Support to fix "error 5" when compiling WW3

[Cesar-IIUNAM]

Hello everyone! best regards.
Please, I need your support to compile the model. I have tried several ways but I have not been able to compile the model on my desktop computer.

I have tried the following:

wget https://github.com/NOAA-EMC/WW3/archive/refs/tags/6.07.tar.1.gz
tar -zxf 6.07.1.tar.gz
cp comp.Gnu comp
cp link.Gnu link
cp switch_Ifremer2 switch
./w3_setup ../
./w3_make

When I do ./w3_make I get the following error:
(base) ctorresm@pcctorres:/media/ctorresm/Datos/CROCO/WW3-6.07.1/model/bin$ ./w3_make

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

Exporting WWATCH3_ENV=/media/ctorresm/Datos/CROCO/WW3-6.07.1/model/bin/wwatch3.env
Main directory : /media/ctorresm/Datos/CROCO/WW3-6.07.1/model
Scratch directory : /media/ctorresm/Datos/CROCO/WW3-6.07.1/model/tmp
Save source codes : yes
Save listings : yes

[INFO] list of the programs selected : ww3_grid ww3_strt ww3_bound ww3_outf ww3_outp ww3_trck ww3_grib ww3_gint gx_outf gx_outp ww3_uprstr ww3_gspl ww3_prep ww3_shel ww3_prnc ww3_ounf ww3_ounp ww3_bounc ww3_trnc ww3_prtide ww3_multi ww3_sbs1 libww3 ww3_systrk

Processing ww3_grid

ad3 : processing constants
2 errors found, see /media/ctorresm/Datos/CROCO/WW3-6.07.1/model/tmp/constants.err
*** compile error ***
file constants.o not found
make: *** [makefile:844: /media/ctorresm/Datos/CROCO/WW3-6.07.1/model/obj/constants.o] Error 5

My variables are defined like this:

export CC=gcc
export FC=gfortran
export F90=gfortran
export F77=gfortran

#Librerias MPI
export CC=mpicc
export FC=mpifort
export F90=mpifort
export F77=mpifort
export MPIF90=mpifort

export WWATCH3_NETCDF=NC4
export NETCDF_CONFIG=/usr/bin/nc-config

#export NETCDF_CONFIG=/usr/bin
#export NETCDF_ROOT=/usr

when I do nc-config --all and nf-config --all, I get:

nf-config --all

This netCDF-Fortran 4.5.4 has been built with the following features:

--cc -> gcc
--cflags -> -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2

--fc -> gfortran
--fflags -> -I/usr/include -I/usr/include
--flibs -> -L/usr/lib/x86_64-linux-gnu -lnetcdff -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lnetcdf -lnetcdf -lm
--has-f90 ->
--has-f03 -> yes

--has-nc2 -> yes
--has-nc4 -> yes

--prefix -> /usr
--includedir-> /usr/include
--version -> netCDF-Fortran 4.5.4

nc-config --all

This netCDF 4.8.1 has been built with the following features:

--cc -> /usr/bin/cc
--cflags -> -I/usr/include -I/usr/include/hdf5/serial
--libs -> -L/usr/lib/x86_64-linux-gnu -L/usr/lib/x86_64-linux-gnu/hdf5/serial -lnetcdf
--static -> -lhdf5_hl -lhdf5 -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm

--has-c++ -> no
--cxx ->

--has-c++4 -> no
--cxx4 ->

--has-fortran -> yes
--fc -> gfortran
--fflags -> -I/usr/include -I/usr/include
--flibs -> -L/usr/lib/x86_64-linux-gnu -lnetcdff -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lnetcdf -lnetcdf -lm
--has-f90 ->
--has-f03 -> yes

--has-dap -> yes
--has-dap2 -> yes
--has-dap4 -> yes
--has-nc2 -> yes
--has-nc4 -> yes
--has-hdf5 -> yes
--has-hdf4 -> no
--has-logging -> no
--has-pnetcdf -> no
--has-szlib -> yes
--has-cdf5 -> yes
--has-parallel4 -> no
--has-parallel -> no
--has-nczarr -> yes

--prefix -> /usr
--includedir -> /usr/include
--libdir -> /usr/lib/x86_64-linux-gnu
--version -> netCDF 4.8.1

At the moment, this is the information I am sharing. If you need anything else, do not hesitate to ask for it. Please, any suggestions would be greatly appreciated.

