I am having some problems in running Yambo (v4.0.1 r.88) with Netcdf libraries on a Cray machine.
I have successfully configured and compiled the code by linking with the cray-optimized Netcdf and HDF5 libraries. In particular, after running the configure script with the machine-specific flags, I get the following:
Code: Select all
#
# [VER] 4.0.1 r.88
#
# - GENERAL CONFIGURATIONS -
#
# [SYS] linux@x86_64
# [SRC] /home/e411/e411/fcaruso/espresso-5.1.2/yambo-4.0.1-epl
# [BIN] /home/e411/e411/fcaruso/espresso-5.1.2/yambo-4.0.1-epl/bin
# [-] Double precision
# [X] Redundant compilation
# [-] Run-Time timing profile
#
# - PARALLEL SUPPORT -
#
# [X] MPI (open-mpi kind)
# [-] OpenMP
# [-] Blue-Gene specific procedures
#
# - LIBRARIES (E=external library; I=internal library; -=not used;) -
#
# I/O
# [ E ] IOTK : /home/e411/e411/fcaruso/espresso-5.1.2/iotk//src/libiotk.a (QE 5.0)
# [ - ] ETSF_IO:
# [ E ] NETCDF : -L/opt/cray/netcdf-hdf5parallel/4.3.2/INTEL/140//lib -lnetcdff -lnetcdf (No large files support)
# [ E ] HDF5 : -L/opt/cray/hdf5-parallel/1.8.13/INTEL/140//lib -L/opt/cray/hdf5-parallel/1.8.13/INTEL/140//lib -lhdf5_fortran -lhdf5_hl -lhdf5 (No specific HDF5-IO support)
#
# MATH
# [ E ] FFT : -L/opt/cray/fftw/3.3.4.2/sandybridge//lib -lfftw3 (FFTW v3)
# [ E ] BLAS : -L/opt/intel/composer_xe_2013_sp1.4.211/mkl/lib/intel64/ -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
# [ E ] LAPACK : -L/opt/intel/composer_xe_2013_sp1.4.211/mkl/lib/intel64/ -Wl,--start-group -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -Wl,--end-group -ldl
# [ E ] SCALAPACK: -L/opt/intel/composer_xe_2013_sp1.4.211/mkl/lib/intel64/ -lmkl_scalapack_lp64
#
# OTHER
# [ I ] LibXC : -lxc
# [ - ] MPI library:
#
# - COMPILERS, MAKE and EDITOR -
#
# [ CPP ] cc -E -ansi -D_NETCDF_IO -D_MPI -D_FFTW -D_FFTW_OMP -D_SCALAPACK -D_OPENMPI
# [ C ] cc -g -O2 -D_C_US -D_FORTRAN_US
# [MPICC] cc -g -O2 -D_C_US -D_FORTRAN_US
# [ F90 ] ftn -assume bscc -O2 -static -ip -nofor\_main
# [MPIF ] ftn -assume bscc -O2 -static -ip -nofor\_main
# [ F77 ] ftn -assume bscc -O2 -static -ip -nofor\_main
# [Cmain] -Mnomain
# [NoOpt] -assume bscc -O0 -static -nofor\_main
#
# [ MAKE ] make
# [EDITOR] vim
#
However, when I run yambo for calculating the PPA quasi-particle corrections for Silicon I systematically run into the following error:
P0002: [ERROR] STOP signal received while in :[07] Dynamic Dielectric Matrix (PPA)
P0002: [ERROR][NetCDF] NetCDF: Unknown file format
This occurs whenever yambo finishes the computation of the first q point of the polarizability.
Additionally, the calculation does not crash and it keeps occupying the nodes of the cluster unless I delete the job manually.
I attach the input/output files of the calculation.
Any idea of the origin of this problem?
Thanks in advance for your help!
Best,
Fabio