Error in compile

[pwd1]

Below is the last several lines that report errors in my compile process. I am installing in Ubuntu Linux 9.10 with ifort.
The file upwelling.h is in the directory that is being called out.
Your help would be appreciated. Attached are my build.bash and Linux-ifort.mk files.

***************************************

In file included from ROMS/Nonlinear/bbl.F:2:
ROMS/Include/cppdefs.h:749: error: /usr/temp/ROMS/Bin/upwelling.h: No such file or directory
In file included from ROMS/Nonlinear/bc_2d.F:2:
ROMS/Include/cppdefs.h:749: error: /usr/temp/ROMS/Bin/upwelling.h: No such file or directoryIn file included from ROMS/Nonlinear/exchange_2d.F:2
:
ROMS/Include/cppdefs.h:749: error: /usr/temp/ROMS/Bin/upwelling.h: No such file or directory
In file included from ROMS/Modules/mod_param.F:2:
ROMS/Include/cppdefs.h:749: error: /usr/temp/ROMS/Bin/upwelling.h: No such file or directory
make: *** [/usr/temp/ROMS/Bin/Build/bbl.f90] Error 1
make: *** Waiting for unfinished jobs....
make: *** [/usr/temp/ROMS/Bin/Build/bc_2d.f90] Error 1
make: *** [/usr/temp/ROMS/Bin/Build/exchange_2d.f90] Error 1
make: *** [/usr/temp/ROMS/Bin/Build/mod_param.f90] Error 1

[kate]

ROMS/Include/cppdefs.h:749: error: /usr/temp/ROMS/Bin/upwelling.h: No such file or directory

The question should be "why is it looking for upwelling.h in that directory?". Was it there and then moved? Can you "make clean" then try again?

[pwd1]

Maybe I chose an unfortunate name for the Source Code directory: /usr/temp. I used snv to check out the code there, but didn't know how to move them afterward.

I will try "make clean" also.

-Thanks

[kate]

Actually, upwelling.h is usually in the ROMS/Include directory. It looks like the distributed build.bash comes with:

Code: Select all

 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}

and

Code: Select all

 export     MY_PROJECT_DIR=${PWD}

These are not the defaults I would have picked. Come to think of it, I kind of gave up on the build scripts after an experience like this.

[pwd1]

Thanks for the guidance. I am a newbie to ROMS and fortran compiling, so I believe a lot of my problems were path related.

I am also new to Ubuntu and am learning that the "make clean" command doesn't appear to work. I found references to this by Googling and there appears to be an equivalent command that is run from the make-kpkg kernel-package. Not sure about this though.

After correcting several path problems in build.bash I believe I am getting stuck on the ifort section and the path required. This section looks like this on my computer.

export USE_MPI=on
export USE_MPIF90=on
export FORT=ifort

#export USE_OpenMP=on

export USE_DEBUG=on
export USE_LARGE=on
#export USE_NETCDF4=on

if [ -n "${USE_MPIF90:+1}" ]; then
case "$FORT" in
ifort )
# export PATH=/opt/intelsoft/mpich/bin:$PATH
export PATH=/opt/intel/Compiler/11.1/069/bin/intel64:$PATH
# export PATH=/opt/intelsoft/openmpi/bin:$PATH

The last lines of my compile are below. --Thanks

cd /usr/temp/ROMS/Bin/Build; -c -heap-arrays -fp-model precise -g -check uninit -ftrapuv -traceback mod_kinds.f90
/bin/sh: -c: not found
make: *** [/usr/temp/ROMS/Bin/Build/mod_kinds.o] Error 127
make: *** Waiting for unfinished jobs....
ROMS/Bin/cpp_clean /usr/temp/ROMS/Bin/Build/master.f90

[kate]

In the makefile, there is this line:

Code: Select all

        cd $$(SCRATCH_DIR); $$(FC) -c $$(FFLAGS) $(notdir $2)

Your FC is blank, even though FORT is set. In Compilers/Linux-ifort.mk, I have:

Code: Select all

              FC := ifort

then

Code: Select all

ifdef USE_MPI
         CPPFLAGS += -DMPI
 ifdef USE_MPIF90
               FC := mpif90
 else
             LIBS += -lfmpi-pgi -lmpi-pgi
 endif
endif

then

Code: Select all

                FC := $(shell which ${FC})

You can type "make -n -p | grep FC" and I'm sure this line will be blank for you:

Code: Select all

FC := /usr/local/pkg/pgi/pgi-9.0.4/linux86-64/9.0-4/bin/pgf90

What do you get from "which ifort" or "which mpif90"?

