Compile ROMS problem via cygwin

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lalvarez
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Compile ROMS problem via cygwin

#1 Unread post by lalvarez »

Hello Everyone

I´m installing ROMS via CYGWIN. I´ve followed the instructions of the Tutorial for Windows and I´ve got to the Compile ROMS process in order to get the executable oceanS file; when I do so, I get this message:

./build.bash: line 40: $'\r': command not found
./build.bash: line 43: $'\r': command not found
./build.bash: line 46: syntax error near unexpected token '$'in\r'
./build.bash: line 46: ' case "$1" in

I applied the dos2unix command as:

$ dos2unix ./build.bash

and I only get this line (blue)

dos2unix: convirtiendo archivo ./build.bash a formato Unix ...
dos2unix: converting file ./build.bash to unix format ... (traslation)


Is my sintax on the dos2unix command wrong? Any clue what am I doing wrong?
Beause no lots of stuff comes out and no oceanS is done.

Thanks in advance
Leo
:shock:

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m.hadfield
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Location: NIWA

Re: Compile ROMS problem via cygwin

#2 Unread post by m.hadfield »

lalvarez wrote:Hello Everyone

I´m installing ROMS via CYGWIN. I´ve followed the instructions of the Tutorial for Windows and I´ve got to the Compile ROMS process in order to get the executable oceanS file; when I do so, I get this message:

./build.bash: line 40: $'\r': command not found
./build.bash: line 43: $'\r': command not found
./build.bash: line 46: syntax error near unexpected token '$'in\r'
./build.bash: line 46: ' case "$1" in

I applied the dos2unix command as:

$ dos2unix ./build.bash

and I only get this line (blue)

dos2unix: convirtiendo archivo ./build.bash a formato Unix ...
dos2unix: converting file ./build.bash to unix format ... (traslation)


Is my sintax on the dos2unix command wrong? Any clue what am I doing wrong?
Beause no lots of stuff comes out and no oceanS is done.

Thanks in advance
Leo
:shock:
Hi Leo

The dos2unix command should convert the line endings in the file from Windows (\r\n or CR LF) to Unix (\n or LF) and maybe print a short, informative message. Which is what it appears to have done.

The next thing to do is try running it again. Have you done that?

Mark

PS: the fact that you had \r's in your build.bash in the first place suggests you have downloaded it with a Windows utility, or maybe edited with a Windows editor that doesn't preserve Unix line endings. These are things you should avoid.

lalvarez
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Joined: Wed Feb 03, 2010 6:59 pm
Location: Universidad Autonoma de Baja California Sur

Re: Compile ROMS problem via cygwin

#3 Unread post by lalvarez »

Hello Mark

Thanks for Your replay

Do I have to run the whole dos2unix ./build.bash command or only the ./build.bash command?

One more thing, I have ROMS installed via cygwin on windows with netcdf-4.1.1 version in a laptop.
How can I update the netcdf on this other computer?

Have a nice day
Leo

lalvarez
Posts: 104
Joined: Wed Feb 03, 2010 6:59 pm
Location: Universidad Autonoma de Baja California Sur

Re: Compile ROMS problem via cygwin

#4 Unread post by lalvarez »

Well I have run the dos2unix ./build.bash command and I get

dos2unix: converting file ./build.bash to unix format ... (traslation), so it is Ok!

and then I run the ./build.bash command only and I get this message

$ ./build.bash
makefile:32: *** This makefile requires one of GNU make version 3.80 3.81 3.82.. Alto.
makefile:32: *** This makefile requires one of GNU make version 3.80 3.81 3.82.. Alto.


Is it related with the netcdf or the cygwin installing process?

Thanks in advance
Leo

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kate
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Re: Compile ROMS problem via cygwin

#5 Unread post by kate »

This new problem is related to gnu make. I get:
delta.arsc.edu 236% make --version
GNU Make 3.81
This version matches one in the list of versions it is looking for. What do you get from "make --version"? Add the response to the makefile, near the top. The line looks like:
NEED_VERSION := 3.80 3.81 3.82
You do need to have GNU make, however, not some other version - you should be fine with Cygwin.

Then you need to try running build.bash again.

lalvarez
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Location: Universidad Autonoma de Baja California Sur

Re: Compile ROMS problem via cygwin

#6 Unread post by lalvarez »

Hello Kate

I´m updating the cygwin, and I had installed the 3.82.90-1 version of the GNU make, I´m going to change it for the 3.81-2 version and try to Compile ROMS again

Thanks a lot

Leo

lalvarez
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Re: Compile ROMS problem via cygwin

#7 Unread post by lalvarez »

Kate

It is compiling now, the GNUmake 3.81-2 version works Ok!

Thanks a lot

Leo

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kate
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Re: Compile ROMS problem via cygwin

#8 Unread post by kate »

Actually, I think Mark Hadfield posted that changing the makefile to account for the weird Cygwin version of make worked just fine. Easier than installing some old make just for ROMS!

lalvarez
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Re: Compile ROMS problem via cygwin

#9 Unread post by lalvarez »

Well the compiling was running until I got this message and the process stops

/usr/lib/gcc/i686-pc-cygwin/4.5.3/../../../../i686-pc-cygwin/bin/ld: final link failed: Invalid operation
collect2: ld devolvió el estado de salida 1
make: *** [/home/Usuario/roms/Projects/Upwelling/oceanS.exe] Error 1


Any clue about it?

Do I have to run the ./configure, make, make check & make install for the netcdf-4.2.1.1 and netcdf-fortran-4.2 again?

Leo

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kate
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Re: Compile ROMS problem via cygwin

#10 Unread post by kate »

Please show us the output line before:
final link failed: Invalid operation
The examples on the web tell what's wrong in the line above it.

lalvarez
Posts: 104
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Location: Universidad Autonoma de Baja California Sur

Re: Compile ROMS problem via cygwin

#11 Unread post by lalvarez »

Hello Kate

Here is the line before final link failed: Invalid operation, I insert the whole paragraph just in case

/usr/lib/gcc/i686-pc-cygwin/4.5.3/../../../../i686-pc-cygwin/bin/ld: /home/Usuar io/roms/Projects/Upwelling/Build/libUTIL.a(lbc.o): bad reloc address 0x48c in se ction `.rdata'
/usr/lib/gcc/i686-pc-cygwin/4.5.3/../../../../i686-pc-cygwin/bin/ld: final link failed: Invalid operation
collect2: ld devolvió el estado de salida 1
make: *** [/home/Usuario/roms/Projects/Upwelling/oceanS.exe] Error 1


