yambo: command not found

[marsusi]

Dear All,

I typed
" ./configure --enable-mpi="yes" --with-mpi-prefix="/usr" --with-netcdf-include="-I/usr/include/" --with-linalg-flavor="atlas" --with-linalg-libs="-L/usr/lib -llapack -lf77blas -lcblas -latlas" --with-netcdf-lib="-L/usr/lib/ -lnetcdf -lnetcdff" "
in order to compile yambo with netcdf,
then typed
" make yambo interfaces".
No problem was reported, and typing ~/bin/yambo results in: "yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)".
That's good till now, but in executing process, when go to SAVE directory of YAMBO and type "yambo", get this message:
"yambo: command not found",
and if type ~/bin/yambo get:
"yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)".
In fact no command is working. Any help would be so appriciated, the config.log file is attached to this mail.

Many thanks in advance,

F.Marsusi,
Amirkabir University of Technology,
Tehran.

[myrta gruning]

Dear Marsusi

there is nothing wrong with your yambo compilation. as you said the yambo executable is created in the bin.

1. If you want to type just yambo then you have to set the PATH environment variable in your unix/linx shell accordingly (see e.g. http://www.codecoffee.com/tipsforlinux/articles/11.html).
2. You should not be in the SAVE directory, but in a directory containing the SAVE.

Hope this helps
Myrta

[marsusi]

Dear Myrta,

Thanks a lot. I set envierment variable in .bashrc, and yambo command is recognized now. But again yambo complains of access to CORE database (SAVE/*db1 and/or SAVE/*wf)", even in SAVE directory.

Marsusi,
Amirkabir university,
Tehran.

[myrta gruning]

Dear Marsusi

as I said in my previous post

2. You should not be in the SAVE directory, but in a directory containing the SAVE.

Further, did you use the interfaces (a2y/p2y)?
the SAVE directory has to contain the core files generated using the interfaces (or downloaded in case of some tutorial) to convert the results from a previous DFT calculations (follow the links in http://www.yambo-code.org/doc/index.php to see how)

m

[marsusi]

Dear Myrta,

Thank you very much for the so quick answer. Unfortunately still it doesn't work. I am using tutorial examples. Taking a list shows:
> ls SAVE
>ns.db1 ns.wf
>yambo
>yambo: cannot access CORE database (SAVE/*db1 and/or SAVE/*wf)
Is any problem in configuration?

Marsusi.

[Daniele Varsano]

Dear Marsusi,
Most probably the netcdf libs have not been properly linked. Unfortunately right now I can't see your config.log files as I do not have a laptop with me. Check it or otherwise produce new databases without the netcdf support.
Best
Daniele

[marsusi]

Dear Myrta and Daniel,

Yambo is working without netcdf support, but still I don't understand, why it was faild to compile netcdf within yambo.

Marsusi.

[myrta gruning]

I looked at the config.log and indeed yambo did not linked to netcdf.
Note that after the configure you get somthing like:

Code: Select all

#
# [VER] 3.4.1 r.3187
# 
# [SYS] linux@x86_64
# [SRC] /data/myrta/Src/yambo-gpl/stable
# [BIN] /data/myrta/Src/yambo-gpl/stable/bin
# [FFT] External Fast Fourier transform
#
# [ ] Double precision
# [X] Redundant compilation  
# [X] MPI 
# [ ] OpenMP 
# [X] PW (5.0) support
# [ ] ETSF I/O support
# [ ] SCALAPACK
# [X  ] NETCDF/HDF5/Large Files 
# [  X] Built-in BLAS/LAPACK/LOCAL
#
# [ CPP ] icc -E -ansi  
# [  C  ] icc -g -O2 -D_C_US -D_FORTRAN_US
# [MPICC] mpicc -g -O2 -D_C_US -D_FORTRAN_US
# [ F90 ] ifort -assume bscc -O3 -ip -xHost   
# [MPIF ] mpif90 -assume bscc -O3 -ip -xHost   
# [ F77 ] ifort -assume bscc -O3 -ip -xHost
# [Cmain] -nofor_main
# [NoOpt] -assume bscc -O0 -xHost
#
# [ MAKE ] make
# [EDITOR] vim
#

This information is then stored in the config/report.
The X in

Code: Select all

# [X  ] NETCDF/HDF5/Large Files 

tells you that yambo will link to NETCDF.

There can be two main reasons that the link does not work.
1. Error in the path
2. Netcdf is compiled with a different c compiler.

2. is quite unfortunate as that means you would need to compile the netcdf. Just assume this is not the case.

Try (after a make clean_all)

Code: Select all

./configure --enable-mpi="yes" --with-mpi-prefix="/usr" --with-netcdf-include="/usr/include/" --with-linalg-flavor="atlas" --with-linalg-libs="-L/usr/lib -llapack -lf77blas -lcblas -latlas" --with-netcdf-lib="/usr/lib/"

After the configure, from the report you can check if it worked or not.

Best
m

[marsusi]

Dear Myrta,

Many thank. I followed your proposed configure expression.
At the end, I received this report:

configure: WARNING: unrecognized options: --enable-mpi, --with-mpi-prefix, --with-linalg-flavor, --with-linalg-libs

#
# [VER] 3.4.1 r.3187
#
# [SYS] linux@x86_64
# [SRC] /home/farah/local/yambo-3.4.1
# [BIN] /home/farah/local/yambo-3.4.1/bin
# [FFT] Goedecker Fast Fourier transform with 0 cache
#
# [ ] Double precision
# [X] Redundant compilation
# [X] MPI
# [ ] OpenMP
# [ ] PW (5.0) support
# [ ] ETSF I/O support
# [ ] SCALAPACK
# [X ] 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] vim
#
./configure: line 38: sort: No such file or directory
./configure: line 35: sed: No such file or directory

But, unfortunately it still doesn't work. The log file is attached.

Marsusi.

[myrta gruning]

Dear Marsusi

yes some options you used do not applied to yambo. Using

Code: Select all

.configure -help

you see which options you have and their usage.

Coming to the netcdf problem, I cannot see much from the config.log, just that netcdf libs and include files were found and worked in small dummy programs.

Just to double check:
you did 'make clean_all'
you rerun the .configure with the options as above
then you did again
make yambo
(make interfaces etc..)
and then you use the recompiled yambo again in a directory containing the SAVE (containing ndb.* and ns.* files) and you get the same error message?

Just want to be sure before let you go into compiling netcdf.

Best
m