Linking with NETCDF

[devsharma]

hi sir,
Thanks for guidance. I will use Abinit for all my calculations.

Sir, as u suggested,i tried to install the yambo with netcdf. Please tell one thing.
I download netcdf -4.01, extract it in home folder(/home/sushil) and compile it with
./configure --prefix=/home/sushil/net (where net is a folder i created)
make check install
i got netcdf compiled with no error. and all tests were passed.
Now i have , in net folder ,
bin include lib src
and in netcdf-4.0.1 folder ,
cxx cxx4 examples f90 fortran libncdap libsrc libsrc4 m4 man4 ncdap_test ncdump ncgen ncgen4 nctest nc_test nf_test win32

Sir, i want to ask, now if i have to compile the yambo with netcdf libraries which path to specify??
i tried
./configure --with-netcdf=/home/sushil/net/lib
but the configuration was not with netcdf. Please guide
thanks
with regards
Dev

[Conor Hogan]

Dear Dev,
Unfortunately the web page has not been updated to show this for the latest versions of the code, but you can always check the correct configure options using

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./configure --help

It this case it shows you:

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  --with-netcdf-include=<path>
                          Path of the NetCDF include directory
  --with-netcdf-lib=<path>
                          Path of the NetCDF lib directory

so you need to make the appropriate modifications.
Regards,
Conor

[feffeficus]

Hi guys,

netcdf compiling error, I presume:

I'm compiling on this machine in CCRT:

952 Machines Bull modèles 3045 et 3045c sous OS Bull Advanced Server 4 version 5
64-bit
i load this modules (that are supposed to be coherent each other I hope..)

1) mpibull2/1.3.9-5.s(default) 2) intel/11.1.056(default) 3) fftw3/3.2.1 4) netcdf/3.6.2 5) mkl/10.1.0.015

i use this configure:

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./configure --with-iotk=/home/cont003/feffe/CODES/PLATINE/espresso-4.1.2/iotk --with-fftw=/applications/fftw3-3.2.1/ --with-netcdf-lib=/opt/scilibs/NETCDF/netCDF-3.6.2/lib --with-netcdf-include=/opt/scilibs/NETCDF/netCDF-3.6.2/include --with-p2y=4.0 --enable-largedb FC=/opt/mpi/mpibull2-1.3.9-5.s/bin/mpif90 FCFLAGS=-nofor-main

and after a good configure, doing make yambo, I found en error with these two modules:

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home/cont003/feffe/CODES/PLATINE/yambo-3.2.1_rev576/lib/libmodules.a
/home/cont003/feffe/CODES/PLATINE/yambo-3.2.1_rev576/lib/libio.a

make[1]: *** [yambo] Error 1
make[1]: Leaving directory `/home/cont003/feffe/CODES/PLATINE/yambo-3.2.1_rev576/driver'
make: *** [yambo] Error 2

Now: I ask of course to the ccrt guys, but in the meanwhile, since they don't reply yet, do you think is a problem of netcdf precompilation or not?

Thanks!
ff

[myrta gruning]

Ciao Feffe

Usually netcdf problems appear from the configure...
It seems you have the problem at the final stage while yambo is linking all the libs
libmodules.a
libio.a
that are generated by the yambo compilation.
Maybe they were not properly cleaned from a previous compilation well this is just an hypothesis, the compiler error message is not really helpful.
You may try with a
make clean
checking that all the *.a and *.o are cleaned and then re-do
make yambo

m

[feffeficus]

ciao Myrta!
thanks.

I will try as you suggest. I will let you know!
ciau!
ff

[feffeficus]

sorry no way.

i still get this as last of a long list of errors:

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/home/cont003/feffe/CODES/PLATINE/yambo-prova/yambo-3.2.1_rev576/lib/libmodules.a(mod_IO.o)(.text+0x6192): In function `io_m_mp_variable_is_found_':
: undefined reference to `netcdf_mp_nf90_inq_varid_'

sigh.

[andrea marini]

Feffe, do a make clean_all and after the configure list the contents of the lib/ and include/ folders (before compiling). They should look like

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include/:
bison  gsl_complex.h  gsl_complex_math.h  netcdfcpp.h  netcdf.h  netcdf.hh  netcdf.inc  netcdf.mod  parser.h  symbols.h  typesizes.mod  version.inc

lib/:
blas  lapack  libiotk.a  libnetcdf.a  libnetcdf_c++.a  local  slatec

[feffeficus]

Feffe, do a make clean_all and after the configure list the contents of the lib/ and include/ folders (before compiling). They should look like

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include/:
bison  gsl_complex.h  gsl_complex_math.h  netcdfcpp.h  netcdf.h  netcdf.hh  netcdf.inc  netcdf.mod  parser.h  symbols.h  typesizes.mod  version.inc

lib/:
blas  lapack  libiotk.a  libnetcdf.a  libnetcdf_c++.a  local  slatec

yes, they are like that.

[andrea marini]

Ok. so the problem is at the linking time. Last you think we can try is to compile using

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configure (...) --enable-msgs-comps

Then you can redirect configure and compilation log with

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./configure (...) >& CONFIGURE_LOG
make (...) >& COMPILATION_LOG

then tar the two files and post them here om the forum. Maybe from the messages of the configure/make we can guess where the problem is.

[feffeficus]

Ok. so the problem is at the linking time. Last you think we can try is to compile using

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configure (...) --enable-msgs-comps

Then you can redirect configure and compilation log with

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./configure (...) >& CONFIGURE_LOG
make (...) >& COMPILATION_LOG

then tar the two files and post them here om the forum. Maybe from the messages of the configure/make we can guess where the problem is.

thanks. ok. the file are in attachement.
sorry to bother, since now no improvement.