Ocean Modeling Discussion

longmtm

Thanks.

The u2dbc_im.F file https://www.myroms.org/svn/src/trunk/ROMS/Nonlinear/u2dbc_im.F treated EAST_M2FLATHER so that BOUNDARY(ng)%zeta_east is used to specify ubar.

# elif defined EAST_M2FLATHER
!
! Eastern edge, Flather boundary condition.
!
DO j=Jstr,Jend
# if defined SSH_TIDES ...

longmtm

Dear all,

Please help, I'm a bit confused here. I wonder how open boundary tidal water level is picked up by the model when EAST_FSCHAPMAN condition is used.

Code: https://www.myroms.org/svn/src/trunk/ROMS/Nonlinear/zetabc.F

In the following section of Nonlinear/zetabc.F

# elif defined ...

longmtm

Thanks a lot! Since a 2D radiation boundary for (ubar,vbar) is not yet implemented and nesting version of ROMS is not yet released, for now do you think EAST_M2RADIATION + EAST_M2NUDGING is better than EAST_M2FLATHER for nesting a model inside of an external model?

The reason that I'm asking is ...

longmtm

Dear all

Can some one explain the following section of the code Nonlinear/u2dbc_im.F ?
Link: https://www.myroms.org/svn/src/trunk/ROMS/Nonlinear/u2dbc_im.F

# elif defined SOUTH_M2FLATHER || defined SOUTH_M2REDUCED
!
! Southern edge, Chapman boundary condition.
!
DO i=IstrU,Iend
cff=dt2d*0.5 ...

longmtm

Good to know the new ecological model has more flexibility and the ROMS3.3 or later is already stable.

We will move forward to keep up with you guys.

Wen

longmtm

Other passive surface fluxes are less known, so it is a good approximation to set them to zero, using ANA_SPFLUX. There is not such thing as surface flux of phytoplankton, zooplankton, dyes, and so on. The bottom flux of tracer should be zero too, unless that you have hydrothermal vents in you ...

longmtm

I'm here referring to ROMS3.0 tagged version.

Here is a segment in ROMS3.0 Utility/def_avg.F
https://www.myroms.org/svn/src/tags/roms-3.0/ROMS/Utility/def_avg.F

!
! Define surface net salt flux.
!
IF (Hout(idTsur(isalt),ng)) THEN
Vinfo( 1)=Vname(1,idTsur(isalt))
WRITE (Vinfo( 2),'(a,1x,a ...

longmtm

Same interesting/odd things occurred with my runs of Chesapeake Bay with TS_MPDATA:

I have TS_MPDATA and biology (fasham/fennel) on and tried it on two different machines. It works on one machine, but not on another when using MPI. Both machines work with serial model (no MPI). So I guess it is ...

longmtm

John, many thanks.

Conserving mass is probably the most compelling reason that negativity is preserved using the first RHS term (firstly chopped off, and then added back). I guess the other reason should be trying to avoid rapid change of signs/values before and after bio reaction terms being ...

longmtm

We experienced negative concentrations for NO3 and also Temperature and Salinity with CPP options for tracers being:

#define TS_SVADVECTION
#define TS_U3HADVECTION

It seems to us that most likely the negativity is produced by the advection scheme for T and S are not updated in fennel.h/fasham.h at ...

longmtm

https://www.myroms.org/projects/src/bro ... /inp_par.F

Code: Select all

      WRITE (out,100) ZooER(ng), 'ZooMR',                         &

line 3702, it is reporting ZooER as ZooMR, should be ZooMR

Wen

longmtm

Katja,

After some checking, I think you are right. It is accumulating and the unit should be [millimole N/m3/diag-period]

Wen

longmtm

Hi Katja,

Thanks for the input! Certainly I think millimole-N/m3/day is not accurate, but I'm not sure if it is millimole-N/m3/dtdays or millimole-N/m3/diag-period as you indicated. If it is [millimole-N/m3/diag-period], the code must be accumulating for multi-dtdays to get diag-period.

