Linking with NETCDF

[mpayami]

Dear Claudio,

Thank you so much.
mahmoud

Mahmoud Payami
Physics Group, AEOI, Tehran, Iran

[claudio]

Dear all

we fixed some configuration problem with NetCDF 4.1.2 in the new Yambo version 3.2.4, please download it

http://www.yambo-code.org/download.php

and check if it solves your compilation problems.

regards
Claudio

[a.marani]

Dear Yambo support,

I'm trying to compile Yambo with netcdf built from hdf5. I think it may be useful for me to visit the page linked on your guide, about how to use the flag --with-netcdf-link=... . However, it looks like that page (http://mailman.unidata.ucar.edu/softwar ... Flags.html) isn't online anymore.

Can somebody explain me what was its content and what should i use that flag for?

Many thanks,
Marani Alessandro (CINECA, Italy)

[myrta gruning]

Dear Alessandro

in my case I used
--with-netcdf-link='$NETCDFLINK'
with
NETCDFLINK='-lnetcdff -lnetcdf -lhdf5hl_fortran -lhdf5_hl -lhdf5_fortran -lhdf5 -lz '

but I am not sure this is general, it probably depends on netcdf/hdf5 are compiled and on the architecture.

m

[claudio]

Dear Alessandro

if you have properly installed NetCDF you can get the NETCDFLINK variable doing

nc-config --libs

notice that you are compiling yambo in a cluster you should load the NetCDF module before doing nc-config.

Claudio

[a.marani]

Thank you everybody,
my correct netcdf-link options were: -lnetcdf -lnetcdff -lsz -lz -lm
Now the problem is solved!

Alessandro

[kopinjol]

Hi,

I am running into a similar problem with compiling netcdf-4.1.3. Thr library compiles very well. But when i type make check I get an error.

Here is my configure line:

./configure --prefix=/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3 FC=gfortran44 CC=gcc44 --with-zlib=/home/kbaish2/DFT-GW-Codes/zlib-1.2.7 --disable-dap --disable-netcdf-4

And Here is the error message I get:

make[1]: Entering directory `/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test'
make nf_test tst_f77_v2 ftest tst_f90
make[2]: Entering directory `/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test'
/bin/sh ../libtool --tag=F77 --mode=link gfortran44 -I../fortran -I../include -I../f90 -g -O2 -L/home/kbaish2/DFT-GW-Codes/hdf5-1.8.9/lib -o nf_test test_get.o test_put.o nf_error.o nf_test.o test_read.o test_write.o util.o fortlib.o ../fortran/libnetcdff.la -lm -lcurl
libtool: link: gfortran44 -I../fortran -I../include -I../f90 -g -O2 -o .libs/nf_test test_get.o test_put.o nf_error.o nf_test.o test_read.o test_write.o util.o fortlib.o -L/home/kbaish2/DFT-GW-Codes/hdf5-1.8.9/lib ../fortran/.libs/libnetcdff.so /home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/liblib/.libs/libnetcdf.so -lm -lcurl -Wl,-rpath -Wl,/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/lib
test_get.o: In function `test_nf_get_att_double_':
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5511: undefined reference to `nf_open_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5521: undefined reference to `nf_get_att_double_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5526: undefined reference to `nf_get_att_double_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5529: undefined reference to `nf_get_att_double_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5547: undefined reference to `nf_get_att_double_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5594: undefined reference to `nf_close_'
test_get.o: In function `test_nf_get_att_real_':
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5403: undefined reference to `nf_open_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5413: undefined reference to `nf_get_att_real_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5418: undefined reference to `nf_get_att_real_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5421: undefined reference to `nf_get_att_real_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5439: undefined reference to `nf_get_att_real_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5486: undefined reference to `nf_close_'
test_get.o: In function `test_nf_get_att_int_':
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5295: undefined reference to `nf_open_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5305: undefined reference to `nf_get_att_int_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5310: undefined reference to `nf_get_att_int_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5313: undefined reference to `nf_get_att_int_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5331: undefined reference to `nf_get_att_int_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5378: undefined reference to `nf_close_'
test_get.o: In function `test_nf_get_att_int2_':
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5186: undefined reference to `nf_open_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5196: undefined reference to `nf_get_att_int2_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5201: undefined reference to `nf_get_att_int2_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5204: undefined reference to `nf_get_att_int2_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5222: undefined reference to `nf_get_att_int2_'
/home/kbaish2/DFT-GW-Codes/netcdf-4.1.3/nf_test/test_get.F:5269: undefined reference to `nf_close_'
test_get.o: In function `test_nf_get_att_int1_':


