I am following https://www.myroms.org/wiki/Plotting_Pa ... stallation page in an attempt to plot the output from the Upwelling test case.
I don't know if this page is outdated or whether I am doing something wrong, I am a little lost at this step:
Here, I am in the ~/plot/src directory, from the recently svn'd plot package. Following every step, I encounter the problem of setting NETCDF path again. The instruction in this step (quoted above) tells me that I need to change NETCDF paths for NETCDF4, similar to compiling ROMS itself. However, in the makefile file, I suspect that there has been updates and not reflected on the tutorial page. In makefile file, I do not see anywhere that I can specify my NETCDF4 directory paths, despite that it has this information:Machine Dependent Include File
Next you should check the paths and options of the machine dependent include file you chose with the FORT macro variable in the makefile. In particular you should check that LD points to the correct ncargf90 and that NETCDF_INCDIR and NETCDF_LIBDIR are set correctly. It is important that your NetCDF libraries are compatible with your NCL install. The most common compatibility issue is the infamous second underscore problem. A simple google search will tell you more than you wish to know on this subject as will a search in the ROMS forum. The binary distributions of NCL 5.0.0 appear to have been built with the -fno-second-underscore compiler option set where applicable.
The last thing to check is FFLAGS. You may have to experiment with these to get the ROMS Plotting Package to compile. For example, if you installed the 64-bit binary for x86_64 chips for Linux compiled with gcc 3.x you would would want to add -fno-second_underscore to FFLAGS in the Linux-g77.mk file.
NOTE: If you are running ROMS it is likely that your NetCDF library is already built with single underscores at the end of symbol names.
For compiling ROMS itself, there was a separate build_my_path.sh file for me specify the path. But here for the plotting compilation, I don't see such a file, neither does it give me option to set directory paths under NETCDF_INCDIR and NETCDF_LIBDIR, as suggested. Now I am encountering the following issue:# Use NetCDF-4/HDF5 libraries. Notice that the NetCDF-4/HDF5 libraries
# are backwards compatible with NetCDF classic format file. Therefore,
# when compiled with the NetCDF-4/HDF5 libraries this plotting package
# can plot both NetCDF format files.
#
# There are serial and parallel NetCDF-4 and HDF5 libraries. The
# parallel libraries also requires the MPI library. The plotting
# package is serial but it can be compiled with the parallel
# libraries. In order to allow compiling with both serial and
# parallel libraries, the NCAR's library loader script "ncargf90"
# is not longer used in the make configuration files located in the
# Compilers directory. The required plotting libraries are specified
# explicitly as:
#
# LIBS := -L$(NCARG_ROOT)/lib -lncarg -lncarg_gks -lncarg_c
# LIBS += -L/usr/X11R6/lib64 -lX11
USE_NETCDF4 ?= ON
Which I understand as saying it cannot find netcdf, because I couldn't find where to set the path... Any solution?make: /opt/gfortransoft/serial/netcdf4/bin/nc-config: Command not found
make: /opt/gfortransoft/serial/netcdf4/bin/nc-config: Command not found
cd Build_plt; /usr/local/bin/gfortran -c -frepack-arrays -O3 opencdf.f90
opencdf.f9053:
1912 | status=nf_get_vara_real(ncid1,varid,1,nfcst1,fcst1)
| 2
......
2028 | status=nf_get_vara_real(ncid1,varid,1,Nr,zinp1)
| 1
Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(4)/REAL(8)).
opencdf.f9054:
2068 | status=nf_get_vara_double(ncid1,varid,start,count,time1)
| 2
......
2213 | status=nf_get_vara_double(ncid1,varid,1,ntime1,time1)
| 1
Error: Rank mismatch between actual argument at (1) and actual argument at (2) (rank-1 and scalar)
opencdf.f9058:
1912 | status=nf_get_vara_real(ncid1,varid,1,nfcst1,fcst1)
| 2
......