Thanks for You help

Leo

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m.hadfield
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Re: Compile ROMS problem via cygwin

#12 Unread post by m.hadfield »

A quick Google search on "bad reloc address" indicates that this message is usually preceded by other error messages, eg undefined reference, that give you a better indication of the problem. Please, if you can, reply on the forum attaching the *entire* output of your ROMS build, or at least the last few screenfuls of it.

lalvarez
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Location: Universidad Autonoma de Baja California Sur

Re: Compile ROMS problem via cygwin

#13 Unread post by lalvarez »

Hello Kate & Mark

Here it is, the entire output of the Compile ./build.bash
Hope You can help me

Thanks in advance
Attachments
CompileRoms-build.bash-Error.docx
(30.05 KiB) Downloaded 313 times

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kate
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Re: Compile ROMS problem via cygwin

#14 Unread post by kate »

This could be the second bullet described here. Look at Compilers/CYGWIN-gfortran.mk where there's an ifdef USE_NETCDF4. Did you define it in the build script? Which NetCDF do you have? Does the command "nc-config --flibs" work for you and what does it give?

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m.hadfield
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Re: Compile ROMS problem via cygwin

#15 Unread post by m.hadfield »

Yes, Kate is on the right track.

The command that triggers the error is

Code: Select all

/usr/bin/gfortran-4 -frepack-arrays -O3 -ffast-math  /home/Usuario/roms/Projects/Upwelling/Build/esmf_roms.o /home/Usuario/roms/Projects/Upwelling/Build/master.o /home/Usuario/roms/Projects/Upwelling/Build/ocean_control.o /home/Usuario/roms/Projects/Upwelling/Build/ocean_coupler.o /home/Usuario/roms/Projects/Upwelling/Build/propagator.o /home/Usuario/roms/Projects/Upwelling/Build/roms_export.o /home/Usuario/roms/Projects/Upwelling/Build/roms_import.o -o /home/Usuario/roms/Projects/Upwelling/oceanS.exe /home/Usuario/roms/Projects/Upwelling/Build/libUTIL.a /home/Usuario/roms/Projects/Upwelling/Build/libNLM.a /home/Usuario/roms/Projects/Upwelling/Build/libNLM_bio.a /home/Usuario/roms/Projects/Upwelling/Build/libNLM_sed.a /home/Usuario/roms/Projects/Upwelling/Build/libANA.a /home/Usuario/roms/Projects/Upwelling/Build/libUTIL.a /home/Usuario/roms/Projects/Upwelling/Build/libMODS.a -L/usr/local/lib -lnetcdf
The error messages that follow indicate that the linker can't find several routines from the netCDF Fortran 90 interface.

Leo, you said earlier in the thread that you are using netcdf-4.2 and netcdf-fortran-4.2 or similar. With those versions the Fortran library is separate from the C library, so you would also need "-lnetcdff" in the linker command to find the netCDF Fortran library. And maybe also -lhdf5 and others, depending on the options chosen when netCDF was built. The necessary information should be passed to the build process by nc-config or nf-config (either should work, actually) but it's not.

lalvarez
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Re: Compile ROMS problem via cygwin

#16 Unread post by lalvarez »

Hello Mark

Yes I´m using the netcdf-4.2.1.1 version and the netcdf-fortran-4.2version.

Anyway I guess my mistake is in here, I configured netcdf-4.2.1.1 with this:

./configure --prefix=/usr/local --disable-shared --enable-netcdf-4 --enable-dap --disable-dap-remote-tests

and configured netcdf-fortran-4.2 with:

CC=gcc FC=gfortran LIBS="$(nc-config --libs)" CPPFLAGS="-I$(nc-config --includedir)" nice ./configure --disable-shared --prefix=/usr/local

instead of this sintax:

CC=gcc FC=gfortran LIBS="$(nf-config --libs)" CPPFLAGS="-I$(nf-config --includedir)" nice ./configure --disable-shared --prefix=/usr/local

As Kate once suggested in thread 2766

I´m going to try this last sintax and see what happen

Thanks in advance

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m.hadfield
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Re: Compile ROMS problem via cygwin

#17 Unread post by m.hadfield »

lalvarez wrote:Hello Mark

Yes I´m using the netcdf-4.2.1.1 version and the netcdf-fortran-4.2version.

Anyway I guess my mistake is in here, I configured netcdf-4.2.1.1 with this:

./configure --prefix=/usr/local --disable-shared --enable-netcdf-4 --enable-dap --disable-dap-remote-tests

and configured netcdf-fortran-4.2 with:

CC=gcc FC=gfortran LIBS="$(nc-config --libs)" CPPFLAGS="-I$(nc-config --includedir)" nice ./configure --disable-shared --prefix=/usr/local

instead of this sintax:

CC=gcc FC=gfortran LIBS="$(nf-config --libs)" CPPFLAGS="-I$(nf-config --includedir)" nice ./configure --disable-shared --prefix=/usr/local

As Kate once suggested in thread 2766

I´m going to try this last sintax and see what happen

Thanks in advance
No!! :shock:

Your configure command for building netcdf-fortran was fine. As far as I can tell, you have built & installed it with no problems. Your problem is that the information about the netcdf-fortran configuration is not being passed properly to ROMS.

Re nc-config & nf-config, nc-config is created when netcdf is built and it is installed in ${prefix}/bin (where prefix in your case is /usr/local). It is available to any application that wants to call the netcdf C library. Then you build netcdf-fortran: the cleanest way to tell the configure command where to find everything is with nc-config, hence the form of the configure command that I recommended. The netcdf-fortran build process creates its own counterpart to nc-config, called nf-config, and likewise installs it in ${prefix}/bin. That's not the command you want when building netcdf-fortran, because the first time you build netcdf-fortran it doesn't exist.

The ROMS build process needs to know how to link to netcdf-fortran and for that the most elegant way is to call the appropriate configuration command, which in your case is nf-config (but see below). This is what should happen if you define USE_NETCDF4 (which can be done just by creating an environment variable in build.bash). Then the following line in the platform-specific make file comes into play

Code: Select all

        NC_CONFIG ?= nc-config
That tells ROMS that the netCDF configuration command is nc-config but allows it to be overridden by the environment. You want nf-config (but see below) so in your build.bash you need to set

Code: Select all

  export NC_CONFIG=nf-config
But perhaps /usr/local/bin is not on your PATH (which might well be the problem in your case). In that case you could set this

Code: Select all

  export NC_CONFIG=/usr/local/bin/nf-config
or you could ensure it is on your path (near the front, I suggest):

Code: Select all

  export PATH=/usr/local/bin:$PATH
This could be in build.bash but is better in one of your startup files, I think.

