Search found 185 matches

by shchepet
Sat Jun 29, 2019 9:47 am
Forum: ROMS Discussion
Topic: Alongshore currents with periodic alongshore boundaries
Replies: 9
Views: 1089

Re: Alongshore currents with periodic alongshore boundaries

Is this an idealized problem? If yes, you have to make a your own routine which creates these field analytically. As an example (actually a fairly old one) you may use http://people.atmos.ucla.edu/alex/ROMS/IslandWakeNotes.pdf The technique is essentially the same as using side boundary forcing in r...
by shchepet
Fri Jun 28, 2019 9:24 pm
Forum: ROMS Discussion
Topic: Alongshore currents with periodic alongshore boundaries
Replies: 9
Views: 1089

Re: Alongshore currents with periodic alongshore boundaries

....The goal is to have the flow fully developed over the alongshore direction.... You want periodicity and simultaneously want to maintain your alongshore velocity be close to a desired value. This is over-specification. You do need periodic boundaries to do that. Instead you need to specify you d...
by shchepet
Wed Nov 28, 2018 9:22 am
Forum: ROMS Discussion
Topic: Set a land mask on the sea in SeaGrid
Replies: 22
Views: 4778

Re: Set a land mask on the sea in SeaGrid

What is the acceptable level of orthogonality errors? I would say none. Or, more precisely, the question is irrelevant, because orthogonality errors can be kept at the level roundoff errors of double precision -- it is technologically achievable, and therefore should be done this way. Then there is ...
by shchepet
Thu Nov 22, 2018 10:21 am
Forum: ROMS Discussion
Topic: Set a land mask on the sea in SeaGrid
Replies: 22
Views: 4778

Re: Set a land mask on the sea in SeaGrid

The answer in "no", all three of them, A,B,C, cannot be made straight at the same time. This is the nature of conformal mapping: once A and C are straight, there is no way to fit a curve which would go along the coast, and be perpendicular to A and C at the junction points. B can me made straight ea...
by shchepet
Tue Nov 20, 2018 3:59 pm
Forum: ROMS Tools and Techniques
Topic: Building ROMS grid topography from scattered, sparse data
Replies: 2
Views: 1300

Building ROMS grid topography from scattered, sparse data

Recently I was asked to help set up ROMS grid for a lake which has its bathymetry data available only as a set of point measurements from a boat: the depth was measured by echo sounder accompanied by GPS, so the data comes as a file of the following structure, three numbers on each line latitude lon...
by shchepet
Wed Nov 14, 2018 11:23 am
Forum: ROMS Discussion
Topic: Set a land mask on the sea in SeaGrid
Replies: 22
Views: 4778

Re: Set a land mask on the sea in SeaGrid

No, you should be able to compile the package using any compiler. I updated the package (see attachment at the end of this post) specifically paying attention to the warnings issued by GCC compiler, which was forced into checking conformance to Fortran 2008 standards in pedantic mode. No bugs were d...
by shchepet
Sun Nov 11, 2018 11:20 am
Forum: ROMS Tools and Techniques
Topic: Courant number Tool
Replies: 1
Views: 1098

Re: Courant number Tool

Hi Steve, Remember me in Florida State back from 1992-1993? It was a nice time back then. You problem will take only a few minutes to overcome because the very same package you have compiled contains command-line operators nc_add_att and nc_del_att which allow you to put all the necessary attributes...
by shchepet
Fri Nov 09, 2018 6:23 pm
Forum: ROMS Discussion
Topic: Set a land mask on the sea in SeaGrid
Replies: 22
Views: 4778

Re: Set a land mask on the sea in SeaGrid

Obviously this should be C$OMP PARALLEL SHARED(Lm,Mm, pm,pn, f,f_q, fnd_rmask,rmask, dm_u,dn_v, C$OMP& iA_q) call init_vort_thread(Lm,Mm, pm,pn, f,f_q, fnd_rmask,rmask, & dm_u,dn_v, iA_q) C$OMP END PARALLEL i.e., change "& into "C$OMP&" in continuation line for OpenMP directive in the original vort....
by shchepet
Tue May 29, 2018 12:05 pm
Forum: ROMS Discussion
Topic: Set a land mask on the sea in SeaGrid
Replies: 22
Views: 4778

Re: Set a land mask on the sea in SeaGrid

Try the tool editmask which is in the myroms/landmask folder of Matlab tools John, Here is the problem: At first many thanks to Andrey Scherbina for creating editmask tool back in 1999. I checked editmask in myroms/landmask today by getting it from via svn, svn checkout --username shchepet https://...
by shchepet
Fri Feb 16, 2018 9:24 am
Forum: ROMS Discussion
Topic: Set a land mask on the sea in SeaGrid
Replies: 22
Views: 4778

Re: Set a land mask on the sea in SeaGrid

Error: Symbol ‘nf_netcdf4’ at (1) has no IMPLICIT type This one you should be able to overcome yourself. At first, my package comes with several README.something files: just look through them. Among them is README.compiling which tells what to do. Then, it is quite obvious that your netcdf.inc file...
by shchepet
Wed Feb 14, 2018 11:35 pm
Forum: ROMS Discussion
Topic: Set a land mask on the sea in SeaGrid
Replies: 22
Views: 4778

Re: Set a land mask on the sea in SeaGrid

you can fit weird shapes after some practice...
Black Sea grid.
Black Sea grid.
by shchepet
Wed Feb 14, 2018 11:25 pm
Forum: ROMS Discussion
Topic: Set a land mask on the sea in SeaGrid
Replies: 22
Views: 4778

Re: Set a land mask on the sea in SeaGrid

The reason why you have these compiling problems is a faulty version of mpc.F supplied with the package at some point in the past. This was corrected, but it appears that the old version came back because at some point the web page was restored from the backup after disk failure and I did not realiz...
by shchepet
Sun Feb 11, 2018 11:53 am
Forum: ROMS Discussion
Topic: Set a land mask on the sea in SeaGrid
Replies: 22
Views: 4778

Re: Set a land mask on the sea in SeaGrid

The procedure for generating ROMS land mask from USGS coastline data described here:
viewtopic.php?f=23&t=3878&p=14908
by shchepet
Sun Feb 11, 2018 11:27 am
Forum: ROMS Discussion
Topic: Set a land mask on the sea in SeaGrid
Replies: 22
Views: 4778

Re: Set a land mask on the sea in SeaGrid

Is this the kind of grid you want to generate?
by shchepet
Wed Oct 04, 2017 3:42 pm
Forum: ROMS Problems
Topic: Docker container for ROMS?
Replies: 7
Views: 3511

Re: Docker container for ROMS?

What is the motivation for doing this? I inspected WRF file and it looks like this
is just another layer of software toward black-boxing it one level further. What is
wrong with standard build procedures?
by shchepet
Wed Jul 26, 2017 5:22 am
Forum: ROMS Benchmarks
Topic: Ryzen 1800x Benchmarking and memory bandwidth
Replies: 2
Views: 2078

Re: Ryzen 1800x Benchmarking and memory bandwidth

Jamie, This is very useful as you bringing it in, and actually encouraging. The first time I heard about AMD Ryzen is from my son, who is a kind of enthusiast, but I have no first hand experience. Over long period of time Intel and AMD had very different design philosophies: let's just assume that t...
by shchepet
Mon Jul 10, 2017 5:19 am
Forum: ROMS Benchmarks
Topic: Understanding ROMS output
Replies: 5
Views: 2480

Re: Understanding ROMS output

The profile above indicates that the most computationally expensive part is seawater Equation of State. Is this actually true?
by shchepet
Tue May 30, 2017 6:44 am
Forum: ROMS Discussion
Topic: CFL condition
Replies: 3
Views: 2128

Re: CFL condition

There are several of them associated with different processes. 1. Barotropic mode. The easiest to predict and control -- based on speed of the external waves, c_g=sqrt(g*h) where h is local depth, then Cg = c_g*dtfast*sqrt{1/dx^2 +1/dy^2} with dx and dy evaluated locally; Cg_max=max{Cg} over all hor...
by shchepet
Sun May 07, 2017 3:13 am
Forum: ROMS Benchmarks
Topic: Strange Upwelling Performance on Different Architectures
Replies: 2
Views: 1741

Re: Strange Upwelling Performance on Different Architectures

.....16 cores. 4*4 grid: wall time 17s .... 16 cores. 4*4 grid: wall time 27s .... 64 cores (KNL). 8*8 grid, wall time 28s Am I interpret correctly that "4*4 grid" means tiling 4x4? If yes, read https://www.myroms.org/forum/viewtopic.php?f=17&t=2001&p=7771 -- used to be hot topic sometime in the pa...
by shchepet
Tue Mar 14, 2017 3:30 pm
Forum: ROMS Installation
Topic: Netcdf incompatibility error: i386 architecture
Replies: 3
Views: 1340

Re: Netcdf incompatibility error: i386 architecture

....is there a website you could direct me to?
please read
http://people.atmos.ucla.edu/alex/techn ... g_sequence
by shchepet
Sat Sep 24, 2016 9:30 pm
Forum: ROMS Problems
Topic: Help on installing NETCDF/HDF5/ROMS
Replies: 10
Views: 5484

Re: Help on installing NETCDF/HDF5/ROMS

Another problem I noticed is Operating system : Linux CPU/hardware : x86_64 Compiler system : gfortran Compiler command : /usr/bin/gfortran Compiler flags : -frepack-arrays -fopenmp -O3 -ffast-math -ffree-form -ffree-line-length-none -ffree-form -ffree-line-length-none which means that you use gfort...
by shchepet
Sat Sep 24, 2016 4:40 am
Forum: ROMS Problems
Topic: Help on installing NETCDF/HDF5/ROMS
Replies: 10
Views: 5484

Re: Help on installing NETCDF/HDF5/ROMS

The errors you are reporting are unrelated to netCDF installation. The error message from your roms model says it all: Resolution, Grid 01: 0041x0080x016, Parallel Threads: 2, Tiling: 001x001 ROMS/TOMS: Wrong choice of domain 001 partition or number of parallel threads. NtileI*NtileJ must be a posit...
by shchepet
Fri Sep 23, 2016 4:17 am
Forum: ROMS Problems
Topic: Help on installing NETCDF/HDF5/ROMS
Replies: 10
Views: 5484

Re: Help on installing NETCDF/HDF5/ROMS

This means that XML packages from Linux distribution are not installed. Type (assuming that you have rpm-based Linux; Debian uses different command) rpm -qa | grep XML you should get something like this perl-XML-SAX-0.990.0-7.mga5 perl-XML-SAX-Base-1.80.0-5.mga5 perl-XML-NamespaceSupport-1.110.0-7.m...
by shchepet
Sat Sep 10, 2016 6:02 am
Forum: ROMS Usage
Topic: Bathymetry and grid for a small lake
Replies: 2
Views: 7964

Re: Bathymetry and grid for a small lake

I tried to build grid for lake Shira using the latest available GSHHS version 2.3.6 shoreline data set taken at full resolution, gshhs_f.b, see https://www.soest.hawaii.edu/pwessel/gshhg/ and this is what I managed to get: http://people.atmos.ucla.edu/alex/tmp/shira_lake1.png The lake exists in this...
by shchepet
Wed Aug 17, 2016 5:15 pm
Forum: ROMS Installation
Topic: upwellingcase
Replies: 8
Views: 4659

Re: upwellingcase

Most (most likely all) problems of this kind associated with linking to netCDF library can be avoided if you compile netCDF (including dependencies hdf5, zlib, etc) libraries yourself using matching compiler and compiler flags (the same as you use for ROMS) rather than "install" it from your Linux d...
by shchepet
Mon Aug 08, 2016 1:51 am
Forum: ROMS Discussion
Topic: Why the POTEN_ENRG is so big?
Replies: 2
Views: 1805

Re: Why the POTEN_ENRG is so big?