I have also checked that I have used same compilers for hdf5 and netcdf.4.1.3 and the compilers are the same gcc44 and gfortran44.

I would really appreciate any help.

Thanks in advance.
kopinjol

[Daniele Varsano]

Dear Kopinjol,
the error you are experiencing is in the compilation of the netcdf library and not in linking netcdf to yambo.
There are in the web several forum about netcdf compilation, for instances just typing in google: "undefined reference to `nf_open_'"
you can find several information that can useful to solve your problem.
Anyway, did you type make install, before the make check?
I suspect it is a just a path problem when linking the netcdf library.

Cheers,

Daniele

[kopinjol]

Hello Daniele,

Thanks for the reply. I tried as you suggested, by typing make install before make check. But I still get the same error. I did look at the google results, but I think i'll just post in the netcdf forum. In any case, I was just wondering if anyone had any idea as to what might be going wrong! I am using CC=gcc44, FC=gcc44. Interestingly, if i do along with thesze, CXX=gcc44 , I get an error while compiling, i.e make gives me an error.

Anyway thanks for the reply again. I will check with the netcdf guys and see what they say.

Cheers,
kopinjo,l

[kopinjol]

Hi everyone,

I was able to compile netcdf-4.1.3 after talking to the unidata guys. I just had to add the flag -DgFortran to CFLAGS. But now I get an error in compiling yambo. The error occurs at the 'linking Yambo' step. These are the error messages,