IMHO ensuring the nf-config command you want is on your path is the best solution.

I hope that's clear enough; now I'm going to confuse things again. Why is the ROMS default nc-config, when nf-config is the right command? Because until recently (version 4.2.x) the netCDF C and Fortran libraries were not separate and there was no nf-config. But here's the clever and rather confusing thing: in the very latest version of netcdf-fortran, the nf-config script is still created & installed as I've described, but the pre-existing nc-config is also modified so that it knows where to find the Fortran stuff. (I've included output from nc-config and nf-config on my system at the bottom of this post to demonstrate.) Clever, though a bit dodgy in my opinion. So which to use? I would suggest nf-config if you have it and nc-config if you don't.

Code: Select all

$ nf-config --all

This netCDF-Fortran 4.2 has been built with the following features:

  --cc        -> gcc
  --cflags    ->  -I/usr/local/include -I/usr/local/include
  --libs      -> -L/usr/local/lib  -lnetcdf -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl

  --fc        -> gfortran
  --fflags    -> -g -O2 -I/usr/local/include
  --flibs     -> -L/usr/local/lib -lnetcdff  -lnetcdf -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl
  --has-f90   -> yes

  --has-nc2   -> yes
  --has-nc4   -> yes

  --prefix    -> /usr/local
  --includedir-> /usr/local/include
  --version   -> netCDF-Fortran 4.2

$ nc-config --all

This netCDF 4.2.1.1 has been built with the following features:

  --cc        -> gcc
  --cflags    ->  -I/usr/local/include
  --libs      -> -L/usr/local/lib  -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl

  --has-c++   -> no
  --cxx       ->
  --has-c++4  -> no
  --cxx4      ->

  --fc        -> gfortran
  --fflags    -> -g -O2 -I/usr/local/include
  --flibs     -> -L/usr/local/lib -lnetcdff -lnetcdf -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl
  --has-f90   -> yes

  --has-dap   -> yes
  --has-nc2   -> yes
  --has-nc4   -> yes
  --has-hdf5  -> yes
  --has-hdf4  -> no
  --has-pnetcdf-> no
  --has-szlib ->

  --prefix    -> /usr/local
  --includedir-> /usr/local/include
  --version   -> netCDF 4.2.1.1


csherwood
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Re: Compile ROMS problem via cygwin

#18 Unread post by csherwood »

I think Mark's suggestion about adding the -lnetcdff library might have gotten lost in the noise. You have to do that.

Here is my CYGWIN-gfortran.mk file, which I keep in ../my_ROMS_compilers. I point to that directory in by build.bash file, with:

Code: Select all

export    MY_ROMS_COMPILER=/home/csherwood/src/my_ROMS_compilers
CYGWIN-gfortran.mk:

Code: Select all

# svn $Id: CYGWIN-gfortran.mk 655 2008-07-25 18:57:05Z arango $
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
# Copyright (c) 2002-2010 The ROMS/TOMS Group                           :::
#   Licensed under a MIT/X style license                                :::
#   See License_ROMS.txt                                                :::
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
#
# Include file for GNU g95 on Cygwin (actually gfortran - CRS)
# -------------------------------------------------------------------------
#
# ARPACK_LIBDIR  ARPACK libary directory
# FC             Name of the fortran compiler to use
# FFLAGS         Flags to the fortran compiler
# CPP            Name of the C-preprocessor
# CPPFLAGS       Flags to the C-preprocessor
# NETCDF_INCDIR  NetCDF include directory
# NETCDF_LIBDIR  NetCDF libary directory
# LD             Program to load the objects into an executable
# LDFLAGS        Flags to the loader
# RANLIB         Name of ranlib command
# MDEPFLAGS      Flags for sfmakedepend  (-s if you keep .f files)
#
# First the defaults
#

              BIN := $(BIN).exe

               FC := gfortran
           FFLAGS := -frepack-arrays
              CPP := /usr/bin/cpp
         CPPFLAGS := -P -traditional
          LDFLAGS :=
               AR := ar
          ARFLAGS := -r
            MKDIR := mkdir -p
               RM := rm -f
           RANLIB := ranlib
             PERL := perl
             TEST := test

        MDEPFLAGS := --cpp --fext=f90 --file=- --objdir=$(SCRATCH_DIR)

#
# Library locations, can be overridden by environment variables.
#

ifdef USE_NETCDF4
    NETCDF_INCDIR ?= /usr/local/netcdf4/include
    NETCDF_LIBDIR ?= /usr/local/netcdf4/lib
      HDF5_LIBDIR ?= /usr/local/lib
      CURL_LIBDIR ?= /usr/local/lib
else
    NETCDF_INCDIR ?= /usr/local/include
    NETCDF_LIBDIR ?= /usr/local/lib
endif
             LIBS := -L$(NETCDF_LIBDIR) -lnetcdff -lnetcdf
ifdef USE_NETCDF4
             LIBS += -L$(HDF5_LIBDIR) -lhdf5_hl -lhdf5 -lz -L$(CURL_LIBDIR) -lcurl
endif

ifdef USE_ARPACK
    ARPACK_LIBDIR ?= /usr/local/lib
             LIBS += -L$(ARPACK_LIBDIR) -larpack
endif

ifdef USE_MPI
         CPPFLAGS += -DMPI
 ifdef USE_MPIF90
               FC := mpif90
  ifdef USE_DEBUG
           FFLAGS += -mpe=mpicheck
  endif
 else
  # MPI without mpif90 is not currently supported
 endif
endif

ifdef USE_OpenMP
         CPPFLAGS += -D_OPENMP
           FFLAGS += -fopenmp
endif

ifdef USE_DEBUG
           FFLAGS += -g -fbounds-check -fbacktrace
else
           FFLAGS += -O3 -ffast-math
endif

ifdef USE_MCT
       MCT_INCDIR ?= /usr/local/include
       MCT_LIBDIR ?= /usr/local/lib
           FFLAGS += -I$(MCT_INCDIR)
             LIBS += -L$(MCT_LIBDIR) -lmct -lmpeu
endif

ifdef USE_ESMF
      ESMF_SUBDIR := $(ESMF_OS).$(ESMF_COMPILER).$(ESMF_ABI).$(ESMF_COMM).$(ESMF_SITE)
      ESMF_MK_DIR ?= $(ESMF_DIR)/lib/lib$(ESMF_BOPT)/$(ESMF_SUBDIR)
                     include $(ESMF_MK_DIR)/esmf.mk
           FFLAGS += $(ESMF_F90COMPILEPATHS)
             LIBS += $(ESMF_F90LINKPATHS) -lesmf -lC
endif

