[Wrf-users] Compiling WRF with NETCDF, PNETCDF and PHDF5
Gianluca Meneghello
gianmail at gmail.com
Mon Nov 30 15:30:01 MST 2015
Hi Tabish,
thanks for your quick reply.
I have a working installation using the tutorial configuration, with mpi
but serial output only (io_form_history 2).
I am interested in building WRF with parallel IO (using parallel NETCDF4 is
possible, or using parallel netcdf and PHDF5 otherwise, i.e.
io_form_history 4 or 11). I understand from the manual that PHDF5 and
PNETCDF are supported, I am not clear about parallel NETCDF4.
I had a look at the NETCDF4 test performed by configure script. The line
make nc4_test > tools/nc4_test.log 2>&1
corresponding to
gcc -o nc4_test.exe nc4_test.c
-I/home/gianlu/software/netcdf-4.3.3.1/netcdf/include
-L/home/gianlu/software/netcdf-4.3.3.1/netcdf/lib -lnetcdf
fails. But if I replace the gcc command including mpi, pnetcdf and hdf5
mpicc -o nc4_test.exe nc4_test.c
-L/home/gianlu/software/netcdf-4.3.3.1/netcdf/lib
-L/home/gianlu/software/parallel-netcdf-1.6.1/pnetcdf/lib
-L/home/gianlu/software/hdf5-1.8.16/phdf5/lib -lnetcdf -lpnetcdf -lhdf5_hl
-lhdf5 -ldl -lm -lz
the test compiles correctly.
Is there any specific instruction for compiling with PHDF5 support and
NETCDF4?
I attach the output of the unmodified ./configure
Thanks for your help
Gianluca
checking for perl5... no
checking for perl... found /usr/bin/perl (perl)
Will use NETCDF in dir: /home/gianlu/software/netcdf-4.3.3.1/netcdf
Will use PNETCDF in dir: /home/gianlu/software/parallel-netcdf-1.6.1/pnetcdf
Will use PHDF5 in dir: /home/gianlu/software/hdf5-1.8.16/phdf5
Will use 'time' to report timing information
$JASPERLIB or $JASPERINC not found in environment, configuring to build
without grib2 I/O...
------------------------------------------------------------------------
Please select from among the following Linux x86_64 options:
1. (serial) 2. (smpar) 3. (dmpar) 4. (dm+sm) PGI (pgf90/gcc)
5. (serial) 6. (smpar) 7. (dmpar) 8. (dm+sm) PGI (pgf90/pgcc):
SGI MPT
9. (serial) 10. (smpar) 11. (dmpar) 12. (dm+sm) PGI (pgf90/gcc): PGI
accelerator
13. (serial) 14. (smpar) 15. (dmpar) 16. (dm+sm) INTEL (ifort/icc)
17. (dm+sm) INTEL (ifort/icc):
Xeon Phi (MIC architecture)
18. (serial) 19. (smpar) 20. (dmpar) 21. (dm+sm) INTEL (ifort/icc):
Xeon (SNB with AVX mods)
22. (serial) 23. (smpar) 24. (dmpar) 25. (dm+sm) INTEL (ifort/icc):
SGI MPT
26. (serial) 27. (smpar) 28. (dmpar) 29. (dm+sm) INTEL (ifort/icc):
IBM POE
30. (serial) 31. (dmpar) PATHSCALE
(pathf90/pathcc)
32. (serial) 33. (smpar) 34. (dmpar) 35. (dm+sm) GNU (gfortran/gcc)
36. (serial) 37. (smpar) 38. (dmpar) 39. (dm+sm) IBM (xlf90_r/cc_r)
40. (serial) 41. (smpar) 42. (dmpar) 43. (dm+sm) PGI (ftn/gcc): Cray
XC CLE
44. (serial) 45. (smpar) 46. (dmpar) 47. (dm+sm) CRAY CCE (ftn/gcc):
Cray XE and XC
48. (serial) 49. (smpar) 50. (dmpar) 51. (dm+sm) INTEL (ftn/icc):
Cray XC
52. (serial) 53. (smpar) 54. (dmpar) 55. (dm+sm) PGI (pgf90/pgcc)
56. (serial) 57. (smpar) 58. (dmpar) 59. (dm+sm) PGI (pgf90/gcc):
-f90=pgf90
60. (serial) 61. (smpar) 62. (dmpar) 63. (dm+sm) PGI (pgf90/pgcc):
-f90=pgf90
Enter selection [1-63] : 34
------------------------------------------------------------------------
Compile for nesting? (1=basic, 2=preset moves, 3=vortex following) [default
1]: 3
Configuration successful!
