run yambo

[sdwang]

Dear developers；
I install netcdf first and it run well.Then I install yambo as the following procedure:
1. ./configure --with-netcdf-include=/home/sdwang/netcdf/include/ --with-netcdf-lib=/home/sdwang/netcdf/lib/ --with-iotk=/home/raman/espresso-3.2.3/iotk/ --with-p2y=3.2
2. I got :
[VER] 3.2.1 r.448
#
# [SYS] linux@x86_64
# [SRC] /home/sdwang/yambo-3.2.1-r.448
# [BIN] /home/sdwang/yambo-3.2.1-r.448/bin
# [FFT] Goedecker Fast Fourier transform with 0 cache
#
# [ ] Double precision
# [X] Redundant compilation
# [X] MPI
# [X] PW (3.2) support
# [ ] ETSF I/O support
# [ ] SCALAPACK
# [ ] NETCDF/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 ] ifort -assume bscc -O3 -ip -tpp7
# [MPIF ] mpif90 -assume bscc -O3 -ip -tpp7
# [ F77 ] ifort -assume bscc -O3 -ip -tpp7
# [Cmain] -nofor_main
# [NoOpt] -assume bscc -O0 -tpp7
#
# [ MAKE ] make
# [EDITOR] vi
3. make all

Then I reach in the sample/bulk_silicon/,and do
gunzip database_DB1_NETCDF_format.gz
> /home/sdwang/netcdf/bin/ncgen -o ns.db1 database_DB1_NETCDF_format
> gunzip database_WF_NETCDF_format.gz
> /home/sdwang/netcdf/bin/ncgen -o ns.wf database_WF_NETCDF_format

after this, I input /home/sdwang/yambo-3.2.1-r.448/bin/yambo,but it appears

yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)


What is my problem?

sd wang
Southeast University in Nanjing

[Daniele Varsano]

From your configure oputput, the netcdf option is not crossed.
It means that they are not linked properly. Please check in config.log
what is happening, and if you cannot solve it, post here the config.log file.

Regards,

Daniele

[sdwang]

This is my config.log:
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by Yambo configure 3.2.1 r.448 , which was
generated by GNU Autoconf 2.59. Invocation command line was

$ ./configure --with-netcdf-include=/home/sdwang/net/local/include/ --with-netcdf-lib=/home/sdwang/net/local/lib/ --with-iotk=/home/sdwang/espresso-3.2.3/iotk/ --with-p2y=3.2

[andrea marini]

Dear sdwang, I have edited your post. Please attach big files as gzipped attachments. Otherwise the post is unreadable.

[Daniele Varsano]

Dear Sdwang

looking at the logfile you post, there is not any reference to the netcdf libraries.
Please, be sure to include the right path in the options:
--with-netcdf-include=
and
--with-netcdf-lib=


i.e.: it is present libnetcdf.a in /home/sdwang/net/local/lib/ ?
moreover it is important that the netcdf library are compiled with the same compiler you are
compiling yambo.

Regards,

Daniele

[sdwang]

If I want to configure with f95,should I set :./configure --with-netcdf-include=/home/sdwang/net/local/include/ --with-netcdf-lib=/home/sdwang/net/local/lib/ --with-iotk=/home/sdwang/espresso-3.2.3/iotk/ --with-p2y=3.2 --enable-f95?

Or, I want to use F95 configure the yambo, What I should do?

Thanks!

[Daniele Varsano]

Dear Sdwang,

let me ask you to fill your signature when submitting a post. You can do it directly in your profile. This is a rule of the forum.


In this way it should work:

/configure --with-netcdf-include=/home/sdwang/net/local/include/ --with-netcdf-lib=/home/sdwang/net/local/lib/ --with-iotk=/home/sdwang/espresso-3.2.3/iotk/ --with-p2y=3.2 FC=f95

otherwise export your compiler variable before configuring Yambo:

export FC=f95
./configure .....

Regards,

Daniele

[sdwang]

I compile yambo with:
./configure --with-netcdf-include=/home/sdwang/netcdf/include/ --with-netcdf-lib=/home/sdwang/netcdf/lib/ --with-iotk=/home/sdwang/espresso-3.2.3/iotk/ --with-p2y=3.2 FC=ifort, and then "make all" ,the result is:
#
# [VER] 3.2.1 r.448
#
# [SYS] linux@x86_64
# [SRC] /home/sdwang/yambo-3.2.1-r.448
# [BIN] /home/sdwang/yambo-3.2.1-r.448/bin
# [FFT] Goedecker Fast Fourier transform with 0 cache
#
# [ ] Double precision
# [X] Redundant compilation
# [X] MPI
# [X] PW (3.2) support
# [ ] ETSF I/O support
# [ ] SCALAPACK
# [X ] NETCDF/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 ] ifort -assume bscc -O3 -ip -tpp7
# [MPIF ] mpif90 -assume bscc -O3 -ip -tpp7
# [ F77 ] ifort -assume bscc -O3 -ip -tpp7
# [Cmain] -nofor_main
# [NoOpt] -assume bscc -O0 -tpp7
#
# [ MAKE ] make
# [EDITOR] vi
#

and NETCDF is compiled with ./configure FC=ifort prefix==/home/sdwang/netcdf/, it seems right.
But "yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)" also appears.


Sdwang

Southeast University

[andrea marini]

and NETCDF is compiled with ./configure FC=ifort prefix==/home/sdwang/netcdf/, it seems right.
But "yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)" also appears.

This is very strange. If you compiled with NETCDF support then you should be able to read the databases. So let's move step by step

1. Do a make clean_all and Post the list of files in the lib and include directories immediately after the configure. You should see something like
   

   Code: Select all

   ./lib/libnetcdf_c++.a
   ./lib/libnetcdf.a
   ./config/netcdf_f90.m4
   ./include/netcdf.mod
   ./include/netcdf.h
   ./include/netcdf.inc
   ./include/netcdfcpp.h
   ./include/netcdf.hh
   

   If these files are present then yambo will be properly compiled.
2. Are you sure you're running the code UP of the SAVE folder ? Please post the result of ls -R in the directory where you're running yambo.

Sdwang
Southeast University

Please.... we do need you COMPLETE name and your COMPLETE affiliation. I have no idea where the Southeast University and I am sure your name is not only sdwang! Edit these informations in your signature that you can access via your User control panel.

[sdwang]

This my configure.log of yambo-3.2.1-r.448 and netcdf-4.0.1,please check it.Thanks!

Shudong Wang

Department of Physics os Southeast University in Nanjing ,China