error1 Compiling the Upwelling test for the first time

[PhilipT]

Hi all,

I'm a another new user and have been receiving the following error when I attempt to compile the Upwelling test case:

.
.
. ...more undefined references to `__netcdf_MOD_nf90_put_att_text' follow
/home/philip/MYROMS/MyTest/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_inq_var':
.
.
.
mod_netcdf.f90:(.text+0xecfa): undefined reference to `__netcdf_MOD_nf90_get_att_text'
mod_netcdf.f90:(.text+0xf02a): undefined reference to `__netcdf_MOD_nf90_get_att_one_fourbyteint'
/home/philip/MYROMS/MyTest/upwelling/Build/libMODS.a(mod_netcdf.o): In function `__mod_netcdf_MOD_netcdf_get_dim':
mod_netcdf.f90:(.text+0x103d0): undefined reference to `__netcdf_MOD_nf90_inquire'
mod_netcdf.f90:(.text+0x10476): undefined reference to `__netcdf_MOD_nf90_inquire_dimension'

collect2: ld returned 1 exit status
make: *** [/home/philip/MYROMS/MyTest/upwelling/oceanS] Error 1

Any ideas?
Thank you in advance!
Philip

[kate]

The problem is in linking with the NetCDF library. Do you have it? Did you compile it? What version is it? What does your link command look like? See also https://www.myroms.org/wiki/index.php/F ... _link_time

[agilroy]

Hello,
I'm having a similar problem but I can't quite figure out what exactly is going wrong or where to look for a missing path/file. I have the following error:

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/home/agilroy/src/Projects/Upwelling/Build/libUTIL.a(close_io.o): In function `close_out_':
close_io.f90:(.text+0xb61): undefined reference to `__netcdf_MOD_nf90_strerror'

followed by many more undefined references. FYI (if needed), I'm using Netcdf C 4.2.1.1 and Netcdf fortran 4.2 on a university computing system (so I did not install these myself). Thank you in advance.
-Angelica

[kate]

Can you show us your full link command with all the -lnetcdf and -lnetcdff, etc? Did you set USE_NETCDF4 to on?

[agilroy]

Hi Kate,
Thanks for your reply. I did set USE_NETCDF4 to on and I am using the gfotran compiler. I believe this is the block of code you'd like to see:

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ifdef USE_NETCDF4
        NC_CONFIG ?= nc-config
    NETCDF_INCDIR ?= $(shell $(NC_CONFIG) --prefix)/include
             LIBS := $(shell $(NC_CONFIG) --flibs)
else
    NETCDF_INCDIR ?= /opt/netcdf/4.2/gnu/openmpi/ib/include
    NETCDF_LIBDIR ?= /opt/netcdf/4.2/gnu/openmpi/ib/lib
             LIBS := -L/opt/netcdf/4.2.1.1/gnu/openmpi/ib/lib -L/opt/netcdf/4.2/gnu/openmpi/ib/lib -lnetcdff -lnetcdf
endif

If I'm mistaken please do not hesitate to ask again.
-Angelica

[kate]

Actually, I was asking for something like:

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/usr/local/pkg/openmpi/openmpi-1.4.3.gnu-4.7.3/bin/mpif90 -frepack-arrays -g -fbounds-check -I/usr/include  /center/w/kate/Build_ARCG/esmf_roms.o /center/w/kate/Build_ARCG/master.o /center/w/kate/Build_ARCG/ocean_control.o /center/w/kate/Build_ARCG/ocean_coupler.o /center/w/kate/Build_ARCG/propagator.o /center/w/kate/Build_ARCG/roms_export.o /center/w/kate/Build_ARCG/roms_import.o -o oceanG /center/w/kate/Build_ARCG/libMODS.a /center/w/kate/Build_ARCG/libNLM.a /center/w/kate/Build_ARCG/libNLM_bio.a /center/w/kate/Build_ARCG/libNLM_sed.a /center/w/kate/Build_ARCG/libANA.a /center/w/kate/Build_ARCG/libExtra.a /center/w/kate/Build_ARCG/libUTIL.a /center/w/kate/Build_ARCG/libMODS.a -L/usr/local/pkg/netcdf/netcdf-4.3.0.gnu-4.7.3/lib -lnetcdff -L/usr/local/pkg/hdf5/hdf5-1.8.10-p1.gnu-4.7.3/lib -L/usr/local/pkg/szip/szip-2.1.gnu/lib -L/usr/local/pkg/udunits/udunits-2.1.24.gnu-4.7.3/lib -L/usr/local/pkg/netcdf/netcdf-4.3.0.gnu-4.7.3/lib -lnetcdf -lnetcdf /center/w/kate/Build_ARCG/libCICE.a

OK, so yours won't exactly match this.

One could then go to the appropriate directory and do:

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pacman3 312% pushd /usr/local/pkg/netcdf/netcdf-4.3.0.gnu-4.7.3/lib
pacman3 314% nm libnetcdff.so | grep strerror
0000000000069200 T __netcdf_MOD_nf90_strerror
                 U nc_strerror
00000000000135ed T nf_strerror_

[agilroy]

Hi Kate,
Sorry for the confusion. Here it is.

