WRF 4.4 Build Failure with gcc Ubuntu 11.2.0-19ubuntu1

billcapehart · May 24, 2022

I am having a similar but not identical problem that others are reporting with the more recent Umbutu builds (mine is 22.04 LTS).

Specifics:
* OS: Umbutu 22.04 LTS
* MPICH Version: 4.0 (system native)
* Compilers Version: gcc Ubuntu 11.2.0-19ubuntu1 (system native)
* NetCDF4 Version (installed with above GCC compilers in /usr/local for C [4.8.1] and Fortran [4.5.4] with both static and libraries installed.

I have the configuration.wrf file and compile log (using the dm par option) attached in this post.

Everything seems to be running fine until the final linking in which I get the following error from the link command to create wrf.exe, where this happens... [note also that the in contrast to similar reported problems, I am indeed including the -L and -ls to the libnetcdff and libnetcdf libraries.]. This is the first time an Error shows up in the compile process.

Code:

ranlib  libwrflib.a
time mpif90  -o wrf.exe  -O2 -ftree-vectorize -funroll-loops -w -ffree-form -ffree-line-length-none -fconvert=big-endian -frecord-marker=4 -fallow-argument-mismatch -fallow-invalid-boz    wrf.o ../main/module_wrf_top.o libwrflib.a  /home/wjc/GitHub/SD_Mines_WRF_REALTIME/WRF4/WRF/external/fftpack/fftpack5/libfftpack.a /home/wjc/GitHub/SD_Mines_WRF_REALTIME/WRF4/WRF/external/io_grib1/libio_grib1.a /home/wjc/GitHub/SD_Mines_WRF_REALTIME/WRF4/WRF/external/io_grib_share/libio_grib_share.a /home/wjc/GitHub/SD_Mines_WRF_REALTIME/WRF4/WRF/external/io_int/libwrfio_int.a -L/home/wjc/GitHub/SD_Mines_WRF_REALTIME/WRF4/WRF/external/esmf_time_f90 -lesmf_time /home/wjc/GitHub/SD_Mines_WRF_REALTIME/WRF4/WRF/external/RSL_LITE/librsl_lite.a /home/wjc/GitHub/SD_Mines_WRF_REALTIME/WRF4/WRF/frame/module_internal_header_util.o /home/wjc/GitHub/SD_Mines_WRF_REALTIME/WRF4/WRF/frame/pack_utils.o -L/home/wjc/GitHub/SD_Mines_WRF_REALTIME/WRF4/WRF/external/io_netcdf -lwrfio_nf -L/usr/local/lib -lnetcdff -lnetcdf       -L/usr/local//lib -lhdf5_hl -lhdf5 -lz  
/usr/bin/ld: /tmp/ccscXtvM.ltrans18.ltrans.o: in function `__module_wps_io_arw_MOD_read_wps':
<artificial>:(.text+0xee00e8): undefined reference to `__module_optional_input_MOD_flag_st000010'
/usr/bin/ld: <artificial>:(.text+0xee00f5): undefined reference to `__module_optional_input_MOD_flag_st010040'
/usr/bin/ld: <artificial>:(.text+0xee0102): undefined reference to `__module_optional_input_MOD_flag_st040100'
/usr/bin/ld: <artificial>:(.text+0xee010f): undefined reference to `__module_optional_input_MOD_flag_st100200'
/usr/bin/ld: <artificial>:(.text+0xee011c): undefined reference to `__module_optional_input_MOD_flag_sm000010'
/usr/bin/ld: <artificial>:(.text+0xee0129): undefined reference to `__module_optional_input_MOD_flag_sm010040'
/usr/bin/ld: <artificial>:(.text+0xee0136): undefined reference to `__module_optional_input_MOD_flag_sm040100'
/usr/bin/ld: <artificial>:(.text+0xee0143): undefined reference to `__module_optional_input_MOD_flag_sm100200'
/usr/bin/ld: <artificial>:(.text+0xee0150): undefined reference to `__module_optional_input_MOD_flag_st010200'
/usr/bin/ld: <artificial>:(.text+0xee015d): undefined reference to `__module_optional_input_MOD_flag_sm010200'
/usr/bin/ld: <artificial>:(.text+0xee0174): undefined reference to `__module_optional_input_MOD_flag_soilt040'
/usr/bin/ld: <artificial>:(.text+0xee019f): undefined reference to `__module_optional_input_MOD_flag_soilm040'
/usr/bin/ld: <artificial>:(.text+0xee01c0): undefined reference to `__module_optional_input_MOD_flag_sst'
/usr/bin/ld: <artificial>:(.text+0xee01cd): undefined reference to `__module_optional_input_MOD_flag_toposoil'
/usr/bin/ld: <artificial>:(.text+0xee01da): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xee01e7): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xee0203): undefined reference to `__module_optional_input_MOD_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xee0226): undefined reference to `__module_optional_input_MOD_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xee263e): undefined reference to `__module_optional_input_MOD_flag_snowh'
/usr/bin/ld: <artificial>:(.text+0xee275b): undefined reference to `__module_optional_input_MOD_flag_snow'
/usr/bin/ld: <artificial>:(.text+0xee2885): undefined reference to `__module_optional_input_MOD_flag_metgrid'
/usr/bin/ld: <artificial>:(.text+0xee29cd): undefined reference to `__module_optional_input_MOD_flag_soilhgt'
/usr/bin/ld: <artificial>:(.text+0xee2b1c): undefined reference to `__module_optional_input_MOD_flag_psfc'
/usr/bin/ld: <artificial>:(.text+0xee2c64): undefined reference to `__module_optional_input_MOD_flag_slp'
/usr/bin/ld: <artificial>:(.text+0xee2de3): undefined reference to `__module_optional_input_MOD_num_sw_levels_input'
/usr/bin/ld: <artificial>:(.text+0xee2f17): undefined reference to `__module_optional_input_MOD_flag_soil_levels'
/usr/bin/ld: <artificial>:(.text+0xee305b): undefined reference to `__module_optional_input_MOD_flag_soil_layers'
/usr/bin/ld: <artificial>:(.text+0xee6888): undefined reference to `__module_optional_input_MOD_flag_psfc'
/usr/bin/ld: <artificial>:(.text+0xeeceb5): undefined reference to `__module_optional_input_MOD_flag_st000010'
/usr/bin/ld: <artificial>:(.text+0xeecec2): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeecece): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeeced7): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeecef7): undefined reference to `__module_optional_input_MOD_char2int2'
/usr/bin/ld: <artificial>:(.text+0xeecefe): undefined reference to `__module_optional_input_MOD_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeecfe8): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeecff2): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed006): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed018): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed027): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed198): undefined reference to `__module_optional_input_MOD_flag_st010040'
/usr/bin/ld: <artificial>:(.text+0xeed1a5): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed1b1): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed1ba): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed1da): undefined reference to `__module_optional_input_MOD_char2int2'