home/kbaish2/DFT-GW-Codes/Yambo/yambo-3.2.5/lib/libio.a(io_elemental.o): In function `io_elemental_':
io_elemental.f90:(.text+0xb9a): undefined reference to `__netcdf_MOD_nf90_put_var_fourbyteint'
io_elemental.f90:(.text+0xdc9): undefined reference to `__netcdf_MOD_nf90_put_var_1d_fourbyteint'
io_elemental.f90:(.text+0x10d9): undefined reference to `__netcdf_MOD_nf90_put_var_eightbytereal'
io_elemental.f90:(.text+0x1385): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
io_elemental.f90:(.text+0x175c): undefined reference to `__netcdf_MOD_nf90_put_var_fourbyteint'
io_elemental.f90:(.text+0x1a6b): undefined reference to `__netcdf_MOD_nf90_put_var_1d_text'
io_elemental.f90:(.text+0x1f19): undefined reference to `__netcdf_MOD_nf90_redef'
io_elemental.f90:(.text+0x1ff1): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
io_elemental.f90:(.text+0x201f): undefined reference to `__netcdf_MOD_nf90_enddef'
io_elemental.f90:(.text+0x23a5): undefined reference to `__netcdf_MOD_nf90_get_var_fourbyteint'
io_elemental.f90:(.text+0x286f): undefined reference to `__netcdf_MOD_nf90_get_var_1d_text'
io_elemental.f90:(.text+0x2b99): undefined reference to `__netcdf_MOD_nf90_inq_varid'
io_elemental.f90:(.text+0x2c98): undefined reference to `__netcdf_MOD_nf90_get_var_fourbyteint'
io_elemental.f90:(.text+0x3065): undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
io_elemental.f90:(.text+0x33c5): undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
io_elemental.f90:(.text+0x3645): undefined reference to `__netcdf_MOD_nf90_get_var_eightbytereal'
io_elemental.f90:(.text+0x3dce): undefined reference to `__netcdf_MOD_nf90_def_var_onedim'
io_elemental.f90:(.text+0x49a5): undefined reference to `__netcdf_MOD_nf90_def_var_onedim'
/home/kbaish2/DFT-GW-Codes/Yambo/yambo-3.2.5/lib/libio.a(io_bulk.o): In function `io_bulk_':
io_bulk.f90:(.text+0x695): undefined reference to `__netcdf_MOD_nf90_put_var_fourbyteint'
io_bulk.f90:(.text+0x7bb): undefined reference to `__netcdf_MOD_nf90_put_var_1d_fourbyteint'
io_bulk.f90:(.text+0x919): undefined reference to `__netcdf_MOD_nf90_put_var_2d_fourbyteint'
io_bulk.f90:(.text+0xb2f): undefined reference to `__netcdf_MOD_nf90_put_var_3d_fourbyteint'
io_bulk.f90:(.text+0xd17): undefined reference to `__netcdf_MOD_nf90_put_var_1d_onebyteint'
io_bulk.f90:(.text+0xea3): undefined reference to `__netcdf_MOD_nf90_put_var_3d_eightbytereal'
io_bulk.f90:(.text+0x102b): undefined reference to `__netcdf_MOD_nf90_put_var_eightbytereal'
io_bulk.f90:(.text+0x1152): undefined reference to `__netcdf_MOD_nf90_put_var_1d_eightbytereal'
io_bulk.f90:(.text+0x12b5): undefined reference to `__netcdf_MOD_nf90_put_var_2d_eightbytereal'
io_bulk.f90:(.text+0x14c2): undefined reference to `__netcdf_MOD_nf90_put_var_3d_eightbytereal'
io_bulk.f90:(.text+0x2a32): undefined reference to `__netcdf_MOD_nf90_redef'
io_bulk.f90:(.text+0x2be9): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
io_bulk.f90:(.text+0x2c20): undefined reference to `__netcdf_MOD_nf90_enddef'
io_bulk.f90:(.text+0x2e5b): undefined reference to `__netcdf_MOD_nf90_get_var_3d_eightbytereal'
io_bulk.f90:(.text+0x2fa2): undefined reference to `__netcdf_MOD_nf90_get_var_2d_eightbytereal'
io_bulk.f90:(.text+0x30b6): undefined reference to `__netcdf_MOD_nf90_get_var_1d_eightbytereal'
io_bulk.f90:(.text+0x3175): undefined reference to `__netcdf_MOD_nf90_get_var_fourbyteint'
io_bulk.f90:(.text+0x328e): undefined reference to `__netcdf_MOD_nf90_get_var_1d_fourbyteint'