Anyhow ...

longmtm

Hi Laura,

I want to confirm that Katja is right. The Unit of AttChl in the bioFasham.in file should be[m2/(mg_Chl) rather than [1/(mg_Chl m2).This should be corrected in the file ROMS/External/bioFasham.in

and also Bio(i,k,iChlo) should have unit [milligram CHL/m3]

Wen

longmtm

Hi all,

Not a big issue, but it seems like a unit inconsistency to me here.

in Nonlinear/fasham.h DiaBio3d(i,j,k,iPPro) is given N_Flux_NewProd
which has unit [millimole-N/m3]

#ifdef DIAGNOSTICS_BIO
DiaBio3d(i,j,k,iPPro)=DiaBio3d(i,j,k,iPPro)+ &
& N_Flux_NewProd+N_Flux_RegProd

and in ...

longmtm

Please post your findings with the bug pointed out in the previous post, I'm also interested in seeing how well WET_DRY works

Thanks

Wen

longmtm

The ChesROMS (Chesapeake ROMS) is also operationally running for about 1.5 years now.

More details:

http://ches.communitymodeling.org/models/ChesROMS/index.php

Here are results daily for Sea Nettle, HAB and Pathogen Vibrio Cholerae based on empirical formulars involving ROMS predicted T and S ...

longmtm

I want to come back to this bug fix pointed out by Aijun Zhang:

I believe this bug was introduced when ROMS2.2 is upgraded to ROMS3.0 and when PERFECT_RESTART option was introduced.

The fix was in the previous message and also copied here:

1 #ifdef INI_FILE
2 IF (nrrec(ng).eq.0) THEN
3 !
4 ...

longmtm

Tough but certainly a very good direction to go.

The gaming industry/graphics gang certainly have more money and power than the gozilla gigantic super computer sect

To optimize the entire ROMS in with GPU would be quite challenging, especially that ROMS is still under fast evolution. Yet I think ...

longmtm

Hi all,

People in our group are in the processes of building a server for viewing ROMS outputs online. Yet for velocity fields, rotation and scaling are needed in order to obtain the results into true (East, North) directions on collocated grid points instead of being in the curvilinear and ...

longmtm

Thank god! Oh, no, thanks to the ROMS forum, the restart is working with the PERFECT_RESTART option, GLS_MIXING, and a bug fix pointed out by AiJun and Lyon in NOAA.

Here are the results based on station outputs.

http://131.118.211.30/chesromsweb/inter ... est/zilla/

Wen

longmtm

I guess you can specify a smaller value of the NDEFHIS, so that you will have multiple history outpus per year, then you shall be able to restart from in the middle of a year,

longmtm

AiJun,

Thanks! I feel better since we can corss compare different applications and different platforms,

Will report soon on my trials with SGI

BTW, netcdf3.6.2 is very hard to install on SGI and I didn't have a clue of what to do, so for now, I just use 3.6.0

Wen

longmtm

Hi

I tried to activate the model PERFECT_RESTART cpp option on SGI openMP system using 8 process. I still met some diffriculty which I beileve is related to netcdf:

First of all, I tried activating both PERFECT_RESTART and OUT_DOUBLE and LARGE=on for 64 bit compilation.

Then the model had ...

longmtm

Hi John,

Thanks! I will try and report here.

Wen

longmtm

Hi all,

I did quite some trials to compare restarted runs and straight runs of ROMS3.0 foy my application of the Chesapeake Bay, I didn't get perfect restarted results.

I do see there is a CPP option called PERFECT_RESTART, All my tests did not include definition of this CPP option. Do I have ...

longmtm

> I also tried to restart using the history file of the end of 11'th month, i.e. >day 330, it worked ran into the second year smoothly. If I stop it at the end >of 23'th month i.e. 690 days and restart, I'm not sure whether if it will work.

Just to report, I did try to restart from 23'th month ...

longmtm

I have tried to include t=360(days) in the forcing files as well, still doesn't work.

Anybody tried to use restart for climatological runs before? Thanks.

Wen

longmtm

Hi Kate and all ROMS experts,

You are right, once I restricted the forcing files to only contain data within time range [0 cycle_length) , the model reads forcing correctly and can run multiple years.

Yet there is another problem that I ran into:

I have succesfully run the model for 2 years ...

longmtm

Hi Kate,

Thanks a lot, after quite some poking around, I believe what you suggest is right. I should try not give something EXTRA than it's trying to find.

