Ocean Modeling Discussion

FengZhou

Hi, John,

Thank you very much! You are right. The river sediment concentration is one order lower than the local value caused by erosion and resuspension, that is why it cannot be seen.

regards,

Feng

FengZhou

Hi,
I have the same issue when I would like to add river_mud_01 to the model. I saw the river_temp and river_salt working well but not the sediment.

By the way, which version of ROMS are you using? I didnot find the cpp option River_sediment. I am using ROMS 3.7.

regards,

Feng

FengZhou

Hi, have you solved the problem? Feng Would like to add suspended sediment from a river analytically using ana_psource.h. Have specified CSED value in input file and attempted to add ised value in ana_psource but neither appear to be introducing sediment. Salinity and temperature appear to be ...

FengZhou

Hi, ROMS users, Has anyone succeeded in introduce the river sediments into the model? The effects of rivers' temperature and salinity can be seen clearly in my model but not the sediment. I intended to add a mud to the present circulation model, which has already included the Yangtze River ...

FengZhou

The problem is solved. My biological module (CoSiNE) contains some old cpp definition 'TS_PSOURCE' in ROMS/Nonlinear/Biology/bio_UMAINE13_var.h . The 'TS_PSOURCE' has been removed by the new version of ROMS. So when I try to couple that CoSiNE and the recent ROMS, the model can not find the point ...

FengZhou

In other words, I am wondering if I need to prepare river nutrients in a file other than the file in which river transport/temp/salinity are included? If so, what's the file name? should I put it in ocean_.in or in something like bio_Fennel.in (designated by BPARNAM)?

Thanks in advance!

FengZhou

Hi, all, I am running a coupled model (ROMS svn 713 ＋ CoSiNE), which behaves well when no riverine nutrients put in. The model have completed successfully after being spinned up for two years. And now I would like to add river nutrients like nitrate, silicate and phosphate etc, since they are so m ...

FengZhou

When I simulated 5 tidal components with constant temperature and salinity and no winds, the model didn't yields the correct residual flows even after 1 years running. my configuration in this case is:

NAVG == 12960
NDEFAVG == 155520

NTIMES == 777600
DT == 200.0d0

FengZhou

Hi,all, My ROMS is v3.4, ticket 512, with only one tidal component-M2. These days, I want to obtain the tidal residual currents in my region, so I have tried the following method as supposed as before in the forum. (1) the simple method of time average by: set DT == 216.0104d0 NAVG == 2070 NDEFAVG ...

FengZhou

Hi,

Can you tell me how to fix this problem? what do you mean by "difference of the offsets of River.time between ROMS and Matlab Codes."

Thank you very much!

FengZhou

Hi,Rob, Thank you for proposing a solution! I didn't use mpi1.2, but mpi1.1 + pgi compiler. My job file are: #PBS -N nwpo #PBS -l nodes=4:ppn=4 #PBS -l walltime=500:00:00 #PBS -j oe #PBS -q general #define variables NSLOTS=`cat ${PBS_NODEFILE} | wc -l` echo "This jobs is "$PBS_JOBID@$PBS_QUEUE ...

FengZhou

gcreager wrote:This actually looks like a node crashed on you (node34). I see you're using Torque (pbs). Is there a stderr file that shows any more information?

gerry

Yes I use PBS. There is no other further information.

FengZhou

Ok, I failed to fix the problem completely. Some of problems come from the insufficent time for the model to finish the specified running. However, others didn't. I have the trouble again like this: WRT_HIS - wrote history fields (Index=1,1) into time record = 0000005 169779 406 18:17:33 1.471362E ...

FengZhou

Hi, all, Recently, I want to add a passive tracer like dye together with the river discharge into the ROMS model.I would like to input the initial concentration of the tracer via the initial netcdf file. Then what I should do is: (1) define T_PASSIVE in the cpp file? (2) modify the initial file to ...

FengZhou

My experience is : this message is caused by the limitation of the running time, so please modify the job script to increase running time at this line:

#PBS -l walltime=600:00:00

please try it.

zhou

FengZhou

Thank you, Kate!

