p2y stops with qexml_read_cell IOTK error
Posted: Thu Jun 07, 2012 11:38 pm
Dear all,
I downloaded and compiled Quantum Espresso 5.0 together with tddfpt trying to calculate UV-vis spectroscopy for an extended system. Tests indicated that everything is fine but tddfpt only works for Gamma point at this moment. Therefore I had to resort to Yambo-3.2.5 . Both QE and Yambo are the the latest version. However, I had a problem with p2y, which is described in detail as follows.
Compliers used are composerxe/2011.5.220 and mpi/openmpi-1.4.5-intel. The architecture is x86_64. Compilation aimed at a parallel build. I tried two approaches: (1) compile Yambo together with QE by "$make pw yambo"; (2) complie QE first (tests indicate it was compiled correctly) and then configure and make Yambo afterwards. It seems to make no difference in terms of the problem of p2y. Taking the second approach as an example, the configuration was done by: $ ./configure --with-blas="-L/opt/intel/mkl/10.0.2.018/lib/em64t -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" --with-netcdf-include=/usr/include --with-netcdf-lib=/usr/lib64 --enable-netcdf-hdf5 --with-iotk=/home/hzu/espresso/iotk --with-p2y=4.0 PFC=mpif90 FC=mpif90 FCFLAGS="-O2 -assume byterecl -g -traceback -par-report0 -vec-report0 -nomodule -fpp -D__INTEL -D__FFTW3 -D__MPI -D__PARA -D__SCALAPACK -I../include -nofor_main". And make was done by: $make all.
After an scf run and an nscf run with wave functions collected, in the prefix.save, by typing $p2y, p2y stopped with the following message:
<---> P(W) 2 Y(ambo) Ver. 4.0
<---> DBs path set to .
<---> Index file set to data-file.xml
<---> Header/K-points/Energies...done
<---> Cell data...
[ERROR] STOP signal received while in :
[ERROR]Error in qexml_read_cell IOTK error ierr: 1
I browsed different forums and saw some problems with p2y but those problems came after the cell data stage. I looked at the logfile for make and didn't see anything wrong. The logfile for configure shows the following:
#
# [VER] 3.2.5 r.1015
#
# [SYS] linux@x86_64
# [SRC] /home/hzu/espresso/yambo-3.2.5
# [BIN] /home/hzu/espresso/yambo-3.2.5/bin
# [FFT] Goedecker Fast Fourier transform with 0 cache
#
# [ ] Double precision
# [X] Redundant compilation
# [X] MPI
# [X] PW (4.0) support
# [ ] ETSF I/O support
# [ ] SCALAPACK
# [ ] LibXC
# [ ] NETCDF/HDF5/Large Files
# [XX ] 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 ] mpif90 -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 -nomodule -fpp -D__INTEL -D__FFTW3 -D__MPI -D__PARA -D__SCALAPACK -I../include -nofor_main
# [MPIF ] mpif90 -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 -nomodule -fpp -D__INTEL -D__FFTW3 -D__MPI -D__PARA -D__SCALAPACK -I../include -nofor_main
# [ F77 ] mpif90 -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 -nomodule -fpp -D__INTEL -D__FFTW3 -D__MPI -D__PARA -D__SCALAPACK -I../include -nofor_main
# [Cmain]
# [NoOpt] -O0
#
# [ MAKE ] make
# [EDITOR] vim
#
It can be seen that although NETCDF include and lib paths were specified, somehow it didn't find the files. But I don't think that's the reason. In the config.log file, there are a few warning and error messages associated with conftest. Those may not be the reason either. So I don't know what might be wrong. I'd greatly appreciate your help by examining the attached files including config.log, configure.logfile, make.logfile, silicon.scf.in, silicon.nscf.in, and data-file.xml.