2352 | status=nf_get_vara_real(ncid2,varid,1,nlev2,zinp2)
| 1
Error: Type mismatch between actual argument at (1) and actual argument at (2) (REAL(4)/REAL(8)).
make: *** [Build_plt/opencdf.o] Error 1
53:
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58:Code: Select all
# $Id: makefile 997 2020-01-10 04:33:10Z arango $
#::::::::::::::::::::::::::::::::::::::::::::::::::::: Hernan G. Arango :::
# Copyright (c) 2002-2020 The ROMS/TOMS Group Kate Hedstrom :::
# Licensed under a MIT/X style license :::
# See License_ROMS.txt :::
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
# :::
# ROMS/TOMS Plotting Code Master Makefile :::
# :::
# This makefile is designed to work only with GNU Make version 3.80 or :::
# higher. It can be used in any architecture provided that there is a :::
# machine/compiler rules file in the "Compilers" subdirectory. You :::
# may need to modify the rules file to specify the correct path for :::
# the NetCDF library. :::
# :::
# If appropriate, the USER needs to modify the macro definitions in :::
# in user-defined section below. To activate an option set the macro :::
# to "on". For example, if you want to compile with debugging options :::
# set: :::
# :::
# PLT_DEBUG := on :::
# :::
# Otherwise, leave macro definition blank. :::
# :::
# The USER needs to provide a value for the macro FORT. Choose the :::
# appropriate value from the list below. :::
# :::
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
NEED_VERSION := 3.80 3.81 3.82
$(if $(filter $(MAKE_VERSION),$(NEED_VERSION)),, \
$(error This makefile requires one of GNU make version $(NEED_VERSION).))