ifdef USE_WRF
           FFLAGS += -I$(MCT_INCDIR)
             LIBS += -L$(MCT_LIBDIR) -lmct -lmpeu
             LIBS += WRF/main/module_wrf_top.o
             LIBS += WRF/main/libwrflib.a
             LIBS += WRF/external/fftpack/fftpack5/libfftpack.a
             LIBS += WRF/external/io_grib1/libio_grib1.a
             LIBS += WRF/external/io_grib_share/libio_grib_share.a
             LIBS += WRF/external/io_int/libwrfio_int.a
             LIBS += WRF/external/esmf_time_f90/libesmf_time.a
             LIBS += WRF/external/RSL_LITE/librsl_lite.a
             LIBS += WRF/frame/module_internal_header_util.o
             LIBS += WRF/frame/pack_utils.o
             LIBS += WRF/external/io_netcdf/libwrfio_nf.a
#            LIBS += WRF/external/io_netcdf/wrf_io.o
endif

#
# Use full path of compiler.
#
               FC := $(shell which ${FC})
               LD := $(FC)

#
# Turn off bounds checking for function def_var, as "dimension(*)"
# declarations confuse Gnu Fortran 95 bounds-checking code.
#

$(SCRATCH_DIR)/def_var.o: FFLAGS += -fno-bounds-check

#
# Allow integer overflow in ran_state.F.  This is not allowed
# during -O3 optimization. This option should be applied only for
# Gfortran versions >= 4.2.
#

FC_TEST := $(findstring $(shell ${FC} --version | head -1 | cut -d " " -f 5 | \
                              cut -d "." -f 1-2),4.0 4.1)

ifeq "${FC_TEST}" ""
$(SCRATCH_DIR)/ran_state.o: FFLAGS += -fno-strict-overflow
endif

#
# Set free form format in source files to allow long string for
# local directory and compilation flags inside the code.
#

$(SCRATCH_DIR)/mod_ncparam.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/mod_strings.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/analytical.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/biology.o: FFLAGS += -ffree-form -ffree-line-length-none
ifdef USE_ADJOINT
$(SCRATCH_DIR)/ad_biology.o: FFLAGS += -ffree-form -ffree-line-length-none
endif
ifdef USE_REPRESENTER
$(SCRATCH_DIR)/rp_biology.o: FFLAGS += -ffree-form -ffree-line-length-none
endif
ifdef USE_TANGENT
$(SCRATCH_DIR)/tl_biology.o: FFLAGS += -ffree-form -ffree-line-length-none
endif

#
# Supress free format in SWAN source files since there are comments
# beyond column 72.
#

ifdef USE_SWAN

$(SCRATCH_DIR)/ocpcre.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/ocpids.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/ocpmix.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/swancom1.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/swancom2.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/swancom3.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/swancom4.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/swancom5.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/swanmain.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/swanout1.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/swanout2.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/swanparll.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/swanpre1.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/swanpre2.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/swanser.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/swmod1.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/swmod2.o: FFLAGS += -ffixed-form
$(SCRATCH_DIR)/m_constants.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/m_fileio.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/mod_xnl4v5.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/serv_xnl4v5.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanBpntlist.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanCheckGrid.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanCompdata.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanCompUnstruc.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanComputeForce.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanConvAccur.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanConvStopc.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanCreateEdges.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanCrossObstacle.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanDiffPar.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanDispParm.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanFindObstacles.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanFindPoint.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanGridCell.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanGriddata.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanGridFace.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanGridobjects.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanGridTopology.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanGridVert.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanGSECorr.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanInitCompGrid.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanInterpolateAc.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanInterpolateOutput.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanInterpolatePoint.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanIntgratSpc.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanPointinMesh.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanPrepComp.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanPrintGridInfo.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanPropvelS.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanPropvelX.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanReadADCGrid.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanReadEasymeshGrid.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanReadGrid.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanReadTriangleGrid.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanSweepSel.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanThreadBounds.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanTranspAc.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanTranspX.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/SwanVertlist.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/waves_control.o: FFLAGS += -ffree-form -ffree-line-length-none
$(SCRATCH_DIR)/waves_coupler.o: FFLAGS += -ffree-form -ffree-line-length-none
endif
Chris Sherwood, USGS
1 508 457 2269

User avatar
m.hadfield
Posts: 521
Joined: Tue Jul 01, 2003 4:12 am
Location: NIWA

Re: Compile ROMS problem via cygwin

#19 Unread post by m.hadfield »

csherwood wrote:I think Mark's suggestion about adding the -lnetcdff library might have gotten lost in the noise. You have to do that.
You can let nc-config(*) do that. You just need to ensure that nc-config is on the path and that USE_NETCDF4 is defined. Then the following lines (from the current CYGWIN_gfortran.mk) come into play:

Code: Select all

ifdef USE_NETCDF4
        NC_CONFIG ?= nc-config
    NETCDF_INCDIR ?= $(shell $(NC_CONFIG) --prefix)/include
             LIBS := $(shell $(NC_CONFIG) --flibs)
else
    NETCDF_INCDIR ?= /usr/local/include
    NETCDF_LIBDIR ?= /usr/local/lib
             LIBS := -L$(NETCDF_LIBDIR) -lnetcdf
endif
(*) Or nf-config, but nc-config does fine with the latest netCDF.

lalvarez
Posts: 104
Joined: Wed Feb 03, 2010 6:59 pm
Location: Universidad Autonoma de Baja California Sur

Re: Compile ROMS problem via cygwin

#20 Unread post by lalvarez »

Hello Mark & Chris

Well I did not try the nf-config for the nc-config, as You suggested.
In here I include my $nf-config --all, which is:

Code: Select all

$ nf-config --all

This netCDF-Fortran 4.2 has been built with the following features:

  --cc        -> gcc
  --cflags    ->  -I/usr/local/include -I/usr/local/include
  --libs      -> -L/usr/local/lib  -lnetcdf -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl

  --fc        -> gfortran
  --fflags    -> -g -O2 -I/usr/local/include
  --flibs     -> -L/usr/local/lib -lnetcdff  -lnetcdf -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl
  --has-f90   -> yes

  --has-nc2   -> yes
  --has-nc4   -> yes

  --prefix    -> /usr/local
  --includedir-> /usr/local/include
  --version   -> netCDF-Fortran 4.2
and my $ nc-config --all:

Code: Select all

$ nc-config --all

This netCDF 4.2.1.1 has been built with the following features:

  --cc        -> gcc
  --cflags    ->  -I/usr/local/include
  --libs      -> -L/usr/local/lib  -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl

  --has-c++   -> no
  --cxx       ->
  --has-c++4  -> no
  --cxx4      ->

  --fc        -> gfortran
  --fflags    -> -g -O2 -I/usr/local/include
  --flibs     -> -L/usr/local/lib -lnetcdff -lnetcdf -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl
  --has-f90   -> yes

  --has-dap   -> yes
  --has-nc2   -> yes
  --has-nc4   -> yes
  --has-hdf5  -> yes
  --has-hdf4  -> no
  --has-pnetcdf-> no
  --has-szlib ->

  --prefix    -> /usr/local
  --includedir-> /usr/local/include
  --version   -> netCDF 4.2.1.1
As far as I can see, there are no differences with those of yours Mark.