------------------------------------------------------------------------
testing for MPI_Comm_f2c and MPI_Comm_c2f
MPI_Comm_f2c and MPI_Comm_c2f are supported
testing for fseeko and fseeko64
fseeko64 is supported
------------------------------------------------------------------------
# Settings for Linux x86_64 ppc64le, gfortran compiler with gcc (dmpar)
#
DESCRIPTION = GNU ($SFC/$SCC)
DMPARALLEL = 1
OMPCPP = # -D_OPENMP
OMP = # -fopenmp
OMPCC = # -fopenmp
SFC = gfortran
SCC = gcc
CCOMP = gcc
DM_FC = mpif90 -f90=$(SFC)
DM_CC = mpicc -cc=$(SCC) -DMPI2_SUPPORT
FC = time $(DM_FC)
CC = $(DM_CC) -DFSEEKO64_OK
LD = $(FC)
RWORDSIZE = $(NATIVE_RWORDSIZE)
PROMOTION = #-fdefault-real-8
ARCH_LOCAL = -DNONSTANDARD_SYSTEM_SUBR -DWRF_USE_CLM
$(NETCDF4_IO_OPTS)
CFLAGS_LOCAL = -w -O3 -c
LDFLAGS_LOCAL =
CPLUSPLUSLIB =
ESMF_LDFLAG = $(CPLUSPLUSLIB)
FCOPTIM = -O2 -ftree-vectorize -funroll-loops
FCREDUCEDOPT = $(FCOPTIM)
FCNOOPT = -O0
FCDEBUG = # -g $(FCNOOPT) # -ggdb -fbacktrace -fbounds-check
-ffpe-trap=invalid,zero,overflow
FORMAT_FIXED = -ffixed-form
FORMAT_FREE = -ffree-form -ffree-line-length-none
FCSUFFIX =
BYTESWAPIO = -fconvert=big-endian -frecord-marker=4
FCBASEOPTS_NO_G = -w $(FORMAT_FREE) $(BYTESWAPIO)
FCBASEOPTS = $(FCBASEOPTS_NO_G) $(FCDEBUG)
MODULE_SRCH_FLAG =
TRADFLAG = -traditional $(NETCDF4_IO_OPTS)
CPP = /lib/cpp -P
AR = ar
ARFLAGS = ru
M4 = m4 -G
RANLIB = ranlib
CC_TOOLS = $(SCC)
###########################################################
######################
# POSTAMBLE
FGREP = fgrep -iq
ARCHFLAGS = $(COREDEFS) -DIWORDSIZE=$(IWORDSIZE)
-DDWORDSIZE=$(DWORDSIZE) -DRWORDSIZE=$(RWORDSIZE) -DLWORDSIZE=$(LWORDSIZE) \
$(ARCH_LOCAL) \
$(DA_ARCHFLAGS) \
-DDM_PARALLEL \
\
-DNETCDF \
-DPNETCDF \
\
\
\
\
\
\
\
-DMOVE_NESTS -DVORTEX_CENTER \
-DUSE_ALLOCATABLES \
-DGRIB1 \
-DINTIO \
-DLIMIT_ARGS \
-DCONFIG_BUF_LEN=$(CONFIG_BUF_LEN) \
-DMAX_DOMAINS_F=$(MAX_DOMAINS) \
-DMAX_HISTORY=$(MAX_HISTORY) \
-DNMM_NEST=$(WRF_NMM_NEST)
CFLAGS = $(CFLAGS_LOCAL) -DDM_PARALLEL \
-DMAX_HISTORY=$(MAX_HISTORY)
-DNMM_CORE=$(WRF_NMM_CORE)
FCFLAGS = $(FCOPTIM) $(FCBASEOPTS)
ESMF_LIB_FLAGS =
# ESMF 5 -- these are defined in esmf.mk, included above
ESMF_IO_LIB = -L$(WRF_SRC_ROOT_DIR)/external/esmf_time_f90
-lesmf_time
ESMF_IO_LIB_EXT = -L$(WRF_SRC_ROOT_DIR)/external/esmf_time_f90
-lesmf_time
INCLUDE_MODULES = $(MODULE_SRCH_FLAG) \
$(ESMF_MOD_INC) $(ESMF_LIB_FLAGS) \
-I$(WRF_SRC_ROOT_DIR)/main \
-I$(WRF_SRC_ROOT_DIR)/external/io_netcdf \
-I$(WRF_SRC_ROOT_DIR)/external/io_int \
-I$(WRF_SRC_ROOT_DIR)/frame \
