Yambo Community Forum

Dear all,

I try the Si GW example, but I am unable to generate databases using p2y
When the following command is executed
p2y -F ./Si.save/data-file.xml
after running scf and nscf calulations with espresso I get the following error
[ERROR] STOP signal received while in :
[ERROR]Error in qexml_read_gk IOTK error ierr: 1

This has been addressed in an earlier post viewtopic.php?f=1&t=400&hilit=Error+in+ ... error+ierr
I tried all three remedies proposed by Stik Azzi but could not get around it.

I would appreciate any assistance regarding this error. I have given information about compilation of yambo below.

Thanks
Laalitha


Info:
Yambo version: 3.4.0 rev.2132 as given by yambo -H
espresso version: v.5.0.2 (svn rev. 9656)
Compilers for both yambo and espresso : Intel composer_xe_2013.2.146 on TACC stampede cluster
Yambo configure options

./configure FC=mpif90 F77=mpif90 CC=icc LDFLAGS=-nofor_main \
--with-blas="-L$MKLROOT/lib/intel64 $MKLROOT/lib/intel64/libmkl_blas95_lp64.a $MKLROOT/lib/intel64/libmkl_lapack95_lp64.a -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread -lm" \
--with-lapack="-L$MKLROOT/lib/intel64 $MKLROOT/lib/intel64/libmkl_blas95_lp64.a $MKLROOT/lib/intel64/libmkl_lapack95_lp64.a -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread -lm" \
--with-blacs="-L$MKLROOT/lib/intel64 $MKLROOT/lib/intel64/libmkl_blas95_lp64.a $MKLROOT/lib/intel64/libmkl_lapack95_lp64.a -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread -lm" \
--with-scalapack="-L$MKLROOT/lib/intel64 $MKLROOT/lib/intel64/libmkl_blas95_lp64.a $MKLROOT/lib/intel64/libmkl_lapack95_lp64.a -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread -lm" \
--with-iotk="/home1/02400/laalitha/work/codes/espresso-5.0.2/iotk/" \
--with-p2y=5.0

Output after running configure
#
# [VER] 3.4.0 r.2132
#
# [SYS] linux@x86_64
# [SRC] /home1/02400/laalitha/work/codes/yambo/build
# [BIN] /home1/02400/laalitha/work/codes/yambo/build/bin
# [FFT] Goedecker Fast Fourier transform with 0 cache
#
# [ ] Double precision
# [X] Redundant compilation
# [X] MPI
# [ ] OpenMP
# [X] PW (5.0) support
# [ ] ETSF I/O support
# [X] SCALAPACK
# [ ] 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 ] mpif90 -O
# [MPIF ] mpif90 -O
# [ F77 ] mpif90 -O
# [Cmain]
# [NoOpt] -O0
#
# [ MAKE ] make
# [EDITOR] vim
#

Dear laalitha,
please fill your signature with your name and complete affiliation. This is a rule of the forum.
It is not easy to understand what is going on with the information you provided. The compilation looks successful.
Please post your nscf input and output of quantum espresso, and the complete standard output of the p2y run, as we can
have a look to them.I presume you included in your input the wf_collect flag .true.

Best,

Daniele

Dear Daniele,

Thanks for your reply. I have attached the files and yes I have wf_collect flag set to true.

Dear Laalitha,
I can't see anything wrong in your outputs.
Did you compile the iotk libraries and the p2y converter with the same compiler?

Best,

Daniele

Dear Daniele,

Yes I did use the same compilers and libraries.
I have included the ldd output for each of the binaries for your reference.

pw.x
====
linux-vdso.so.1 => (0x00007fffac5e3000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003f6b800000)
libimf.so => /opt/apps/intel/13/composer_xe_2013.2.146/compiler/lib/intel64/libimf.so (0x00002b70f8bc8000)
libm.so.6 => /lib64/libm.so.6 (0x0000003f6b000000)
libmpichf90.so.8 => /opt/apps/intel13/mvapich2/1.9/lib/libmpichf90.so.8 (0x00002b70f9085000)
libmpich.so.8 => /opt/apps/intel13/mvapich2/1.9/lib/libmpich.so.8 (0x00002b70f9287000)
libopa.so.1 => /opt/apps/intel13/mvapich2/1.9/lib/libopa.so.1 (0x00002b70f985f000)
libmpl.so.1 => /opt/apps/intel13/mvapich2/1.9/lib/libmpl.so.1 (0x00002b70f9a61000)
libibmad.so.5 => /opt/ofed/lib64/libibmad.so.5 (0x00002b70f9c65000)
librdmacm.so.1 => /opt/ofed/lib64/librdmacm.so.1 (0x00002b70f9e7c000)
libibumad.so.3 => /opt/ofed/lib64/libibumad.so.3 (0x00002b70fa085000)
libibverbs.so.1 => /opt/ofed/lib64/libibverbs.so.1 (0x00002b70fa28b000)
librt.so.1 => /lib64/librt.so.1 (0x0000003f6c000000)
liblimic2.so.0 => /opt/apps/limic2/0.5.5//lib/liblimic2.so.0 (0x00002b70fa49a000)
libc.so.6 => /lib64/libc.so.6 (0x0000003f6ac00000)
/lib64/ld-linux-x86-64.so.2 (0x0000003f6a800000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003f70800000)
libdl.so.2 => /lib64/libdl.so.2 (0x0000003f6b400000)
libintlc.so.5 => /opt/apps/intel/13/composer_xe_2013.2.146/compiler/lib/intel64/libintlc.so.5 (0x00002b70fa69c000)
libifport.so.5 => /opt/apps/intel/13/composer_xe_2013.2.146/compiler/lib/intel64/libifport.so.5 (0x00002b70fa8eb000)
libifcore.so.5 => /opt/apps/intel/13/composer_xe_2013.2.146/compiler/lib/intel64/libifcore.so.5 (0x00002b70fab1a000)
libsvml.so => /opt/apps/intel/13/composer_xe_2013.2.146/compiler/lib/intel64/libsvml.so (0x00002b70fae50000)
libirng.so => /opt/apps/intel/13/composer_xe_2013.2.146/compiler/lib/intel64/libirng.so (0x00002b70fb81c000)