About my CYGWIN-gfortran.mk file here I send it as a word file.

I found some differences compared with the CYGWIN-gfortran of Chris

I hope You can help me
Attachments
myCYGWIN-gfortran.mk.docx
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User avatar
m.hadfield
Posts: 521
Joined: Tue Jul 01, 2003 4:12 am
Location: NIWA

Re: Compile ROMS problem via cygwin

#21 Unread post by m.hadfield »

Hi Leo

That's all as I expected. See the string that is returned by "nc-config --flibs" or "nf-config --flibs":

Code: Select all

-L/usr/local/lib -lnetcdff  -lnetcdf -L/usr/local/lib -lnetcdf -lhdf5_hl -lhdf5 -lm -lz -lcurl
The ROMS build process needs to incorporate that string in the command used to link the ROMS executable. At the moment (judging from the error output you gave several posts back) it's not doing so. It's just using this:

Code: Select all

-L/usr/local/lib -lnetcdf
So the linker can't find the netCDF Fortran routines (which would be brought in via "-lnetcdff"), not to mention the hdf5, curl and zlib routines.

The problem is that you're not defining USE_NETCDF4 before calling make. You can do so with a line like this in build.bash:

Code: Select all

export USE_NETCDF4=on
There may be one in there already that's commented out. Just delete the "#' at the start of the line.

Mark

lalvarez
Posts: 104
Joined: Wed Feb 03, 2010 6:59 pm
Location: Universidad Autonoma de Baja California Sur

Re: Compile ROMS problem via cygwin

#22 Unread post by lalvarez »

Hello Mark

I´m a little confuse, jaja

Here is the build.bash script of mine as I already have it, in here I have highlighted the export NC_CONFIG= lines I have found.

Are those lines the ones that You suggest to change for: export NC_CONFIG=nf-config or export NC_CONFIG=/usr/local/bin/nf-config?

Also I have found the lines with the export PATH= text. Are those lines the ones to be change for: export PATH=/usr/local/bin:$PATH?

Thanks in advance for Your help

Code: Select all

#!/bin/bash
#
# svn $Id: build.bash 641 2012-12-19 21:51:03Z arango $
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
# Copyright (c) 2002-2012 The ROMS/TOMS Group                           :::
#   Licensed under a MIT/X style license                                :::
#   See License_ROMS.txt                                                :::
#::::::::::::::::::::::::::::::::::::::::::::::::::::: Hernan G. Arango :::
#                                                                       :::
# ROMS/TOMS Compiling Script                                            :::
#                                                                       :::
# Script to compile an user application where the application-specific  :::
# files are kept separate from the ROMS source code.                    :::
#                                                                       :::
# Q: How/why does this script work?                                     :::
#                                                                       :::
# A: The ROMS makefile configures user-defined options with a set of    :::
#    flags such as ROMS_APPLICATION. Browse the makefile to see these.  :::
#    If an option in the makefile uses the syntax ?= in setting the     :::
#    default, this means that make will check whether an environment    :::
#    variable by that name is set in the shell that calls make. If so   :::
#    the environment variable value overrides the default (and the      :::
#    user need not maintain separate makefiles, or frequently edit      :::
#    the makefile, to run separate applications).                       :::
#                                                                       :::
# Usage:                                                                :::
#                                                                       :::
#    ./build.bash [options]                                             :::
#                                                                       :::
# Options:                                                              :::
#                                                                       :::
#    -j [N]      Compile in parallel using N CPUs                       :::
#                  omit argument for all available CPUs                 :::
#    -noclean    Do not clean already compiled objects                  :::
#                                                                       :::
# Notice that sometimes the parallel compilation fail to find MPI       :::
# include file "mpif.h".                                                :::
#                                                                       :::
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

parallel=0
clean=1

while [ $# -gt 0 ]
do
  case "$1" in
    -j )
      shift
      parallel=1
      test=`echo $1 | grep '^[0-9]\+$'`
      if [ "$test" != "" ]; then
        NCPUS="-j $1"
        shift
      else
        NCPUS="-j"
      fi
      ;;

    -noclean )
      shift
      clean=0
      ;;

    * )
      echo ""
      echo "$0 : Unknown option [ $1 ]"
      echo ""
      echo "Available Options:"
      echo ""
      echo "-j [N]      Compile in parallel using N CPUs"
      echo "              omit argument for all avaliable CPUs"
      echo "-noclean    Do not clean already compiled objects"
      echo ""
      exit 1
      ;;
  esac
done

# Set the CPP option defining the particular application. This will
# determine the name of the ".h" header file with the application
# CPP definitions.

export   ROMS_APPLICATION=UPWELLING

# Set a local environmental variable to define the path to the directories
# where all this project's files are kept.

export        MY_ROOT_DIR=/home/Usuario/roms
export     MY_PROJECT_DIR=${MY_ROOT_DIR}/Projects/Upwelling

# The path to the user's local current ROMS source code.
#
# If using svn locally, this would be the user's Working Copy Path (WCPATH).
# Note that one advantage of maintaining your source code locally with svn
# is that when working simultaneously on multiple machines (e.g. a local
# workstation, a local cluster and a remote supercomputer) you can checkout
# the latest release and always get an up-to-date customized source on each
# machine. This script is designed to more easily allow for differing paths
# to the code and inputs on differing machines.