Kate, this actually exposes a long outstanding problem: how useful ROMS diagnostic of PE? And what would be the most meaningful definition of PE in principle? Yes, the computation of PE diagnostic was there in diag.F from the very beginning inherited from SCRUM and SPEM, yet nobody was wiling to rev...
by shchepet
Sun Apr 17, 2016 4:39 am
Forum: ROMS Discussion
Topic: Set geostrphically balanced initial current
Replies: 4
Views: 2839

Re: Set geostrphically balanced initial current

There is one more thing to add to this topic specifically related to the fact that you may want not just geostrophic balance, but the geostrophic balance as it would be felt by the discrete model , i.e., ROMS. ROMS uses C-grid, which means that discrete u s and v s in Coriolis terms are subject to 4...
by shchepet
Sat Apr 02, 2016 7:41 am
Forum: ROMS Discussion
Topic: Set geostrphically balanced initial current
Replies: 4
Views: 2839

Re: Set geostrphically balanced initial current

I set velocity field first and calculate the temperature field through geostrophic balance
It is usually works the other way around: density field + free surface (via level of no motion or some other idea of this sort) ==> pressure field ==> pressure gradient ==> velocity field
by shchepet
Wed Mar 30, 2016 5:51 am
Forum: ROMS Discussion
Topic: Which most worthy test case to Kuroshio current ?
Replies: 1
Views: 1527

Re: Which most worthy test case to Kuroshio current ?

...In the process, I have rewritten the ROMS source code of the test case “UPWELLING” Obviously, going from upwelling toy problem to a full-complexity, realistic regional nested Kuroshio simulation is a long way to go, and you have to rewrite a lot. But if the question is what pre-configured exampl...
by shchepet
Fri Mar 11, 2016 7:09 pm
Forum: ROMS Discussion
Topic: Reading ROMS files in R (R-project)
Replies: 4
Views: 2624

Re: Reading ROMS files in R (R-project)

Speaking CF-conventions.... Would it be hard to adapt and universally enforce a convention that time dimension and the associated timing variable in any ROMS-related netCDF file have the same name ? This should apply to ROMS code itself as well as all pre- and post-processing software, Matlab, and P...
by shchepet
Thu Mar 10, 2016 9:06 am
Forum: ROMS Discussion
Topic: angle in grid file
Replies: 8
Views: 3423

Re: angle in grid file

The rationale for computing angle is very simple: Consider a small Dxi increment along the direction of ROMS grid curvilinear coordinate xi: the associated displacement in longitudinal direction measured in km is R * cos(Lat) * dLon/dxi * Dxi where R is Earth radius; displacement in latitudinal dire...
by shchepet
Thu Mar 10, 2016 6:28 am
Forum: ROMS Discussion
Topic: angle in grid file
Replies: 8
Views: 3423

Re: angle in grid file

See the bottom half of the following routine. Angle can be either in degrees or radians -- it is just a matter of personal preference. ROMS code itself does not use angle, but various pre- and post- processing routines use it to rotate vectors -- velocities if one needs to prepare files for initial ...
by shchepet
Sun Jan 24, 2016 4:20 am
Forum: ROMS Bugs
Topic: Beware of netCDF STRINGs
Replies: 6
Views: 4559

Re: Beware of netCDF STRINGs

Now, I have the following file: roms_clm_HYCOM_Y2015M10.nc 34GB Another thing to mention here is that 64BIT_OFFSET netCDF format has virtually no restriction of the file size, however to exceed 2 GByte limit the file MUST HAVE UNLIMITED DIMENSION, and (1) all variables not having unlimited dimensio...
by shchepet
Sun Jan 24, 2016 3:57 am
Forum: ROMS Bugs
Topic: Beware of netCDF STRINGs
Replies: 6
Views: 4559

Re: Beware of netCDF STRINGs

Kate (and Angelolemos as well), You should be more specific here: rather than advise to post it on AGRIF forum rather than here, or trying to motivate AGRIF people to be more flexible (good luck with this, huh...) The error GET_TCLIMA - unable to open climatology NetCDF file: ../SCRATCH/roms_clm.nc ...
by shchepet
Tue Nov 24, 2015 6:37 pm
Forum: ROMS Discussion
Topic: cubed sphere in ROMS?
Replies: 4
Views: 1209

Re: cubed sphere in ROMS?

Can the existing nesting mechanism in ROMS handle such corners? No, because coordinates become strongly non-orthogonal there, so equation require extra terms which ROMS lacks. ROMS generally follows Arakawa and Lamb, 1977 orthogonal curvilinear coordinate framework and the associated discretization...
by shchepet
Thu Nov 19, 2015 5:54 pm
Forum: ROMS Discussion
Topic: cubed sphere in ROMS?
Replies: 4
Views: 1209

Re: cubed sphere in ROMS?

I understand the feeling of excitement when one is about to embark on a new adventure, but actually, while cubed-sphere was famously used for many years in ECCO model (this is MITgcm global configuration), the most recent version, ECCO v.4, has abandoned this approach in favor of conformal mapping d...
by shchepet
Wed Sep 30, 2015 6:07 pm
Forum: ROMS Problems
Topic: CPU time and MPI issues with nested grids
Replies: 16
Views: 5751

Re: CPU time and MPI issues with nested grids

Tomasz, you must be more specific: Hernan points to the differences in step2d which dated back to long time ago as reflected in a post from 2005, http://www.myroms.org/forum/viewtopic.php?f=19&t=280 still relevant today ( ? ) -- simply put, AGRIF code was updated with respect to this matter, but Rut...
by shchepet
Fri Jul 10, 2015 3:17 am
Forum: ROMS Tools and Techniques
Topic: Generating ROMS land mask from GSHHS Global Coastline Datase
Replies: 2
Views: 3943

Re: Generating ROMS land mask from GSHHS Global Coastline Da

Generally you want to keep only what is mathematically necessary in the file, so not only u_mask, and v_mask should be discarded, but few other items as well. For a spherical grid this is all what you need: netcdf pac16_grid { dimensions: xi_rho = 1330 ; xi_u = 1329 ; eta_rho = 1218 ; eta_v = 1217 ;...
by shchepet
Mon Jul 06, 2015 11:21 pm
Forum: ROMS Discussion
Topic: Initial shape of the surface
Replies: 4
Views: 1394

Re: Initial shape of the surface

Check your numbers: ..... x=(xr(i,j)-x0) ; y=(yr(i,j)-y0) alfa=(x*x+y*y)/200.0_r8 zeta(i,j,1)=EXP(-alfa) .... where 200.0_r8 means 200 square meters, or same as (14 m)^2, meaning that the semi-width of your Gaussian is only 14 meters. However your Xsize=1000.0E+03_r8 Esize=500.0E+03_r8 are 1000 and ...
by shchepet
Mon Jul 06, 2015 5:08 am
Forum: ROMS Discussion
Topic: Initial shape of the surface
Replies: 4
Views: 1394

Re: Initial shape of the surface

An analytical setup for testing baroptropic Flather- or Orlanskii-type boundary conditions from article Mason, et al., 2010: Procedures for offline grid nesting in regional ocean models, Ocean Modeling, vol. 35, pp. 1-15, especially Sec. 2.1.2 and Figure 3 there (expanding ring in free surface field...
by shchepet
Wed Jun 24, 2015 3:39 am
Forum: ROMS Tools and Techniques
Topic: Generating ROMS land mask from GSHHS Global Coastline Datase
Replies: 2
Views: 3943

Generating ROMS land mask from GSHHS Global Coastline Datase

Dear All, A new automatic tool to construct ROMS land mask from GSHHS (Global Self-consistent Hierarchical High-resolution Shorelines) dataset is now available as a compile-once -- use-forever command-line operator. This is the preferred the way and, in fact superior to the more usual practice of ge...
by shchepet
Wed Mar 26, 2014 8:08 pm
Forum: ROMS Bugs
Topic: 2 possible bugs in Shc boundary conditions
Replies: 6
Views: 3671

Re: 2 possible bugs in Shc boundary conditions

OK. Let's just summarize it. I just downloaded the latest version, ROMS 3.7 svn rev. 726, and the relevant piece of code looks like cff=1.0_r8/(0.5_r8*(GRID(ng)%h(Iend ,j)+ & ! <-- A & GRID(ng)%h(Iend+1,j))) cff1=SQRT(g*cff) ! <-- B Cx=dt2d*cff1*0.5_r8*(GRID(ng)%pm(Iend ,j)+ & ! <-- C & GRID(ng)%pm(...
by shchepet
Fri Mar 21, 2014 3:05 am
Forum: ROMS Bugs
Topic: 2 possible bugs in Shc boundary conditions
Replies: 6
Views: 3671

Re: 2 possible bugs in Shc boundary conditions

The original code in u2dbc_im.F is as follows, and it is correct: cff=0.5*(h(iend,j)+h(iend+1,j)) hx=sqrt(g/cff) cx=dtfast*cff*hx*0.5*(pm(iend,j)+pm(iend+1,j)) zx=(0.5+cx)*zeta(iend,j,kstp)+(0.5-cx)*zeta(iend+1,j,kstp) if (cx > 0.292893218813452) then zx=zx + ( zeta(iend,j,knew) +cx*zeta(iend+1,j,ks...
by shchepet
Mon Jan 27, 2014 1:43 am
Forum: ROMS Discussion
Topic: Problem with large size initial files
Replies: 10
Views: 2458

Re: Problem with large size initial files

The following message forrtl: severe (408): fort: (2): Subscript #1 of the array GRIDNUMBER has value 1 which is greater than the upper bound of 0 says it all, you either have a simple code bug, or an uninitialized index (most likely also due to code bug, or, alternatively, due to allocation/address...
by shchepet
Thu Dec 05, 2013 3:52 am
Forum: ROMS Bugs
Topic: There's always a 1st time...1st time...1st time...1st time
Replies: 1
Views: 1355

Re: There's always a 1st time...1st time...1st time...1st ti

There are in principle two way to handle this situation, which should not be mixed together. 1. The first one is as you suggested: switch first_time should have exactly the same status as any global summation variable, which mans that it should be shared, that is not declared as threadprivate, and s...
by shchepet
Thu Nov 21, 2013 5:33 pm
Forum: ROMS Adjoint
Topic: netcdf closing error
Replies: 2
Views: 2429

Re: netcdf closing error

Pay attention to ncid = 0 in

NETCDF_CLOSE - error during closing of file, ncid = 0

most likely you are trying to close a file which was not opened
at the first place.
by shchepet
Thu Oct 03, 2013 2:21 am
Forum: ROMS Installation
Topic: problem of installing netcdf-fortran
Replies: 3
Views: 3662

Re: problem of installing netcdf-fortran

libifport.so.5 is a part of Intel compiler installation and it belongs to the standard library directory within ifort installation tree, say, go to the directory where your intel compuler(s) are installed and type find . -name libifport.so.5 -print The coutcome should be something like ./Compiler/1...
by shchepet
Thu Sep 19, 2013 4:17 am
Forum: ROMS Tools and Techniques
Topic: matlab script for gebco ?
Replies: 1
Views: 1980

Re: matlab script for gebco ?

