Problems linking with ww3_grib with Wavewatch III

Submitted by jbarrers on Mon, 11/22/2021 - 13:47
Forums
Build Dependencies

I am trying to compile a program in Wavewatch III with a modified version of the switch NCEP_glwu, in which grib files are used. In the modified version of NCEP_glwu I simply deleted the switches NOPA and LRB4, since they have been deprecated. In any case, I have tried with other switches (e.g., Ifremer1) and I always find the same problem. 

Using the modified NCEP_glwu switch, in which NOPA and LRB4 have been removed, I always get an error message during the compilation procedure when ad3, after processing ww3_grib, tries to link this file (ww3_grib). This is the error:

Processing ww3_grib

---------------------

ad3 : processing ww3_grib

Linking ww3_grib

make: *** [makefile:400: /home/tesalia/WW3/model/exe/ww3_grib] Error 1

I checked the makefile located at WW3/model/src. Line 400 in makefile states:

@$(aPb)/link ww3_grib w3parall wmmdatmd w3triamd w3gdatmd w3wdatmd w3adatmd w3idatmd w3odatmd w3sdb1md w3sbt1md w3src4md w3flx1md w3snl3md w3iogrmd w3iogomd constants w3servmd w3timemd w3arrymd w3dispmd w3gsrumd

I also checked the ad3 file, located at WW3/model/bin and I saw that Error 1 refers to Input errors. Therefore, I checked the ww3_grib file that should be located at WW3/model/exe and it does not exist. In other words, it is not created by my model. I think this may be the source of the problem, but I do not know how to handle it. Below I describe my configuration.

Error files (especially ww3_grib.err) and logs located at WW3/model/tmp are empty. The only file with some content is located at WW3/model/obj_SEQ/link.err, and states:

gfortran: error: big_endian: File or directory not found

gfortran: error: byterecl: File or directory not found

gfortran: error: unrecognized command line option ‘-convert’; did you mean ‘-fconvert=’?

gfortran: error: unrecognized command line option ‘-assume’

gfortran: error: unrecognized command line option ‘-prec-div’

gfortran: error: unrecognized command line option ‘-prec-sqrt’

gfortran: error: unrecognized command line option ‘-ip’; did you mean ‘-p’?

I do not know how to handle this information. Reading on the Internet, I found a solution that suggest changing line 111 in link.tmpl (WW3/model/bin/link.tmpl) from:

opt="$opt -convert big_endian -assume byterecl -prec-div -prec-sqrt -ip"

To:

opt="$opt -fconvert=big-endian -assume byterecl -prec-div -prec-sqrt -ip"

As a result, the first line of the aforementioned error disappeared (i.e., "gfortran error: big_endian (...)). I tried to change the remaining parts of line 111 (i.e., -assume byterecl, -prec-div, -prec-sqrt, -ip), but I do not find the proper synthax to do so.

To Reproduce

Since I have other programs using some libraries required for WW3 (e.g., I have install a WRF model that also uses jasper, zlib and png), I am not using a hpc-stack nor something similar. I have installed almost all libraries by hand. Next, I detail the libraries that were installed in my system before installing WW3:

NetCDF

nf-config --version -> Output: netCDF-Fortran 4.5.2 nf-config --has-nc4-> Output: yes

Jasper -> Jasper 1.900.1
HDF5 -> HDF5 1.10.4
zlib -> 1.2.11
libpng -> 1.6.37
libjpeg -> 8.2.2

 

I installed these other libraries (code is described too):

CMake (Please, see https://github.com/Kitware/CMake/tree/21e60da5bb0715e09f2feba5930ea2c8bc8180af) -> Version 3.22.2021

git clone https://github.com/Kitware/CMake.git

cd CMake

./bootstrap --prefix=/home/tesalia/cmake -- -DCMAKE_USE_OPENSSL=OFF

./bootstrap && make && sudo make install

NCEPLIBS (it includes several libraries. Please, see https://github.com/NOAA-EMC/NCEPLIBS)

git clone https://github.com/NOAA-EMC/NCEPLIBS

mkdir -p build && cd build

cmake –DCMAKE_INSTALL_PREFIX=/usr/lib/x86_64-linux-gnu/nceplibs /home/tesalia/NCEPLIBS

sudo make

WAVEWATCH 3 (I am using my own fork, but the library is exactly the same, saving from some modified switches as indicated above)

sudo git clone https://github.com/Josue9740/WW3

cd WW3

sudo sh model/bin/ww3_from_ftp.sh

 

I declared these environment variables in ~/.bash_profile

export PNG_LIB=/usr/lib/x86_64-linux-gnu/libpng.a

export Z_LIB=/usr/lib/x86_64-linux-gnu/libz.a

export JASPER_LIB=/usr/lib/x86_64-linux-gnu/libjasper.a

export G2_LIB4=/usr/local/g2-3.4.1/lib/libg2_4.a

export W3NCO_LIB4=/usr/local/w3nco-2.4.1/lib/libw3nco_4.a

export BACIO_LIB4=/usr/local/bacio-2.4.1/lib/libbacio_4.a

 

Model compilation

sudo ./model/bin/w3_setup model -c gnu -s NCEP_glwu

cd model/bin sudo ./w3_make ww3_grib

As indicated above, NCEP_glwu is a modified version without the switches NOPA and LRB4. I am using gnu compiler since if I use the same code but replacing -c gnu by -c intel I get the next error:

/home/tesalia/WW3/model/bin/ad3: línea 215: ifort: command not found

*** w3adc error ***

file constants.F90 not found (2)

I do not know why the intel compiler does not work (my system has installed ifort 2021.4.0) or why linking the ww3_grib file always produces a linking error if all the required libraries and the environment variables have been set.