#--------------------------------------------------------------------------
# Initialize some things.
#--------------------------------------------------------------------------
sources :=
#==========================================================================
# Start of user-defined options. In some macro definitions below: "on" or
# any other string means TRUE while blank (or spaces) is FALSE.
#==========================================================================
#
# Activate debugging compiler options:
PLT_DEBUG ?=
# If applicable, activate 64-bit compilation:
PLT_LARGE ?= ON
# Sometimes it is desirable to activate one or more CPP options
# using the -D syntax.
MY_CPP_FLAGS ?=
# Use NetCDF-4/HDF5 libraries. Notice that the NetCDF-4/HDF5 libraries
# are backwards compatible with NetCDF classic format file. Therefore,
# when compiled with the NetCDF-4/HDF5 libraries this plotting package
# can plot both NetCDF format files.
#
# There are serial and parallel NetCDF-4 and HDF5 libraries. The
# parallel libraries also requires the MPI library. The plotting
# package is serial but it can be compiled with the parallel
# libraries. In order to allow compiling with both serial and
# parallel libraries, the NCAR's library loader script "ncargf90"
# is not longer used in the make configuration files located in the
# Compilers directory. The required plotting libraries are specified
# explicitly as:
#
# LIBS := -L$(NCARG_ROOT)/lib -lncarg -lncarg_gks -lncarg_c
# LIBS += -L/usr/X11R6/lib64 -lX11
USE_NETCDF4 ?= ON
ifdef USE_NETCDF4
USE_MPIF90 ?=
endif
#--------------------------------------------------------------------------
# We are going to include a file with all the settings that depend on
# the system and the compiler. We are going to build up the name of the
# include file using information on both. Set your compiler here from
# the following list:
#
# Operating System Compiler(s)
#
# AIX: xlf
# ALPHA: f90
# CYGWIN: g95, df, ifort
# Darwin: f90, xlf
# IRIX: f90
# Linux: ftn, ifc, ifort, pgi, path, g95, gfortran
# SunOS: f95
# UNICOS-mp: ftn
# SunOS/Linux: ftn (Cray cross-compiler)
#
# Feel free to send us additional rule files to include! Also, be sure
# to check the appropriate file to make sure it has the right paths to
# NetCDF and so on.
#--------------------------------------------------------------------------
FORT ?= gfortran
#--------------------------------------------------------------------------
# Set directory for executable.
#--------------------------------------------------------------------------
PLT_BINDIR ?= /usr/local/bin
#--------------------------------------------------------------------------
# Provide NCAR library version installed. Several common blocks changes
# in these versions. These switch is used in routines Utility/cnt_frame.F
# and Utility/hbackground.F to tune the appropriate parameters.
#--------------------------------------------------------------------------
#NCAR_VERSION ?= NCARG410
#NCAR_VERSION ?= NCARG422
#NCAR_VERSION ?= NCARG430
#NCAR_VERSION ?= NCARG431
#NCAR_VERSION ?= NCARG441
NCAR_VERSION ?= NCARG662
#==========================================================================
# End of user-defined options. See also the machine-dependent include
# file being used above.
#==========================================================================
#--------------------------------------------------------------------------
# Set directory for temporary objects.
#--------------------------------------------------------------------------
SCRATCH_DIR ?= Build_plt
clean_list := core *.ipo $(SCRATCH_DIR)
ifeq "$(strip $(SCRATCH_DIR))" "."
clean_list := core *.o *.oo *.mod *.f90 lib*.a *.bak
clean_list += $(CURDIR)/*.ipo
endif
ifeq "$(strip $(SCRATCH_DIR))" "./"
clean_list := core *.o *.oo *.ipo *.mod *.f90 lib*.a *.bak
clean_list += $(CURDIR)/*.ipo
endif
#--------------------------------------------------------------------------
# Set Pattern rules.
#--------------------------------------------------------------------------
%.o: %.F
%.o: %.f90
cd $(SCRATCH_DIR); $(FC) -c $(FFLAGS) $(notdir $<)
%.f90: %.F
$(CPP) $(CPPFLAGS) $(MY_CPP_FLAGS) $< > $*.f90
$(CLEAN) $*.f90
CLEAN := Bin/cpp_clean
#--------------------------------------------------------------------------
# Make functions for putting the temporary files in $(SCRATCH_DIR)
# DO NOT modify this section; spaces and blank lines are needed.
#--------------------------------------------------------------------------
# $(call source-dir-to-binary-dir, directory-list)
source-dir-to-binary-dir = $(addprefix $(SCRATCH_DIR)/, $(notdir $1))
# $(call source-to-object, source-file-list)
source-to-object = $(call source-dir-to-binary-dir, \
$(subst .F,.o,$1))
# $(call make-library, library-name, source-file-list)
define make-library
libraries += $(SCRATCH_DIR)/$1
sources += $2
$(SCRATCH_DIR)/$1: $(call source-dir-to-binary-dir, \
$(subst .F,.o,$2))
$(AR) $(ARFLAGS) $$@ $$^
$(RANLIB) $$@
endef
# $(call f90-source, source-file-list)
f90-source = $(call source-dir-to-binary-dir, \
$(subst .F,.f90,$1))
# $(compile-rules)
define compile-rules
$(foreach f, $(local_src), \
$(call one-compile-rule,$(call source-to-object,$f), \
$(call f90-source,$f),$f))
endef
# $(call one-compile-rule, binary-file, f90-file, source-files)
define one-compile-rule
$1: $2 $3
cd $$(SCRATCH_DIR); $$(FC) -c $$(FFLAGS) $(notdir $2)