If this would help, there is a fortran code designed to work as a command-line operator
to transfer topography from Gebco (as well as other datasets like SRTM30) to ROMS
grid file. http://www.atmos.ucla.edu/~alex/ROMS/tools.tar
by shchepet
Sat Jun 29, 2013 1:01 am
Forum: ROMS Ice
Topic: tuning ice model ...
Replies: 9
Views: 7172

Re: tuning ice model ...

Your choice Vtransform=2 ; Vstretching=4 in combination with such small value for critical depth TCLINE=5.0d0 would yield an very tight packing of sigma levels toward the surface: suppose you have 40 layers total. Then your uppermost grid box will be only 12.5cm thick, and so do other grid boxes jus...
by shchepet
Thu Jun 06, 2013 5:00 am
Forum: ROMS Installation
Topic: Plotting Package: "cairo" undefined reference
Replies: 3
Views: 3497

Re: Plotting Package: "cairo" undefined reference

The cause of your problem is the line in your makefile LIBS := -L$(NCARG_ROOT)/lib -lncarg -lncarg_gks -lncarg_c which is way outdated because this is how NCAR Graphics 4.4 used to be. Basically the above line does not specify all the libraries NCAR graphics relies upon. What version of NGAR Graphic...
by shchepet
Mon Jun 03, 2013 5:31 pm
Forum: ROMS Discussion
Topic: Doubts about the new OBC combination (Che + Shc)
Replies: 5
Views: 2485

Re: Doubts about the new OBC combination (Che + Shc)

You have to do both: look for artificial reflections, and look for maximum allowed time step (actually to make sure that your boundary algorithm does not impose additional restrictions on dtfast relative to what is the natural limit of the time stepping algorithm), as well as check how the reflectio...
by shchepet
Sun Jun 02, 2013 5:29 am
Forum: ROMS Discussion
Topic: Doubts about the new OBC combination (Che + Shc)
Replies: 5
Views: 2485

Re: Doubts about the new OBC combination (Che + Shc)

The problem with these values is that they are way all too small. Normally, when you are running the code in 3D configuration you should not waste your CPU time on the barotropic mode, so the time step dt and mode splitting ratio should be set accordingly from the respective stability limits. While ...
by shchepet
Sat Jun 01, 2013 7:06 pm
Forum: ROMS Discussion
Topic: Doubts about the new OBC combination (Che + Shc)
Replies: 5
Views: 2485

Re: Doubts about the new OBC combination (Che + Shc)

What is your barotropic gravity wave Courant number in these experiments?

Cg_max = ?
by shchepet
Sat Apr 06, 2013 10:11 pm
Forum: ROMS Problems
Topic: Slow performance on SGI with Opterons
Replies: 6
Views: 3294

Re: Slow performance on SGI with Opterons

Besides everything else highlighted by David, your code spends ~55% of time computing barotropic mode. This is way too much. What is your barotropic gravity wave Courant number, Cg_max=max_{i,j}{ dtfast*sqrt[g*h*(1/dx^2+1/dy^2)]} computed by "metrics.F" and reported as "Maximum barotropic Courant Nu...
by shchepet
Mon Dec 10, 2012 1:28 am
Forum: ROMS Bugs
Topic: a possible bug in fennel biological model
Replies: 3
Views: 2337

Re: a possible bug in fennel biological model

There is no bug here as far as I can see. cff1=gmax*Zoo*Phyt/(kp + Phyt*Phyt) cff3=1/(1+cff1) Phyt(new)=Phyt(old)*cff3 Zoo(new)=Zoo(old)+Phyt(new)*cff1 The whole biological time stepping procedure is dated back into 1998 -- about 14 years ago, see http://www.atmos.ucla.edu/~alex/biology , and the ma...
by shchepet
Sat Sep 01, 2012 2:15 am
Forum: ROMS Problems
Topic: how to determine the optimal tiling
Replies: 2
Views: 1662

Re: how to determine the optimal tiling

Grid size 960*768*30 ... tiling 8*32 ... Cpu: four 64-core AMD Opteron ...mvapich2 1.6, Let me guess: Based on what said above, you are running code in MPI mode using 4 hardware nodes each of whom has 4 CPU sockets, and each CPU is a 16-core Opteron. The hardware nodes are interconnected by Infinib...
by shchepet
Sat Jul 07, 2012 2:07 am
Forum: ROMS Discussion
Topic: A simple question about the t3dmix2_s
Replies: 2
Views: 905

Re: A simple question about the t3dmix2_s

Because at this moment t(i,j,k,nnew,itrc) has the meaning of tracer concentration multiplied by Hz(i,j,k) . Since Hz changes because of free surface evolution, tracers are multiplied by Hz at time step "n" before the barotropic time stepping begins for the current 3D time step, then all fluxes are a...
by shchepet
Sat Apr 28, 2012 3:57 am
Forum: ROMS Bugs
Topic: Incorrect nesting of OpenMP directives: FLOAT_VWALK
Replies: 11
Views: 5323

Re: Incorrect nesting of OpenMP directives: FLOAT_VWALK

Watching this conversation between Mark and Hernan, I realized today that it has been approximately 10 years (no kidding!) since I eliminated all C$OMP PARALLEL DO directives from my code. Back then I was motivated by making the code more explicit (and, frankly by beauty as well), but it appears tha...
by shchepet
Tue Mar 06, 2012 8:28 pm
Forum: ROMS Bugs
Topic: The perils of floating-point time-step arithmetic
Replies: 14
Views: 5517

Re: The perils of floating-point time-step arithmetic

Hernan, by adding a small increment dt to time as follows from your code, ... time(ng)=time(ng)+dt(ng) ... (see close to the end) you are back to the original problem: you accumulate roundoff errors in counting time. What you should do instead is to change the above into something of the sort of ......
by shchepet
Sat Feb 11, 2012 3:10 am
Forum: ROMS Documentation
Topic: Shchepetkin 2010
Replies: 2
Views: 2983

Re: Shchepetkin 2010

This version of stretched terrain-following coordinate formally appears first as Eqs. (2.2)-(2.4) in Shchepetkin, A. F. and J. C. McWilliams, 2009: Correction and Commentary for "Ocean Forecasting in Terrain-Following Coordinates: Formulation and Skill Assessment of the Regional Ocean Modeling Syste...
by shchepet
Fri Jan 27, 2012 8:51 pm
Forum: ROMS Bugs
Topic: The perils of floating-point time-step arithmetic
Replies: 14
Views: 5517

Re: The perils of floating-point time-step arithmetic

As of right now, ROMS expects to read the 3D-mode time step "dt" and mode-splitting ratio "ndtfast" from the input script. A potentially attractive alternative would be to specify "dt" and fast-time step "dtfast", and let the model figure out the mode-splitting ratio within the code (along with a sl...
by shchepet
Thu Jan 26, 2012 12:26 am
Forum: ROMS Bugs
Topic: The perils of floating-point time-step arithmetic
Replies: 14
Views: 5517

Re: The perils of floating-point time-step arithmetic

Hernan and Mark, Are you serious about your idea of counting REAL-type numbers, like it is proposed in the latest fix, my_StepTime=0.0_r8 MaxDT=MAXVAL(dt) STEP_LOOP : DO WHILE (my_StepTime.le.(RunInterval+0.5_r8*MaxDT)) my_StepTime=my_StepTime+MaxDT ... END DO STEP_LOOP ? It is a bad idea in any cas...
by shchepet
Wed Jan 25, 2012 1:18 am
Forum: ROMS Bugs
Topic: is LMD constancy preserving
Replies: 9
Views: 3557

Re: is LMD constancy preserving

I had a chance to examine the relevant KPP routines from a recent ROMS AGRIF, files lmd_skpp.F and step3d_t.F of the following SVN versions ! $Id: lmd_skpp.F 726 2011-08-12 13:48:44Z gcambon $ ! $Id: step3d_t.F 697 2011-04-11 12:35:17Z gcambon $ and found the following: ghats(i,j,k), the same for al...
by shchepet
Tue Jan 24, 2012 11:39 pm
Forum: ROMS Bugs
Topic: is LMD constancy preserving
Replies: 9
Views: 3557

Re: is LMD constancy preserving

Patrick, First, the purpose of the above post was to fix what is obviously wrong -- mainly the discontinuity of nonlocal flux at the base of PBL -- not to advance the physical accuracy of parameterization (that would be a separate and a much longer subject), and yes, KPP is full of p -traps to fall ...
by shchepet
Sun Jan 22, 2012 4:12 am
Forum: ROMS Bugs
Topic: is LMD constancy preserving
Replies: 9
Views: 3557

Re: is LMD constancy preserving

Just to reply to the original question of John Warner. Yes, KPP is constancy preserving in its NONLOCAL transport part, as well as everywhere else, if you do it right. Unfortunately, the original 1994 LMD paper buries this aspect into a rather sloppy notation making it very hard to understand what i...
by shchepet
Mon Jan 16, 2012 1:44 am
Forum: ROMS Installation
Topic: problem while compiling inlet_test case
Replies: 3
Views: 2851