The problem is solved.

But its weird for ROMS to read in River Id from river forcing file, and then to compare with 'smday' ( start modeling day), it should have compared with 'river_time', am I right?

btw, cycle_length is completely useless for river file.

zhou

FengZhou

Hi, all when I upgrade to ROMS3.2, I met trouble in preparing the river forcing file. The error message is : GET_CYCLE - starting time for variable: river is greater than current model time. TMIN = 1.0000 TDAYS = 0.0000 The start time in ROMS_INI.nc file is 0, and river_time in ROMS_FRC_Rivers.nc is ...

FengZhou

Hi, all I have compiled the code just upgrade to v298 (ROMS3.2), it is ok for default UPWELLING case. But it meet problem when I turned to my own case. The message is : ROMS/Bin/cpp_clean Build/mod_netcdf.f90 cd Build; /opt/mpi/mvapich/1.1/gcc.pgf90/bin/mpif90 -c -O3 -tp k8-64 -Mfree mod_netcdf.f90 ...

FengZhou

Hi, all I got into a new trouble after upgraded to ROMS3.1. The model will quit after several months(some cases longer than 1 year) without blow up messages. I have compared the results that ROMS3.1 behaves better at open boundaries than ROMS3.0, which yield beautiful patterns in the whole domain ...

FengZhou

Hi,

ggerbi wrote:I found the same thing as jacopo. Reducing the time step made it run fine.
Have you tested it with all three stability functions (Kantha-Clayson, Canuto A and Canuto B?)

As you said, Canuto A works.

Thank you!

FengZhou

Hi, John,

I don't know MPI well, so I just check others.

I don't think there are changes between these two versions by comparing Build/gls_corstep.f90.

zhou

FengZhou

Hi, ROMSers, Normally I used k-e (or k-omega) as my default GLS_MIXING scheme while applied ROMS(3.0) to the Bohai Sea (a small north part of the East China Sea). It performs better than others like k-kl, gen, and KPP. So I did the same choice while applied the model(3.1) to the whole East China Sea ...

FengZhou

1. surface relaxation for resetting surface salt and heat fluxes Options 1 and 3 above get the nudging data from a user analytical formulation in ana_tclima.h or from the 3D climatology file CLMNAME set in ocean.in Hi, John, I feel that the SRELAXATION restores the modeled SSS to the SSS in forcing ...

FengZhou

Hi, bronwyn, I have just tested the EcoSim case, but met trouble whiling running 1 step. The messages are: STEP time[DAYS] KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME trd 0 0.00000 0.000000E+00 1.034867E+03 1.034867E+03 2.764606E+11 0 DEF_HIS - creating history file: ocean_his.nc WRT_HIS - error ...

FengZhou

Hi, Amanda,

The bathymetry is steep only at other grids far away from the estuary. While the large salinity value occrus only at the inlet of river, especially on lower levels. The top 5-10 layers sound not weird.

FengZhou

I have just tried the TS_MPDATA option. There are no negative values even in July after 7 month simulation. However I have checked the bottom salinity that the largest salinity exceeds 70 psu . It occurs in both cases : 1st case : The frseh water is only specified on the top 15 layers, almost ...

FengZhou

Dear all, I am running a coarse realistic case (18km*18km) including a large fresh water inflow (annual mean is about 30000 m^3/s, largest is close to 50000m^3/s in normal years). In this case, I focus on the river plume and its interaction with ambient water. Before, a general simulation has been ...

FengZhou

Hi, all,

problem is probably fixed. I forgot to define the nudging block for the realistic case. Its running just by undefining the nudging items. Now I am tracking on...

Thank you all.

FengZhou

which version of pgi are you using? my pgi is 7.0.3. other information: Model Input Parameters: ROMS/TOMS version 3.0 Wednesday - January 30, 2008 - 3:19:38 PM ----------------------------------------------------------------------------- Bohai-YellowSea-EastChinaSea, 1/12 degree Operating system ...

