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initialization [ERROR][NetCDF] NetCDF:
Posted: Wed Oct 23, 2013 10:40 am
by feffefico
Hi all.
I am sorry to open a new topic, but i cannot find any other discussions on that.
I am working on PLX -cineca, I compiled the stable version 340-rev2750 .
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./configure --with-iotk=/cineca/prod/build/applications/qe/4.3.1/openmpi--1.4.4--intel--co-2011.6.233--binary/BA_WORK/espresso-4.3.1/iotk --with-p2y=4.3 --with-mpi --enable-netcdf-LFS --enable-netcdf-hdf5 --with-netcdf-include=/plx/userexternal/mpalummo/D_sources/netcdf/try/include --with-netcdf-lib=/plx/userexternal/mpalummo/D_sources/netcdf/try/lib --with-netcdf-link=-lnetcdf -lnetcdff -lsz -lz -lm
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Currently Loaded Modulefiles:
1) autoload/0.1/verbose
2) profile/advanced
3) intel/co-2011.6.233--binary
4) openmpi/1.4.4--intel--co-2011.6.233--binary
5) szip/2.1--intel--co-2011.6.233--binary
6) hdf5/1.8.7_ser--intel--co-2011.6.233--binary
7) qe/4.3.1
No problem in compilation.
I run my p2y I got the database fine.
I initialize: /pathtoyambo/yambo -i -V RL
and I got my yambo.in file
when then I run with the submission script or even from command line yambo, I got this message:
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ERROR] STOP signal received while in :
[ERROR][NetCDF] NetCDF: Variable not found
I put in attachement the tar file with all the interesting files to look at.
Someone can give me an advice?
Before using this version I was using the developement one of ver 340 - rev2132 and I didn't get any problem.
Thanks in advance.
federico iori
postdoc at DISMI - University of Modena and Reggio Emilia
Re: initialization [ERROR][NetCDF] NetCDF:
Posted: Wed Oct 23, 2013 11:11 am
by feffefico
I got the code working. I do not know what happened. maybe the database was not well writte. I redid everythign from scratch now p2y and initialization with yambo are ok.
sorry about that.
Re: initialization [ERROR][NetCDF] NetCDF:
Posted: Tue Apr 22, 2014 8:37 am
by leoteo
Dear all,
we are using yambo Version 3.4.1 Revision 3187 and experiencing the same problem.
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__ __ ______ ____ _____
/\ \ /\ \\ _ \ /"\_/`\/\ _`\ /\ __`\
\ `\`\\/"/ \ \L\ \/\ \ \ \L\ \ \ \/\ \
`\ `\ /" \ \ __ \ \ \__\ \ \ _ <" \ \ \ \
`\ \ \ \ \ \/\ \ \ \_/\ \ \ \L\ \ \ \_\ \
\ \_\ \ \_\ \_\ \_\\ \_\ \____/\ \_____\
\/_/ \/_/\/_/\/_/ \/_/\/___/ \/_____/
<11s> [01] Files & I/O Directories
<12s> [02] CORE Variables Setup
<12s> [02.01] Unit cells
<22s> [02.02] Symmetries
<22s> [02.03] RL shells
<24s> Shells finder | | [000%] --(E) --(X)
<24s> P001: Shells finder |####################| [100%] --(E) --(X)
<22s> P034: [02.04] K-grid lattice<24s> P020: [02.04] K-grid lattice
<24s> P018: [02.05] Energies [ev] & Occupations
<22s> P025: [02.05] Energies [ev] & Occupations<26s> P001: [03] Transferred momenta grid
<26s> P001: X indexes | | [000%] --(E) --(X)
<26s> P001: X indexes |####################| [100%] --(E) --(X)
<26s> SE indexes | | [000%] --(E) --(X)
<22s> P025: [03] Transferred momenta grid
P025: [ERROR] STOP signal received while in :[03] Transferred momenta grid
P025: [ERROR][NetCDF] NetCDF: Variable not found
It seems that (at least sometimes) the error occurs only during the
first setup run. When the setup run is simply repeated, it can finish without problems (attached are l_ and r_ files from the two runs).
Still, it would be very helpful to get to the bottom of this issue, also in order to make sure that it does not potentially lead to other problems in the calculation.
We are using netcdf 4.2.1.1 together with the intel compiler 13.1.3. Below are the result of the configure when making yambo.
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#
# [VER] 3.4.1 r.3187
#
# [SYS] linux@x86_64
# [SRC] /gpfs/work/pr89mi/pr3da262/TEST/yambo-fat/devel
# [BIN] /gpfs/work/pr89mi/pr3da262/TEST/yambo-fat/devel/bin
# [FFT] External Fast Fourier transform
#
# [ ] Double precision
# [X] Redundant compilation
# [X] MPI
# [ ] OpenMP
# [X] PW (5.0) support
# [ ] ETSF I/O support
# [X] SCALAPACK
# [X ] 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 ] ifort -assume bscc -O3 -ip -xHost
# [MPIF ] mpif90 -assume bscc -O3 -ip -xHost
# [ F77 ] ifort -assume bscc -O3 -ip -xHost
# [Cmain] -nofor_main
# [NoOpt] -assume bscc -O0 -xHost
#
# [ MAKE ] make
# [EDITOR] vim
#
Best,
Leopold
Re: initialization [ERROR][NetCDF] NetCDF:
Posted: Tue Apr 22, 2014 10:26 am
by Daniele Varsano
Dear Leopold,
NECDF problem, never easy to spot.
Just a question, does it happen also if you run the initialization in serial mode?
Moreover, the second run it looks is doing nothing, looking at report is just reading the previously stored databases (RD), while the first run even if it crash looks to write them (WR).
We will have a look at it.
Best,
Daniele
Re: initialization [ERROR][NetCDF] NetCDF:
Posted: Tue Apr 22, 2014 11:01 am
by leoteo
Dear Daniele,
thanks a lot for the fast reply!
And yes - when I removed the gops and kindx databases and redid the setup with 1 MPI task, it ran without problems (reports attached).
So, for the moment I will switch to one MPI task for the setup and if this error pops up again I will report.
Best,
Leo