Re: problem while compiling inlet_test case

First, go to include subdirectory of your MPI directory three and inspect content of file "mpif.h" to make sure that parameter MPI_PROC_NULL is present there [for MPICH versions 1.0.5p4 through 1.4.1p1 (current) it is just an integer parameter with value -1]. Secondly, this directory should also con...
by shchepet
Tue Dec 13, 2011 3:06 am
Forum: ROMS Discussion
Topic: river salinity overshoot
Replies: 11
Views: 4460

Re: river salinity overshoot

I vaguely remembered some flags such as MPDATA (or TS_MPDATA) could alleviate such problems This sounds like a fairly standard answer in ROMS comminity (and, in fact, in general oceanographic comminity), however, it should be noted that contrary to a very popular belief MPDATA is not a monotonicity...
by shchepet
Tue Dec 06, 2011 3:40 am
Forum: ROMS Discussion
Topic: how about nudging sst and ssh in ROMS
Replies: 3
Views: 2114

Re: how about nudging sst and ssh in ROMS

Nudging of Sea Surface Height (SSH) is a very bad idea and should not be used under any circumstances. The only way the model naturally accepts external SSH data is through lateral boundary conditions of the so-called Flather type. The main point here is that the dynamical balance between SSH and th...
by shchepet
Wed Nov 09, 2011 1:06 am
Forum: ROMS Documentation
Topic: Pressure gradient documentation conundrum and a request
Replies: 2
Views: 3447

Re: Pressure gradient documentation conundrum and a request

Shchepetkin, 2000 (also cited in Ezer, Arango, Shchepetkin, 2002) refers to http://www.atmos.ucla.edu/~alex/ROMS/pgf1A.ps http://www.atmos.ucla.edu/~alex/ROMS/pgf1B.ps which are odd and even pages of the same document (these files are designed to generate a two-sided printout using one-sided black-a...
by shchepet
Thu Nov 03, 2011 5:14 am
Forum: ROMS Discussion
Topic: what's going on with my zeta field?
Replies: 3
Views: 1044

Re: what's going on with my zeta field?

And is it possible to plot two consecutive time steps to see how
the phase of zeta field changes from one 3D time step to the next?
by shchepet
Tue Oct 25, 2011 3:57 am
Forum: ROMS Discussion
Topic: NONLIN_EOS in upwelling example creates velocities
Replies: 6
Views: 2444

Re: NONLIN_EOS in upwelling example creates velocities

Yes, the problem here is due to the fact that the pressure gradient scheme described in the 2003 paper WAS NEVER FULLY implemented in Rutgers ROMS. That paper introduces the notion of adiabatic differences and harmonic averaging of adiabatic differences as a method to enforce non-oscillatory stratif...
by shchepet
Fri Sep 30, 2011 1:19 am
Forum: ROMS Installation
Topic: netcdf-4.1.3
Replies: 4
Views: 3229

Re: netcdf-4.1.3

With NetCDF 4.1.3 it is quite easy to specify what you want. For example, if you want to use Intel Compiler, then you have to execute the following sequence of commands (literally, just copy-paste and execute them one-by-one): tcsh setenv CC icc setenv CXX icpc setenv FC ifort setenv F77 ifort seten...
by shchepet
Fri Aug 19, 2011 6:27 pm
Forum: ROMS Discussion
Topic: how is it define baroclinic velocity in ROMS?
Replies: 2
Views: 1553

Re: how is it define baroclinic velocity in ROMS?

how is it define baroclinic velocity: for practical purposes it is simply u_bcl(i,j,k)=u(i,j,k,nstp)-ubar(i,j,nstp) v_bcl(i,j,k)=v(i,j,k,nstp)-vbar(i,j,nstp) where u,v_bcl(i,j,k) are baroclinic velocities; u,v(i,j,k,nstp) are ROMS 3D velocities at certain time step as they occur in ROMS output histo...
by shchepet
Wed Jul 20, 2011 7:03 pm
Forum: ROMS Results
Topic: Some questions about using ncview
Replies: 11
Views: 6670

Re: Some questions about using ncview

This would be a very natural behavior of netCDF writing (and, as a matter of fact, any buffered writing to the disk): as long as file is not closed or forcefully synchronized, the data does not land onto the disk, but in the memory of the machine, and consequently, is not accessible by any process o...
by shchepet
Thu Jul 14, 2011 3:46 am
Forum: ROMS Tools and Techniques
Topic: plot package and ncl linking problem
Replies: 7
Views: 3752

Re: plot package and ncl linking problem

...... -L/opt/gfortransoft/s_netcdf4/lib -lnetcdf -L/opt/gfortransoft/s_hdf5/lib -lhdf5_hl -lhdf5 -lz resulted in /home/rpacheco/PLOTROMS/src/crash.f90:1562: undefined reference to `nf_close_' /home/rpacheco/PLOTROMS/src/crash.f90:1563: undefined reference to `nf_close_' /home/rpacheco/PLOTROMS/src...
by shchepet
Sun Jul 10, 2011 5:52 am
Forum: ROMS Tools and Techniques
Topic: plot package and ncl linking problem
Replies: 7
Views: 3752

Re: plot package and ncl linking problem

Pay attention to this: /usr/bin/ld: Warning: size of symbol `mapcm1_' changed from 28 in libUTIL.a(hbackground.o) to 40 in /usr/local/lib/libncarg.a(mapbd.o) /usr/bin/ld: Warning: size of symbol `mapcm2_' changed from 60 in libUTIL.a(cnt_frame.o) to 128 in /usr/local/lib/libncarg.a(mapbd.o) /usr/bin...
by shchepet
Fri Jul 08, 2011 10:26 pm
Forum: ROMS Results
Topic: Some questions about using ncview
Replies: 11
Views: 6670

Re: Some questions about using ncview

For the purpose of Ncview and my post above 2D-, 3D-, and 4D-variables means 2-, 3-, 4-dimensional arrays. The picture you attaching is exactly what is expected: your netCDF file have shown all four netCDF dimensions, namely xi_rho, eta_rho, s_w, and ocean_time for the variable you are trying to see...
by shchepet
Fri Jul 08, 2011 7:03 pm
Forum: ROMS Results
Topic: Some questions about using ncview
Replies: 11
Views: 6670

Re: Some questions about using ncview

what level are they plotted at? maybe in the free surface? No, not necessarily at surface or bottom. Ncview plots exactly what you see on your screen at the time you hit its "Print" button. Using main window of ncview you can navigate through variables present in your file and select axes. Ncview (...
by shchepet
Fri Jul 08, 2011 1:39 am
Forum: ROMS Problems
Topic: fortran runtime error with inp_par.f90
Replies: 4
Views: 2934

Re: fortran runtime error with inp_par.f90

What is the input entry in your "ocean.in" file you are attempting to read when the error occurs? What compiler/version do you use? The problem with the code string=Vstring(is:ie) LenS=LEN_TRIM(string) READ (string(1:LenS),*) Rval(Nval) is that the READ statement is not IOSTAT-protected, so if there...
by shchepet
Wed Jul 06, 2011 9:46 pm
Forum: ROMS Discussion
Topic: Computing Advective CFL in diag.F
Replies: 1
Views: 1205

Computing Advective CFL in diag.F

Hernan, and all whoever may find it useful, Some time ago I found that Computation of Courant number for the purpose of diagnostics in done by averaging velocities toward the tracer point (see around line 220 of diag.F), my_Cu=0.5_r8*ABS(u(i,j,k,nstp)+u(i+1,j,k,nstp))* & & dt(ng)*pm(i,j) my_Cv=0.5_r...
by shchepet
Fri Jul 01, 2011 1:31 am
Forum: ROMS Discussion
Topic: ROMS Large File I/O
Replies: 8
Views: 3150

Re: ROMS Large File I/O

All you have to do is to edit file "ROMS/Modules/mod_netcdf.F" around line 135 and change ! ! Netcdf file creation mode flag. ! #if defined HDF5 integer :: CMODE = nf90_hdf5 ! NetCDF-4/HDF5 format file #else integer :: CMODE = nf90_clobber ! NetCDF classic format file #endif into #if defined HDF5 in...
by shchepet
Thu Jun 30, 2011 5:21 pm
Forum: ROMS Discussion
Topic: ROMS Large File I/O
Replies: 8
Views: 3150

Re: ROMS Large File I/O

So if we do not define HDF5, the NetCDF file creation mode is "classic" and if you look at the unidata website, this option limits file sizes to 2Gb. Hence, if we run ROMS with a PERFECT_RESTART option and write-out the fields in double precision and our application is somewhat big, we can easily e...
by shchepet
Fri Jun 24, 2011 2:36 am
Forum: ROMS Results
Topic: Some questions about using ncview
Replies: 11
Views: 6670

Re: Some questions about using ncview

As far as I can tell, the answer is "no", you cannot save colorbar from ncview. There are few controls about axes, title, etc... including option for none in each category, that is to save plain plot of the field without any extra decorations, axes, etc. This turns out to be the most useful, since s...
by shchepet
Thu Jun 09, 2011 3:03 am
Forum: ROMS Discussion
Topic: ROMS Large File I/O
Replies: 8
Views: 3150

Re: ROMS Large File I/O

This thread continues on viewtopic.php?t=2289
because the last post from Lyon was actually placed twice, here and following the link.
by shchepet
Thu Jun 09, 2011 2:17 am
Forum: ROMS Bugs
Topic: Possible bug in writing out restart file?
Replies: 3
Views: 2925

Re: Possible bug in writing out restart file?