Permalink

Submitted by jbarrers on Tue, 11/23/2021 - 10:21

In order to provide further explanations on my problem, I have tried to run the next example test: 

sudo ./bin/run_test -s MPI -w ../model_examples/work_ww3_ufs1.1 -m grdset_c -f -p mpirun -n 24 -o all ../model ww3_ufs1.1

However, the next error arises:

+--------------------+
|  Grid preprocessor |
+--------------------+


                *****************************
              ***   WAVEWATCH III make      ***
                *****************************

Main directory    : /home/tesalia/WW3/model
Scratch directory : /home/tesalia/WW3/model/tmp
Save source codes : yes
Save listings     : yes
Shared Object     : No

[INFO] list of the programs selected : ww3_grid

Processing ww3_grid
---------------------
ad3 : processing w3gdatmd
ad3 : processing scrip_kindsmod [no w3adc]
mv: cannot stat 'scrip_kindsmod.o': No such file or directory
mv: cannot stat 'w3gdatmd.o': No such file or directory
ad3 : processing scrip_iounitsmod [no w3adc]
ad3 : processing scrip_timers [no w3adc]
ad3 : processing scrip_constants [no w3adc]
ad3 : processing w3odatmd
mv: cannot stat 'scrip_iounitsmod.o': No such file or directory
mv: cannot stat 'scrip_constants.o': No such file or directory
mv: cannot stat 'scrip_timers.o': No such file or directory
mv: cannot stat 'w3odatmd.o': No such file or directory
ad3 : processing w3idatmd
ad3 : processing scrip_errormod [no w3adc]
ad3 : processing w3timemd
ad3 : processing w3dispmd
mv: cannot stat 'scrip_errormod.o': No such file or directory
mv: cannot stat 'w3idatmd.o': No such file or directory
mv: cannot stat 'w3timemd.o': No such file or directory
ad3 : processing w3nmlgridmd
mv: cannot stat 'w3dispmd.o': No such file or directory
ad3 : processing scrip_netcdfmod [no w3adc]
ad3 : processing wmmdatmd
ad3 : processing w3flx1md
mv: cannot stat 'scrip_netcdfmod.o': No such file or directory
mv: cannot stat 'w3nmlgridmd.o': No such file or directory
ad3 : processing w3adatmd
ad3 : processing w3src4md
mv: cannot stat 'w3flx1md.o': No such file or directory
mv: cannot stat 'wmmdatmd.o': No such file or directory
ad3 : processing scrip_grids [no w3adc]
mv: cannot stat 'w3src4md.o': No such file or directory
mv: cannot stat 'w3adatmd.o': No such file or directory
mv: cannot stat 'scrip_grids.o': No such file or directory
ad3 : processing w3triamd
ad3 : processing w3snl1md
ad3 : processing w3parall
ad3 : processing scrip_remap_vars [no w3adc]
mv: cannot stat 'w3snl1md.o': No such file or directory
mv: cannot stat 'w3parall.o': No such file or directory
mv: cannot stat 'w3triamd.o': No such file or directory
mv: cannot stat 'scrip_remap_vars.o': No such file or directory
ad3 : processing w3iogrmd
ad3 : processing w3wdatmd
ad3 : processing scrip_remap_write [no w3adc]
ad3 : processing scrip_remap_conservative [no w3adc]
mv: cannot stat 'w3iogrmd.o': No such file or directory
mv: cannot stat 'w3wdatmd.o': No such file or directory
mv: cannot stat 'scrip_remap_conservative.o': No such file or directory
mv: cannot stat 'scrip_remap_write.o': No such file or directory
ad3 : processing scrip_remap_read [no w3adc]
mv: cannot stat 'scrip_remap_read.o': No such file or directory
ad3 : processing scrip_interface
mv: cannot stat 'scrip_interface.o': No such file or directory
ad3 : processing wmscrpmd
mv: cannot stat 'wmscrpmd.o': No such file or directory
ad3 : processing w3gridmd
mv: cannot stat 'w3gridmd.o': No such file or directory
ad3 : processing ww3_grid
mv: cannot stat 'ww3_grid.o': No such file or directory
: no valid option
make: *** [makefile:43: /home/tesalia/WW3/model/exe/ww3_grid] Error 1

ERROR: Error occured during WW3 ww3_grid build
 

There is an error message in some files contained into the path WW3/model/tmp, which states:


/home/tesalia/WW3/model/bin/comp: line 98: -c: command not found

Can anybody help me? Thank you so much.

Permalink

Submitted by Jessica.meixner on Wed, 12/08/2021 - 01:13

I'd recommend two things: 

First: Try cleaning the model using: 

./model/bin/w3_clean -c  

I think your issues with the run_test likely just needs to be cleaned before being run again. 

Second: For your grib issues, likely a variable just needs to be defined.  WW3 expects the following (see https://github.com/NOAA-EMC/WW3/blob/develop/model/bin/link.tmpl#L111) to be defined based on your library locations: 

${G2_LIB4} ${W3NCO_LIB4} ${BACIO_LIB4} ${JASPER_LIB} ${PNG_LIB} ${Z_LIB}" 

I'd recommend using echo $var for each of these variables and make sure that they are defined and point to an existing library.  

 

 

 

Permalink

Submitted by jbarrers on Wed, 12/08/2021 - 12:40

Dear Jessica,

None of this worked. I have declared the environment variables and I did check they exist, among many other checks. In fact, I have added additional environment variables I read about on different forums. I have discovered that my system is also running the WRF model, which was installed some time ago. There seems to be some kind of incompatibility between the libraries. Finally, I handle this problem by constructing the WW3 program into a Docker. It is working perfectly right now. 

Thank you so much for all your kind help and assitance.

Copyright © 2022. All rights reserved.