Best regards,
Cesar.

[mickaelaccensi]

Hi Cesar,
To know the exact error message, you need to open the log file : /media/ctorresm/Datos/CROCO/WW3-6.07.1/model/tmp/constants.err

I really recommend you to move to the latest release of the develop branch of WW3 and to use cmake to build WW3, it is more robust and user friendly.

There is a tutorial about ww3 installation that we do during our annual training course:
https://docs.google.com/document/d/1azvnWsozWDpSo6c7gSFwZVAsqQ5wcpLndsXDXe1W4gY/edit?usp=sharing

[Cesar-IIUNAM]

Hi Mickael,
Thank for your kind reply and for sharing de training material.
I have tried several ways to install and compile the model on my computer. Perhaps with your tutorial I can do it.

As for the contents of the log file, it says the following:

gfortran: error: unrecognized command line option ‘-fallow-invalid-boz’
gfortran: error: unrecognized command line option ‘-fallow-argument-mismatch’; did you mean ‘-Wno-argument-mismatch’?

Best regards,
César.

[mickaelaccensi]

@MatthewMasarik-NOAA , we should be able to install WW3 without MPI library, it was possible before cmake.
We probably need to set an environment variable like :
export MPICC=gcc
@Cesar-IIUNAM can you try this also ?

[Cesar-IIUNAM]

Hi @mickaelaccensi, in fact I just tried it and I get the same error. Likewise, I installed the openMPI library (I think it shouldn't be necessary since I use a desktop computer), getting the same error.
I honestly don't understand why I'm having these problems.

[mickaelaccensi]

looking back to your environment variables, you have overwritten the CC and FC variables :

export CC=gcc
export FC=gfortran
export F90=gfortran
export F77=gfortran

#Librerias MPI
export CC=mpicc
export FC=mpifort
export F90=mpifort
export F77=mpifort
export MPIF90=mpifort

Also, do you have the exe /usr/bin/mpicc ?

[Cesar-IIUNAM]

I had already corrected the definition of the variables for CC and FC. Now I define them like this:

export CC=gcc
export FC=gfortran
export F90=gfortran
export F77=gfortran
export MPICC=gcc

About if i have the exe /usr/bin/mpicc, it's not clear to me what I should check, but doing "$ which mpicc", I get the following:
/usr/bin/mpicc
Although, perhaps, it's not what you want me to review. Can you tell me exactly what I should check?

Thank very much for your kind support,
César.

[MatthewMasarik-NOAA]

César,
please try this following call (the only thing to change is the path to the switch file):

cmake -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_C_COMPILER=gcc -DSWITCH=/path/to/switchfile ..    

[mickaelaccensi]

the official installation procedure is described in the readme :
https://github.com/NOAA-EMC/WW3/blob/develop/model/README.md

[CarstenHansen]

Thank you @mickaelaccensi for disclosing this location of the CMake Build information, and for the details (in the Ifremer tutorial) about how to make a local installation of CMake. Now I realized that the WW3 build requires CMake 3.19+ to work, and it actually appears to work smoothly.

[MatthewMasarik-NOAA]

Hi @Cesar-IIUNAM,
I wanted to circle back and see if you had a chance to try this latest cmake call:

cmake -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_C_COMPILER=gcc -DSWITCH=/path/to/switchfile ..    

I think it should resolve the error you displayed at the C compiler check.

[MatthewMasarik-NOAA]

@Cesar-IIUNAM, that's great -- progress. Regarding the .. at the end, yes, those need to be included. You're calling cmake from ../WW3/build/, so the two dot specify the directory location one level up, ../WW3/ as the root of the source to be built. In the first screenshot you are doing it correctly.

So, in that first screenshot you got passed the cmake compiler check, and now this new error is with the switch file. It is telling you that the switch you are using, switch_IINGEN_st4, is not set up to support grib, so I would look into the switches in your file.

[Cesar-IIUNAM]

Hi @MatthewMasarik-NOAA ,
Thanks for your support! I have changed my switch and at least now I don't get errors anymore. After "cmake -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_C_COMPILER=gcc -DSWITCH=/media/ctorresm/Datos/CROCO/WW3/model/bin/switch_IINGEN_st4 .."

