WRF 4.3.3. Compilation on Ubuntu 21.10

[jozamm]

Dear all,

I am trying to compile WRF 4.3.3 on Ubuntu 21.10 with no success. For compilation I am using the following libraries

netcdf version 4.7.4 (Came with distribution)
gcc/gfortran 11.2 (comes with OS)
jasper lib downloaded from Xenial sources

The directories for netcdf and netcdff are in /usr/lib/x86_64-linux-gnu/

The mpich library is in : /usr/lib/x86_64-linux-gnu/

The HDF5 ibrary is in : /usr/lib/x86_64-linux-gnu/hdf5/mpich

During compilation I am getting the following error when wrf.exe is being compiled which than propagates down the compilation

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/joseph/WRF/external/fftpack/fftpack5/libfftpack.a /home/joseph/WRF/external/io_grib1/libio_grib1.a /home/joseph/WRF/external/io_grib_share/libio_grib_share.a /home/joseph/WRF/external/io_int/libwrfio_int.a -L/home/joseph/WRF/external/esmf_time_f90 -lesmf_time /home/joseph/WRF/external/RSL_LITE/librsl_lite.a /home/joseph/WRF/frame/module_internal_header_util.o /home/joseph/WRF/frame/pack_utils.o -L/home/joseph/WRF/external/io_netcdf -lwrfio_nf -L/usr/lib -lnetcdff -lnetcdf    -L/home/joseph/WRF/external/io_grib2 -lio_grib2 -L/usr/lib/x86_64-linux-gnu -ljasper  -L/usr/lib/x86_64-linux-gnu/hdf5/mpich/lib -lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran -lhdf5 -lm -lz    
/usr/bin/ld: /tmp/cc9PtMZs.ltrans21.ltrans.o: in function `__module_wps_io_arw_MOD_read_wps':
<artificial>:(.text+0x1eae6b0): undefined reference to `__module_optional_input_MOD_flag_st000010'
/usr/bin/ld: <artificial>:(.text+0x1eae6bd): undefined reference to `__module_optional_input_MOD_flag_st010040''

The "undefined reference to" error repeats for different nf_ variables and results in a failure. Here are the details of the NetCDF version

This netCDF 4.7.4 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 -lpthread -lsz -lz -ldl -lm -lcurl

--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
--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 -> no
--has-cdf5 -> yes
--has-parallel4 -> no
--has-parallel -> no

--prefix -> /usr
--includedir -> /usr/include
--libdir -> /usr/lib/x86_64-linux-gnu
--version -> netCDF 4.7.4


I am attaching the compile log, configure.wrf and details on the

 

[kwerner]

Hi,
It doesn't look like you have the netcdf path set. Before configuring you must set the NETCDF environment variable to the path where all netcdf lib, bin, and include directories are. Take a look at this document to use as a template for ensuring that your environment is set up properly.

 

[miroilias]

Hello !

I have similar problem, I specified export NETCDF="/usr"; export NETCDF_classic=1 and dmpar ;

But got missing libraries, looks like from netcdf-fortran, but nc-config says "--has-fortran -> yes --fc -> gfortran"


~~~
wrf_io.f.text+0x1c0f5): undefined reference to `nf_open_'
/usr/bin/ld: wrf_io.f.text+0x1c12c): undefined reference to `nf_inq_varid_'
/usr/bin/ld: wrf_io.f.text+0x1c174): undefined reference to `nf_inq_var_'
/usr/bin/ld: wrf_io.f.text+0x1c5f8): undefined reference to `nf_inq_dimlen_'
/usr/bin/ld: wrf_io.f.text+0x1c630): undefined reference to `nf_inq_dimlen_'
~~~

 

[kwerner]

@mirollias,
Did you follow the steps in the =https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.phpcompiling tutorial document I linked above?

 

[billcapehart]

I am having a similar problem but my system build does indeed touch the NetCDF libraries (installed on /usr/local) before the compile gets to that final link for wrf.exe. ldconfig and the LD_LIBRARY_PATH both touch the compilers and they are hard pointed to the /usr/local area. This only happened to me with the GNU compilers, the Intel HPC one-api compilers were able to compile and run wrf [but only on one node and UPP-for-WRF will not build].

Is this a problem with the GCC 11.2 compiles for Umbut? 21.10 uses 11.2.0-7ubuntu2 and 22.04 LTS uses 11.2.0-19ubuntu1.

Bill Capehart
SD Mines

 

[musaidpp]

I was getting some different error using GCC/Gfortran version 11 and what i could find is that gcc/gfortran version 10 or later has some compatibility issues with netcdf. please try version 9

 

[bakamotokatas]

Use openmpi instead mpich for Ubuntu 21.10 and Ubuntu 22.04. Then you will be able to complete the compilation without any problems.

sudo apt install libopenmpi-dev libhdf5-openmpi-dev

 

[Deleted member 3607]

This will also work.

./configure --prefix=$DIR/MPICH --with-device=ch3 FFLAGS=-fallow-argument-mismatch FCFLAGS=-fallow-argument-mismatch

But the issue is gcc/gfortran 10 or greater.

 

[bakamotokatas]

This will also work.

./configure --prefix=$DIR/MPICH --with-device=ch3 FFLAGS=-fallow-argument-mismatch FCFLAGS=-fallow-argument-mismatch

But the issue is gcc/gfortran 10 or greater.

I'm not saying there is a problem installing mpich. WRF installation fails when trying to install WRF with GCC 10+ and mpich on Ubuntu 21.10+. Currently, the only way to have a successful installation on Ubuntu 21.10+ with GCC 10+ is to use openmpi instead of mpich.

Openmpi is an alternative open source Message Passing Interface program that works the same as mpich. Many distributions like Archlinux use openmpi instead of mpich.

 

[Deleted member 3607]

Update

Using the fflags and fcflags with mpich install. Compiles wrf.