installing chem_prep_sources on yellowstone

[apattant]

I am trying to install chem_prep_sources on yellowstone. Does anyone have any tips because I am not having much luck getting the executable to build.

[meteorrosie]

Did you ever receive resolution to this problem? Which include.mk file should be edited for building prep-chem-sources on Yellowstone? Also, what should "UTILS_VERSION" be? What other parts should be changed other than "NETCDF_LIBS", "HDF_LIBS"? Thanks very much.

[meteorrosie]

Yellowstone Help Desk provided the locations of the libraries. I received this warning message:
"ld: warning: libhdf5_hl.so.7, needed by /glade/apps/opt/netcdf/4.2/intel/default/lib/libnetcdf_c++4.so.1, may conflict with libhdf5_hl.so.8
ld: warning: libhdf5.so.7, needed by /glade/apps/opt/netcdf/4.2/intel/default/lib/libnetcdf_c++4.so.1, may conflict with libhdf5.so.8

Finished building === ../prep_chem_sources_RADM_WRF_FIM.exe"

I'll see how to fix this. In the meantime, here is my include.mk.intel.wrf file for anyone who can use it:

#Makefile include include.mk.opt
############################## Change Log ##################################
# 1.0.0.2
#
# 000908 MJB include.mk-mrc ##
# Added MAKE environment varaible.
# Added free format option to F_OPTS for some platforms. ##
# 000907 MJB include.mk-mrc ##
# Changed the defualts to no NCAR Graphics and no parallel.
# Also commented out the machine specifics to force the user to
# select the appropriate machine for them. ##
# 000823 MJB include.mk-mrc ##
# New - defines all make environment varaibles and is included
# in all make files. ##
#
############################################################################

# Define make (gnu make works best).

MAKE=/usr/bin/make

# Activate appropriate parts below, comment out others.

# NCAR Graphics.

#---------------------------------------------------------------
# If you are using a standard installation of NCAR Graphics, set:
# LOADER=ncargf90
# in the machine-dependent sections below
#LIBNCARG=
#---------------------------------------------------------------
# If you are using the NCAR dummy libraries...

NCARG_DIR=$(BASE)
#LIBNCARG=-L$(NCARG_DIR) -lncarg-$(UTILS_VERSION) -lncarg_c-$(UTILS_VERSION) \
# -lncarg_gks-$(UTILS_VERSION)
#LIBNCARG=-L$(NCARG_DIR) -lncarg-$(UTILS_VERSION)
LIBNCARG=$(BASE)/libncarg-$(UTILS_VERSION)-$(OPT).a
#---------------------------------------------------------------# If you are using a real distribution of NCAR Graphics...
#NCARG_DIR=/usr/local/ncarg-4.3.0/lib#LIBNCARG=-L$(NCARG_DIR) -lncarg -lncarg_gks -lncarg_c -L/usr/X11R6/lib -lX11 -ldl
#---------------------------------------------------------------

# NETCDF libraries


#NETCDF=/home/stockler/projetos/libs/intel/netcdf
NETCDF=/glade/apps/opt/netcdf/4.3.0/intel/12.1.5
NETCDF_INC=-I$(NETCDF)/include
NETCDF_LIBS=-L$(NETCDF)/lib -lnetcdf

# More libraries not originally in this include.mk.intel.wrf file
JPEG=/glade/apps/opt/libjpeg/9a/intel/12.1.5
ZLIB=/glade/apps/opt/zlib/1.2.7/intel/12.1.4
SZLIB=/glade/apps/opt/szlib/2.1/intel/12.1.4

# HDF libraries
HDF5=/glade/apps/opt/hdf5/1.8.11/intel/12.1.5
HDF5_INC=-I$(HDF5)/include
#HDF5_LIB=-L$(HDF5)/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -L/scratchin/grupos/catt-brams/shared/libs/intel/zlib-1.2.4/lib -lz
HDF5_LIB=-L$(HDF5)/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -L$(ZLIB)/lib -lz -L$(SZLIB)/lib -lsz -L$(JPEG)/lib -ljpeg

# Machine-dependent options.

#----------------- LINUX Portland Group pgf77/gcc ---------------
CMACH=PC_LINUX1
F_COMP=/glade/u/ssg/ys/opt/intel/12.1.0.233/composer_xe_2013.1.117/bin/intel64/ifort
C_COMP=/glade/u/ssg/ys/opt/intel/12.1.0.233/composer_xe_2013.1.117/bin/intel64/icc
LOADER=/glade/u/ssg/ys/opt/intel/12.1.0.233/composer_xe_2013.1.117/bin/intel64/ifort
C_LOADER=/glade/u/ssg/ys/opt/intel/12.1.0.233/composer_xe_2013.1.117/bin/intel64/icc
LIBS=
MOD_EXT=mod

