Linking with NETCDF

[feffeficus]

Ok. The CCRT replied:


they say " apparently I should not use the precompiled nectdf from the module".

So on the machine Platine cluster bull from CCRT center compile like this:

Code: Select all

./configure --with-iotk=/home/cont003/feffe/CODES/PLATINE/espresso-4.1.2/iotk/src --with-fftw=/applications/fftw3-3.2.1/ --with-p2y=4.0 --enable-largedb FC=mpif90 FCFLAGS=-nofor-main LIBS="-lnetcdff -lnetcdf"

make yambo
make interfaces

it works.
Now I should only understand if it links properly or not the iotk....but this wil be eventually another nice post!

Thanks to all.
I will let you know.

[c3031929]

Hi,

I seem to have a similar problem to Feffe here. I don't understand how he solved his. I have previously compiled YAMBO successfully without NetCDF, but now I need to re-compile YAMBO with NetCDF included. I can successfully compile NetCDF, but when it comes to linking YAMBO I keep running into the following error:

...
/home/dwalton/NetCDF/netcdf-4.1.1/libncdap3/oc/curlfunctions.c:49: undefined reference to `curl_easy_setopt'
/home/dwalton/Yambo_NetCDF/yambo-3.2.1-r.448/lib/libnetcdf.a(liboc_la-curlfunctions.o):/home/dwalton/NetCDF/netcdf-4.1.1/libncdap3/oc/curlfunctions.c:53: more undefined references to `curl_easy_setopt' follow
make[1]: *** [yambo] Error 1
make[1]: Leaving directory `/home/dwalton/Yambo_NetCDF/yambo-3.2.1-r.448/driver'
make: *** [yambo] Error 2

Any help here would be appreciated. The configure and compilation logs are attached.

Cheers,

Danno

[claudio]

Dear Daniel

may you compile Yambo with the option --enable-msgs-comps and send us again all the log files
and also the file config.log

[c3031929]

All three files are now attached.

Cheers,

Danno

[claudio]

Dear Danno

I think you have a problem in the NetCdf libraries, for some reason your system cannot find the curl libraries that are necessary for NetCdf.
It is a general problem not related directly to yambo, but to any code that uses netcdf.

Try to recompile netcdf with the option --disable-dap and the same compilers you use for yambo

You can also check these forums:
http://curl.haxx.se/mail/lib-2005-04/0251.html
http://ubuntuforums.org/showthread.php?p=8041499

[c3031929]

Claudio,

Thank you, that did the trick!

Cheers,

Danno

[mpayami]

Dear All,

I am using the latest version netcdf-4.1.2. I had problem in "./configure" command, and followed Myrta's advice using "--disable-dap --without-curl", so that the configure, compilation, check, and install was ok.
Now, in configuring yambo, I use the command:
./configure F77=ifort FC=ifort CC=icc CXX=icpc --with-netcdf-lib=/opt/NetCDF412/lib --with-netcdf-include=/opt/NetCDF412/include --with-iotk=/opt/QE421/iotk/ --with-p2y=4.0

The configure process completes successfully. When I try to compile, using "make yambo interfaces", in the linking step the following error message appears:

