Daniel Thomas' Blog

Tag: grm

  • Compiling JULES on Ubuntu Intrepid Linux

    I have obtained the source code for JULES which is one of the components that the Met Office uses to forecast the weather. Compiling it was not straightforward and required the modification of several source files.

    The modified files and .patch files can be found here.

    First I will outline the route I took to the most working binary.

    An almost working way

    1) in Makefile:

    1.1) Setting the location of the netcdf libaries (you will probably need to install these)

    JULESDIR=$(PWD)
    CDF_LIB_PATH=/usr/lib/
    CDF_MOD_PATH=/usr/include/

    1.2) and to enable the use of the gfortran compiler

    ifeq ($(COMPILER),g95)
    include $(JULESDIR)/Makefile.comp.g95
    endif
    ifeq ($(COMPILER),gfortran)
    include $(JULESDIR)/Makefile.comp.gfortran
    endif
    ifeq ($(COMPILER),nag)
    include $(JULESDIR)/Makefile.comp.nag
    endif

    rather than

    ifeq ($(COMPILER),g95)
    include $(JULESDIR)/Makefile.comp.g95
    endif
    ifeq ($(COMPILER),nag)
    include $(JULESDIR)/Makefile.comp.nag
    endif

    2) in Makefile.common.mk:

    GRMPATH=$(which grm)

ifneq ($(strip $(GRMPATH)),)
    RM=grm -f
endif

RMPATH=$(which rm)

ifneq ($(strip $(RMPATH)),)
    RM=rm -f
endif

ifndef RM
    $(error No rm equivalent command found)
endif

    rather than

    RM=grm -f

    grm means GNU rm, on a linux system rm is GNU rm, so rm should be used rather than grm the conditionals mean that if the met office run the code on their setup it ‘should work’ and if someone runs it on a normal linux distribution it should still work.

    cp Makefile.comp.g95 Makefile.comp.gfortran

    3) in Makefile.comp.gfortran:

    In order to select the gfortran compiler rather than g95, as gfortran is available for Ubutnu/debian while g95 is not.

    FC=gfortran -fno-underscoring

    rather than:

    FC=g95

    and

    MOD_PUT=-J

    rather than:

    MOD_PUT=-fmod=

    4) Then to compile

    make BUILD=run COMPILER=gfortran CDFDUMMY=true

    #BUILD could also be debug or fast.
    #CDFDUMMY is needed even though you can install netcdf from the repositories – because if you set it false you get:

    /home/daniel/dev/JULES/jules-v2-0/libjules.a(RWERR_MOD.o): In function `__rwerr_mod_MOD_rwerr':
RWERR_MOD.f90:(.text+0xaae): undefined reference to `__netcdf_MOD_nf90_inquire_dimension'
RWERR_MOD.f90:(.text+0xed7): undefined reference to `__netcdf_MOD_nf90_strerror'
/home/daniel/dev/JULES/jules-v2-0/libjules.a(JULES_NETCDF.o): In function `__jules_netcdf_MOD_closecdf':
JULES_NETCDF.f90:(.text+0xd): undefined reference to `__netcdf_MOD_nf90_close'
/home/daniel/dev/JULES/jules-v2-0/libjules.a(JULES_NETCDF.o): In function `__jules_netcdf_MOD_check_nc_dims':
JULES_NETCDF.f90:(.text+0x2e1): undefined reference to `__netcdf_MOD_nf90_inq_dimid'
/home/daniel/dev/JULES/jules-v2-0/libjules.a(JULES_NETCDF.o): In function `__jules_netcdf_MOD_readvar2dreal_ncvector_gswp2':
JULES_NETCDF.f90:(.text+0x566): undefined reference to `__netcdf_MOD_nf90_inq_varid'
JULES_NETCDF.f90:(.text+0x8b1): undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbytereal'
JULES_NETCDF.f90:(.text+0xbb9): undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbytereal'
JULES_NETCDF.f90:(.text+0xeed): undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbytereal'
JULES_NETCDF.f90:(.text+0x1160): undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbytereal'
JULES_NETCDF.f90:(.text+0x1477): undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbytereal'
/home/daniel/dev/JULES/jules-v2-0/libjules.a(JULES_NETCDF.o):JULES_NETCDF.f90:(.text+0x178e): more undefined references to `__netcdf_MOD_nf90_get_var_1d_fourbytereal' follow
/home/daniel/dev/JULES/jules-v2-0/libjules.a(JULES_NETCDF.o): In function `__jules_netcdf_MOD_opencdf':
JULES_NETCDF.f90:(.text+0x1c24): undefined reference to `__netcdf_MOD_nf90_open'
collect2: ld returned 1 exit status
make: *** [jules.exe] Error 1