/usr/bin/ld: <artificial>:(.text+0xeed1e1): undefined reference to `__module_optional_input_MOD_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed2cb): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed2d5): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed2e9): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed2fb): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed30a): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed3db): undefined reference to `__module_optional_input_MOD_flag_st040100'
/usr/bin/ld: <artificial>:(.text+0xeed3e8): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed3f4): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed3fd): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed41d): undefined reference to `__module_optional_input_MOD_char2int2'
/usr/bin/ld: <artificial>:(.text+0xeed424): undefined reference to `__module_optional_input_MOD_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed50e): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed518): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed52c): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed53e): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed54d): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed61e): undefined reference to `__module_optional_input_MOD_flag_st100200'
/usr/bin/ld: <artificial>:(.text+0xeed62b): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed637): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed640): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed660): undefined reference to `__module_optional_input_MOD_char2int2'
/usr/bin/ld: <artificial>:(.text+0xeed667): undefined reference to `__module_optional_input_MOD_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed751): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed75b): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed76f): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed781): undefined reference to `__module_optional_input_MOD_num_st_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed790): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeed861): undefined reference to `__module_optional_input_MOD_flag_sm000010'
/usr/bin/ld: <artificial>:(.text+0xeed86e): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed87a): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed883): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed8a3): undefined reference to `__module_optional_input_MOD_char2int2'
/usr/bin/ld: <artificial>:(.text+0xeed8aa): undefined reference to `__module_optional_input_MOD_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed994): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeed99e): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeed9b2): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeed9c4): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeed9d3): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeedaa4): undefined reference to `__module_optional_input_MOD_flag_sm010040'
/usr/bin/ld: <artificial>:(.text+0xeedab1): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeedabd): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeedac6): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeedae6): undefined reference to `__module_optional_input_MOD_char2int2'
/usr/bin/ld: <artificial>:(.text+0xeedaed): undefined reference to `__module_optional_input_MOD_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeedbd7): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeedbe1): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeedbf5): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeedc07): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeedc16): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeedce7): undefined reference to `__module_optional_input_MOD_flag_sm040100'
/usr/bin/ld: <artificial>:(.text+0xeedcf4): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeedd00): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeedd09): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeedd29): undefined reference to `__module_optional_input_MOD_char2int2'
/usr/bin/ld: <artificial>:(.text+0xeedd30): undefined reference to `__module_optional_input_MOD_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeede1a): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeede24): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeede38): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeede4a): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeede59): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeedf2a): undefined reference to `__module_optional_input_MOD_flag_sm100200'
/usr/bin/ld: <artificial>:(.text+0xeedf37): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeedf43): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeedf4c): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeedf6c): undefined reference to `__module_optional_input_MOD_char2int2'
/usr/bin/ld: <artificial>:(.text+0xeedf73): undefined reference to `__module_optional_input_MOD_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeee05d): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeee067): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeee07b): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeee08d): undefined reference to `__module_optional_input_MOD_num_sm_levels_input'
/usr/bin/ld: <artificial>:(.text+0xeee09c): undefined reference to `__module_optional_input_MOD_sm_input'
/usr/bin/ld: <artificial>:(.text+0xeee17d): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeee187): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeee192): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeee19d): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: <artificial>:(.text+0xeee1a8): undefined reference to `__module_optional_input_MOD_st_input'
/usr/bin/ld: /tmp/ccscXtvM.ltrans18.ltrans.o:<artificial>:(.text+0xeee1b3): more undefined references to `__module_optional_input_MOD_st_input' follow
collect2: error: ld returned 1 exit status
Command exited with non-zero status 1[/color]
4531.39user 59.60system 18:31.13elapsed 413%CPU (0avgtext+0avgdata 7266876maxresident)k
2536inputs+839120outputs (36major+14087411minor)pagefaults 0swaps
make[1]: [Makefile:17: em_wrf] Error 1 (ignored)
make[1]: Leaving directory '/home/wjc/GitHub/SD_Mines_WRF_REALTIME/WRF4/WRF/main'
( cd run ; /bin/rm -f wrf.exe ; ln -s ../main/wrf.exe . )