#export       MY_ROMS_SRC=${MY_ROOT_DIR}/branches/arango
 export       MY_ROMS_SRC=${MY_ROOT_DIR}/trunk

# Set path of the directory containing makefile configuration (*.mk) files.
# The user has the option to specify a customized version of these files
# in a different directory than the one distributed with the source code,
# ${MY_ROMS_SRC}/Compilers. If this is the case, the you need to keep
# these configurations files up-to-date.

 export         COMPILERS=${MY_ROMS_SRC}/Compilers
#export         COMPILERS=${HOME}/Compilers

# Set tunable CPP options.
#
# Sometimes it is desirable to activate one or more CPP options to run
# different variants of the same application without modifying its header
# file. If this is the case, specify each options here using the -D syntax.
# Notice also that you need to use shell's quoting syntax to enclose the
# definition.  Both single or double quotes work. For example,
#
#export      MY_CPP_FLAGS="-DAVERAGES"
#export      MY_CPP_FLAGS="${MY_CPP_FLAGS} -DDEBUGGING"
#
# can be used to write time-averaged fields. Notice that you can have as
# many definitions as you want by appending values.

#export      MY_CPP_FLAGS="-D"

# Other user defined environmental variables. See the ROMS makefile for
# details on other options the user might want to set here. Be sure to
# leave the switches meant to be off set to an empty string or commented
# out. Any string value (including off) will evaluate to TRUE in
# conditional if-statements.

 export           USE_MPI=            # distributed-memory parallelism
 export        USE_MPIF90=            # compile with mpif90 script
#export         which_MPI=mpich         # compile with MPICH library
#export         which_MPI=mpich2        # compile with MPICH2 library
 export         which_MPI=openmpi       # compile with OpenMPI library

#export        USE_OpenMP=on            # shared-memory parallelism

 export              FORT=ifort
 export              FORT=gfortran
#export              FORT=pgi

#export         USE_DEBUG=on            # use Fortran debugging flags
 export         USE_LARGE=on            # activate 64-bit compilation
 export       USE_NETCDF4=on            # compile with NetCDF-4 library
#export   USE_PARALLEL_IO=on            # Parallel I/O with Netcdf-4/HDF5

 export       USE_MY_LIBS=on            # use my library paths below

# There are several MPI libraries available. Here, we set the desired
# "mpif90" script to use during compilation. This only works if the make
# configuration file (say, Linux-pgi.mk) in the "Compilers" directory
# has the following definition for FC (Fortran Compiler) in the USE_MPI
# section:
#
#              FC := mpif90
#
# that is, "mpif90" defined without any path. Notice that the path
# where the MPI library is installed is computer dependent. Recall
# that you still need to use the appropriate "mpirun" to execute.

if [ -n "${USE_MPIF90:+1}" ]; then
  case "$FORT" in
    ifort )
      if [ "${which_MPI}" = "mpich" ]; then
        [color=#BF0000]export PATH=/opt/intelsoft/mpich/bin:$PATH[/color]
      elif [ "${which_MPI}" = "mpich2" ]; then
        [color=#BF0000]export PATH=/opt/intelsoft/mpich2/bin:$PATH[/color]
      elif [ "${which_MPI}" = "openmpi" ]; then
        [color=#BF0000]export PATH=/opt/intelsoft/openmpi/bin:$PATH[/color]
      fi
      ;;

    pgi )
      if [ "${which_MPI}" = "mpich" ]; then
        [color=#BF0000]export PATH=/opt/pgisoft/mpich/bin:$PATH[/color]
      elif [ "${which_MPI}" = "mpich2" ]; then
        [color=#BF0000]export PATH=/opt/pgisoft/mpich2/bin:$PATH[/color]
      elif [ "${which_MPI}" = "openmpi" ]; then
        [color=#BF0000]export PATH=/opt/pgisoft/openmpi/bin:$PATH[/color]
      fi
      ;;

    gfortran )
      if [ "${which_MPI}" = "mpich2" ]; then
        [color=#BF0000]export PATH=/opt/gfortransoft/mpich2/bin:$PATH[/color]
      elif [ "${which_MPI}" = "openmpi" ]; then
        [color=#BF0000]export PATH=/opt/gfortransoft/openmpi/bin:$PATH[/color]
      fi
      ;;

  esac
fi

# If the USE_MY_LIBS is activated above, the path of the libraries
# required by ROMS can be set here using environmental variables
# which take precedence to the values specified in the make macro
# definitions file (Compilers/*.mk). For most applications, only
# the location of the NetCDF library is needed during compilation.
#
# Notice that when the USE_NETCDF4 macro is activated, we need the
# serial or parallel version of the NetCDF-4/HDF5 library. The
# configuration script NC_CONFIG (available since NetCDF 4.0.1)
# is used to set up all the required libraries according to the
# installed options (openDAP, netCDF4/HDF5 file format). The
# parallel library uses the MPI-I/O layer (usually available
# in MPICH2 and OpenMPI) requiring compiling with the selected
# MPI library.
#
# In ROMS distributed-memory applications, you may use either the
# serial or parallel version of the NetCDF-4/HDF5 library. The
# parallel version is required when parallel I/O is activated
# (ROMS cpp option PARALLEL_IO and HDF5).
#
# However, in serial or shared-memory ROMS applications, we need
# to use the serial version of the NetCDF-4/HDF5 to avoid conflicts
# with the compiler. We cannot activate MPI constructs in serial
# or shared-memory ROMS code. Hybrid parallelism is not possible.
#
# Recall also that the MPI library comes in several flavors:
# MPICH, MPICH2, OpenMPI, etc.

if [ -n "${USE_MY_LIBS:+1}" ]; then
  case "$FORT" in
    ifort )
      export             ESMF_OS=Linux
      export       ESMF_COMPILER=ifort
      export           ESMF_BOPT=O
      export            ESMF_ABI=64
      export           ESMF_COMM=mpich
      export           ESMF_SITE=default

      export       ARPACK_LIBDIR=/opt/intelsoft/serial/ARPACK
      if [ -n "${USE_MPI:+1}" ]; then
        if [ "${which_MPI}" = "mpich" ]; then
          export        ESMF_DIR=/opt/intelsoft/mpich/esmf
          export      MCT_INCDIR=/opt/intelsoft/mpich/mct/include
          export      MCT_LIBDIR=/opt/intelsoft/mpich/mct/lib
          export  PARPACK_LIBDIR=/opt/intelsoft/mpich/PARPACK
        elif [ "${which_MPI}" = "mpich2" ]; then
          export        ESMF_DIR=/opt/intelsoft/mpich2/esmf
          export      MCT_INCDIR=/opt/intelsoft/mpich2/mct/include
          export      MCT_LIBDIR=/opt/intelsoft/mpich2/mct/lib
          export  PARPACK_LIBDIR=/opt/intelsoft/mpich2/PARPACK
        elif [ "${which_MPI}" = "openmpi" ]; then
          export        ESMF_DIR=/opt/intelsoft/openmpi/esmf
          export      MCT_INCDIR=/opt/intelsoft/openmpi/mct/include
          export      MCT_LIBDIR=/opt/intelsoft/openmpi/mct/lib
          export  PARPACK_LIBDIR=/opt/intelsoft/openmpi/PARPACK
        fi
      fi