The clocking of Tmono is really fancy,,,

Wen

longmtm

Folks, I still need your help on this.

Now I have set all time variables in forcing files with an attribute cycle_length= 360, and the model is reading that correctly.

Yet the model complains about the time interpolation.

To rephrase the problem: I'm trying to run ROMS for chesapeake bay for ...

longmtm

For me, I have

DSTART = 6940.0d0 ! days after TIME_REF, i.e. 1999 01 01
TIDE_START =0.0 ! days after tide forcing time axis origin
TIME_REF = 19800101.0d0 ! yyyymmdd.dd

TIDE_START totally depends on how you prepare the tidal forcing, i.e. how you generate the nodal factors and equilibrium ...

longmtm

J, Thanks a lot. I will try it out and report.

Wen

longmtm

Dear all,

I'm trying to run ROMS3.0 with a case for the Chesapeake Bay with climatological forcing. I set TIME_REF=-1 so that the model will take 360 day with 12 30-day months as a year.

I have forcings (river, wind, OBC etc) prepared from day -10 to day 368 or so, with days [-10,0] and [360 ...

longmtm

Hi Hernan,

Thanks for the clarification. We will move to ROMS3.0.

Wen

longmtm

The compile error is solved after I installed latest version of ifort and icc. (10.0.023, IA32, 686,)

So I guess it is due to a bug in icc version 9.1.038 or earlier.

I also installed mpich1.2.7 using ifort .

A Linux-mpif90.mk is used instead of Linux-ifort.mk. Here is the contents of Linux ...

longmtm

Hi

Since ROMS has now been hosted by SVN. After we retrieve the 2.2 version, we still need to apply corrections file for bugs reported above.

Yet if I follow the post above and download:

http://www.myroms.org/links/corrections-2-2.tar.gz

And untar this corrections-2-2.tar.gz file, under ...

longmtm

I got the same problem with ifort and mpich1.2.6, the compiler complains about mp_scatter in white_noise.f90, no clue what is the problem

Wen

longmtm

Hi,

Just to point out a tiny typo in bulk_flux.F of ROMS 2.2

!
! Mean absoption in cool-skin layer.
!
Fc=0.065_r8+11.0_r8*Hcool- &
& (1.0_r8-EXP(-Hcool*1250.0_8))*6.6E-5_r8/Hcool

where 1250.0_8 should be 1250.0_r8 ? Don't know what the effect will be with "r" left out.

Wen

longmtm

Are you using ROMS2.2?

The fix I mentioned works for me. Would you please try replacing two files with the following link and post back?

http://131.118.211.30/chesroms/LatestRO ... tationfix/

Thanks,

Wen

longmtm

Finally here is the quickest fix the problem,,

We only need to change two places in file grid_coords.F in Utility

1) use a larger search box, LBi, UBi, LBj,UBj instead of Istr, Iend, Jstr, Jend
2) replace spv by -1.0_r8 in the call of hindices() and mp_collect() i as the following (only this call ...

longmtm

I have to take it back. The fix doesn't realy work. The out put of (lat lon) are correct but the (Ipos and Jpos) are not.

Wen

longmtm

I tried to modify the grid_coords.F in directory Utility, and it seemed to be working.

The old and new results are located at:

http://131.118.211.30/chesroms/retrospectrun/1999/MedusaMPIstn/ROMSMPIcodeStationCheck.fig

and

http://131.118.211.30/chesroms/retrospectrun/1999/MedusaMPIstn ...

longmtm

Comrades,

There seems to be a bug in 2.2 version for the station location interpolation.

Here, in my case, I have 126 stations for the Chesapeake Bay (Red) in the following link. In the code, the station input file can take (lat, lon) as input data. And ROMS is supposed to find the (Ipos, Jpos ...

longmtm

I couldn't find the -bmaxdata option in my compiler options, insead I tried to use something like -mcmodel=large for the ifort, yet still didn't work.