I get the following, is it ok?:

Based on the guide (https://github.com/NOAA-EMC/WW3/blob/develop/model/README.md), from the build directory, I did:
"make"
"make install"
Which does not seem to be correct. Then I ran it in one level up, ../WW3/
Well I am not doing something right yet...

Again, thank very much for your support!

César.

[MatthewMasarik-NOAA]

Hi @Cesar-IIUNAM, sure thing. I'm glad you're making progress. The error above looks like in the install stage, it is trying to write to a system location that your user does not have permissions for. You can fix this by adding an additional option to the cmake call:

-DCMAKE_INSTALL_PREFIX=<path/to/install/dir>

use any path that your user can write to.

[Cesar-IIUNAM]

@MatthewMasarik-NOAA, thank you very much, I was able to execute the commands without problems. It seems that the model was installed and compiled.
What caught my attention is that the /model/exe directory was not created with the programs like "ww3_grid", "ww3_strt" and others. Instead I have seen that in the model directory there is a directory with these programs. I guess it is due to this new version of WW3.

I can only say thank for your support and patience!

[MatthewMasarik-NOAA]

@MatthewMasarik-NOAA, thank you very much, I was able to execute the commands without problems. It seems that the model was installed and compiled.

@Cesar-IIUNAM , that's great, and you're welcome!

What caught my attention is that the /model/exe directory was not created with the programs like "ww3_grid", "ww3_strt" and others. Instead I have seen that in the model directory there is a directory with these programs. I guess it is due to this new version of WW3.

That's correct. cmake allows (and encourages) building projects outside of the model source code area. It looks like you used the WW3/ dir as the INSTALL_PREFIX. This is OK, though I tend to specify a sub-directory of WW3/, for instance WW3/install, that will put the build output in during the install step. In this case, you don't need to manually create the 'install' sub-dir, cmake will do that for you.

At any rate that's just a preference, and the important part is you got over the compile hurdle!

[MatthewMasarik-NOAA]

@Cesar-IIUNAM also, if this has been addressed to your satisfaction, please feel free to close the discussion thread. Cheers

[aronroland]

Hi, … u need to run make in the build directory … and u can chose the binaries by saying … e.g. make ww3_shel, u can compile in parallel by using make -j 4 ww3_shel … let us know! Aron Von: Cesar-IIUNAM ***@***.***> Gesendet: Dienstag, 19. September 2023 19:55 An: NOAA-EMC/WW3 ***@***.***> Cc: Subscribed ***@***.***> Betreff: Re: [NOAA-EMC/WW3] Support to fix "error 5" when compiling WW3 (Discussion #1066) Hi @MatthewMasarik-NOAA <https://github.com/MatthewMasarik-NOAA> , Thanks for your support! I have changed my switch and at least now I don't get errors anymore. After "cmake -DCMAKE_Fortran_COMPILER=gfortran -DCMAKE_C_COMPILER=gcc -DSWITCH=/media/ctorresm/Datos/CROCO/WW3/model/bin/switch_IINGEN_st4 .." I get the following, is it ok?: <https://user-images.githubusercontent.com/113042121/269043212-ce09cd19-7441-4529-8f77-48efe45c8ee4.png> Based on the guide (https://github.com/NOAA-EMC/WW3/blob/develop/model/README.md), from the build directory, I did: "make" "make install" Which does not seem to be correct. Then I ran it in one level up, ../WW3/ Well I am not doing something right yet... <https://user-images.githubusercontent.com/113042121/269049670-6ee39aad-985c-4401-b74f-b33987b58cec.png> Again, thank very much for your support! César. — Reply to this email directly, view it on GitHub <#1066 (reply in thread)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB2S43XS4AVPAO4LDSF26ODX3HL7NANCNFSM6AAAAAA4KXYREA> . You are receiving this because you are subscribed to this thread. <https://github.com/notifications/beacon/AB2S43RZDUA4JLPGV2ICYH3X3HL7NA5CNFSM6AAAAAA4KXYRECWGG33NNVSW45C7OR4XAZNRIRUXGY3VONZWS33OINXW23LFNZ2KUY3PNVWWK3TUL5UWJTQANOIHG.gif> Message ID: ***@***.*** ***@***.***> >