FengZhou

Yes, I use PGI compiler.

FengZhou

hi,Kate, Thanks for your reply. My grid dimension is as following( need only to input into External/byesea.h in Roms3 ?): Lm == 167 ! Number of I-direction INTERIOR RHO-points Mm == 243 ! Number of J-direction INTERIOR RHO-points N == 30 ! Number of vertical levels while in ROMS2, they were written ...

FengZhou

Hi, all, I just tried ROMS3 and compiled the codes successfully with Upwelling case and a realistic case. But there is an error during executing the latter. The message is : 0: Subscript out of range for array scalars%sc_w (set_scoord.f90: 49) subscript=0, lower bound=0, upper bound=-1, dimension=1 ...

FengZhou

Yes, I use a window 'svnversion' to down the codes and then transfer to the Linux workstation. I use pgf90 compiler with the default case 'UPWELLING'. After I applied the command 'dos2unix', there are still some error messages: $ make : No such file or directory makefile:231: INCLUDING FILE ...

FengZhou

Hi, all I use ROMS2.2 for some time. It workes well. But now v3.0 is recommended. I have trouble in compiling the ROMS3.0. The system said: [zhoufeng@oceanfe Ocean]$ make : No such file or directory makefile:231: INCLUDING FILE Compilers/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE ...

FengZhou

Hi, I have the same issue too. I've just ask our administrator to install make3.81 version. After 'make', it gives as follows : [zhoufeng@oceanfe Ocean]$ make : No such file or directory makefile:230: INCLUDING FILE Compilers/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS make ...

FengZhou

About the interconnect, due to the mismatch between mpi-1.2.7 and Myrinet 2000, I have to use a low level 1000m bps hub.

FengZhou

Hi, Jamie, My configuration: CPU/hardware: Dell PowerEdge 1850, Xeon 3.2G / 2G DDR / SCSI Compiler location : pgi location /opt/pgi/linux86/7.0-3/; mpi location ~/mpi-1.2.7pgi/ Operating system : Linux CPU/hardware : i686 Compiler system : mpif90 Compiler command : mpif90 Compiler flags : -r8 -i4 ...

FengZhou

Hi, Jamie, Thank you!
A simple shell script works!

Hi, Weifeng,
Thank you for the suggestions. I will bother you if necessary:)
Do I know you? I have a friend has the close name with you from Zhejiang University. He is in U.S.A now:)

FengZhou

Hi, everyone. Has anyone compared the ROMS efficency of CPU usage under serial mode and parallel mode ? I got ridiculous results. In serial mode, the cpu efficiency is close to 99%, comparing to the 33% cpu used under parallel mode. And parallel takes longer time than serial mode. All the setups of ...

FengZhou

Hi, Can everyone tell me how to run roms2.3 backgroundly under PGI+MPI environments? With serial mode, it can be done as: ./oceanS <External> logbohai_200709.out & While in parallel mode, it have been compiled to get the executable file oceanM with MPIf90 using PGF90 compiler. And submitted as ...

FengZhou

Thanks, problem fixed.

cancel -Vaxlib.

FengZhou

yes, I modified the Compiler/Linux-mpif90.mk, and got in new trouble: mpif90 -c -fastsse -Mipa=fast -tp p6 -Vaxlib master.o ocean_control.o -o oceanM libNLM.a libUTIL.a libMODS.a -L./netcdf_ifc -lnetcdf pgf90-Fatal-Could not find alternate compiler: /opt/pgi/linux86/axlib/bin/pgf90 make: *** [oceanM ...

FengZhou

Hi, Scott, I have met similar problems like you, mpif90 -c -g -check bounds mod_kinds.f90 pgf90-Error-Unknown switch: -check make: *** [mod_kinds.o] Error 1 rm mod_kinds.f90 Would you please tell which file shall I modify? I can't find the parameters you said above. Thanks in advance! zhou Thanks, I ...

FengZhou

Thanks, Kate!

you are right. The EAST_M2RADIATION is missing in check_defs.F.

