#1 NetCDF Inc file

Hi @pbarriat,

I'm compiling the ensemble Kalman filter code on Zenobe and the Fortran code needs at some point a file called netcdf.inc which should be in the directory of the NetCDF libraries:

From nfw.F90:

...
!                                         length, v)
! 06/11/2009 PS: added nfw_dim_exists(ncid, name)
!                nfw_put_att_real(fname, ncid, varid, attname, type, length, v)
!                nfw_get_att_real(fname, ncid, varid, attname, v)

module nfw_mod
  implicit none
  include 'netcdf.inc'

  character(*), private, parameter :: nfw_version = "0.03"
  integer, private, parameter :: logunit = 6
  character(*), private, parameter :: errprefix = "nfw: error: "
  private quit1, quit2, quit3

contains
...

The file is not there:

fmasson@frontal1 09:17:54 ~/git/EnKF/EnKF-MPI-TOPAZ 11 > ls /projects/acad/ecearth/opt/software/netCDF/4.4.1-foss-2016b/include/
netcdf.h  netcdf_mem.h  netcdf_meta.h

but I know what it should be from previous runs at BSC:

bsc32526@login3:/gpfs/scratch/bsc32/bsc32526> ls /apps/NETCDF/4.3.2/INTEL/IMPI/include/
netcdf4_f03.mod            netcdf4_nf_interfaces.mod  netcdf_fortv2_c_interfaces.mod  netcdf.inc  netcdf_nc_data.mod        netcdf_nf_data.mod        netcdf_par.h
netcdf4_nc_interfaces.mod  netcdf_f03.mod             netcdf.h                        netcdf.mod  netcdf_nc_interfaces.mod  netcdf_nf_interfaces.mod  typesizes.mod

The file is on my home:

ls /home/acad/ucl-elic/fmasson/netcdf.inc

Could you copy it to the lib directory?

Not sure it will fix my compilation error but I can still try.

Thanks,

François

Hi @fmasson,

This file comes with the netCDF-Fortran module.

It seems that BSC merge netCDF and netCDF-Fortran during the install process.

You should load netCDF-Fortran/4.4.4-foss-2016b and you will have:

ls /projects/acad/ecearth/opt/software/netCDF-Fortran/4.4.4-foss-2016b/include/
netcdf4_f03.mod  netcdf4_nc_interfaces.mod  netcdf4_nf_interfaces.mod  netcdf_f03.mod  netcdf_fortv2_c_interfaces.mod  netcdf.inc  netcdf.mod  netcdf_nc_data.mod  netcdf_nc_interfaces.mod  netcdf_nf_data.mod  netcdf_nf_interfaces.mod  typesizes.mod

@fmasson,

On zenobe (frontal3), just do:

module purge
module load netCDF-Fortran/4.4.4-foss-2016b

And:

cd ~/git/EnKF/EnKF-MPI-TOPAZ
make

FYI, make.inc with GNU is:

# Library and include

INC_NETCDFF = -I${EBROOTNETCDFMINFORTRAN}/include
INC_NETCDF = -I${EBROOTNETCDF}/include
LIB_NETCDF = -L${EBROOTNETCDF}/lib64 -lnetcdf
LIB_NETCDFF = -L${EBROOTNETCDFMINFORTRAN}/lib -lnetcdff
INC_LAPACK = -I${EBROOTSCALAPACK}/include
LIB_LAPACK = -L${EBROOTSCALAPACK}/lib -lscalapack
LIB_BLAS = -L${EBROOTOPENBLAS}/lib -lopenblas
INC_BLAS = -I${EBROOTOPENBLAS}/include
INC_FFT = -I${EBROOTFFTW}/include
LIB_FFT = -L${EBROOTFFTW}/lib -lfftw3 -lfftw3_mpi

INCS = $(INC_NETCDF) $(INC_FFT) $(INC_NETCDFF) $(INC_LAPACK) $(INC_BLAS)
LIBS = $(LIB_NETCDF) $(LIB_NETCDFF) $(LIB_FFT) $(LIB_LAPACK) $(LIB_BLAS)