-I$(WRF_SRC_ROOT_DIR)/share \
-I$(WRF_SRC_ROOT_DIR)/phys \
-I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \
-I$(NETCDFPATH)/include \
REGISTRY = Registry
CC_TOOLS_CFLAGS = -DNMM_CORE=$(WRF_NMM_CORE)
LIB_BUNDLED = \
$(WRF_SRC_ROOT_DIR)/external/fftpack/fftpack5/libfftpack.a \
$(WRF_SRC_ROOT_DIR)/external/io_grib1/libio_grib1.a \
$(WRF_SRC_ROOT_DIR)/external/io_grib_share/libio_grib_share.a \
$(WRF_SRC_ROOT_DIR)/external/io_int/libwrfio_int.a \
$(ESMF_IO_LIB) \
$(WRF_SRC_ROOT_DIR)/external/RSL_LITE/librsl_lite.a \
$(WRF_SRC_ROOT_DIR)/frame/module_internal_header_util.o \
$(WRF_SRC_ROOT_DIR)/frame/pack_utils.o
LIB_EXTERNAL = \
-L$(WRF_SRC_ROOT_DIR)/external/io_netcdf -lwrfio_nf
-L/home/gianlu/software/netcdf-4.3.3.1/netcdf/lib -lnetcdff -lnetcdf
-L$(WRF_SRC_ROOT_DIR)/external/io_pnetcdf -lwrfio_pnf
-L/home/gianlu/software/parallel-netcdf-1.6.1/pnetcdf/lib -lpnetcdf
LIB = $(LIB_BUNDLED) $(LIB_EXTERNAL) $(LIB_LOCAL)
$(LIB_WRF_HYDRO) $(NETCDF4_DEP_LIB)
LDFLAGS = $(OMP) $(FCFLAGS) $(LDFLAGS_LOCAL)
ENVCOMPDEFS =
WRF_CHEM = 0
CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG)
NETCDFPATH = /home/gianlu/software/netcdf-4.3.3.1/netcdf
PNETCDFPATH = /home/gianlu/software/parallel-netcdf-1.6.1/pnetcdf
bundled: io_only
external: io_only $(WRF_SRC_ROOT_DIR)/external/RSL_LITE/librsl_lite.a
gen_comms_rsllite module_dm_rsllite $(ESMF_TARGET)
io_only: esmf_time wrfio_nf wrfio_pnf \
wrf_ioapi_includes wrfio_grib_share wrfio_grib1 wrfio_int fftpack
######################
------------------------------------------------------------------------
Settings listed above are written to configure.wrf.
If you wish to change settings, please edit that file.
If you wish to change the default options, edit the file:
arch/configure_new.defaults
Testing for NetCDF, C and Fortran compiler
This installation of NetCDF is 64-bit
C compiler is 64-bit
Fortran compiler is 64-bit
It will build in 64-bit
************************** W A R N I N G
************************************
There are some Fortran 2003 features in WRF that your compiler does not
recognize
The IEEE signaling call has been removed. That may not be enough.
*****************************************************************************
/home/gianlu/software/netcdf-4.3.3.1/netcdf
************************** W A R N I N G
************************************
NETCDF4 IO features are enabled, but this installation of NetCDF
/home/gianlu/software/netcdf-4.3.3.1/netcdf
sounds like DO NOT support these IO features.