io_bulk.f90:(.text+0x33d5): undefined reference to `__netcdf_MOD_nf90_get_var_2d_fourbyteint'
io_bulk.f90:(.text+0x3546): undefined reference to `__netcdf_MOD_nf90_get_var_3d_fourbyteint'
io_bulk.f90:(.text+0x365e): undefined reference to `__netcdf_MOD_nf90_get_var_1d_onebyteint'
io_bulk.f90:(.text+0x37df): undefined reference to `__netcdf_MOD_nf90_get_var_3d_onebyteint'
io_bulk.f90:(.text+0x3893): undefined reference to `__netcdf_MOD_nf90_get_var_eightbytereal'
io_bulk.f90:(.text+0x3974): undefined reference to `__netcdf_MOD_nf90_def_var_manydims'
io_bulk.f90:(.text+0x3aa2): undefined reference to `__netcdf_MOD_nf90_get_var_2d_eightbytereal'
io_bulk.f90:(.text+0x3c00): undefined reference to `__netcdf_MOD_nf90_get_var_3d_onebyteint'
io_bulk.f90:(.text+0x3d55): undefined reference to `__netcdf_MOD_nf90_put_var_3d_eightbytereal'
io_bulk.f90:(.text+0x3e84): undefined reference to `__netcdf_MOD_nf90_put_var_2d_eightbytereal'
io_bulk.f90:(.text+0x3fe9): undefined reference to `__netcdf_MOD_nf90_put_var_3d_onebyteint'
io_bulk.f90:(.text+0x4031): undefined reference to `__netcdf_MOD_nf90_inq_varid'
io_bulk.f90:(.text+0x418d): undefined reference to `__netcdf_MOD_nf90_get_var_3d_eightbytereal'
/home/kbaish2/DFT-GW-Codes/Yambo/yambo-3.2.5/lib/libmodules.a(mod_IO.o): In function `__io_m_MOD_file_is_open':
mod_IO.f90:(.text+0x1165): undefined reference to `__netcdf_MOD_nf90_inquire'
/home/kbaish2/DFT-GW-Codes/Yambo/yambo-3.2.5/lib/libmodules.a(mod_IO.o): In function `__io_m_MOD_netcdf_call':
mod_IO.f90:(.text+0x1285): undefined reference to `__netcdf_MOD_nf90_strerror'
/home/kbaish2/DFT-GW-Codes/Yambo/yambo-3.2.5/lib/libmodules.a(mod_IO.o): In function `__io_m_MOD_netcdf_dim':
mod_IO.f90:(.text+0x141f): undefined reference to `__netcdf_MOD_nf90_inq_dimid'
mod_IO.f90:(.text+0x1443): undefined reference to `__netcdf_MOD_nf90_def_dim'
/home/kbaish2/DFT-GW-Codes/Yambo/yambo-3.2.5/lib/libmodules.a(mod_IO.o): In function `__io_m_MOD_variable_is_found':
mod_IO.f90:(.text+0x14ab): undefined reference to `__netcdf_MOD_nf90_inq_varid'
mod_IO.f90:(.text+0x14ce): undefined reference to `__netcdf_MOD_nf90_inq_varid'
/home/kbaish2/DFT-GW-Codes/Yambo/yambo-3.2.5/lib/libmodules.a(mod_IO.o): In function `__io_m_MOD_file_is_open.clone.0':
mod_IO.f90:(.text+0x1605): undefined reference to `__netcdf_MOD_nf90_inquire'
/home/kbaish2/DFT-GW-Codes/Yambo/yambo-3.2.5/lib/libmodules.a(mod_IO.o): In function `__io_m_MOD_io_disconnect':
mod_IO.f90:(.text+0x171c): undefined reference to `__netcdf_MOD_nf90_close'
/home/kbaish2/DFT-GW-Codes/Yambo/yambo-3.2.5/lib/libmodules.a(mod_IO.o): In function `__io_m_MOD_io_connect':
mod_IO.f90:(.text+0x3367): undefined reference to `__netcdf_MOD_nf90_open'
mod_IO.f90:(.text+0x38bc): undefined reference to `__netcdf_MOD_nf90_open'
mod_IO.f90:(.text+0x3d95): undefined reference to `__netcdf_MOD_nf90_create'
mod_IO.f90:(.text+0x3ddf): undefined reference to `__netcdf_MOD_nf90_enddef'
mod_IO.f90:(.text+0x3fd8): undefined reference to `__netcdf_MOD_nf90_create'
mod_IO.f90:(.text+0x4024): undefined reference to `__netcdf_MOD_nf90_enddef'
collect2: ld returned 1 exit status
make[1]: *** [yambo] Error 1
make[1]: Leaving directory `/home/kbaish2/DFT-GW-Codes/Yambo/yambo-3.2.5/driver'
make: *** [yambo] Error 2


I ran configure with the --enable-msgs-comps flag and saved the output in CONFIG.LOG and ran make all the output of which is in MAKE.LOG. The two files are attached as a tar archive named FILES.tar. I would really appreciate any help regarding this.

Thanks in advance,
kopinjol