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Ali.Abdolali edited this page Apr 17, 2024 · 7 revisions

Frequently Asked Questions

This page is a collection of frequently asked questions from WW3 users and developers.

Index

General:

Develop Branch (CMAKE build):

How to cite WAVEWATCH III®

The WAVEWATCH III® Development Group (WW3DG), 2019: User manual and system documentation of WAVEWATCH III® version 6.07. Tech. Note 333, NOAA/NWS/NCEP/MMAB, College Park, MD, USA, 326 pp. + Appendices.

BibTex Format:

@article{wavewatch6.07, title="{User Manual and System Documentation of WAVEWATCH III version 6.07, The {WAVEWATCH III} Development Group}", author={WW3DG}, journal={Tech. Note 326 pp. + Appendices, NOAA/NWS/NCEP/MMAB}, year={2019}} Please note that "WAVEWATCH III" should be in all capital letters and that the preferred way to shorten WAVEWATCH III is to use WW3.

CFL condition

There are 4 timesteps for WW3 with explicit scheme:
1- Global time step (Should be a multiple of spatial time step).
2- Spatial time step (Should satisfy CFL).
3- Spectral time step (Should be a multiple of spatial time step).
4- Minimum source term time step.

The maximum allowable time step for spatial propagation is given by:

Δt=123766 * Δx * cosd(max(latitude))*f

where Δx is the resolution in degrees,cosd(max(latitude)) is the cosine of the maximum latitude in degrees and f is the first frequency from ww3_grid.inp(nml).

The spatial time step should be chosen as an integer close to this number (no fraction of seconds).

Executing heavy serial jobs

Users might need to allocate a larger memory if a segmentation fault occurs at model definition preparation step (ww3_grid) due to a large grid, preprocessing of field inputs (i.e. ww3_prnc), or postprocessing of model outputs (i.e. ww3_ounf/outf) due to a heavy out_grd.ww3. In this case, it is recommended to use compute nodes instead of login nodes on HPC environments for serial executables.

How to avoid common cmake error with Intel IMPI 2018.1.163?

A common error when using Intel IMPI 2018.1.163 is the following:

b47f:edada740: 683 us(683 us): open_hca: device mlx5_0 not found [0] MPI startup(): dapl fabric is not available and fallback fabric is not enabled

to avoid this error, the workaround is to disable the environment variable I_MPI_DEVICE by doing either :

unsetenv I_MPI_DEVICE export -n I_MPI_DEVICE

How to debug error messages:

A common question is: I got the following error

forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source

ww3_shel 00000000006C1E45 Unknown Unknown Unknown ww3_shel 00000000006BFC07 Unknown Unknown Unknown ww3_shel 0000000000661A64 Unknown Unknown Unknown ww3_shel 0000000000661876 Unknown Unknown Unknown ww3_shel 00000000005F1976 Unknown Unknown Unknown ww3_shel 00000000005F7440 Unknown Unknown Unknown libpthread.so.0 00002AAAABC71850 Unknown Unknown Unknown ww3_shel 00000000004F042D Unknown Unknown Unknown ww3_shel 00000000004E91D3 Unknown Unknown Unknown ww3_shel 00000000004936C3 Unknown Unknown Unknown ww3_shel 0000000000415929 Unknown Unknown Unknown ww3_shel 0000000000404E5E Unknown Unknown Unknown libc.so.6 00002AAAAC117C36 Unknown Unknown Unknown ww3_shel 0000000000404D69 Unknown Unknown Unknown

what do I do?

First, add traceback flags in the comp. (This will either be comp. or in cmplr.env depending on which you are using). Then you should get a line number of the program so that you can then traceback the error to.

Linking error when compiling

Here gx_outp was not compiling and giving the following error:

The error was: ad3 : processing w3triamd ad3 : processing w3iopomd ad3 : processing w3flx2md ad3 : processing wmmdatmd ad3 : processing w3sic3md ad3 : processing gx_outp Linking gx_outp *** error in linking ***

gx_outp.o: In function gxoutp_IP_gxexpo_': gx_outp.F90:(.text+0x390a): undefined reference to w3flx2md_mp_w3flx2_'

If you look in the makefile for the line of what all in linked and is set as a dependency, look at:

$(aPe)/gx_outp : $(aPo)/w3odatmd.o $(aPe)/gx_outp : $(aPo)/wmmdatmd.o $(aPe)/gx_outp : $(aPo)/w3parall.o $(aPe)/gx_outp : $(aPo)/w3triamd.o $(aPe)/gx_outp : $(aPo)/w3flx2md.o $(aPe)/gx_outp : $(aPo)/w3sic3md.o $(aPe)/gx_outp : $(aPo)/w3iogrmd.o $(aPe)/gx_outp : $(aPo)/w3iopomd.o $(aPe)/gx_outp : $(aPo)/gx_outp.o @$(aPb)/link gx_outp w3gdatmd w3wdatmd w3adatmd w3idatmd w3odatmd wmmdatmd w3parall w3triamd w3flx2md w3sic3md w3iogrmd w3iopomd constants w3servmd w3timemd w3arrymd w3dispmd w3gsrumd in the original makefile the w3flx2md was not included, but needed to be there.