Paul, I guess you are using Scali MPI, while in my MVAPICH, I don't get an option like -inherit_limits,,,

Thanks,

wen

longmtm

Hi Kate, thanks for the detailed questions,

Here are my settings for the limits:

> ulimit -SHacdflmnpstuv
core file size (blocks, -c) 0
data seg size (kbytes, -d) unlimited
file size (blocks, -f) unlimited
max locked memory (kbytes, -l) 32
max memory size (kbytes, -m) unlimited
open files (-n ...

longmtm

Thanks to kate and john for the discussion.

I believe it is, as kate said, due to memory limit. I have used unlimited stack size, and it still deosn't work for my case (100*150*30 grid). Yet I tested the upwelling case, it is okay.

I wonder whether kate and john know what compiler option I ...

longmtm

Dear all,

I'm trying to test whether ROMS MPI parallel run and serial runs give different results.

In my case I found that MPI 1 by 8 (NtileI=1, NtileJ=8 ) compiled by mpich1.2.6 gives somewhat different results as compared to serial run compiled by ifort. Since the two compilers are different ...

longmtm

Dear Hernan and Kate,

Thanks a lot for the quick reply.

Wen

longmtm

Dear all,

About the recent bug fix https://www.myroms.org/blog/?p=113

I couldn't find the corresponding codes in the 2.2 version. For example, I only have mp_gather in stead of mp_gather_state in distribute.F

I also coudn't find pdnaupd.f in the 2.2 version.

Are these bugs solely related ...

longmtm

We have similar problems using MPI. The sequential run and MPI runs results are different especially at open Boundary. Also results are different when we use different number of partitions using MPI . We did use IBM cpp compiler and mvapich 1.2.6.

We have a 20 node linux cluster, if you don't ...

longmtm

Jpringle:

Thank you very much for the suggestions.

I did make the MPI work for cpi.c . The problem is solved after we recheck the OpenPBS settings and restart the PBS server and mom daemons.

Wen Long

longmtm

Hi,

Hope you can tell me the trick here. I'm trying to run ROMS on a 10 node(computer) Linux X86 64b cluster. (MVAPICH + Open PBS)

Each node has 2 processors. Am I right if I want to use more than 10 processes in parallel to run the code?

Fore example, the following run is sucessful ...

longmtm

The problem is solved, reason is that I put the run mpirun directory in the PATH. The machine has two copies of mpich, and they are not the same.

Thanks,

longmtm

Hi,

I start to work with ROMS in the last few days.

I used ifort to install ROMS and MPICH-1.2.6 . After the compile, I do get a oceanM executable, it runs with the following case:

mpirun -np 4 ./oceanM ocean_upw.in

But when I looked at the output, it says wrong choice of domain 01 ...

Ocean Modeling Discussion

Search found 55 matches

Re: FSCHAPMAN and SSH_TIDES, ADD_FSOBC

FSCHAPMAN and SSH_TIDES, ADD_FSOBC

Re: question on SOUTH_M2FLATHER and NORTH_M2FLATHER

question on SOUTH_M2FLATHER and NORTH_M2FLATHER

Re: bug in def_avg.F , get_data.F, wrt_hessian.F etc

Re: bug in def_avg.F , get_data.F, wrt_hessian.F etc

bug in def_avg.F , get_data.F, wrt_hessian.F etc

Re: MPI error when define TS_MPDATA???

Re: negative tracer and preserving negativity in fennel.h

negative tracer and preserving negativity in fennel.h

Very slight bug in inp_par.F

Re: unit inconsistency in DiaBio3d outputs in fasham.h?

Re: unit inconsistency in DiaBio3d outputs in fasham.h?

Re: Light attenuation in Fasham

unit inconsistency in DiaBio3d outputs in fasham.h?

Re: blows up in shallow water! wet_dry problem?

Re: Operating ROMS nowcast/forecast models

velocity outputs rotated to true East, ture North ?

PERFECT_RESTART cpp option

recycle of forcing for climatological runs

Internal Compile Error

roms 2.2 corrections tar file uptodate?

typo in bulk_flux.F

MPI code bug in interpolating station locations

MPI 1 by 1 tile configuration --segmentation error

About the recent parallel bug

How to run ROMS with MPI + OpenPBS with every processors?

wrong choice of domain 01 partition error?