CF90 = mpif90
CPPFLAGS = -D_G95_ -DQMPI
CF77 = $(CF90)
LD = $(CF90)
CPP = cpp -traditional-cpp
CC = mpicc

CPPARCH =
CPPFLAGS +=

SIZEO = -fdefault-real-8
OPTO = -O3
DEBUG_FLAGS = #-g -traceback -W1 -warn unused -warn uncalled -debug extended -debug-parameters -ftrapuv -fpe0

FFLAGS = $(SIZEO) $(OPTO) $(DEBUG_FLAGS) $(INCS)
CFLAGS = -Df2cFortran $(OPTO) $(INCS)
LINKFLAGS = $(SIZEO) $(OPTO) $(DEBUG_FLAGS) $(LIBS)

# language-specific flags
#
F77FLG =
F90FLG =

That's OK with the following bug fix (it's done) in EnKF.F90:

integer, external :: iargc

becomes:

#if defined(_G95_)
  integer, intrinsic :: iargc
#else
  integer, external :: iargc
#endif

Many thanks, much appreciated and very useful.

François

Hi @pbarriat,

I'm trying to recompile this code on zenobe but it looks like the commands above do not work anymore:

fmasson@frontal3 13:34:46 ~/git/EnKF 27 > module purge
fmasson@frontal3 13:34:50 ~/git/EnKF 28 > module load netCDF-Fortran/4.4.4-foss-2016b
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'netCDF-Fortran/4.4.4-foss-2016b'

Still the path to the library exists:

fmasson@frontal3 13:36:04 ~/git/EnKF 30 > ls /projects/acad/ecearth/opt/software/netCDF-Fortran/4.4.4-foss-2016b/include/
netcdf4_f03.mod            netcdf4_nf_interfaces.mod  netcdf_fortv2_c_interfaces.mod  netcdf.mod          netcdf_nc_interfaces.mod  netcdf_nf_interfaces.mod
netcdf4_nc_interfaces.mod  netcdf_f03.mod             netcdf.inc                      netcdf_nc_data.mod  netcdf_nf_data.mod        typesizes.mod

More generally a couple of modules that was I able to load back then, seem not available anymore:

fmasson@frontal3 13:39:21 ~/git/EnKF 36 > module purge
fmasson@frontal3 13:39:23 ~/git/EnKF 37 > module load intel
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'intel'
fmasson@frontal3 13:39:23 ~/git/EnKF 38 > module load impi
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'impi'
fmasson@frontal3 13:39:23 ~/git/EnKF 39 > module load MKL
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'MKL'
fmasson@frontal3 13:39:23 ~/git/EnKF 40 > module load NETCDF/4.4.1.1
ModuleCmd_Load.c(213):ERROR:105: Unable to locate a modulefile for 'NETCDF/4.4.1.1'

Any idea how to fix this? Thanks! François

Hi @fmasson,

Pfff... the modules on Zenobe, such a shame!

I recently did a function in my ~/.bashrc file to by-pass the official modules system.

my_modules()
{
  module() { eval $($LMOD_CMD bash "$@"); }
  export -f module
  MODULESHOME=""
  export MODULESHOME
  LOADEDMODULES=""
  export LOADEDMODULES
   . /projects/acad/ecearth/opt/lmod/lmod/init/bash
  MODULEPATH="/projects/acad/ecearth/opt/modules/all"
  export MODULEPATH
}

Once this function called, module av should show you some modules installed by myself (with easybuild = state of the art!)

Now, if I take a look in ~fmasson/git/EnKF/EnKF-MPI-TOPAZ, I think you just have to do:

module load netCDF-Fortran/4.4.4-foss-2016b
cd ~fmasson/git/EnKF/EnKF-MPI-TOPAZ
make

That's it!

Works, thanks.

François