F_OPTS=-fpp -D$(CHEM) -O2 -convert big_endian
C_OPTS= -O2
LOADER_OPTS= -O2

#-----------------------------------------------------------------


# If compiling for a single-CPU platform only (without MPI):

#-----------------------------------------------------------------
PAR_LIBS=
PAR_DEFS=
#-----------------------------------------------------------------


# For IBM,HP,SGI,ALPHA use these:
ARCHIVE=ar rs
# For NEC SX-6
#ARCHIVE=sxar rs
# For SUN,CONVEX
#ARCHIVE=ar r'

[meteorrosie]

Here's an update include.mk.intel.wrf. The changes are that the paths have been commented out and the ncarcompilers have been amended. This successfully builds the prep chem source executable in the bin folder. The libcdf compatibility warning remains, but it doesn't seem to harm the next step in the emissions build:

#Makefile include include.mk.opt
############################## Change Log ##################################
# 1.0.0.2
#
# 000908 MJB include.mk-mrc ##
# Added MAKE environment varaible.
# Added free format option to F_OPTS for some platforms. ##
# 000907 MJB include.mk-mrc ##
# Changed the defualts to no NCAR Graphics and no parallel.
# Also commented out the machine specifics to force the user to
# select the appropriate machine for them. ##
# 000823 MJB include.mk-mrc ##
# New - defines all make environment varaibles and is included
# in all make files. ##
#
############################################################################

# Define make (gnu make works best).

MAKE=/usr/bin/make

# Activate appropriate parts below, comment out others.

# NCAR Graphics.

#---------------------------------------------------------------
# If you are using a standard installation of NCAR Graphics, set:
# LOADER=ncargf90
# in the machine-dependent sections below
#LIBNCARG=
#---------------------------------------------------------------
# If you are using the NCAR dummy libraries...

NCARG_DIR=$(BASE)
#LIBNCARG=-L$(NCARG_DIR) -lncarg-$(UTILS_VERSION) -lncarg_c-$(UTILS_VERSION) \
# -lncarg_gks-$(UTILS_VERSION)
#LIBNCARG=-L$(NCARG_DIR) -lncarg-$(UTILS_VERSION)
LIBNCARG=$(BASE)/libncarg-$(UTILS_VERSION)-$(OPT).a
#---------------------------------------------------------------# If you are using a real distribution of NCAR Graphics...
#NCARG_DIR=/usr/local/ncarg-4.3.0/lib#LIBNCARG=-L$(NCARG_DIR) -lncarg -lncarg_gks -lncarg_c -L/usr/X11R6/lib -lX11 -ldl
#---------------------------------------------------------------

# NETCDF libraries


#NETCDF=/home/stockler/projetos/libs/intel/netcdf
#NETCDF=/glade/apps/opt/netcdf/4.3.0/intel/12.1.5
#NETCDF_INC=-I$(NETCDF)/include
#NETCDF_LIBS=-L$(NETCDF)/lib -lnetcdf

# More libraries not originally in this include.mk.intel.wrf file
#JPEG=/glade/apps/opt/libjpeg/9a/intel/12.1.5
#ZLIB=/glade/apps/opt/zlib/1.2.7/intel/12.1.4
#SZLIB=/glade/apps/opt/szlib/2.1/intel/12.1.4

# HDF libraries
#HDF5=/glade/apps/opt/hdf5/1.8.11/intel/12.1.5
#HDF5_INC=-I$(HDF5)/include
#HDF5_LIB=-L$(HDF5)/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -L/scratchin/grupos/catt-brams/shared/libs/intel/zlib-1.2.4/lib -lz
#HDF5_LIB=-L$(HDF5)/lib -lhdf5hl_fortran -lhdf5_fortran -lhdf5_hl -lhdf5 -L$(ZLIB)/lib -lz -L$(SZLIB)/lib -lsz -L$(JPEG)/lib -ljpeg

# Machine-dependent options.

#----------------- LINUX Portland Group pgf77/gcc ---------------
CMACH=PC_LINUX1
F_COMP=ifort
C_COMP=icc
LOADER=ifort
C_LOADER=icc
LIBS=
MOD_EXT=mod

F_OPTS=-fpp -D$(CHEM) -O2 -convert big_endian
C_OPTS= -O2
LOADER_OPTS= -O2

#-----------------------------------------------------------------


# If compiling for a single-CPU platform only (without MPI):

#-----------------------------------------------------------------
PAR_LIBS=
PAR_DEFS=
#-----------------------------------------------------------------


# For IBM,HP,SGI,ALPHA use these:
ARCHIVE=ar rs
# For NEC SX-6
#ARCHIVE=sxar rs
# For SUN,CONVEX
#ARCHIVE=ar r'