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Ali.Abdolali edited this page Nov 18, 2021 · 57 revisions

Frequently Asked Questions

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

Index

1 - How to cite WAVEWATCH III®
2 - How to debug error messages
3 - How to add a new switch to the makefile
4 - How to install netcdf
5 - How to install Metis/Parmetis
6 - How to compile with PDLIB
7 - For MACOSX with gfortran
8 - How to compile WW3 using NOAA hpc-stack
9 - Executing heavy serial jobs
10 - CFL condition
11 - 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}}

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 add a new switch to makefile?

The main key here is find a switch that would behave similar to yours, and then follow the patterns. The two files you need to update are make_makefile.sh and w3_new.

In model/bin/make_makefile.sh

  • Add your case to the list in section 2.b, then copy a similar situation:
#sort:mach:
#sort:dstress:
      dstress) TY='upto1'
               ID='Diagnostic stress comp'
               TS='FLD'
               OK='FLD0 FLD1 FLD2' ;;

So in the above the case is "dstress". TY can be "one" (that means 1 switch is required), 'upto1' (up to one switch), or 'upto2' (up to two switches can be used). The OK variable lists the possible switch options.

  • Then add your case in the section of code, that for dstress for example is:
      dstress) dstress=$sw ;;
  • Then add the modules/files for your switches (if needed) in the section like below:
  case $dstress in
   FLD0) ds=$NULL
         dsx=$NULL ;;
   FLD1) ds=$NULL
         dsx='w3fld1md' ;;
   FLD2) ds=$NULL
         dsx='w3fld1md w3fld2md' ;;
  esac

If you have a case like an 'upto1' your block of code will look more like:

  is=$NULL
  case $s_is in
   IS1) is='w3sis1md' ;;
   IS2) is='w3sis2md' ;;
  esac
  • In the last step, you defined which files/modules you need to be compiled. So in the first one 'dsx' and in the second one 'is'. You now need to add this variable where needed in section 2c, such as:
    case $prog in
     ww3_grid) IDstring='Grid preprocessor'
               core=
               data='w3wdatmd w3gdatmd w3adatmd w3idatmd w3odatmd'
               prop=
             source="w3triamd $stx $nlx $btx $is"
                 IO='w3iogrmd'
                aux='constants w3servmd w3arrymd w3dispmd w3gsrumd w3timemd' ;;
  • In section 3b, you need to add the file and module file. So first add the module in:
    for mod in W3INITMD W3WAVEMD W3WDASMD W3UPDTMD W3FLDSMD W3CSPCMD \
               W3GDATMD W3WDATMD W3ADATMD W3ODATMD W3IDATMD \
               W3FLD1MD  W3FLD2MD \
               W3IOGRMD W3IOGOMD W3IOPOMD W3IOTRMD W3IORSMD W3IOBCMD \
                        W3IOSFMD W3PARTMD W3BULLMD \
....

and then add in the list, such as:

         'W3FLD1MD'     ) modtest=w3fld1md.o ;;

In model/bin/w3_new

  • Update w3_new with the new switch case. Again, copy a template from the switch before adding to the list any routine that has the new switch.

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):

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

Download the Metis and Parmetis from the link
for Metis
module purge
load compiler and mpi libraries
module load intel impi
setenv CFLAGS -fPIC
make config cc=mpiicc CXX=mpiicc prefix=</path/to/your/parmetis> | & tee config.out-rr
make install | & tee make-install.out-rr
It adds libmetis.a under > /path/to/your/parmetis/lib/libmetis.a
For Parmetis
module purge
module load intel impi
setenv CFLAGS -fPIC
make config cc=mpiicc cxx=mpiicc prefix=/path/to/your/parmetis/ | & tee config.out-rr
make install | & tee make-install.out-rr
It adds libparmetis.a under /path/to/your/parmetis/lib/ libparmetis.a
set the path to metis/parmetis
setenv METIS_PATH /path/to/your/parmetis

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

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.

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).

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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