Yambo Community Forum

Respected Sir
I am installing yambo parallel in a cluster machine. For this I have configure with the command

./configure FC=/opt/intel/2013/bin/ifort --enable-msgs-comps F77=/opt/intel/2013/bin/ifort CC=/opt/intel/2013/bin/icc --with-iotk=/opt/espresso/5.1/intel/espresso-5.1/S3DE/iotk --with-p2y=5.1

But I get a warning massage highlighted below- Then when I have tried to make interfaces using the command “make interfaces” and get the following error massage. Could you please help me to solve this problem? I am waiting for your kind response.
Here I have attached the config.log . Thanking you.

Sincerely
Barnali Bhattacharya
Ph.D student
Assam University, India

Dear Barnali Bhattacharya

regarding the first problem:
if you do not specify where the mpif90 is, yambo checks the standard paths, and there it cannot find any.
Try to specify which mpif90 it has to use with in the ./configure command line.
For more details type in the yambo dir

Best,
m

Dear Barnali,
this looks a problem of the configuration of the MPI in your machine and not of Yambo.
Are the MPI in your cluster correctly installed?
Try to specify the parallel compiler by hand, as suggested by Myrta, if it is not present, you should ask some hep to your system administrator.
Best,
Daniele

Respected Sir (Daniele Varsano and Myrta Grüning),

Thanks a lot for your quick reply. I have checked the parallel version of quantum espresso which works fine.
Here I have attached the make.sys file for quantum espresso . Please help me to set 'PFC=' in the time of configuration.

I am waiting for your reply.
Thank you in advance.

Sincerely
Barnali Bhattacharya
Ph.D student
Assam university

Dear Barnali,
try to specify PFC=mpif90,
be sure that the mpif90 is in your PATH, otherwise you need to specify the PATH: somethinkg like:
/opt/intel/impi/version_number/intel64/bin/mpif90 (check which mpi is installed in your machine).

Anyway in you previous post it looks that the mpi path is not found, is it the case that in your cluster you need to load the MPI module first?
somehing like
module load mpi-module-name?

I'm just wondering as I do not know how your machine is configured.
Best,
Daniele

Respected Sir
According to your suggestion I have specify the path of mpif90 using PFC . Now I have used the command

./configure FC=/opt/intel/2013/bin/ifort --enable-msgs-comps F77=/opt/intel/2013/bin/ifort PFC=/opt/openmpi/1.6.5/intel/2013/bin/mpif90 CC=/opt/intel/2013/bin/icc --with-iotk=/opt/espresso/5.1/intel/espresso-5.1/S3DE/iotk --with-p2y=5.1

But I have found the same warning

...................................................................checking whether we are using the GNU Fortran 77 compiler... no
checking whether /opt/intel/2013/bin/ifort accepts -g... yes
checking if Fortran 77 compiler /opt/intel/2013/bin/ifort works... yes
checking for mpif90... /opt/openmpi/1.6.5/intel/2013/bin/mpif90
checking for MPI_Init... no
checking for MPI_Init in -lmpi... no
checking for MPI_Init in -lmpich... no
checking for a working mpif.h... no
checking for a working mpi.h... no
checking for a working mpi module... no
configure: WARNING: could not compile a FORTRAN mpi test program. YAMBO serial only.
checking for FFTW... no
checking the configuration of the LIBXC internal library... yes
configure: creating ./config.status
config.status: creating config/setup
config.status: creating config/Makefile
config.status: creating config/report
config.status: creating src/wf_and_fft/sgfft.F
...................................................................

And in the time of making interfaces again I have found the following error-
............................................................................
PP_PWscf_driver.o PP_PWscf_comp.o p2y_db1.o p2y_wf.o p2y_i.o -lint_modules -L/home/usarkar1/Y/yambo-3.4.1/lib -lbz_ops -lio -lcommon -lcommunicate -lparser -lmodules -lexternal_c -liotk -llapack -lblas -lxc -lm ) > /dev/null
/home/usarkar1/Y/yambo-3.4.1/lib/libiotk.a(iotk_error.o): In function `iotk_error_handler_x':
/opt/espresso/5.1/intel/espresso-5.1/S3DE/iotk/src/iotk_error.f90:497: undefined reference to `mpi_abort_'
make[1]: *** [p2y] Error 1
make[1]: Leaving directory `/home/usarkar1/Y/yambo-3.4.1/interfaces/p2y'
make: *** [interfaces] Error 2
.............................................................................................
Could you please tell me how can i overcome this problem?
I am waiting for your suggestion.
Thanking you.

Sincerely
Barnali Bhattacharya
Ph.D student, Assam university

Dear Barnali Bhattacharya

yambo cannot find the mpi library as it is not in the library path
http://www.open-mpi.org/faq/?category=r ... see%20here
You should probably ask the sys admin of the machine you are using for assistance.

Best
m

Respected sir,

Still I am trying to install Yambo parallel in my account. At that time I am using gfortran compiler. I have Configured with iotk by using the command -

./configure PFC=/opt/openmpi/1.4.3/gcc/4.5.2/bin/mpif90 MPICC=/opt/openmpi/1.4.3/gcc/4.5.2/bin/mpicc MPIF90=/opt/openmpi/1.4.3/gcc/4.5.2/bin/mpif90 --with-mpi=/opt/openmpi/1.4.3/gcc/4.5.2/lib/libmpi_f90.la --with-iotk=/opt/espresso/5.0.3/intel/2013/espresso-5.0.2/S3DE/iotk --with-p2y=5.0.2/

Now in the time of configuration the yambo found the mpi library;

.....................................................................................................
# [ ] Double precision
# [X] Redundant compilation
# [X] MPI
# [ ] OpenMP
# [X] PW (5.0) 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] /opt/openmpi/1.4.3/gcc/4.5.2/bin/mpicc -g -O2 -D_C_US -D_FORTRAN_US
# [ F90 ] gfortran -O3 -mtune=native
# [MPIF ] /opt/openmpi/1.4.3/gcc/4.5.2/bin/mpif90 -O3 -mtune=native
# [ F77 ] gfortran -O3 -mtune=native
# [Cmain]
# [NoOpt] -O0 -mtune=native
#
# [ MAKE ] make
# [EDITOR] vim

................................................................................................................................
Here I have attached the config.log for detail information. But I meet the following error when I am trying to make interfaces by using the command

make interfaces
....................................................................................................................

make[1]: Entering directory `/home/usarkar1/Y/yambo-3.4.1/interfaces/a2y'

/opt/openmpi/1.4.3/gcc/4.5.2/lib/libmpi_f90.la: file not recognized: File format not recognized
collect2: ld returned 1 exit status
make[1]: *** [a2y] Error 1
make[1]: Leaving directory `/home/usarkar1/Y/yambo-3.4.1/interfaces/a2y'
make: *** [interfaces] Error 2
..................................................................................................................
Please help me to overcome this problem.
I am waiting for your suggestion.
Thanking you.

Sincerely
Barnali Bhattacharya
Ph.D student, Assam university

Dear Barnali,
this is quite strange anyway, it is not really important to have the interfaces compiled in parallel.
I think that the easiest way to overcome the problem is to compile and use them in serial.
Best,
Daniele