NETCDF_ENDDEF - unable to end definition mode for file: ocean_rst1.nc call from: def_rst.F Now it is something a bit new: it looks like it went through several netCDF calls regarding creation of all dimensions and the variables, and then cannot finish its definition. Do you have any other error mes...
by shchepet
Tue Jun 07, 2011 1:23 am
Forum: ROMS Discussion
Topic: ROMS Large File I/O
Replies: 8
Views: 3150

Re: ROMS Large File I/O

Interestingly enough, in the netCDF web suite pointed by Lyon, among other things it says Should I start using the new 64-bit offset format for all my netCDF files? No, we discourage users from making use of the new format unless they need it for very large files. It may be some time until third-par...
by shchepet
Tue Jun 07, 2011 1:04 am
Forum: ROMS Discussion
Topic: ROMS Large File I/O
Replies: 8
Views: 3150

Re: ROMS Large File I/O

Official netCDF limitations for 64-bit format are practically unlimited, and are described here: http://www.unidata.ucar.edu/software/netcdf/docs/netcdf/NetCDF-64-bit-Offset-Format-Limitations.html i.e., there is still 4GByte limit on a fix-size variable and on record length (aggregate size of a sin...
by shchepet
Tue Mar 22, 2011 10:44 pm
Forum: ROMS Sediment
Topic: diagnosing vertical coordinate from history/grid files
Replies: 8
Views: 6339

Re: diagnosing vertical coordinate from history/grid files

So the distributed code had one version and now has a different, older version? It changed without warning? And now we've built all these tools with the old version? Gotta love it. Kate, I understand your frustration, which is, obviously an outcome of a communication screw up on our side. But to sa...
by shchepet
Tue Mar 08, 2011 6:40 am
Forum: ROMS Sediment
Topic: diagnosing vertical coordinate from history/grid files
Replies: 8
Views: 6339

Re: diagnosing vertical coordinate from history/grid files

I do not object adhering with CF conventions in principle -- there is nothing wrong with them, but I do not see how CF compliance changes this discussion, in sense that that I do not see what it has to do with the way how the information about the specific type of vertical coordinate is stored in a ...
by shchepet
Tue Mar 08, 2011 4:26 am
Forum: ROMS Sediment
Topic: diagnosing vertical coordinate from history/grid files
Replies: 8
Views: 6339

Re: diagnosing vertical coordinate from history/grid files

Jamie Pringle: ...I would prefer to know the "official" answers. File sniffing is easy to do poorly... Actually it looks like you already provided the official answer yourself: it is what you call "file sniffing". The whole story of "new" coordinate emerged from the dissatisfaction with the "old" c...
by shchepet
Tue Feb 22, 2011 2:25 am
Forum: ROMS Problems
Topic: ifort i7 optimization flags issue
Replies: 11
Views: 5410

Re: Intel’s new i7 980x CPU gives disappointing speedup

Now it looks like this time your problem is different than before (when it was compiled without -g -extra_flags ): now the code terminates immediately when attempts it to call set_avg for the very first time, not when finalizing averaging. Based on the fact that word 'hola' never gets printed in log...
by shchepet
Fri Feb 18, 2011 9:59 pm
Forum: ROMS Problems
Topic: ifort i7 optimization flags issue
Replies: 11
Views: 5410

Re: Intel’s new i7 980x CPU gives disappointing speedup

It appears that you are looking at very basic segmentation fault, which may be associated with either ROMS itself, or to the particular netCDF version you are using. set_avg_tile is a long routine. Most likely the breaking point occurs inside ! Convert accumulated sums into time-averages, if appropr...
by shchepet
Mon Feb 07, 2011 5:20 pm
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

HP.txt Compiler flags : -heap-arrays -fp-model strict -openmp -fpp -ip -O3 -msse2 -free Resolution, Grid 01: 0384x0176x030, Parallel Threads: 8, Tiling: 001x016 Compiler flags are not optimal: -heap-arrays ---> -no-heap-arrays , but you have to adjust stacksize limit. Instruction set: -msse2 --> -x...
by shchepet
Sun Feb 06, 2011 10:58 pm
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

Kate, Hernan, Bárður, and whoever cares, Here is a little test program to illustrate finiteness of cache lines -- the fact that cache_line is more than just one number, as well as the pitfalls associated with memory system architecture. It is worth spending 15 minutes playing with it. All the progra...
by shchepet
Sun Feb 06, 2011 8:56 am
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

People are going to more and more processors these days, not faster processors. I've used about 100 at a time, but don't feel I can usefully use 1000. How do we get there? Kate, Do you mean "cores" or "CPUs" or MPI nodes or hardware nodes (motherboards)? We routinely use 256 cores "in house", and t...
by shchepet
Wed Feb 02, 2011 8:41 pm
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

...This use of private storage to minimize memory requirements is fatal and not possible in adjoint computations when the model is run backward in time... Hernan, the horrendous practice in v.1.9 you are referring to is merely to reuse the same scratch memory for two different purposes in a sequenc...
by shchepet
Tue Feb 01, 2011 8:45 pm
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

Do we spend our time staring at the code or waiting for the numbers to come out? Do we want the fastest code that's perhaps more challenging to debug? Kate, or perhaps anybody else: just compare step2d.F from v.3.4 vs. v.1.9 and explain to me and to everybody else why v.3.4 is easier to debug than ...
by shchepet
Sun Jan 30, 2011 9:38 pm
Forum: ROMS Discussion
Topic: a possible improvement of the spline vertical viscosity
Replies: 2
Views: 1145

Re: a possible improvement of the spline vertical viscosity

DC(i,N(ng)-1)=DC(i,N(ng)-1)-CF(i,N(ng)-1)*sustr(i,j)/AK(i,N(ng)-1) Yes, this is potentially a strong move, but it is also dangerous and can backfire. What you are proposing is essentially to set the uppermost grid-box-side derivative of the velocity field to du/dz = sustr/Akv at the free surface. T...
by shchepet
Sat Jan 29, 2011 10:48 pm
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

Regarding the performance comparison between ROMS 1.9 vs. 3.4: what you are observing can be called as Fortran90 penalty . The fact that pre-Fortran 90 codes run faster than their supposedly more advanced successors actively using new Fortran 90 features is nothing new, and it is actually noticed i...
by shchepet
Thu Jan 27, 2011 6:54 am
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

It must nevertheless be mentioned that the run-times reported above are single run run-times and not averages over several runs, which would be the accurate procedure. No, comparing averages is not the proper way to analyze it. Comparing the best against the best would be more representative. This ...
by shchepet
Thu Jan 13, 2011 1:01 am
Forum: ROMS Usage
Topic: Problems with basic model
Replies: 9
Views: 4273

Re: Problems with basic model

....
Maximum barotropic Courant Number = 9.27620490E-01
....
is a bit too much. Increase ndtfast slightly, by 10...20%,
or reduce main time step by the same fraction.

Also make output at every time step to see how the instability
develops.
by shchepet
Wed Jan 12, 2011 7:26 am
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

...So what? The best results for the SOLITON problem are: for ROMS 1.9 23.0 sec using 6 threads, 12x32 tiling vs. for the new code 32.8 sec also 6 threads, 12x32 tiling, Compiler flags: -pc80 -xSSE4.2 -auto -stack_temps -openmp -fpp -ip -O3 -free The above slightly degrades to 35.6 sec with 6 thread...
by shchepet
Mon Jan 10, 2011 5:29 pm
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

/opt/intel/Compiler/11.1/072/lib/intel64/for_main.o: In function `main': /export/users/nbtester/efi2linux_nightly/branch-11_1/20100415_000000/libdev/frtl/src/libfor/for_main.c:(.text+0x38): undefined reference to `MAIN__' This is caused by an attempt to compile code without compiling mpc first. Exp...
by shchepet
Mon Jan 10, 2011 4:59 pm
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

..... analytical.F:446: error: missing binary operator before token "ISWAKE" ..... There is a type on line 446: It says #if defined ANA_FSOBC && !defines ISWAKE should be #if defined ANA_FSOBC && !defined ISWAKE i.e., !define s --> define d On my machines it still compiles and runs correctly -- CPP...
by shchepet
Thu Jan 06, 2011 7:01 pm
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

Answer to 2: Running with FFLAGS := -no-heap-arrays -fp-model precise -openmp -fpp -ip -O3 - axSSE4.2 -free and increased stack size (16384) using same tilling (6 x 32) on : 12 treads the time was: 39 sec. 8 treads the time was: 44 sec. This is a good news: looks like hyperthreading works now. Runn...
by shchepet
Thu Jan 06, 2011 5:58 pm
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

I usually run current version of ROMS using the build.bash script, where netcdf is located by the following lines: export NETCDF_INCDIR=/usr/local/include export NETCDF_LIBDIR=/usr/local/lib Then you should set CPP = /lib/cpp -traditional -D_OPENMP -D__IFC -I/usr/local/include LCDF = -L/usr/local/l...
by shchepet
Tue Jan 04, 2011 10:25 pm
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

...and relative to where I began the simulations are running much faster now. The point is that you know exactly where you have started, but you do not know where are you heading in sense that you do not know when it is good enough to stop. And I feel that it will take several iterations from where...
by shchepet
Mon Nov 15, 2010 4:58 pm
Forum: ROMS Problems
Topic: ROMS not running on 1024 cores for 17532 iterations
Replies: 12
Views: 4522

Re: ROMS not running on 1024 cores for 17532 iterations

So what was the problem?

Was it just because changing the brand of MPI?

If so, what kind of MPI you was using before?

Any specific setting on tunable parameters?
by shchepet
Mon Nov 15, 2010 2:51 am
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

So as long as ROMS runs with default stack size there is no point in changing it right? In Ubuntu/bash I can increase the stack size by setting e.g. ‘ulimit -s 16384’. This time you actually made me do my homework because what you are reporting -- essentially insensitivity of your code performance ...
by shchepet
Sat Nov 13, 2010 7:20 am
Forum: ROMS Problems
Topic: ROMS not running on 1024 cores for 17532 iterations
Replies: 12
Views: 4522

Re: ROMS not running on 1024 cores for 17532 iterations

This sounds more like MPI problem, not directly ROMS problem, although it is triggered by ROMS pushing MPI to the limit. ............ 0 00:00:00 0.000000E+00 1.963001E+04 1.963001E+04 1.659940E+17 DEF_HIS - creating history file: ./output/ocean_his_0001.nc rank 447 in job 1 n104_34487 caused collect...
by shchepet
Sat Nov 13, 2010 4:35 am
Forum: ROMS Problems
Topic: ROMS not running on 1024 cores for 17532 iterations
Replies: 12
Views: 4522

Re: ROMS not running on 1024 cores for 17532 iterations

Did you create directory called "output" within your working/scratch directory where you running your job? ..... STEP Day HH:MM:SS KINETIC_ENRG POTEN_ENRG TOTAL_ENRG NET_VOLUME 0 0 00:00:00 0.000000E+00 1.963001E+04 1.963001E+04 1.659940E+17 DEF_HIS - creating history file: ./output/ocean_his_0001.n...
by shchepet
Tue Nov 09, 2010 3:38 am
Forum: ROMS Installation
Topic: More nodes or higher clock?
Replies: 1
Views: 1191

Re: More nodes or higher clock?