      if [ -n "${USE_NETCDF4:+1}" ]; then
        if [ -n "${USE_PARALLEL_IO:+1}" ] && [ -n "${USE_MPI:+1}" ]; then
          if [ "${which_MPI}" = "mpich" ]; then
            [color=#0040BF]export     NC_CONFIG=/opt/intelsoft/mpich/netcdf4/bin/nc-config[/color]
            export NETCDF_INCDIR=/opt/intelsoft/mpich/netcdf4/include
          elif [ "${which_MPI}" = "mpich2" ]; then
            [color=#0040BF]export     NC_CONFIG=/opt/intelsoft/mpich2/netcdf4/bin/nc-config[/color]
            export NETCDF_INCDIR=/opt/intelsoft/mpich2/netcdf4/include
          elif [ "${which_MPI}" = "openmpi" ]; then
            [color=#0040BF]export     NC_CONFIG=/opt/intelsoft/openmpi/netcdf4/bin/nc-config[/color]
            export NETCDF_INCDIR=/opt/intelsoft/openmpi/netcdf4/include
          fi
        else
          [color=#0040BF]export       NC_CONFIG=/opt/intelsoft/serial/netcdf4/bin/nc-config[/color]
          export   NETCDF_INCDIR=/opt/intelsoft/serial/netcdf4/include
        fi
      else
        export     NETCDF_INCDIR=/opt/intelsoft/serial/netcdf3/include
        export     NETCDF_LIBDIR=/opt/intelsoft/serial/netcdf3/lib
      fi
      ;;

    pgi )
      export             ESMF_OS=Linux
      export       ESMF_COMPILER=pgi
      export           ESMF_BOPT=O
      export            ESMF_ABI=64
      export           ESMF_COMM=mpich
      export           ESMF_SITE=default

      export       ARPACK_LIBDIR=/opt/pgisoft/serial/ARPACK
      if [ -n "${USE_MPI:+1}" ]; then
        if [ "${which_MPI}" = "mpich" ]; then
          export        ESMF_DIR=/opt/pgisoft/mpich/esmf
          export      MCT_INCDIR=/opt/pgisoft/mpich/mct/include
          export      MCT_LIBDIR=/opt/pgisoft/mpich/mct/lib
          export  PARPACK_LIBDIR=/opt/pgisoft/mpich/PARPACK
        elif [ "${which_MPI}" = "mpich2" ]; then
          export        ESMF_DIR=/opt/pgisoft/mpich2/esmf
          export      MCT_INCDIR=/opt/pgisoft/mpich2/mct/include
          export      MCT_LIBDIR=/opt/pgisoft/mpich2/mct/lib
          export  PARPACK_LIBDIR=/opt/pgisoft/mpich2/PARPACK
        elif [ "${which_MPI}" = "openmpi" ]; then
          export        ESMF_DIR=/opt/pgisoft/openmpi/esmf
          export      MCT_INCDIR=/opt/pgisoft/openmpi/mct/include
          export      MCT_LIBDIR=/opt/pgisoft/openmpi/mct/lib
          export  PARPACK_LIBDIR=/opt/pgisoft/openmpi/PARPACK
        fi
      fi

      if [ -n "${USE_NETCDF4:+1}" ]; then
        if [ -n "${USE_PARALLEL_IO:+1}" ] && [ -n "${USE_MPI:+1}" ]; then
          if [ "${which_MPI}" = "mpich" ]; then
            [color=#0040BF]export     NC_CONFIG=/opt/pgisoft/mpich/netcdf4/bin/nc-config[/color]
            export NETCDF_INCDIR=/opt/pgisoft/mpich/netcdf4/include
          elif [ "${which_MPI}" = "mpich2" ]; then
            [color=#0040BF]export     NC_CONFIG=/opt/pgisoft/mpich2/netcdf4/bin/nc-config[/color]
            export NETCDF_INCDIR=/opt/pgisoft/mpich2/netcdf4/include
          elif [ "${which_MPI}" = "openmpi" ]; then
            [color=#0040BF]export     NC_CONFIG=/opt/pgisoft/openmpi/netcdf4/bin/nc-config[/color]
            export NETCDF_INCDIR=/opt/pgisoft/openmpi/netcdf4/include
          fi
        else
          [color=#0040BF]export       NC_CONFIG=/opt/pgisoft/serial/netcdf4/bin/nc-config[/color]
          export   NETCDF_INCDIR=/opt/pgisoft/serial/netcdf4/include
        fi
      else
        export     NETCDF_INCDIR=/opt/pgisoft/serial/netcdf3/include
        export     NETCDF_LIBDIR=/opt/pgisoft/serial/netcdf3/lib
      fi
      ;;

    gfortran )
      export             ESMF_OS=Linux
      export       ESMF_COMPILER=gfortran
      export           ESMF_BOPT=O
      export            ESMF_ABI=64
      export           ESMF_COMM=mpich
      export           ESMF_SITE=default

      export       ARPACK_LIBDIR=/opt/gfortransoft/serial/ARPACK
      if [ -n "${USE_MPI:+1}" ]; then
        if [ "${which_MPI}" = "mpich2" ]; then
          export        ESMF_DIR=/opt/gfortransoft/mpich2/esmf
          export      MCT_INCDIR=/opt/gfortransoft/mpich2/mct/include
          export      MCT_LIBDIR=/opt/gfortransoft/mpich2/mct/lib
          export  PARPACK_LIBDIR=/opt/gfortransoft/mpich2/PARPACK
        elif [ "${which_MPI}" = "openmpi" ]; then
          export        ESMF_DIR=/opt/gfortransoft/openmpi/esmf
          export      MCT_INCDIR=/opt/gfortransoft/openmpi/mct/include
          export      MCT_LIBDIR=/opt/gfortransoft/openmpi/mct/lib
          export  PARPACK_LIBDIR=/opt/gfortransoft/openmpi/PARPACK
        fi
      fi

      if [ -n "${USE_NETCDF4:+1}" ]; then
        if [ -n "${USE_PARALLEL_IO:+1}" ] && [ -n "${USE_MPI:+1}" ]; then
          if [ "${which_MPI}" = "mpich2" ]; then
            [color=#0040BF]export     NC_CONFIG=/opt/gfortransoft/mpich2/netcdf4/bin/nc-config[/color]
            export NETCDF_INCDIR=/opt/gfortransoft/mpich2/netcdf4/include
          elif [ "${which_MPI}" = "openmpi" ]; then
            [color=#0040BF]export     NC_CONFIG=/opt/gfortransoft/openmpi/netcdf4/bin/nc-config[/color]
            export NETCDF_INCDIR=/opt/gfortransoft/openmpi/netcdf4/include
          fi
        else
          [color=#0040BF]export       NC_CONFIG=/opt/gfortransoft/serial/netcdf4/bin/nc-config[/color]
          export   NETCDF_INCDIR=/opt/gfortransoft/serial/netcdf4/include
        fi
      else
        export     NETCDF_INCDIR=/usr/local/include
        export     NETCDF_LIBDIR=/usr/local/lib
      fi
      ;;

  esac
fi

# The rest of this script sets the path to the users header file and
# analytical source files, if any. See the templates in User/Functionals.
#
# If applicable, use the MY_ANALYTICAL_DIR directory to place your
# customized biology model header file (like fennel.h, nemuro.h, ecosim.h,
# etc).

