mpi.h error in netcdf

[fchemam]

Hi,
after installation Nedcdf-4.3.2 in ubuntu 12.04 64 bit with ifort composer 2013, im blocked in the case of ../include/netcdf_par.h:13:17: fatal error: mpi.h: No such file or directory
the file of mpi.h is in directory /usr/include/mpi,

regards

[Daniele Varsano]

Dear Chemam,
it looks mpi library are not correctly seen:
Just to understand, the problem is found in the netcdf or in yambo compilation?
in order to have a first look can you post your config.log file?
Best,
Daniele

[fchemam]

Hi,
the problem is in netcdf compilation, after compilation with only ''make'', or ''make check install''
the config.log is in attached.
regards

[Daniele Varsano]

Dear Chemam,
this is not a yambo issue, but netcdf problem, and you should eventually ask to netcdf people.
Anyway: please note that
1. Parallel compilation is not needed for the netcdf
2. the fortran compiler has not been recognized, in general you can try to compile by using ./configure FC=gfortran
3. Moreover it looks me that 4.3.2 is the c library, next you have to install a fortran library (after compiling the c libraries):
https://www.unidata.ucar.edu/downloads/ ... /index.jsp
4. If you have problem you can try to installa an older release of netcdf (netcdf 3.6.3 is working for yambo) where c and fortran source were not separated.

Best,
Daniele

[fchemam]

Hi, again,
thank you very much for u help,
ive used the netcdf3.6.3 its work, make , make check and make install no error
now the problem is the yambo linking with netcdf, isn't appear.
like this
#
# [VER] 3.4.1 r.3187
#
# [SYS] linux@x86_64
# [SRC] /home/chemam/yambo-3.4.1
# [BIN] /home/chemam/yambo-3.4.1/bin
# [FFT] Goedecker Fast Fourier transform with 0 cache
#
# [ ] Double precision
# [X] Redundant compilation
# [X] MPI
# [ ] OpenMP
# [X] PW (4.0) support
# [ ] ETSF I/O support
# [ ] SCALAPACK
# [ ] NETCDF/HDF5/Large Files
# [XX ] Built-in BLAS/LAPACK/LOCAL
#
# [ CPP ] gcc -E -P
# [ C ] gcc -g -O2 -D_C_US -D_FORTRAN_US
# [MPICC] mpicc -g -O2 -D_C_US -D_FORTRAN_US
# [ F90 ] gfortran -O3 -mtune=native
# [MPIF ] mpif90 -O3 -mtune=native
# [ F77 ] gfortran -O3 -mtune=native
# [Cmain]
# [NoOpt] -O0 -mtune=native
#
# [ MAKE ] make
# [EDITOR] vi
ive used this instruction ./configure --with-netcdf-include=/home/chemam/netcdf-3.6.3/include/ --with-netcdf-lib=/home/chemam/netcdf-3.6.3/lib/ --with-iotk=/home/chemam/espresso-5.0.2/iotk/ --with-p2y=4.0
best regards

[Daniele Varsano]

Dear Chemam,
Please verify that netcdf and yambo are compiled with the same compiler, next please post the config.log file and we will try to spot the problem.
Regards,
Daniele

[fchemam]

Hi,
the config.log is in attached
regards

[Daniele Varsano]

Dear Chemam,
I can't see anything strange in your configure, the netcdf are ignored so it is not easy to spot the problem.
As told before be sure you are using the same compiler for compiling netcdf and configuring yambo. In order to look exactly to which compiler your mpif90 is linked you can type mpif90 --version
You can also try to add in your configure --with-netcdf-link="-lnetcdff -lnetcdf" , but I do not think it will solve the problem.
You can also add --enable-msgs-comps, in order to add more verbosity in the config.log, this could help.
Finally, please note that netcdf library are not mandatory, you can run the code without using that, the advantage of netcdf is that you can move databases in machines with different architectures, and you need them to run the tutorials. The tutorials can be also run without netcdf but you have to run the ground state calculations first, and use the interface.

Best,
Daniele

[fchemam]

Hi,
if ive understand that after runnig yambo in terminal
u have this instruction, yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf), but u need to install netcdf to escape
this instruction.
me now im in this case, i cant undesrtand how to procede after.
i see the tutorial but no thing in my mind,
Best regards

[Daniele Varsano]

Dear Chemam,
yes, if you are running the tutorial you need the netcdf linked in order to run using the databases stored in the SAVE directory,
Anyway there are also the input for the ground state calculations under the PWSCF directory. If you run the ground state using pwscf (quantum espresso),
and generate your SAVE directory using p2y, you will have in the SAVE directos the s.db and s.wf databases (instead of ns.*) if p2y (and Yambo) are compiled without nectdf support and all the calculations can be run without using the netcdf.
Anyway the error you mention appears when you run yambo without having the SAVE directory in the directory you are running.
Are you running the tutorial or you system of interest?
In the latter case, did you perform the ground state calculation and run the interface (p2y or a2y)? Yambo have to be run in the directory where the SAVE directory is present. The SAVE directory is generated by the p2y, or a2y, interface. If you can't solve it, please report all the step you did before running yambo.
Best,
Daniele