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
#
IOTK error in p2y for espresso-5.0.2
Moderators: Davide Sangalli, andrea.ferretti, myrta gruning, andrea marini, Daniele Varsano, Conor Hogan, Nicola Spallanzani
Forum rules
If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
(2) the architecture (e.g. 64-bit IBM SP5)
(3) if the problems occur compiling in serial/in parallel
(4) the version of Yambo (revision number/major release version)
(5) the relevant compiler error message
If you have trouble compiling Yambo, please make sure to list:
(1) the compiler (vendor and release: e.g. intel 10.1)
(2) the architecture (e.g. 64-bit IBM SP5)
(3) if the problems occur compiling in serial/in parallel
(4) the version of Yambo (revision number/major release version)
(5) the relevant compiler error message
-
- Posts: 4
- Joined: Fri Jun 21, 2013 10:12 pm
IOTK error in p2y for espresso-5.0.2
Laalitha Liyanage, Ph.D.
Central Michigan University
University of North Texas
URL:https://sites.google.com/site/lsiliyanage
Central Michigan University
University of North Texas
URL:https://sites.google.com/site/lsiliyanage
- Daniele Varsano
- Posts: 4198
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: IOTK error in p2y for espresso-5.0.2
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
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
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
-
- Posts: 4
- Joined: Fri Jun 21, 2013 10:12 pm
Re: IOTK error in p2y for espresso-5.0.2
Dear Daniele,
Thanks for your reply. I have attached the files and yes I have wf_collect flag set to true.
Thanks for your reply. I have attached the files and yes I have wf_collect flag set to true.
You do not have the required permissions to view the files attached to this post.
Laalitha Liyanage, Ph.D.
Central Michigan University
University of North Texas
URL:https://sites.google.com/site/lsiliyanage
Central Michigan University
University of North Texas
URL:https://sites.google.com/site/lsiliyanage
- Daniele Varsano
- Posts: 4198
- Joined: Tue Mar 17, 2009 2:23 pm
- Contact:
Re: IOTK error in p2y for espresso-5.0.2
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
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
Dr. Daniele Varsano
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
S3-CNR Institute of Nanoscience and MaX Center, Italy
MaX - Materials design at the Exascale
http://www.nano.cnr.it
http://www.max-centre.eu/
-
- Posts: 4
- Joined: Fri Jun 21, 2013 10:12 pm
Re: IOTK error in p2y for espresso-5.0.2
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
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
Laalitha Liyanage, Ph.D.
Central Michigan University
University of North Texas
URL:https://sites.google.com/site/lsiliyanage
Central Michigan University
University of North Texas
URL:https://sites.google.com/site/lsiliyanage
- Conor Hogan
- Posts: 111
- Joined: Tue Mar 17, 2009 12:17 pm
- Contact:
Re: IOTK error in p2y for espresso-5.0.2
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
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
Dr. Conor Hogan
CNR-ISM, via Fosso del Cavaliere, 00133 Roma, Italy;
Department of Physics and European Theoretical Spectroscopy Facility (ETSF),
University of Rome "Tor Vergata".
CNR-ISM, via Fosso del Cavaliere, 00133 Roma, Italy;
Department of Physics and European Theoretical Spectroscopy Facility (ETSF),
University of Rome "Tor Vergata".
-
- Posts: 4
- Joined: Fri Jun 21, 2013 10:12 pm
Re: IOTK error in p2y for espresso-5.0.2
Dear Conor,
Yes that solved the problem. Thanks very much.
Laalitha
Yes that solved the problem. Thanks very much.
Laalitha
Laalitha Liyanage, Ph.D.
Central Michigan University
University of North Texas
URL:https://sites.google.com/site/lsiliyanage
Central Michigan University
University of North Texas
URL:https://sites.google.com/site/lsiliyanage