your ocean.in that causes the trouble?
is there a way I can download it. dont just copy it to this widget.
-j
by jcwarner
Fri Jul 20, 2018 12:26 pm
Forum: ROMS Discussion
Topic: Blowing up problem using GLS mixing
Replies: 8
Views: 2435

Re: Blowing up problem using GLS mixing

if the closure is making it unstable, then look at temp, salt, u, v, and AKv and AKt. perhaps the options of #define LIMIT_VDIFF --> use to impose an upper limit on vertical diffusion ** #define LIMIT_VVISC --> use to impose an upper limit on vertical viscosity ** might help ??? Also, when the depth...
by jcwarner
Fri Jul 13, 2018 2:54 pm
Forum: ROMS Sediment
Topic: Wave-current BBL drag coefficient as output
Replies: 4
Views: 3211

Re: Wave-current BBL drag coefficient as output

Parker- the routine set_vbc.F computes the bottom stresses (in case you want to look at the code). For QDRAG, it essentially uses (for u-direction) bustr = rdrag2 * u(z=1) * |V| For this option, as u(z=1) changes elevation, the roughness (rdrag2) stays the same. Another option is to use UV_LOGDRAG b...
by jcwarner
Fri Jul 13, 2018 12:43 pm
Forum: ROMS Tools and Techniques
Topic: wind vector direction in NAM and NARR data
Replies: 7
Views: 4386

Re: wind vector direction in NAM and NARR data

possibly. they all get data from here: https://www.ncdc.noaa.gov/nomads/data-products but there had been some changes at the noaa site. I remember they add the 's' to https and that was a problem in matlab. Matblab had been comparing the first 5 letters of a file, and if it started with http:, then ...
by jcwarner
Fri Jul 13, 2018 12:28 pm
Forum: ROMS Discussion
Topic: Blowing up problem using GLS mixing
Replies: 8
Views: 2435

Re: Blowing up problem using GLS mixing

this is a situation where you will need to dig in a little deeper. You say with n2s2 avg turned on, it blows up near the beginning. Suggest you see how many steps it takes before it blows up, lets say it is a 100. then save the model output in a his file every 5 times (or so). that will give you 20 ...
by jcwarner
Fri Jul 06, 2018 11:59 am
Forum: ROMS Discussion
Topic: on the wave mixing
Replies: 4
Views: 1496

Re: on the wave mixing

i believe you are understanding correctly.
-j
by jcwarner
Thu Jul 05, 2018 2:54 pm
Forum: ROMS Discussion
Topic: on the wave mixing
Replies: 4
Views: 1496

Re: on the wave mixing

These features are best described in Kumar, N., Voulgaris, G., Warner, J.C., and M., Olabarrieta (2012). Implementation of a vortex force formalism in a coupled modeling system for inner-shelf and surf-zone applications. Ocean Modelling, 47, 65-95. and Carniel, S., Warner, J.C., Chiggiato, J., and S...