Please make sure NETCDF version is 4.1.3 or later and was built with
--enable-netcdf4
OR unset NETCDF4 variable
bash/ksh : unset NETCDF4
csh : unsetenv NETCDF4
Then re-run this configure script
!!! configure.wrf WAS REMOVED !!!
*****************************************************************************
On Mon, Nov 30, 2015 at 12:00 PM, Tabish Ansari <tabishumaransari at gmail.com>
wrote:
> Hi
>
> Could you do EXACTLY as mentioned in the tutorial below and then see if
> you have more success:
> http://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php#STEP1
>
> bests,
>
> Tabish
>
> Tabish U Ansari
> PhD student, Lancaster Environment Center
> Lancaster Univeristy
> Bailrigg, Lancaster,
> LA1 4YW, United Kingdom
>
> On 30 November 2015 at 17:32, Gianluca Meneghello <gianmail at gmail.com>
> wrote:
>
>> Hi,
>>
>> I am having some difficulties in compiling WRF using NETCDF, PNETCDF as
>> well as PHDF5 (and using PHDF5 for NETCDF). I am using MVAPICH2 as the MPI
>> implementation.
>>
>> I copy in the following the configures commands for all libraries, as
>> well as the configure for WRF. The WRF configure fails by saying that the
>> NETCDF installation does not support NETCDF4 features, despite the fact
>> that I am using the --enable-netcdf-4 flag when compiling netcdf. All
>> libraries are working correctly according to their make check command
>>
>> Please do not hesitate to ask if you need more information. Thanks in
>> advance for any suggestion,
>>
>> Gianluca
>>
>> -------
>>
>> The configure step for the libraries are (executed in order, each one
>> followed by make, make check, make install)
>>
>> -- HDF5
>> CC=mpicc FC=mpif90 ./configure --enable-parallel --prefix=${H5DIR}
>>
>> -- PNETCDF
>> MPICC=mpicc MPICXX=mpic++ MPIF77=mpif77 MPIF90=mpif90 ./configure
>> --prefix=${PNDIR}
>>
>> -- NETCDF-C
>> CC=mpicc CPPFLAGS="-I${H5DIR}/include -I${PNDIR}/include"
>> LDFLAGS="-L${H5DIR}/lib -L${PNDIR}/lib" ./configure --disable-shared
>> --enable-pnetcdf --enable-parallel-tests --prefix=${NCDIR}
>> *--enable-netcdf-4*
>>
>> -- NETCDF-FORTRAN
>> CC=mpicc FC=mpif90 CPPFLAGS="-I${NCDIR}/include -I${H5DIR}/include"
>> LD_LIBRARY_PATH=${H5DIR}/lib:${NCDIR}/lib:${LD_LIBRARY_PATH}
>> LDFLAGS="-L${H5DIR}/lib -L${NCDIR}/lib -lnetcdf" ./configure
>> --disable-shared --prefix=$NFDIR
>>
>> The configure step for WRF is
>> export NETCDF4=1
>> export NETCDF=${NCDIR}
>> export PNETCDF=${PNDIR}
>> export PHDF5=${H5DIR}
>> export WRFIO_NCD_LARGE_FILE_SUPPORT=1
>> ./configure
>>
>> but the configure step fails saying that the NETCDF installation does not
>> support netcdf4, despite the *--enable--netcdf-4* flag in the
>> compilation of NETCDF-C
>> ************************** W A R N I N G ****************************
>> NETCDF4 IO features are enabled, but this installation of NetCDF
>> /home/gianlu/software/netcdf-4.3.3.1/netcdf
>> sounds like DO NOT support these IO features.
>>
>> Please make sure NETCDF version is 4.1.3 or later and was built with
>> --enable-netcdf4
>>
>> OR unset NETCDF4 variable
>> bash/ksh : unset NETCDF4
>> csh : unsetenv NETCDF4
>>
>> Then re-run this configure script
>>
>> !!! configure.wrf WAS REMOVED !!!
>>
>> *********************************************************************
>>
>>
>>
>> _______________________________________________
>> Wrf-users mailing list
>> Wrf-users at ucar.edu
>> http://mailman.ucar.edu/mailman/listinfo/wrf-users
>>
>>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.ucar.edu/pipermail/wrf-users/attachments/20151130/f5895085/attachment-0001.html
More information about the Wrf-users
mailing list