...Dell ... Xeon X5560 - 2.80GHz .... What should I do ... 1) A processor with higher clock? 2) Or increase the number of nodes? Absolutely increase the number of nodes and absolutely stay away from Dell. Your machine is already too expensive and any further increase of clock speed would bring only...
by shchepet
Tue Oct 19, 2010 4:21 am
Forum: ROMS Problems
Topic: help regarding the time step
Replies: 5
Views: 3168

Re: help regarding the time step

First, it is a common experience with such a problems that they may be a bit tricky to start up. How did you create initial conditions? Possibly some kind of Matlab script. Because your kinetic energy starts with zero, it looks like you have created temperature and salinity field for the initial sta...
by shchepet
Sat Oct 09, 2010 7:04 pm
Forum: ROMS Benchmarks
Topic: Serial faster then openmp
Replies: 6
Views: 6258

Re: Serial faster then openmp

Also caught my attention is leommcruz cpu: Intel(R) Xeon(R) CPU E5410 @ 2.33GHz cache size : 6144 KB I'm running a grid with 200x256x30 ...With a 1x8 tile I got the best openmp result ... and leommcruz Regarding the tile option, in my case the best results I got were using 2x2 tile (my grid - 200x25...
by shchepet
Sat Oct 09, 2010 6:14 pm
Forum: ROMS Benchmarks
Topic: Serial faster then openmp
Replies: 6
Views: 6258

Re: Serial faster then openmp

the cpu time should be the sum of all the cpu-times together since a parallel run is never 1/P as fast as a sequential run (in SMPs), the sum of cpu time will be higher. ROMS reports two times: CPU time spent and wall-clock time. This is the intent, Wall clock time is easy to understand. CPU time s...
by shchepet
Thu Sep 30, 2010 11:13 pm
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

So you recover some of the performance loss, but there is still a way to go. QUESTION: where does the 8x81 tiling come from, memory configurations? I made it up just as a first guess. Generally for these kind of problems one wants to chose the size of tile to reach the best possible compromise to sa...
by shchepet
Mon Sep 27, 2010 4:52 pm
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

Grid size: 1398 x 726 x 1 Tilling: is 3 x 2 This is not the best way to run ROMS. Try to set tiling to 8 x 81 (yes, meaning eight by eighty one), rerun it and report your finding back to this forum. We will continue after that... Motherboard: ASUS P6T SE, X58 chipset RAM: DDR3 1333MHz , in triple c...
by shchepet
Sun Sep 26, 2010 3:01 am
Forum: ROMS Problems
Topic: Intel’s new i7 980x CPU gives disappointing speedup
Replies: 48
Views: 24381

Re: Intel’s new i7 980x CPU gives disappointing speedup

I just saw this thread of conversation and to my amusement found what I would characterize as pristine naiveness: did not we been through this before? MPI vs. OpenMP .... influence of I/O, and, ... the usual award winning phrase that "benchmarking ROMS is not trivial..." Contrary to popular belief i...
by shchepet
Thu Jul 08, 2010 4:35 am
Forum: ROMS Installation
Topic: New colormaps for ncview
Replies: 7
Views: 5833

Re: New colormaps for ncview

Lucky you, -- you have system administrator. Well, these are colors ... so they are just a matter of taste. "bright" is general purpose and works for local SST. On a large scale model, that is the whole Pacific "banded" can show more detail, while keeping wide range; "rainbow" is overused here in UC...
by shchepet
Sat Jul 03, 2010 1:08 am
Forum: ROMS Installation
Topic: New colormaps for ncview
Replies: 7
Views: 5833

New colormaps for ncview

This post is for people who like to use "ncview" as a quick tool to visualize netCDF files, such as ROMS output (or of any other origin), and who wants to customize color palettes built-in into by this tool. Ncview is designed by David Pierce, http://meteora.ucsd.edu/~pierce/home_page.html and it so...
by shchepet
Tue Apr 20, 2010 8:38 pm
Forum: ROMS Results
Topic: some suggestion with history file and average file
Replies: 7
Views: 4785

Re: some suggestion with history file and average file

What I want to do is I want to store 2d variables (zeta, ubar,vbar) frequently (say hourly or daily) without 3d variables (temperature, salinity, u, v) on history file. And I want to store 3d vaiable with longer time step(say 10day or month) on average file. This is possible "as is" with the existi...
by shchepet
Wed Mar 31, 2010 4:42 am
Forum: ROMS Problems
Topic: limits on netcdf sizes
Replies: 7
Views: 2637

Re: limits on netcdf sizes

Hernan, According to netCDF manual nf90_64bit_offset is additive to the primary netCDF flag, so it makes sense to use ierr=nf_create(ncname, nf_clobber+nf_64bit_offset, ncid) when you want to create file with nf_clobber status (i.e., overwrite whatever file may already exist) AND with 64bit offset a...
by shchepet
Mon Mar 29, 2010 3:06 am
Forum: ROMS Problems
Topic: limits on netcdf sizes
Replies: 7
Views: 2637

Re: limits on netcdf sizes

No, Mark, it is much simpler that that: you do not have to go to netCDF 4, although you can. Version 3.6.3 -- the latest and final version of 3rd generation of netCDF is perfectly capable to by-pass the 2GByte limitation. All you have to do is to change ierr=nf_create(ncname, nf_clobber, ncid) into ...
by shchepet
Fri Dec 11, 2009 1:44 am
Forum: ROMS Installation
Topic: seamount test case
Replies: 1
Views: 1212

Re: seamount test case

Yes, what you did is correct, and what it was before is wrong, and, in fact, is a parallel bug if the code is compiled/used in Open MP mode. The explanation is as follows: if you examine ./roms-3.1/ROMS/Functionals/ana_grid.h You will find that shared arrays xr(i,j)=... and yr(i,j)=... are assigned ...
by shchepet
Mon Oct 05, 2009 5:23 pm
Forum: ROMS Discussion
Topic: different compiler commands
Replies: 10
Views: 5286

Re: different compiler commands

./oceanO < ROMS/External/ocean_esh.in ./oceanO: error while loading shared libraries: libiomp5.so: cannot open shared object file: No such file or directory This is easy to fix: libiomp5.so belongs to intel compiler, and is located in /opt/intel/Compiler/11.1/056/lib/intel64 for the compiler you us...
by shchepet
Sat Oct 03, 2009 2:49 am
Forum: ROMS Discussion
Topic: different compiler commands
Replies: 10
Views: 5286

Re: different compiler commands

rm -f -r /usr/local/Compilers/make_macros.mk cd /usr/local/Build; -c -heap-arrays -fp-model precise -openmp -fpp -ip -O3 -xW mod_kinds.f90 /bin/sh: -c: command not found from Kate The command not found is your compiler. What happens when you type "which ifort"? No, the error message says "-c: comma...
by shchepet
Thu Oct 01, 2009 5:48 am
Forum: ROMS Discussion
Topic: different compiler commands
Replies: 10
Views: 5286

Re: different compiler commands

What is in your .cshrc file in home directory of the machine you use? A typical practice in supercomputer centers to install a new version of the compiler when it becomes available, but keep the old one, for just in case. This is also what we are doing here at home. As the result, at any given time ...
by shchepet
Thu Oct 01, 2009 3:55 am
Forum: ROMS Discussion
Topic: different compiler commands
Replies: 10
Views: 5286

Re: different compiler commands

Intels keeps modifying both compiler and compiler usage, along with hardware, so compiler flags are generally chanhing all the time. Compiler setting and flags like Compiler command : ifort -fpp2 -openmp -pc80 -axP -align dcommon -auto -stack_temp Compiler flags : -O3 -IPF_fma -ip -xW -free are orig...
by shchepet
Sun Sep 13, 2009 2:28 am
Forum: ROMS Usage
Topic: several doubts for my first application
Replies: 5
Views: 2988

Re: several doubts for my first application

1. is Akv the classic eddy viscosity or is it VISC? No. VISC is horizontal viscosity, sometimes known as "eddy viscosity", basically parameterization of horizontal momentum exchange by interaction of eddies smaller than horizontal grid size. In practice it is chosen most of the time to ensure smoot...
by shchepet
Fri Jun 12, 2009 7:50 am
Forum: ROMS Installation
Topic: Question about the PASCAL compiler
Replies: 5
Views: 1710

Re: Question about the PASCAL compiler

Several years ago I have tested a FORTRAN compiler called PathScale and compared it against the usual suspects -- ifort and pgi. What I found is that when using intel CPUs (Xeon, Pentium 4 at that time) ifort was definitely superior to both alternatives; when using Opteron CPUs (these were older CPU...
by shchepet
Thu Jun 04, 2009 3:55 am
Forum: ROMS Problems
Topic: OMP_NUM_THREADS or NCPUS (2) greater than available cpus (1)
Replies: 1
Views: 1294

Re: OMP_NUM_THREADS or NCPUS (2) greater than available cpus (1)

Most likely your problem is related not to the ROMS code you use, but to the machine and/or its operating system. Open MP programs can be executed in a single processor machine, but, of course, threads go sequentially from one synchronization barrier to the next, resulting in no parallel gain. To te...
by shchepet
Wed May 13, 2009 5:29 pm
Forum: ROMS Installation
Topic: Intel Fortran compiler bug report (this is not bug in ROMS)
Replies: 3
Views: 1894

Re: Intel Fortran compiler bug report (this is not bug in ROMS)

OK, I is kind of serious, since it affects several of our codes. I investigated it a little bit further, and I found that: 1. the failure to return non-zero error status depends on the initial symbol of the string. To see it, compile and execute the following code: program reading_error implicit non...
by shchepet
Wed May 13, 2009 6:00 am
Forum: ROMS Installation
Topic: Intel Fortran compiler bug report (this is not bug in ROMS)
Replies: 3
Views: 1894

Intel Fortran compiler bug report (this is not bug in ROMS)

I encountered the following behavior: internal Fortran reading operation fails to return non-zero status if one attempts to read a real*8 from a string which is does not contain a valid number, and therefore the reading operation must fail. This may have some implication for ROMS, ever more for plot...
by shchepet
Tue Apr 21, 2009 1:55 am
Forum: ROMS Discussion
Topic: What means GRho0*z_w(N) in prsgrd32.h?
Replies: 1
Views: 1110

Re: What means GRho0*z_w(N) in prsgrd32.h?