    Successful compilation should result in:

    gfortran -fno-underscoring -o jules.exe /home/daniel/dev/JULES/jules-v2-0/JULES.o \
	    /home/daniel/dev/JULES/jules-v2-0/UTILS/netcdf_dummy/JULES_NETCDF_DUMMY.o \
	    -L/home/daniel/dev/JULES/jules-v2-0  -L/home/daniel/dev/JULES/jules-v2-0/UTILS/netcdf_dummy  \
	    -J/home/daniel/dev/JULES/jules-v2-0/MODS -I/home/daniel/dev/JULES/jules-v2-0/MODS -I/home/daniel/dev/JULES/jules-v2-0/UTILS/netcdf_dummy  \
	    -ljules

    Alternatively try to use g95 as recommended

    1) Install g95

    From here: http://www.gfd-dennou.org/library/cc-env/g95/index.htm.en#label-5
    g95 is not available in either Ubuntu or Debian repositories – for unknown reasons.

    2) follow steps 1.1 and 2 from the instructions for gfortran.

    3) try to compile

    make BUILD=run COMPILER=g95 CDFDUMMY=true

    If you do this there is no possibility of using netcdf prebuilt binaries according to: http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg04125.html
    This is because they were built for gfortran and so will only work with gfortran.

    unfortunately this results in:

    g95 -o jules.exe /home/daniel/dev/JULES/jules-v2-0/JULES.o \
	    /home/daniel/dev/JULES/jules-v2-0/UTILS/netcdf_dummy/JULES_NETCDF_DUMMY.o \
	    -L/home/daniel/dev/JULES/jules-v2-0  -L/home/daniel/dev/JULES/jules-v2-0/UTILS/netcdf_dummy  \
	    -fmod=/home/daniel/dev/JULES/jules-v2-0/MODS -I/home/daniel/dev/JULES/jules-v2-0/MODS -I/home/daniel/dev/JULES/jules-v2-0/UTILS/netcdf_dummy  \
	    -ljules
/home/daniel/dev/JULES/jules-v2-0/libjules.a(SOILHY7A.o):(.data+0x0): undefined reference to `darcy_'
/home/daniel/dev/JULES/jules-v2-0/libjules.a(SOILHY7A.o):(.data+0x4): undefined reference to `hyd_con__'
make: *** [jules.exe] Error 1

    Running Jules

    To run jules you will need to

    mkdir OUTPUT

    after successfully compiling

    and then to run a test run using one of the shipped examples:

    ./jules.exe < point_loobos_example.jin

    unfortunately doing this I got:

    At line 152 of file SFSNOW7A.f
    Fortran runtime error: Array reference out of bounds for array 'snowcanpft', upper bound of dimension 1 exceeded (6 > 5)

    Also trying:

    ./jules.exe < grid_gswp2_example.jin

    fails because:

    Opening /users/global/rjel/jules/gswp2_files/lsmask_vector.nc
     fileFormat=nc
     ERROR: attempting to use a netCDF procedure, but netCDF library not available.
     This is a 'dummy' procedure.
     To use netCDF, remake model with the 'proper' netCDF library.

    as we compiled with CDFDUMMY=true …

    Conclusion

    It is possible to compile JULES on Ubuntu Linux with a bit of work. However compiling a working version of JULES on Ubuntu Linux may be beyond my current ability (I don’t know any FORTRAN).

    Hopefully this will help someone.

    Thanks as always go to the denizens of #srcf on irc.srcf.ucam.org