This is a new one for me, any ideas would be most helpful.

Cheers
Bill Capehart
SD Mines.

kwerner · May 26, 2022

Hi Bill,
Can you issue the following command?
ls -l share/module_optional_input.* >& ls.txt
and then send that ls.txt file, along with the module_optional_input.f90 file?

Another question: Does this only happen with WRFV4.4, or with other versions, as well? Thanks!

billcapehart · May 27, 2022

Thanks, Kelly:

I just tried building under the same circumstances with WRF-4.3.3 and I got the same error.

I am attaching 4.3.3's module_optional_input.f90 and the resulting run for ls.txt.

Thanks
Bill Capehart
SD Mines.

bakamotokatas · May 28, 2022

Hello, I had the same problem with Ubuntu 22.04. By using openmpi instead mpich I fix the problem.

Code:

sudo apt install libopenmpi-dev libhdf5-openmpi-dev

Also you can use the following script

https://github.com/bakamotokatas/WRF-Install-Script/releases/tag/WRF4.4_Install

Deleted member 3607 · May 28, 2022

Which version of gfotran and gcc are you using?

I have run into issues with anything greater then gfortran/gcc version 9.

Can you enter these commands

gfortran --version
gcc --version

billcapehart · May 28, 2022

The compilers are in the OP above [and topic title]. I DID try to build it on my Mac (via homebrew) successfully and that runs gcc and gfortran (Homebrew GCC 11.3.0) 11.2.0

Bill

Deleted member 3607 · May 28, 2022

Okay so it looks like you are using gfortran/gcc 11.

Do you have FFLAGS & FCFLAGS defined?

If not try this solution from the WRF-Hydro forum.

FFLAGS = -fallow-argument-mismatch
FCFLAGS = -fallow-argument-mismatch

Another option is to download and use gfortran-9 gcc-9 g++-9 when installing.

WRF 4.4 Build Failure with gcc Ubuntu 11.2.0-19ubuntu1

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