The difference between the 2003 paper and what you see in the code is explained by the fact that equations in the paper are written assuming that density "rho" is the whole density (meaning that it is about 1030. kg/m^3), while the code is written assuming that density "rho" is density perturbation ...
by shchepet
Thu Oct 02, 2008 12:43 am
Forum: ROMS Discussion
Topic: sign convention for radiation
Replies: 3
Views: 2127

Re: sign convention for radiation

It depends upon which code are you using. But it easy to track it down in all three cases. Let's Check it out. Rutgers (say. v. 3.1): file pre_step3d.F: array "swdk" is assigned its value at/near line 345, and it is a positive-definite field. Then it is used at about line 784, an now observe the evo...
by shchepet
Tue Sep 30, 2008 4:10 am
Forum: ROMS Discussion
Topic: sign convention for radiation
Replies: 3
Views: 2127

Re: sign convention for radiation

There is a bit of logical inconsistency within ROMS convention, but as the result, it makes it more in line with oceanographic tradition, and somewhat with common sense. The rules are: --- Positive direction of vertical axis Z is upward. --- Model INTERNAL fluxes are positive if they are pointing UP...
by shchepet
Wed Jul 30, 2008 9:48 pm
Forum: ROMS Discussion
Topic: roms.in
Replies: 17
Views: 5182

Re: roms.in

Then you should use Makedefs.generic as Makedefs, or make your own, depending on what type of computer, operating system, and FORTRAN/C compilers you have. I usually supply about 10...15 Makedefs.XXXX files, which are for different machines and advise people how to create their own: basically use a ...
by shchepet
Wed Jul 23, 2008 9:15 pm
Forum: ROMS Discussion
Topic: roms.in
Replies: 17
Views: 5182

Re: roms.in

The "ncrename" I was was referring to belongs to a collection of several basic "tools" designed to manipulate netCDF files (look at target/macro tools/TOOLS in your Makefile for AGRIF ROMS; in order to use them, you must compile them first, hence type "make tools" command; this creates several execu...
by shchepet
Tue Jul 22, 2008 6:48 pm
Forum: ROMS Discussion
Topic: roms.in
Replies: 17
Views: 5182

Re: roms.in

NRREC in keyword-block "initial" specifies record number within the file from which you want to start simulation, say initial: NRREC filename 2 rst.0000.nc means that you have have file "rst.0000.nc" which contains several records, and and you want to use record 2 as the initial condition. NOTE: Dep...
by shchepet
Sun Jul 20, 2008 6:49 am
Forum: ROMS Discussion
Topic: roms.in
Replies: 17
Views: 5182

Re: roms.in

F.Daryabor, Based on the format of your roms.in file, and your working habits (e.g. subdirectory named ROMS_FILES) you are using AGRIF ROMS. This code has capability to arrange your output into sequence of netCDF files, rather than single file with unlimited dimension. This way you can avoid letting...
by shchepet
Wed Aug 22, 2007 3:42 am
Forum: ROMS Discussion
Topic: reasonable value for maximum Haney number?
Replies: 2
Views: 2542

Beckmann-Haidvogel "rx0" number is relevant only because it controls Haney number "rx1" (under all other conditions -- number of vertical levels and stretching -- other kept the same, the two are proportional to each other), and also because you know Haney number only after you setup your vertical g...
by shchepet
Thu Aug 16, 2007 1:24 am
Forum: ROMS Discussion
Topic: Bulk fluxes, surface-relative winds and gustiness
Replies: 12
Views: 6174

coare algorithm

But what about Ekman spiral? If you solve the problem analytically, then you find that water velocity vector always starts at 45 degrees to the wind stress applied. That applies to both classical Ekman problem as well as turbulent. Then, once you start subtracting something like 0.5*(u(i,j,N)+u(i+1,...
by shchepet
Tue Jun 26, 2007 11:03 pm
Forum: ROMS Discussion
Topic: Will new sigma formulation give problems?
Replies: 3
Views: 3320

identification standard for vertical coordinates

It reminds me that we, as a community, should come up with an identification standard for different types of vertical coordinates in order for pre- and post-processing software to recognize it correctly and automatically. I personally no longer use the original S-coordinate for quite a while, more t...
by shchepet
Thu Jun 14, 2007 8:11 pm
Forum: ROMS Problems
Topic: barotropic wave in the channel (no forcing, no dissipation)
Replies: 9
Views: 4032

It should not dissipate, if that number is 0.47. However, you specified the whole length of your channel as "wavelenght_of_interest". I suspect that the actual wave is shorter than that, so it may be not 0.47, but is more. As of right now, your signal travels 7.5km per time step, and it takes about ...
by shchepet
Thu Jun 14, 2007 5:30 pm
Forum: ROMS Problems
Topic: barotropic wave in the channel (no forcing, no dissipation)
Replies: 9
Views: 4032

What is your time step "dt" (for 3D mode) and mod splitting ratio "ndtfast", and maximum barotropic Courant number "Cu_max" as it is reported by the model standard output? Also try to estimate wtat is the ratio of 2*pi * dt * wave_phase_speed / wave_length_of_interest ? where pi=3.141596..., wave_ph...
by shchepet
Tue May 29, 2007 2:55 am
Forum: ROMS Documentation
Topic: Numerical Issues
Replies: 7
Views: 7435

The difference between "finite differences" and "finite volume" is saddle, but significant. The main thing is interpretation of the gridded data: "finite-volume" assumes that u(i,j,k) is AVERAGE of field "u" over control volume dV(i,j,k), while finite difference assumes that it is instantaneous valu...
by shchepet
Fri May 25, 2007 4:32 pm
Forum: ROMS Discussion
Topic: ROMS 3.0 - VAR_RHO_2D
Replies: 2
Views: 1365

The rationale here is that some CPP-switches are project-dependent and are to be defined for a specific physical configuration according to its needs. They are usually set by cppdefs.h (or what ever small configurational include files in roms-3.0) . But there is another group of CPP-switches which s...
by shchepet
Tue May 08, 2007 7:22 pm
Forum: ROMS Documentation
Topic: Numerical Issues
Replies: 7
Views: 7435

There is no emphasis for description of the particular main 3D time stepping procedure used in ROMS v. 1.8....2.2 in the Shchepetkin McWilliams,2005 ROMS paper because this algorithm was always considered as a provisional variant to be replaced with a more refined one. The main 3D procedure of v. 1....
by shchepet
Thu May 03, 2007 12:47 am
Forum: ROMS Benchmarks
Topic: Benchmarks
Replies: 31
Views: 23135

Steve, I did not see your message until recently. Regarding my post about establishing 1CPU reference point is to evaluate the performance of "internal code", which is consistently overlooked. Not only in ROMS discussion on this board, but in a wider community as well: people tend to be happy with "...
by shchepet
Fri Apr 27, 2007 5:23 pm
Forum: ROMS Problems
Topic: 2D momentum boundary conditions missing in running log
Replies: 3
Views: 1624

There is a permanent solution to this problem

There is a permanent solution to this problem practiced in UCLA and Agrif codes for the last 7+ years: create a mechanism for automatic tracking of the status of each CPP switch in "cppdefs.h" by automatically generating an analog of Rutgers "checkdefs.F" (known as "check_switches1.F" in UCLA and Ag...
by shchepet
Sat Mar 31, 2007 7:35 pm
Forum: ROMS Installation
Topic: a problem in compiling ROMS
Replies: 15
Views: 9165

The remarks like "LOOP WAS VECTORIZED" are actually a good sign. It means that compiler is able to optimize the code in some situation. Ideally every innermost loop should be vectorized. [ in Intel's terminology "vectorized" means that consecutive 8-byte real numbers are loaded in quads, that is fou...
by shchepet
Thu Mar 29, 2007 8:40 pm
Forum: ROMS Installation
Topic: a problem in compiling ROMS
Replies: 15
Views: 9165

At first, I suggest you compile netCDF library and the code using GCC compilers, because now you have to solve double problem: you have code-specific problems and you have Intel specific problems as well (for example, you say that you are not able to install 64-bit version of Intel compiler on you m...
by shchepet
Tue Mar 27, 2007 6:30 pm
Forum: ROMS Installation
Topic: a problem in compiling ROMS
Replies: 15
Views: 9165

First, Intel Core 2 dual core processors is a good choice, by far the best computing power per unit price. However, to utilize this fully, you must use Intel IFC compiler: no substitution. You can download a free non-commercial version of it from Intel's web suite http://www.intel.com/cd/software/pr...
by shchepet
Mon Mar 26, 2007 4:51 pm
Forum: ROMS Installation
Topic: a problem in compiling ROMS
Replies: 15
Views: 9165

Yes, it is better to fix the problem by controlling your environment rather that hardcoding parth inside FORTRAN code, so you are better off by setting -I/directory/of/netcdf/include/lile among you CPP flags, and -L/directory/of/netcdf/library -lnetcdf among your linker flags, but this time it is ac...
by shchepet
Wed Feb 28, 2007 10:52 pm
Forum: ROMS Bugs
Topic: Slipperiness, psi-masking and analytical grid
Replies: 4
Views: 3375

pmask settings have any effect only if viscosity is nonzero. The code may be run with or without explicit viscosity, if the upstream-biased advection is used, because the advection scheme is already dissipative enough on grid scale to avoid numerical issues. If, on the other hand, centered advection...
by shchepet
Wed Feb 28, 2007 7:11 pm
Forum: ROMS Bugs
Topic: Slipperiness, psi-masking and analytical grid
Replies: 4
Views: 3375

Pmask settings for no-slip boundaries

As a side remark here is that setting pmask=2 is acceptable along straight boundaries to account for the fact that tangential velocity is located half-grid interval from the boundary, and therefore pmask(i,j)*(u(i,j,k) - u(i,j-1,k)) accurate evaluates derivarive near the boundary, if one of the poin...
by shchepet
Fri Jan 26, 2007 4:56 pm
Forum: ROMS Installation
Topic: Intel Core 2 Duo processor
Replies: 14
Views: 7725

Reply to Lefevre

We have several Tyan Thunder K8W (S2885) in our lab. Although frequently advertized as "DUAL CORE READY", this board MAY or MAY NOT accept dual-core CPUs, depending on revision number. So before you decide to upgrade CPUs get your flashlight and make sure that you can read revision number 04MOAb in ...
by shchepet
Thu Jan 25, 2007 4:59 pm
Forum: ROMS Installation
Topic: Intel Core 2 Duo processor
Replies: 14
Views: 7725

reply to Rich Signell

I am running both WindowsXP (whatever come with the Laptop made by Dell) and Linux Mandriva 2007 with 2.6.17-8mdv kernel. This kernel is SMP cabable: with the release of 2007 operating system Mandrake (now Mandriva) makes ints "normal" kernels be SMP, thus abolishing the distinction between SMP and ...
by shchepet
Wed Jan 24, 2007 5:11 pm
Forum: ROMS Installation
Topic: Intel Core 2 Duo processor
Replies: 14
Views: 7725

ROMS on Dual Core

MPI is useless in this type of configuration, predominantly because of slow and shared memory bus, see http://www.atmos.ucla.edu/~alex/ROMS/poorman_revisited.pdf On the other hand, OpenMP works remarkably well and I can get perfect scaling, and overall excellent performance: my CoreDuo 1.83GHz lapto...
by shchepet
Fri Nov 03, 2006 9:05 pm
Forum: ROMS Problems
Topic: Creating Boundary Netcdf Files
Replies: 2
Views: 2364

Extracting BRY from climatology

...There is an also easy-to-use, compule once --> use forever FORTRAN code which does generic extraction of perimeter from ROMS climatology file, http://www.atmos.ucla.edu/~alex/ROMS/perim.F Just compile it, name executable "perim" and save it into your ~/bin directory, and then say perim WS climato...
by shchepet
Fri Sep 29, 2006 5:21 pm
Forum: ROMS Bugs
Topic: Potential Energy and Kinteic Energy use different unit?
Replies: 4
Views: 2904