FengZhou

Hi,

Could anyone tell me why 2d momentum boundary conditions donot work. I do define :

#define EAST_M2RADIATION
#define EAST_M2NUDGING

in cppdefs.h, but they don't show up in running log file. While if I defined EAST_M2GRADIENT, it shows up its working.

Thanks in andvance!

feng

FengZhou

Hi, Has anyone tried to run roms on 64-bit platform. Usually it works under 32-bit platform with intel ifort compiler. Now I am trying to move them on the 64-bit platform, which is a supercomputer: NEC with redhat linux system. I can't make them compile because I haven't got a netcdf library of 64 ...

FengZhou

Hi, Kate,

Only the Eastern boundary is open. I chose

#define EAST_VOLCONS

#define EAST_FSGRADIENT
#define EAST_M3RADIATION
#define EAST_TRADIATION

and also I use
#define ZCLIMATOLOGY
#define ZCLM_NUDGING

FengZhou

Hi everybody, I am trying to compile ROMS on linux with pgi fortran compiler, 1) My first error: -Unable to open include file: mpif.h (mod_parallel.f90: 18) I go to line and change the following line include 'mpif.h' to include '/usr/mpich/pgi/include/mpif.h' it works, but is there anyway to do ...

FengZhou

Hi, I make a test running in Bohai Sea. It's all closed but the eastern boundary. The inner domain of circulation and temperature are all realsonable as I expect. Howeever the temperature at the eastern bondary (the most eastern column: Lm) is abnormally low and the gradient is pretty strong and ...

FengZhou

Hi,
If you just want to know how to prepare initial, forcing and so on data, you can try the case of Damee_4. They are already for download on the ROMS websit.

ZHOU

FengZhou

Many thanks to both of you. Yes I am running west coast and east coast version of ROMS at the same time. The former is easy to start and I've got powerful preprocessing tools (Roms_tools). The results looks good, but I can't run them with MPI. The problem is as above. Any way, thank you so much! I ...

FengZhou

I got trouble when I wanted to use 2 or more nodes to run ROMS MPI,but it works with only one node. The basic configuration of my model is : parameter (LLm0=167, MMm0=244, N=20) ! <--East China Sea parameter (NP_XI=2, NP_ETA=3, NNODES=NP_XI*NP_ETA) parameter (NSUB_X=1, NSUB_E=2, NPP=1) so horizontal ...

Ocean Modeling Discussion

Search found 52 matches

Re: Cannot introduce river sediment in ROMS (svn 713)

Re: Sediment model

Re: Sediment from river!

Cannot introduce river sediment in ROMS (svn 713)

Re: Model cannot find riverine nutrients like NO3

Re: Model cannot find riverine nutrients like NO3

Model cannot find riverine nutrients like NO3

Re: Confused results when using 'AVERAGE_DETIDE'

Confused results when using 'AVERAGE_DETIDE'

Re: SET_NGFLD - current model time exceeds ending value for var

Re: MPI process terminated unexpectedly

Re: MPI process terminated unexpectedly

Re: MPI process terminated unexpectedly

how to add a passive tracer?

Re: MPI process terminated unexpectedly

Re: start time for river is greater than current model time??

start time for river is greater than current model time??

probably a small bug for public variable : exit_flag

MPI process terminated unexpectedly

Re: meet trouble with GLS_MIXING

Re: meet trouble with GLS_MIXING

meet trouble with GLS_MIXING

Re: how to radiate and damping out waves ?

Re: Initialization for Fasham and EcoSim BioToys applications

salinity goes negative and large in a river plume testing

array scalars%sc_w is out of range?

Is the "svnversion" necessary for compiling the RO

How to increase ROMS parallel efficiency

ROMS2.3 background running problem under PGI + MPI

2D momentum boundary conditions missing in running log

require netcdf for 64-bit platform!

reply for boundary condition

Re: pgf90 compilation problem

abnormally low temperature at the open doundary

I recommend to try the case of Damee_4

another questions: how to start MPI with ROMS/Rutgers 2.2

MPI error ? and how to run MPI ?