p2y
======
linux-vdso.so.1 => (0x00007fff37dff000)
libmkl_scalapack_lp64.so => /opt/apps/intel/13/composer_xe_2013.2.146/mkl/lib/intel64/libmkl_scalapack_lp64.so (0x00002ba6985c2000)
libmkl_intel_lp64.so => /opt/apps/intel/13/composer_xe_2013.2.146/mkl/lib/intel64/libmkl_intel_lp64.so (0x00002ba698e70000)
libmkl_sequential.so => /opt/apps/intel/13/composer_xe_2013.2.146/mkl/lib/intel64/libmkl_sequential.so (0x00002ba699596000)
libmkl_core.so => /opt/apps/intel/13/composer_xe_2013.2.146/mkl/lib/intel64/libmkl_core.so (0x00002ba699c3d000)
libmkl_blacs_intelmpi_lp64.so => /opt/apps/intel/13/composer_xe_2013.2.146/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so (0x00002ba69aea0000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x0000003f6b800000)
libm.so.6 => /lib64/libm.so.6 (0x0000003f6b000000)
libmpichf90.so.8 => /opt/apps/intel13/mvapich2/1.9/lib/libmpichf90.so.8 (0x00002ba69b0ee000)
libmpich.so.8 => /opt/apps/intel13/mvapich2/1.9/lib/libmpich.so.8 (0x00002ba69b2f0000)
libopa.so.1 => /opt/apps/intel13/mvapich2/1.9/lib/libopa.so.1 (0x00002ba69b8c9000)
libmpl.so.1 => /opt/apps/intel13/mvapich2/1.9/lib/libmpl.so.1 (0x00002ba69baca000)
libibmad.so.5 => /opt/ofed/lib64/libibmad.so.5 (0x00002ba69bcce000)
librdmacm.so.1 => /opt/ofed/lib64/librdmacm.so.1 (0x00002ba69bee6000)
libibumad.so.3 => /opt/ofed/lib64/libibumad.so.3 (0x00002ba69c0ee000)
libibverbs.so.1 => /opt/ofed/lib64/libibverbs.so.1 (0x00002ba69c2f4000)
librt.so.1 => /lib64/librt.so.1 (0x0000003f6c000000)
liblimic2.so.0 => /opt/apps/limic2/0.5.5//lib/liblimic2.so.0 (0x00002ba69c503000)
libc.so.6 => /lib64/libc.so.6 (0x0000003f6ac00000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x0000003f70800000)
libdl.so.2 => /lib64/libdl.so.2 (0x0000003f6b400000)
/lib64/ld-linux-x86-64.so.2 (0x0000003f6a800000)
libifport.so.5 => /opt/apps/intel/13/composer_xe_2013.2.146/compiler/lib/intel64/libifport.so.5 (0x00002ba69c706000)
libifcore.so.5 => /opt/apps/intel/13/composer_xe_2013.2.146/compiler/lib/intel64/libifcore.so.5 (0x00002ba69c935000)
libimf.so => /opt/apps/intel/13/composer_xe_2013.2.146/compiler/lib/intel64/libimf.so (0x00002ba69cc6b000)
libintlc.so.5 => /opt/apps/intel/13/composer_xe_2013.2.146/compiler/lib/intel64/libintlc.so.5 (0x00002ba69d128000)
libsvml.so => /opt/apps/intel/13/composer_xe_2013.2.146/compiler/lib/intel64/libsvml.so (0x00002ba69d376000)
libirng.so => /opt/apps/intel/13/composer_xe_2013.2.146/compiler/lib/intel64/libirng.so (0x00002ba69dd42000)


Thanks
Laalitha

Hi Laalitha,
Can you try going into the Si.save folder, and running
p2y
without any -F options? The -F is there for back compatibility with an old interface method (pw_export) which generated a file called index.xml instead of data-file.xml, and isn't meant to be used in a different folder. Probably it causes more confusion now than anything else and can be removed.
Conor

Dear Conor,

Yes that solved the problem. Thanks very much.

Laalitha