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ROMS/Bin/cpp_clean /home/agilroy/src/Projects/Upwelling/Build/master.f90
cd /home/agilroy/src/Projects/Upwelling/Build; /usr/bin/gfortran -c -frepack-arrays -O3 -ffast-math master.f90
/usr/bin/gfortran -frepack-arrays -O3 -ffast-math  /home/agilroy/src/Projects/Upwelling/Build/esmf_roms.o /home/agilroy/src/Projects/Upwelling/Build/master.o /home/agilroy/src/Projects/Upwelling/Build/ocean_control.o /home/agilroy/src/Projects/Upwelling/Build/ocean_coupler.o /home/agilroy/src/Projects/Upwelling/Build/propagator.o /home/agilroy/src/Projects/Upwelling/Build/roms_export.o /home/agilroy/src/Projects/Upwelling/Build/roms_import.o -o /home/agilroy/src/Projects/Upwelling/oceanS /home/agilroy/src/Projects/Upwelling/Build/libUTIL.a /home/agilroy/src/Projects/Upwelling/Build/libNLM.a /home/agilroy/src/Projects/Upwelling/Build/libNLM_bio.a /home/agilroy/src/Projects/Upwelling/Build/libNLM_sed.a /home/agilroy/src/Projects/Upwelling/Build/libANA.a /home/agilroy/src/Projects/Upwelling/Build/libUTIL.a /home/agilroy/src/Projects/Upwelling/Build/libMODS.a
/home/agilroy/src/Projects/Upwelling/Build/libUTIL.a(close_io.o): In function `close_out_':
close_io.f90:(.text+0xb61): undefined reference to `__netcdf_MOD_nf90_strerror'
/home/agilroy/src/Projects/Upwelling/Build/libUTIL.a(lbc.o): In function `lbc_putatt_':
lbc.f90:(.text+0x149f): undefined reference to `__netcdf_MOD_nf90_put_att_text'
/home/agilroy/src/Projects/Upwelling/Build/libUTIL.a(lbc.o): In function `lbc_getatt_':
lbc.f90:(.text+0x48af): undefined reference to `__netcdf_MOD_nf90_get_att_text'
/home/agilroy/src/Projects/Upwelling/Build/libUTIL.a(nf_fwrite2d.o): In function `__nf_fwrite2d_mod_MOD_nf_fwrite2d':
nf_fwrite2d.f90:(.text+0x498): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/home/agilroy/src/Projects/Upwelling/Build/libUTIL.a(nf_fwrite3d.o): In function `__nf_fwrite3d_mod_MOD_nf_fwrite3d':
nf_fwrite3d.f90:(.text+0x5f8): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
/home/agilroy/src/Projects/Upwelling/Build/libUTIL.a(def_dim.o): In function `def_dim_':
def_dim.f90:(.text+0xbc): undefined reference to `__netcdf_MOD_nf90_def_dim'

and

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[agilroy@tscc-login2 lib]$ nm libnetcdff.so | grep strerror
0000000000012740 T __netcdf_MOD_nf90_strerror
                 U nc_strerror
000000000000cd30 T nf_strerror_
[agilroy@tscc-login2 lib]$ pwd
/opt/netcdf/4.2/gnu/openmpi/ib/lib

-Angelica

[kate]

There's nothing wrong with your libnetcdff.so, but you aren't linking to it. The code you showed before should be invoking "nc-config --flibs" as part of the link. What does it give you?

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einstein 228% nc-config --flibs
-L/usr/local/pkg/netcdf/netcdf-4.3.0.gnu-4.7.3/lib -lnetcdff -L/usr/local/pkg/hdf5/hdf5-1.8.10-p1.gnu-4.7.3/lib -L/usr/local/pkg/szip/szip-2.1.gnu/lib -L/usr/local/pkg/udunits/udunits-2.1.24.gnu-4.7.3/lib -L/usr/local/pkg/netcdf/netcdf-4.3.0.gnu-4.7.3/lib -lnetcdf -lnetcdf

[agilroy]

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[agilroy@tscc-login1 bin]$ nc-config --flibs

[agilroy@tscc-login1 bin]$ nc-config --all

This netCDF 4.2.1.1 has been built with the following features:

  --cc        -> gcc
  --cflags    ->  -I/opt/netcdf/4.2.1.1/gnu/openmpi/ib/include -O2 -I/opt/hdf5/gnu/openmpi/ib/include -I/opt/openmpi/gnu/ib/include -L/opt/hdf5/gnu/openmpi/ib/lib
  --libs      -> -L/opt/netcdf/4.2.1.1/gnu/openmpi/ib/lib -lnetcdf

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

  --fc        ->
  --fflags    ->
  --flibs     ->
  --has-f90   -> no

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

  --prefix    -> /opt/netcdf/4.2.1.1/gnu/openmpi/ib
  --includedir-> /opt/netcdf/4.2.1.1/gnu/openmpi/ib/include
  --version   -> netCDF 4.2.1.1

and then if I switch directories to Netcdf fortran bin, I get:

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[agilroy@tscc-login1 bin]$ nf-config --flibs
-L/opt/netcdf/4.2/gnu/openmpi/ib/lib -lnetcdff -lnetcdf

I guess I'm not sure how link to the libnetcdff.so properly.

[kate]

In your case, you need to change that nc-config to nf-config. You need to make sure it is on your path so that you can execute it during the ROMS build, instead of from inside its directory:

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einstein 233% which nc-config
/usr/local/pkg/netcdf/netcdf-4.3.0.gnu-4.7.3/bin/nc-config
einstein 234% which nf-config
/usr/local/pkg/netcdf/netcdf-4.3.0.gnu-4.7.3/bin/nf-config