 export     MY_HEADER_DIR=${MY_PROJECT_DIR}

 export MY_ANALYTICAL_DIR=${MY_PROJECT_DIR}

# Put the binary to execute in the following directory.

 export            BINDIR=${MY_PROJECT_DIR}

# Put the f90 files in a project specific Build directory to avoid conflict
# with other projects.

 export       SCRATCH_DIR=${MY_PROJECT_DIR}/Build

# Go to the users source directory to compile. The options set above will
# pick up the application-specific code from the appropriate place.

 cd ${MY_ROMS_SRC}

# Remove build directory.

if [ $clean -eq 1 ]; then
  make clean
fi

# Compile (the binary will go to BINDIR set above).

if [ $parallel -eq 1 ]; then
  make $NCPUS
else
  make
fi

User avatar
kate
Posts: 4088
Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA

Re: Compile ROMS problem via cygwin

#23 Unread post by kate »

export FORT=ifort
export FORT=gfortran
You have selected both ifort and gfortran, but gfortran is second and overwrites the other. The instances of NC_CONFIG you need to focus on are in the gfortran section. You aren't doing parallel I/O, so it's this one:
export NC_CONFIG=/opt/gfortransoft/serial/netcdf4/bin/nc-config

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arango
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Re: Compile ROMS problem via cygwin

#24 Unread post by arango »

This stuff in the build.bash script is trivial. It is well documented in the script. Several environmental variables are defined and used temporarily in the bash session to pass those values to the respective compilation macro *.mk in Compilers. The build script provides you an interface to customize all these directory paths. You do not need to modify either the makefile or the compilation macros. These paths are different in everybody's computer. The values in the distributed scripts are for our system and are given as an example. It is impossible for us to guess the directories where everybody installed all the libraries needed by ROMS.

:idea: Notice that the temporary variable NC_CONFIG is the full path where nc-config is, if not already in your PATH. If that directory is already in global PATH, it is not necessary to put the full path. But it does not matter if you specify the full path. It is the safest way and give you full control and you don't need to change PATH. This is convenient if you have more than one Fortran compiler or several versions of the NetCDF library :!: It is that simple :!: It seems to me that you need to learn basic Unix and check how the environmental variables work.

lalvarez
Posts: 104
Joined: Wed Feb 03, 2010 6:59 pm
Location: Universidad Autonoma de Baja California Sur

Re: Compile ROMS problem via cygwin

#25 Unread post by lalvarez »

Kate and Hernan

Thank You for you advice, i´m going to check that out and be more careful.
Any good site for basic unix learning?

Leo

robjenkinsiii
Posts: 34
Joined: Tue Jan 22, 2013 5:28 pm
Location: University of Delaware

Re: Compile ROMS problem via cygwin

#26 Unread post by robjenkinsiii »

Hi, lalvarez

Did you ever manage to correct this linking problem and get ROMS to compile?
I'm just a beginner and I've just run up on the same issue. Not really sure where to begin.

Upon, entering the build.bash command I got the same compilation ending in the error. (Which I believe is the same bit at the end which you received.

Code: Select all

/home/Robert/software/roms/Projects/Upwelling/Build/libUTIL.a(lbc.o):lbc.f90:(.text+0x2279): undefined reference to `___netcdf_MOD_nf90_get_att_text'
/home/Robert/software/roms/Projects/Upwelling/Build/libUTIL.a(lbc.o):lbc.f90:(.text+0x2d6f): undefined reference to `___netcdf_MOD_nf90_put_att_text'
/usr/lib/gcc/i686-pc-cygwin/4.5.3/../../../../i686-pc-cygwin/bin/ld: /home/Robert/software/roms/Projects/Upwelling/Build/libUTIL.a(lbc.o): bad reloc address 0x48c in section `.rdata'
/usr/lib/gcc/i686-pc-cygwin/4.5.3/../../../../i686-pc-cygwin/bin/ld: final link failed: Invalid operation
collect2: ld returned 1 exit status
Master/Module.mk:22: recipe for target `/home/Robert/software/roms/Projects/Upwelling/oceanS.exe' failed
make: *** [/home/Robert/software/roms/Projects/Upwelling/oceanS.exe] Error 1

User avatar
m.hadfield
Posts: 521
Joined: Tue Jul 01, 2003 4:12 am
Location: NIWA

Re: Compile ROMS problem via cygwin

#27 Unread post by m.hadfield »

Hi robjenkinsiii

You could begin by reading all the posts in this thread.

The linker is failing to find a netCDF Fortran routine, probably because the linker command is lacking a "-lnetcdff", and the most likely reason for that is that you have netcdf-4.x installed but have failed to define USE_NETCDF4 in build.bash.

If you want further help with this, please give the linker command that produced this error and describe your netCDF installation (what version? where installed? does the command "nc-config" work in the shell?).

Mark

lalvarez
Posts: 104
Joined: Wed Feb 03, 2010 6:59 pm
Location: Universidad Autonoma de Baja California Sur

Re: Compile ROMS problem via cygwin

#28 Unread post by lalvarez »

Hello robjenkinsiii

I´m enclosing here my build.bash file, You have to look where the shaded rows are, perhaps that´s the problem, as Mark says
You could begin by reading all the posts in this thread.

The linker is failing to find a netCDF Fortran routine, probably because the linker command is lacking a "-lnetcdff", and the most likely reason for that is that you have netcdf-4.x installed but have failed to define USE_NETCDF4 in build.bash.

If you want further help with this, please give the linker command that produced this error and describe your netCDF installation (what version? where installed? does the command "nc-config" work in the shell?).

Mark
The trick in here is "where things are, and that's your directories"

Have a nice day
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