[pwd1]

Thanks for explaining the logic of the Linux-ifort.mk code. My file does have the same lines.

After typing "make -n -p | grep FC" in terminal I get this:

root@Phil:~# make -n -p | grep FC
make: *** No targets specified and no makefile found. Stop.
PREPROCESS.F = $(FC) $(FFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -F
LINK.r = $(FC) $(FFLAGS) $(RFLAGS) $(LDFLAGS) $(TARGET_ARCH)
COMPILE.f = $(FC) $(FFLAGS) $(TARGET_ARCH) -c
COMPILE.F = $(FC) $(FFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -c
PREPROCESS.r = $(FC) $(FFLAGS) $(RFLAGS) $(TARGET_ARCH) -F
FC = f77
F77 = $(FC)
COMPILE.r = $(FC) $(FFLAGS) $(RFLAGS) $(TARGET_ARCH) -c
LINK.F = $(FC) $(FFLAGS) $(CPPFLAGS) $(LDFLAGS) $(TARGET_ARCH)
LINK.f = $(FC) $(FFLAGS) $(LDFLAGS) $(TARGET_ARCH)

[kate]

OK, well I typed it from the top directory containing the makefile.

What do you get from "which ifort" or "which mpif90"?

[arango]

Mostly everybody uses the build scripts. I use them all te time. It is the best way to compile ROMS without a need to change the distributed makefile. The makefile is very complicated and it is easy to intruduce mistakes. This is the first time that I heard problems in the build script. Of course that you need to customize this script for a particular application, computer, and compiler. There is a lot of instructions about this in WikiROMS.

[pwd1]

OK, different but the same:

root@Phil:/usr/temp# make -n -p | grep FC
makefile:235: INCLUDING FILE /home/phil/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
cp: cannot stat `/opt/pgisoft/netcdf/include/netcdf.mod': No such file or directory
make: *** No rule to make target `Build/MakeDepend', needed by `all'. Stop.
PREPROCESS.F = $(FC) $(FFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -F
LINK.r = $(FC) $(FFLAGS) $(RFLAGS) $(LDFLAGS) $(TARGET_ARCH)
COMPILE.f = $(FC) $(FFLAGS) $(TARGET_ARCH) -c
COMPILE.F = $(FC) $(FFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -c
PREPROCESS.r = $(FC) $(FFLAGS) $(RFLAGS) $(TARGET_ARCH) -F
cd $$(SCRATCH_DIR); $$(FC) -c $$(FFLAGS) $(notdir $2)
FC :=
F77 = $(FC)
COMPILE.r = $(FC) $(FFLAGS) $(RFLAGS) $(TARGET_ARCH) -c
LINK.F = $(FC) $(FFLAGS) $(CPPFLAGS) $(LDFLAGS) $(TARGET_ARCH)
LINK.f = $(FC) $(FFLAGS) $(LDFLAGS) $(TARGET_ARCH)
cd $(SCRATCH_DIR); $(FC) -c $(FFLAGS) $(notdir $<)
cd $(SCRATCH_DIR); $(FC) -c $(FFLAGS) mod_param.f90
cd $(SCRATCH_DIR); $(FC) -c $(FFLAGS) def_gst.f90
...

[kate]

FC :=

Here is your problem. It is the result of the "which" test as above. Do you have mpif90 on your system? Ifort? Have you tried to compile in serial first?

[pwd1]

I thought I was getting closer to resolution by going through the ifort installation again. It seems that I didn't have RPM installed before the first installation. After uninstalling/reinstalling and verifying that the problematic [for Ubuntu] libstdc++5 was installed properly, I tried to verify a test compilation. It appeared successful when I typed "./ifort /path/test.f90" and got the expected a.out file. Strangely, when I type ifort alone, I get the error "command not found".

But when I tried your test command, it still failed with "FC: " blank as shown below.