$2: $3
$$(CPP) $$(CPPFLAGS) $$(MY_CPP_FLAGS) $$< > $$@
$$(CLEAN) $$@
endef
#--------------------------------------------------------------------------
# Set executables file names.
#--------------------------------------------------------------------------
ifdef PLT_DEBUG
CNT := $(PLT_BINDIR)/cntG
CCNT := $(PLT_BINDIR)/ccntG
SEC := $(PLT_BINDIR)/secG
CSEC := $(PLT_BINDIR)/csecG
else
CNT := $(PLT_BINDIR)/cnt
CCNT := $(PLT_BINDIR)/ccnt
SEC := $(PLT_BINDIR)/sec
CSEC := $(PLT_BINDIR)/csec
endif
#--------------------------------------------------------------------------
# "uname -s" should return the OS or kernel name and "uname -m" should
# return the CPU or hardware name. In practice the results can be pretty
# flaky. Run the results through sed to convert "/" and " " to "-",
# then apply platform-specific conversions.
#--------------------------------------------------------------------------
OS := $(shell uname -s | sed 's/[\/ ]/-/g')
OS := $(patsubst CYGWIN_%,CYGWIN,$(OS))
OS := $(patsubst MINGW%,MINGW,$(OS))
OS := $(patsubst sn%,UNICOS-sn,$(OS))
CPU := $(shell uname -m | sed 's/[\/ ]/-/g')
ifndef FORT
$(error Variable FORT not set)
endif
COMPILERS ?= $(CURDIR)/Compilers
ifneq "$(MAKECMDGOALS)" "clean"
include $(COMPILERS)/$(OS)-$(strip $(FORT)).mk
endif
#--------------------------------------------------------------------------
# Pass the platform variables to the preprocessor as macros. Convert to
# valid, upper-case identifiers.
#--------------------------------------------------------------------------
CPPFLAGS += -D$(shell echo ${OS} | tr "-" "_" | tr [a-z] [A-Z])
CPPFLAGS += -D$(shell echo ${CPU} | tr "-" "_" | tr [a-z] [A-Z])
CPPFLAGS += -D$(shell echo ${FORT} | tr "-" "_" | tr [a-z] [A-Z])
#--------------------------------------------------------------------------
# Add NCAR library version. The library common blocks used in routine
# hbackground.F depend on the NCAR version installed in your system.
# Execute "ncargversion" to find your installed version.
#--------------------------------------------------------------------------
CPPFLAGS += -D$(NCAR_VERSION) -Drmdocinc
#--------------------------------------------------------------------------
# Build target directories.
#--------------------------------------------------------------------------
.PHONY: all
all: $(SCRATCH_DIR) $(SCRATCH_DIR)/MakeDepend $(CNT) $(CCNT) $(SEC) $(CSEC)
modules := Utility Drivers
includes := Include Utility
vpath %.F $(modules)
vpath %.h $(includes)
vpath %.f90 $(SCRATCH_DIR)
vpath %.o $(SCRATCH_DIR)
include $(addsuffix /Module.mk,$(modules))
MDEPFLAGS += $(patsubst %,-I %,$(includes)) --silent --moddir $(SCRATCH_DIR)
CPPFLAGS += $(patsubst %,-I%,$(includes))
$(SCRATCH_DIR):
$(shell $(TEST) -d $(SCRATCH_DIR) || $(MKDIR) $(SCRATCH_DIR) )
#--------------------------------------------------------------------------
# Target to create libraries and dependecies.
#--------------------------------------------------------------------------
.PHONY: libraries
libraries: $(libraries)
#--------------------------------------------------------------------------
# Target to create ROMS/TOMS dependecies.
#--------------------------------------------------------------------------
$(SCRATCH_DIR)/MakeDepend: makefile | $(SCRATCH_DIR)
$(SFMAKEDEPEND) $(MDEPFLAGS) $(sources) > $(SCRATCH_DIR)/MakeDepend
.PHONY: depend
SFMAKEDEPEND := Bin/sfmakedepend
depend: $(SCRATCH_DIR)
$(SFMAKEDEPEND) $(MDEPFLAGS) $(sources) > $(SCRATCH_DIR)/MakeDepend
ifneq "$(MAKECMDGOALS)" "clean"
-include $(SCRATCH_DIR)/MakeDepend
endif
#--------------------------------------------------------------------------
# Target to create tar file.
#--------------------------------------------------------------------------
.PHONY: tarfile
tarfile:
tar --exclude=".svn"-cvf plot-3_0.tar *
.PHONY: zipfile
zipfile:
zip -r plot-3_0.zip *
.PHONY: gzipfile
gzipfile:
gzip -v plot-3_0.gzip *
#--------------------------------------------------------------------------
# Cleaning targets.
#--------------------------------------------------------------------------
.PHONY: clean
clean:
$(RM) -r $(clean_list)
#--------------------------------------------------------------------------
# A handy debugging target. This will allow to print the value of any
# makefile defined macro (see http://tinyurl.com/8ax3j). For example,
# to find the value of CPPFLAGS execute:
#
# gmake print-CPPFLAGS
# or
# make print-CPPFLAGS
#--------------------------------------------------------------------------
.PHONY: print-%
print-%:
@echo $* = $($*)
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