...something else caught my attention. It looks like there is a missing factor of 1/2 in KE computation, since KE = intergal of V^2/2 and not just of V^2. The factor of 0.5 in ke2d computation comes from averaging, 0.5*(u(i+1,j)^2+u(i,j)^2) approximates u^2 and not u^2/2. So, unless ke2d is renormal...
by shchepet
Fri Sep 29, 2006 5:47 am
Forum: ROMS Bugs
Topic: Potential Energy and Kinteic Energy use different unit?
Replies: 4
Views: 2904

There is an error here: multiplier *(rho(i,j,k)+1000.0_r8) should not be present in ke2d calculation. Just change it ke2d(i,j) = ke2d(i,j) + Hz(i,j,k*(0.5_r8*(u(i ,j,k,nstp)*u(i,j,k,nstp)+.... You may also look at diag.F routine from http://www.atmos.ucla.edu/~alex/ROMS/roms.tar to use it for a refe...
by shchepet
Fri Sep 22, 2006 4:24 pm
Forum: ROMS Tools and Techniques
Topic: Grid generation
Replies: 61
Views: 36316

RE: grid generation

Dear Kate, Rich, and all, I am just wondering: sometime ago, back in February 2004 Hernan asked me to revise mex-function interface and fortran code "mexsepeli" in order to enable it to work on Linux platform and being called from Matlab on Linux. Which I succeeded to do. I knew that it was needed f...
by shchepet
Thu May 04, 2006 7:53 pm
Forum: ROMS Information
Topic: compressibility
Replies: 3
Views: 2449

Re: compressibility and UCLA ROMS

Regarding which code to use: the short answer is use a version which is the most suitable for your particular needs. This is because there are many peripheral developments and submodels driving my applications for which you (and most people except those directly involved) probably do not care about...
by shchepet
Mon Apr 10, 2006 6:44 am
Forum: ROMS Bugs
Topic: ROMS KINETIC_ENRG is half volume-average KE
Replies: 3
Views: 3392

Actually what is proposed by Hernan is not consistent with Lilly discretization on a C-grid, even thought it may be viewed as approximatrely correct. Hernan's procedure implies that velocity components are averaged from their U-,V-points to RHO-points first, and then squered there. This is a WRONG w...
by shchepet
Mon Apr 03, 2006 6:42 pm
Forum: ROMS Information
Topic: compressibility
Replies: 3
Views: 2449

RE: compressibility switch

...as far as I know, the compressibility switch has never been implemented in Rutgers codes, but is now standard in UCLA codes (SPLIT_EOS is #defined all the time). ...and yes, it leads to additional pressure gradient errors, if EOS does not allow you to distinguish between in-situ and adiabatic dif...
by shchepet
Mon Mar 20, 2006 7:40 pm
Forum: ROMS Discussion
Topic: Default Boundary Conditons?
Replies: 7
Views: 3590

RE: default boundary conditions...

This reply is not a to be understood as statement of policy, but rather explanation of de-facto settled practices. If no boundary conditions are specified, then it means that they are CLOSED everywhere. It means: (1) no normal flow; (2) Neumann (zero-gradient extrapolation rule) for T,S; and (3) eit...
by shchepet
Mon Feb 06, 2006 7:16 pm
Forum: ROMS Information
Topic: Large Files on Linux Systems
Replies: 3
Views: 2855

netCDF files larger that 2GBytes

At first, I consider it a bad habit, because it can be avoided by arranging your output into sequence of files, rather than single big file. Secondly, it restricts portability: you must have an operating system which has Large File Support and you can no longer open it from a 32-bit Matlab, and any ...
by shchepet
Mon Jan 23, 2006 7:08 pm
Forum: ROMS Information
Topic: ROMS on Linux Fedora Core 4
Replies: 4
Views: 3177

What exactly is the problem?

We routinely run this code on FC4 as well as on other flavors of Linux. Furthermore, from user's point of view in makes no difference, whether it it FC4 or Redhat 9, or Enterprise Linux or Mandrale 9.0, 9.1, 9.2, 10.0. 10.1, 10.2/200LE or 2006. All you have to have is: Intel Fortran compiler compati...
by shchepet
Sun Dec 18, 2005 6:50 pm
Forum: ROMS Discussion
Topic: Will new sigma formulation give problems?
Replies: 3
Views: 3320

RE: Will new sigma formulation give problems?

No, changes of this kind will not cause any conflict. All ROMS codes are written in such a way that any physical code interacts only with arrays z_r and z_w and makes no assumption about where these arrays are coming from. In fact, the only places in the code which are aware of the S-coordinate are ...
by shchepet
Sun Dec 18, 2005 7:18 am
Forum: ROMS Bugs
Topic: 2D time stepping and 2D/3D coupling
Replies: 2
Views: 2811

RE: 2D time stepping and 2D/3D coupling

The second aspect of this problem --- interference between computation of 3D--> baroclinic mode forcing term and the restart of barotropic mode --- is a more serious issue because all ROMS codes (UCLA, Rutgers, Agrif) are affected by this issue. The problem comes from the fact that the full 3D press...
by shchepet
Thu Dec 15, 2005 10:46 pm
Forum: ROMS Bugs
Topic: 2D time stepping and 2D/3D coupling
Replies: 2
Views: 2811

RE: 2D time stepping and 2D/3D coupling

This observation is generally correct: the timestepping algorithm of barotropic modes of both Agrif and Rutgers code (all versions of both) cannot be accurately mapped into Eqs. (2.27)---(2.30) of the time stepping paper because r.h.s. terms saved from previous time step contain barotropic pressure ...
by shchepet
Mon Dec 12, 2005 7:10 pm
Forum: ROMS Installation
Topic: ifort 9.0 with Red Hat Linux EM64T
Replies: 11
Views: 7834

ifort + EM64T

I forgot to mention: because on my machine(s) I always have multiple compilers and multiple operating systems, I always place netCDF library into the "lib" directory of the compiler which was used to compile it. This way, I just have to specify LCDF = -lnetcdf without path to it. The path is actuall...
by shchepet
Mon Dec 12, 2005 6:50 pm
Forum: ROMS Installation
Topic: ifort 9.0 with Red Hat Linux EM64T
Replies: 11
Views: 7834

Ifort + EM64T

I start my reply with nganju's question about light speed-up (~1-2%) when hyperthreading is turned off. Yes, this is consistent with my own experience and you should always turn hyperthreading OFF in BIOS of your dual-Xeon machine. I observed improvement by as much as 7...10%. In the case of single ...
by shchepet
Mon Nov 07, 2005 6:39 pm
Forum: ROMS Installation
Topic: ROMS/TOMS 2.1 array size limitation problem
Replies: 3
Views: 3470

Dear Mark, and everybody, The problem, as already pointed out, is related with stack size limitation and may be fixed in many cases if one can increase or even unlimit stacksize. This, however, is not as innocent as it might sound. In older days (ROMS 1.9 and earlier) scratch arrays were pre-allocat...
by shchepet
Thu Mar 17, 2005 8:06 pm
Forum: ROMS Bugs
Topic: Time-averaging of barotropic fields and Power Law Filter
Replies: 5
Views: 5089

Dear All, First remark is that this set_weight modification is not a bug fix, but it would better fall into category of optimization of code usage. The purpose of filter is to remove fast frequences of the barotropic motions to prevent their aliasing and instability of the model. The downside of it ...
by shchepet
Wed Mar 16, 2005 1:34 am
Forum: ROMS Bugs
Topic: Time-averaging of barotropic fields and Power Law Filter
Replies: 5
Views: 5089

Time-averaging of barotropic fields and Power Law Filter

It is known that the power function weights for time filtering of the vertically integrated fields ( POWER_LAW CPP option) result in unstable code when the splitting ratio ( ndtfast ) becomes too small. For a natural setting of ndtfast=60 to ndtfast=70 (most of the realistic basin-scale problems) wo...
by shchepet
Tue Feb 15, 2005 12:59 am
Forum: ROMS Bugs
Topic: Nasty bug in the computation of ROMS grid metrics
Replies: 5
Views: 4630

Dear All, I was well aware of this feature of SPEM/SCRUM/ROMS codes for years (at least 5 years) and do not consider this feature as a bug. Neither I consider the latest fix as an urgent measure to be done immediately, and I do not see any reason for panic or statements like I cannot believe that we...
by shchepet
Tue Feb 01, 2005 7:01 pm
Forum: ROMS Discussion
Topic: Applying Atm. Pressure as a body force
Replies: 2
Views: 2479

Atmospheric pressure forcing can be easily included into the pressure gradient routine without messing with body-force-type algorithm. As the matter of fact, any pressure gradient force calculation algorithm involves (explicitly or implicitly) vertical integration of density field from surface to th...
by shchepet
Mon Nov 15, 2004 9:01 pm
Forum: ROMS Benchmarks
Topic: Benchmarks
Replies: 31
Views: 23135

I glanced the whole thread of conversation and found it quite disapointing, in sense that there is virtually no attempt to make a meaningful interpretation of the results. Because of split-explicit time stepping in ROMS code (all of them), most MPI-related latencies occur in 2D mode, where many smal...
by shchepet
Wed Oct 27, 2004 1:38 am
Forum: ROMS Information
Topic: ROMS 2.1 successfully built with g95
Replies: 4
Views: 3441

I found it successful and easy to install too (I am using Mandrake Linux 9.2 and 10.0). However performance is significantly lower that that of Intel IFC compiler. For a test problem I am getting 45 seconds run time while the same test, but using Intel compiler takes only 28 seconds and 36, if PGF c...
by shchepet
Tue Oct 26, 2004 10:52 pm
Forum: ROMS Usage
Topic: Modified LMD mixing
Replies: 2
Views: 3065

As you probably know, I made some revision of KPP codes in ROMS last summer (2003) with the view to (1) update it first to the state of NCAR model of Bill Large of 2003 as much as I can; and (2) move on with some new ideas about handling of Ekman Boundary Layers and other things, like Monin-Obukhow ...
by shchepet
Fri Jan 09, 2004 9:38 pm
Forum: ROMS Information
Topic: The "ROMS" paper?
Replies: 1
Views: 2614

Dear All, The main difference is that Rutgers ROMS (all versions 1.x...2.0/TOMS) use Adams-Bashforth 3 time step for 3D momentum equation (inherited from SCRUM 3.0 code) and LF-TR predictor-corrector (PC) algorithm for tracers. The barotropic mode uses LF-AM3 PC algorithm with some forward-backward ...
by shchepet
Thu Nov 06, 2003 12:00 am
Forum: ROMS Discussion
Topic: ROMS list
Replies: 2
Views: 2157

ROMS list

Hernan, and All, I think the idea to abandon the ROMS e-mail list in favor of bulletin board is not a good one: the discussion actually died out. I understand that this was done because of hacker attacks who sent viruses, but in reality we just yield to hackers. Frankly, these viruses affect only Wi...