root@Phil:/usr/temp# make -n -p | grep FC
makefile:235: INCLUDING FILE /home/phil/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
cp: cannot stat `/opt/pgisoft/netcdf/include/netcdf.mod': No such file or directory
make: *** No rule to make target `Build/MakeDepend', needed by `all'. Stop.
PREPROCESS.F = $(FC) $(FFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -F
LINK.r = $(FC) $(FFLAGS) $(RFLAGS) $(LDFLAGS) $(TARGET_ARCH)
COMPILE.f = $(FC) $(FFLAGS) $(TARGET_ARCH) -c
COMPILE.F = $(FC) $(FFLAGS) $(CPPFLAGS) $(TARGET_ARCH) -c
PREPROCESS.r = $(FC) $(FFLAGS) $(RFLAGS) $(TARGET_ARCH) -F
cd $$(SCRATCH_DIR); $$(FC) -c $$(FFLAGS) $(notdir $2)
FC :=
F77 = $(FC)
COMPILE.r = $(FC) $(FFLAGS) $(RFLAGS) $(TARGET_ARCH) -c
LINK.F = $(FC) $(FFLAGS) $(CPPFLAGS) $(LDFLAGS) $(TARGET_ARCH)
LINK.f = $(FC) $(FFLAGS) $(LDFLAGS) $(TARGET_ARCH)
cd $(SCRATCH_DIR); $(FC) -c $(FFLAGS) $(notdir $<)
cd $(SCRATCH_DIR); $(FC) -c $(FFLAGS) mod_param.f90

My attempt to compile ROMS in serial also failed.

I also did a "make clean" before this.

Any suggestions would be greatly appreciated.

Thanks!

[kate]

cp: cannot stat `/opt/pgisoft/netcdf/include/netcdf.mod': No such file or directory
make: *** No rule to make target `Build/MakeDepend', needed by `all'. Stop.

These are also problems. Thing you need to do:

1. Check the wiki for dependencies: https://www.myroms.org/wiki/index.php/Getting_Started
2. Dependencies include a working f90 compiler and the netcdf library compiled with it - generating the netcdf.mod file. Check https://www.myroms.org/wiki/index.php/ROMS_UNSW2008 too.
3. Get that compiler onto your unix path. See http://www.arsc.edu/~kate/ROMS/Slides/Intro_UNIX.ppt for some tips.

[fereshteh]

Hi dear
after having problem with netcdf4.0 which does not have nc-config i decide to use netcdf4.21.1. I have install it in this way:

1-
Cd /home/fkomijani/zlib 1.2.7
./configure --prefix=/home/fkomijani/NETCD4.2.1.1
make check install
2-
cd /home/fkomijani/HDF5 1.8.9
./configure --with-zlib=/home/fkomijani/NETCD4.2.1.1 --prefix=//home/fkomijani/NETCD4.2.1.1
make check install

3-
cd /home/fkomijani/netcdf4.2.1.1
CPPFLAGS=-Ihome/fkomijani/NETCD4.2.1.1/ include LDFLAGS=L/home/fkomijani/NETCD4.2.1.1 /lib ./configure --prefix=/home/fkomijani/NETCD4.2.1.1
make check install

and then add PATH=/home/fkomijani/NETCD4.2.1.1/bin:$PATH; export PATH” to .bashrc file

and then modify build.bash as below:
export FORT=gfortran
USE_MY_LIBS=on
export NC_CONFIG=/home/fkomijani/NETCD4.2.1.1/bin/nc-config
export NETCDF_INCDIR=/home/fkomijani/NETCD4.2.1.1/include
but after running this error appear:
rm -f -r core *.ipo /home/fkomijani/projects/upwelling6/Build /home/fkomijani/make_macros.mk
makefile:238: INCLUDING FILE /home/fkomijani/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS
cp -f /home/fkomijani/NETCD4.2.1.1/include/netcdf.mod /home/fkomijani/projects/upwelling6/Build
cp: cannot stat `/home/fkomijani/NETCD4.2.1.1/include/netcdf.mod': No such file or directory
make: *** No rule to make target `/home/fkomijani/projects/upwelling6/Build/netcdf.mod', needed by `/home/fkomijani/projects/upwelling6/Build/MakeDepend'. Stop.

I have checked NETCD4.2.1.1/include directory, there are some H5...h files and netcdf.h ,hdf5.h files and it has not netcdf.mod.
what do i do now?
And please tell me that my way to install netcdf4.2.1.1 is correct or not?
Please help me to solve this problem with roms error?
Thanks in advance
fershte

[ymamoutos]

fereshteh,

perhaps you have download and build only the
C libraries of netcdf. Check here
http://www.unidata.ucar.edu/downloads/netcdf/index.jsp
and you will see that if you want to use the latest version of the
netcdf library you must download two zip files. The first contains the
C language libraries and the second contains the fortran libs. Also
i remember that when i compiled the hdf libraries for my pc, to
enable netcdf4/hdf5 support for netcdf lib i used the --enable-hl
flag. Good luck

Giannis

[fereshteh]

hi dear
i am really really appreciate for your reply
finally my problem soleved by downloading and installing netcdf4.2-fortran lib, and ocean.G is built.
But please tell me how and where you add --enable-hl flag? is this falg necessary for parallel I/O?
thanks again
sincerely yours
fereshte