Best regards,
Jingsong Huang
Computer Sciences and Mathematics
Center for Nanophase Materials Sciences
Oak Ridge National Laboratory
Oak Ridge, TN 38831, USA
I downloaded and compiled Quantum Espresso 5.0 together with tddfpt trying to calculate UV-vis spectroscopy for an extended system. Tests indicated that everything is fine but tddfpt only works for Gamma point at this moment. Therefore I had to resort to Yambo-3.2.5 . Both QE and Yambo are the the latest version. However, I had a problem with p2y, which is described in detail as follows.
Compliers used are composerxe/2011.5.220 and mpi/openmpi-1.4.5-intel. The architecture is x86_64. Compilation aimed at a parallel build. I tried two approaches: (1) compile Yambo together with QE by "$make pw yambo"; (2) complie QE first (tests indicate it was compiled correctly) and then configure and make Yambo afterwards. It seems to make no difference in terms of the problem of p2y. Taking the second approach as an example, the configuration was done by: $ ./configure --with-blas="-L/opt/intel/mkl/10.0.2.018/lib/em64t -lmkl_intel_lp64 -lmkl_sequential -lmkl_core" --with-netcdf-include=/usr/include --with-netcdf-lib=/usr/lib64 --enable-netcdf-hdf5 --with-iotk=/home/hzu/espresso/iotk --with-p2y=4.0 PFC=mpif90 FC=mpif90 FCFLAGS="-O2 -assume byterecl -g -traceback -par-report0 -vec-report0 -nomodule -fpp -D__INTEL -D__FFTW3 -D__MPI -D__PARA -D__SCALAPACK -I../include -nofor_main". And make was done by: $make all.
After an scf run and an nscf run with wave functions collected, in the prefix.save, by typing $p2y, p2y stopped with the following message:
<---> P(W) 2 Y(ambo) Ver. 4.0
<---> DBs path set to .
<---> Index file set to data-file.xml
<---> Header/K-points/Energies...done
<---> Cell data...
[ERROR] STOP signal received while in :
[ERROR]Error in qexml_read_cell IOTK error ierr: 1
I browsed different forums and saw some problems with p2y but those problems came after the cell data stage. I looked at the logfile for make and didn't see anything wrong. The logfile for configure shows the following:
#
# [VER] 3.2.5 r.1015
#
# [SYS] linux@x86_64
# [SRC] /home/hzu/espresso/yambo-3.2.5
# [BIN] /home/hzu/espresso/yambo-3.2.5/bin
# [FFT] Goedecker Fast Fourier transform with 0 cache
#
# [ ] Double precision
# [X] Redundant compilation
# [X] MPI
# [X] PW (4.0) support
# [ ] ETSF I/O support
# [ ] SCALAPACK
# [ ] LibXC
# [ ] NETCDF/HDF5/Large Files
# [XX ] 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 ] mpif90 -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 -nomodule -fpp -D__INTEL -D__FFTW3 -D__MPI -D__PARA -D__SCALAPACK -I../include -nofor_main
# [MPIF ] mpif90 -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 -nomodule -fpp -D__INTEL -D__FFTW3 -D__MPI -D__PARA -D__SCALAPACK -I../include -nofor_main
# [ F77 ] mpif90 -O2 -assume byterecl -g -traceback -par-report0 -vec-report0 -nomodule -fpp -D__INTEL -D__FFTW3 -D__MPI -D__PARA -D__SCALAPACK -I../include -nofor_main
# [Cmain]
# [NoOpt] -O0
#
# [ MAKE ] make
# [EDITOR] vim
#
It can be seen that although NETCDF include and lib paths were specified, somehow it didn't find the files. But I don't think that's the reason. In the config.log file, there are a few warning and error messages associated with conftest. Those may not be the reason either. So I don't know what might be wrong. I'd greatly appreciate your help by examining the attached files including config.log, configure.logfile, make.logfile, silicon.scf.in, silicon.nscf.in, and data-file.xml.
Best regards,
Jingsong Huang
Computer Sciences and Mathematics
Center for Nanophase Materials Sciences
Oak Ridge National Laboratory
Oak Ridge, TN 38831, USA