FAQs page

Frequently Asked Questions

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

Index

General:

• How to cite WAVEWATCH III^®
• CFL condition
• Executing heavy serial jobs

Develop Branch (CMAKE build):

• How to avoid common cmake error with Intel IMPI 2018.1.163?

Main Branch/Public Release (GNU Make build):

• How to debug error messages?
• How to install netcdf
• How to install Metis/Parmetis
• How to install SCOTCH
• How to compile with PDLIB
• For MACOSX with gfortran
• How to compile WW3 using NOAA hpc-stack
• ww3_grib compilation

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 (most likely this is more of a development group FAQ than users group):

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):

• GNU netcdf installer (Download only)
• Intel netcdf installer (Download only)

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=mpiicc               \
            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=mpiicc               \
            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 v7.0.4
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

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

Note that using SCOTCH 7.0.4 is recommended as it has fixes for issues encountered when using large number of MPI tasks and an issue when building with OpenMPI.

Note: PRIu64 error

If compiling scotch leads to the following error

error: expected ‘)’ before ‘PRIu64’

(or similar), the fix is as follows. Edit the file scotch/src/libscotch/common_integer.c by adding the following two lines at the top of the file:

#define __STDC_FORMAT_MACROS
#include <inttypes.h>

save and then recompile.

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

How to compile WW3 using NOAA hpc-stack

Official installations of hpc-stack can be found on NOAA HPC platforms.

hpc-stack uses a hierarchical module structure that starts with a generic hpc metamodule that then reveal specific compilers, MPI builds, and libraries link to github page.

Load stack
Hera
module use /scratch2/NCEPDEV/nwprod/hpc-stack/libs/hpc-stack/modulefiles/stack
orion
module use /apps/contrib/NCEP/libs/hpc-stack/modulefiles/stack
Load Modules
Check the available hpc-modules
module -r spider '.*hpc.*'
Module load hpc/1.1.0
module load hpc-intel hpc-impi netcdf bacio w3nco g2 jasper png zlib
Set environmental variables
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 WWATCH3_NETCDF NC4
setenv NETCDF_CONFIG $NETCDF/bin/nc-config
clone WW3
git clone -b develop https://github.com/NOAA-EMC/WW3.git WW3
cd WW3/model
Set WW3 environmetal variables (model/bin/wwatch3.env)
./bin/w3_setup ./ -c intel
WW3 Compilation
cd bin
cp switch<user_defined> switch
./w3_make or ./w3_automake

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