>>>[Linking yambo]<<<
make[1]: Entering directory `/tmp/yambo-3.2.3-rev.11/driver'
yambo_driver.F
/opt/intel/Compiler/11.1/072/lib/intel64/libimf.so: warning: warning: feupdateenv is not implemented and will always fail
/tmp/yambo-3.2.3-rev.11/lib/libio.a(io_elemental.o): In function `io_elemental_':
io_elemental.f90:(.text+0x143): undefined reference to `netcdf_mp_nf90_redef_'
io_elemental.f90:(.text+0x264): undefined reference to `netcdf_mp_nf90_def_var_manydims_'
io_elemental.f90:(.text+0x2bd): undefined reference to `netcdf_mp_nf90_def_var_onedim_'
io_elemental.f90:(.text+0x2ec): undefined reference to `netcdf_mp_nf90_enddef_'
io_elemental.f90:(.text+0x96b): undefined reference to `netcdf_mp_nf90_inq_varid_'
io_elemental.f90:(.text+0xab4): undefined reference to `netcdf_mp_nf90_put_var_fourbyteint_'
io_elemental.f90:(.text+0xc0c): undefined reference to `netcdf_mp_nf90_get_var_fourbyteint_'
io_elemental.f90:(.text+0xe7e): undefined reference to `netcdf_mp_nf90_put_var_1d_fourbyteint_'
io_elemental.f90:(.text+0x1377): undefined reference to `netcdf_mp_nf90_get_var_1d_fourbyteint_'
io_elemental.f90:(.text+0x195f): undefined reference to `netcdf_mp_nf90_put_var_fourbytereal_'
io_elemental.f90:(.text+0x1ad3): undefined reference to `netcdf_mp_nf90_get_var_fourbytereal_'
io_elemental.f90:(.text+0x1d9b): undefined reference to `netcdf_mp_nf90_put_var_1d_fourbytereal_'
io_elemental.f90:(.text+0x249a): undefined reference to `netcdf_mp_nf90_get_var_1d_fourbytereal_'
io_elemental.f90:(.text+0x2d55): undefined reference to `netcdf_mp_nf90_put_var_fourbyteint_'
io_elemental.f90:(.text+0x2ee9): undefined reference to `netcdf_mp_nf90_get_var_fourbyteint_'
io_elemental.f90:(.text+0x323a): undefined reference to `netcdf_mp_nf90_put_var_1d_text_'
io_elemental.f90:(.text+0x3437): undefined reference to `netcdf_mp_nf90_get_var_1d_text_'
/tmp/yambo-3.2.3-rev.11/lib/libio.a(io_bulk.o): In function `io_bulk_':
io_bulk.f90:(.text+0x1506): undefined reference to `netcdf_mp_nf90_redef_'
io_bulk.f90:(.text+0x1678): undefined reference to `netcdf_mp_nf90_def_var_manydims_'
io_bulk.f90:(.text+0x16a8): undefined reference to `netcdf_mp_nf90_enddef_'
io_bulk.f90:(.text+0x16f9): undefined reference to `netcdf_mp_nf90_inq_varid_'
io_bulk.f90:(.text+0x17be): undefined reference to `netcdf_mp_nf90_put_var_fourbyteint_'
io_bulk.f90:(.text+0x1876): undefined reference to `netcdf_mp_nf90_get_var_fourbyteint_'
io_bulk.f90:(.text+0x1949): undefined reference to `netcdf_mp_nf90_put_var_1d_fourbyteint_'
io_bulk.f90:(.text+0x1a17): undefined reference to `netcdf_mp_nf90_get_var_1d_fourbyteint_'
io_bulk.f90:(.text+0x1af9): undefined reference to `netcdf_mp_nf90_put_var_2d_fourbyteint_'
io_bulk.f90:(.text+0x1bc7): undefined reference to `netcdf_mp_nf90_get_var_2d_fourbyteint_'
io_bulk.f90:(.text+0x1cbd): undefined reference to `netcdf_mp_nf90_put_var_3d_fourbyteint_'
io_bulk.f90:(.text+0x1d8c): undefined reference to `netcdf_mp_nf90_get_var_3d_fourbyteint_'
io_bulk.f90:(.text+0x1e9d): undefined reference to `netcdf_mp_nf90_put_var_1d_onebyteint_'
io_bulk.f90:(.text+0x1f6c): undefined reference to `netcdf_mp_nf90_get_var_1d_onebyteint_'
io_bulk.f90:(.text+0x1ffa): undefined reference to `netcdf_mp_nf90_put_var_3d_fourbytereal_'
io_bulk.f90:(.text+0x2064): undefined reference to `netcdf_mp_nf90_get_var_3d_onebyteint_'
io_bulk.f90:(.text+0x2163): undefined reference to `netcdf_mp_nf90_put_var_fourbytereal_'
io_bulk.f90:(.text+0x221c): undefined reference to `netcdf_mp_nf90_get_var_fourbytereal_'
io_bulk.f90:(.text+0x22f4): undefined reference to `netcdf_mp_nf90_put_var_1d_fourbytereal_'
io_bulk.f90:(.text+0x23c3): undefined reference to `netcdf_mp_nf90_get_var_1d_fourbytereal_'
io_bulk.f90:(.text+0x2452): undefined reference to `netcdf_mp_nf90_put_var_2d_fourbytereal_'
io_bulk.f90:(.text+0x24bc): undefined reference to `netcdf_mp_nf90_get_var_2d_fourbytereal_'
io_bulk.f90:(.text+0x2559): undefined reference to `netcdf_mp_nf90_put_var_3d_fourbytereal_'
io_bulk.f90:(.text+0x25c2): undefined reference to `netcdf_mp_nf90_get_var_3d_fourbytereal_'