To fix this, go into make_makefile and search for w3flx2md you will find:

FLX2) str_st1='OK' ; str_st2='OK' ; str_st3='no' ; str_st6='OK' flx='w3flx2md' flxx=$NULL ;; So you need to add the variable flx into the make_makefile for the appropriate program:

gx_outp) IDstring='GrADS input file generation for point output' core= data="$memcode w3gdatmd w3wdatmd w3adatmd w3idatmd w3odatmd" prop= source="$pdlibcode $pdlibyow $db $bt $setupcode wmmdatmd w3parall w3triamd $ln $flx $stx $nlx $btx $tr $bs $xx $is $ic" IO='w3iogrmd w3iopomd' aux='constants w3servmd w3timemd w3arrymd w3dispmd w3gsrumd' ;;

How to install netcdf

Method 1 (aptitude)

  • prerequisites apt install gcc g++ gfortran build-essential
  • netcdf4 library apt install libhdf5-serial-dev libnetcdff-dev libnetcdf-dev
  • netcdf tool (ncview, nco) apt install netcdf-bin netcdf-doc ncview libudunits2-0 libgsl0-dev nco Method 2 (scripts - recommended - no support available) The following scripts provide guidelines to install netcdf4 on hpc environment properly for use with WAVEWATCH III® with given FORTRAN compilers (Ifremer):

netcdf installer (Download only) Method 3 (scripts - not recommended - no support available) The following scripts provide guidelines to install netcdf4 properly for use with WAVEWATCH III® with given FORTRAN compilers (NCEP):

How to install Metis and Parmetis

Follow these instructions to download the Parmetis-4.3.0 tarball, which includes both Metis and Parmetis. Then build Metis, followed by Parmetis, as shown below

PARMETIS_INSTALL=<path-to-install> # User sets location for where to install

# Dependencies # * cmake # * Fortran90 compiler # * MPI # export CFLAGS=-fPIC

wget https://launchpad.net/ubuntu/+archive/primary/+sourcefiles/parmetis/4.0.3-4/parmetis_4.0.3.orig.tar.gz tar xvfz parmetis_4.0.3.orig.tar.gz cd parmetis-4.0.3

# Build: Metis

cd metis make config cc=mpiicc \ CXX=mpiixx \ prefix=$PARMETIS_INSTALL |& tee metis-make-config.out make VERBOSE=1 |& tee metis-make.out make install

# Build: ParMetis

cd .. make config cc=mpiicc \ CXX=mpiixx \ prefix=$PARMETIS_INSTALL |& tee parmetis-make-config.out make VERBOSE=1 |& tee parmetis-make.out make install

After a successful install the files libmetis.a libparmetis.a, will be located at $PARMETIS_INSTALL/lib. To reference Metis/Parmetis from a bash script use

export METIS_PATH=$PARMETIS_INSTALL

How to install SCOTCH

A recent version GNU is needed for part of the SCOTCH build, even if your Fortran90 compiler is not GNU (ex, Intel). So in this case both compilers need to be available. In the instructions below the user needs to fill in the SCOTCH_PATH variable to your desired path, as well as replace the placeholders in the cmake command <C-compiler>, and <F90-compiler>

SCOTCH_INSTALL=<path-to-install> # User sets location for where to install

# Dependencies: # - cmake # - Fortran90 compiler # - MPI # - GNU #

git clone https://gitlab.inria.fr/scotch/scotch.git cd scotch git checkout v7.0.3 mkdir build && cd build

cmake -DCMAKE_Fortran_COMPILER=<F90-compiler> \ -DCMAKE_C_COMPILER=<C-compiler> \ -DCMAKE_INSTALL_PREFIX=$SCOTCH_INSTALL \ -DCMAKE_BUILD_TYPE=Release .. |& tee cmake.out make VERBOSE=1 |& tee make.out make install

i.e.

module purge module load cmake/3.20.1 module load intel module load impi module load gnu

mkdir build cd build

cmake VERBOSE=1 -DCMAKE_Fortran_COMPILER=ifort -DCMAKE_C_COMPILER=icc -DCMAKE_INSTALL_PREFIX=<path to scotch>/install -DTHREADS=OFF -DCMAKE_BUILD_TYPE=Release .. | & tee cmake.out-rr

make VERBOSE=1 | & tee make.out-rr make install make scotch make ptscotch

SCOTCH has the ability to make use of pthreads which are set to"ON"by default. If this functionality is not desired, the options to turn off threads (-DTHREADS="OFF") and MPI multiple threads (-DMPI_THREAD_MULTIPLE="OFF"), can be added to the SCOTCH cmake build command above.

After a successful install the files libptscotch.a and libscotch.a among others, will be located at $SCOTCH_INSTALL/lib. To reference SCOTCH from a bash script use

export SCOTCH_PATH=$SCOTCH_INSTALL

How to compile WW3 with PDLIB

  1. Compile metis and parmetis libraries following link.
  2. Set the path to METIS_PATH in the environment.
  3. Compile all the required serial executable without PDLIB in the switch: cd WW3/model/bin ./w3_make ww3_grid ww3_prnc ww3_bounc ...
  4. Add PDLIB to the switch and compile ww3_shel and ww3_multi ./w3_make ww3_shel ww3_multi

For MACOSX with gfortran

Compile gfortran brew install gcc brew install gnu-getopt clone WW3 git clone -b develop https://github.com/NOAA-EMC/WW3.git WW3 cd WW3/model Set environmetal variables (model/bin/wwatch3.env) ./bin/w3_setup ./ WW3 Compilation cd bin ln -s comp.Gnu comp ln -s link.Gnu link cp switch<user_defined> switch ./w3_make

ww3_grib compilation

In order to compile ww3_grib, the following modules are required:

netcdf, bacio, w3nco, g2, jasper, png, zlib, hdf5, w3nco

and setenv PNG_LIB $PNG_ROOT/lib64/libpng.a setenv Z_LIB $ZLIB_ROOT/lib/libz.a setenv JASPER_LIB $JASPER_ROOT/lib64/libjasper.a setenv NETCDF_CONFIG $NETCDF/bin/nc-config

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