io_bulk.f90:(.text+0x4cb3): undefined reference to `netcdf_mp_nf90_put_var_3d_onebyteint_'
io_bulk.f90:(.text+0x4d6c): undefined reference to `netcdf_mp_nf90_get_var_3d_onebyteint_'
io_bulk.f90:(.text+0x4e25): undefined reference to `netcdf_mp_nf90_put_var_2d_fourbytereal_'
io_bulk.f90:(.text+0x4ede): undefined reference to `netcdf_mp_nf90_get_var_2d_fourbytereal_'
io_bulk.f90:(.text+0x4f90): undefined reference to `netcdf_mp_nf90_put_var_3d_fourbytereal_'
io_bulk.f90:(.text+0x5048): undefined reference to `netcdf_mp_nf90_get_var_3d_fourbytereal_'
/tmp/yambo-3.2.3-rev.11/lib/libmodules.a(mod_IO.o): In function `io_m_mp_io_connect_':
mod_IO.f90:(.text+0x147b): undefined reference to `netcdf_mp_nf90_create_'
mod_IO.f90:(.text+0x14a4): undefined reference to `netcdf_mp_nf90_enddef_'
mod_IO.f90:(.text+0x1acd): undefined reference to `netcdf_mp_nf90_open_'
mod_IO.f90:(.text+0x1c1a): undefined reference to `netcdf_mp_nf90_strerror_'
mod_IO.f90:(.text+0x1d17): undefined reference to `netcdf_mp_nf90_strerror_'
mod_IO.f90:(.text+0x1e1f): undefined reference to `netcdf_mp_nf90_open_'
mod_IO.f90:(.text+0x1e87): undefined reference to `netcdf_mp_nf90_create_'
mod_IO.f90:(.text+0x1eb0): undefined reference to `netcdf_mp_nf90_enddef_'
mod_IO.f90:(.text+0x1f5a): undefined reference to `netcdf_mp_nf90_strerror_'
mod_IO.f90:(.text+0x2067): undefined reference to `netcdf_mp_nf90_strerror_'
mod_IO.f90:(.text+0x2161): undefined reference to `netcdf_mp_nf90_strerror_'
mod_IO.f90:(.text+0x2782): undefined reference to `netcdf_mp_nf90_strerror_'
/tmp/yambo-3.2.3-rev.11/lib/libmodules.a(mod_IO.o): In function `io_m_mp_io_disconnect_':
mod_IO.f90:(.text+0x2b50): undefined reference to `netcdf_mp_nf90_close_'
mod_IO.f90:(.text+0x2d51): undefined reference to `netcdf_mp_nf90_strerror_'
mod_IO.f90:(.text+0x2df7): undefined reference to `netcdf_mp_nf90_inquire_'
/tmp/yambo-3.2.3-rev.11/lib/libmodules.a(mod_IO.o): In function `io_m_mp_file_is_open_':
mod_IO.f90:(.text+0x49bd): undefined reference to `netcdf_mp_nf90_inquire_'
/tmp/yambo-3.2.3-rev.11/lib/libmodules.a(mod_IO.o): In function `io_m_mp_netcdf_call_':
mod_IO.f90:(.text+0x4ab4): undefined reference to `netcdf_mp_nf90_strerror_'
/tmp/yambo-3.2.3-rev.11/lib/libmodules.a(mod_IO.o): In function `io_m_mp_netcdf_dim_':
mod_IO.f90:(.text+0x4c06): undefined reference to `netcdf_mp_nf90_inq_dimid_'
mod_IO.f90:(.text+0x4c2a): undefined reference to `netcdf_mp_nf90_def_dim_'
mod_IO.f90:(.text+0x4cc2): undefined reference to `netcdf_mp_nf90_strerror_'
/tmp/yambo-3.2.3-rev.11/lib/libmodules.a(mod_IO.o): In function `io_m_mp_variable_is_found_':
mod_IO.f90:(.text+0x4d77): undefined reference to `netcdf_mp_nf90_inq_varid_'
mod_IO.f90:(.text+0x4d9b): undefined reference to `netcdf_mp_nf90_inq_varid_'
make[1]: *** [yambo] Error 1
make[1]: Leaving directory `/tmp/yambo-3.2.3-rev.11/driver'
make: *** [yambo] Error 2

Any suggestions is highly appreciated.

With Best regards,
Mahmoud Payami
Physics Group, AEOI, Tehran, Iran

[claudio]

Dear All

did Yambo work with the version 4.1.1?
if it is so, I advise you to continue to use the 4.1.1 version, because
there are not relevant changes in NetCDF from 4.1.1 to 4.1.2 that can affect yambo code.

Otherwise if you want to use the 4.1.2, try to recompile everythings from scratch,
make a "make clean_all" in yambo and then check
1) that the compiler options are exactly the same in yambo and netcdf
2) that NetCDF are compiled without CURL library

let us know
Claudio

[mpayami]

Dear Claudio,

I succeeded to install yambo using "parallel-netcdf" from http://trac.mcs.anl.gov/projects/parallel-netcdf and the errors I posted above is disappeared. There was no need to install zlib-1.2.5 and hdf5-1.8.6. Do you use zlib and hdf5 for installing netsdf?

Bests,
mahmoud
Phys. Group, AEOI, Tehran, Iran

[claudio]

Dear mahmoud

> Do you use zlib and hdf5 for installing netsdf?

not yet, but in the next version of yambo we will implement the possibility
to use netcdf with hdf5

Cla