strange crashes when using "heredocs" for convergence tests

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Moderator: Daniele Varsano

strange crashes when using "heredocs" for convergence tests

Postby chwolf » Mon Dec 31, 2018 2:47 am

Dear all,

I am using Yambo with QE 6.3 (GPL Version 4.2.1 Revision 110. (Based on r.14778 h.7b4dc3 MPI Build) and I encounter a strange problem when using Bash
's heredocs (cat >yambo.in <<EOF...) which I use for parameter optimization. When using Yambo interactively everything works but for convergence tests this is rather cumbersome..

I am only doing simple yambo -o c optics on graphene and I cat >yambo.in <<EOF the input file with simple $variable replacement. When I do this, yambo only runs through the initialization step but then stops just after [04] optics

Code: Select all
 [04] Optics
 ===========

 [RD./SAVE//ndb.dip_iR_and_P]--------------------------------
  Brillouin Zone Q/K grids (IBZ/BZ):  545  1089   545  1089
  RL vectors                   (WF):  3567
  Fragmentation                    :yes
  Electronic Temperature        [K]: 0.0000000
  Bosonic    Temperature        [K]: 0.0000000
  X band range           :   1   60
  X band range limits    :  8   9
  X e/h energy range [ev]:-1.0000000 -1.0000000
  RL vectors in the sum  :  3567
  [r,Vnl] included       :yes
  Using shifted grids    :no
  Using covariant dipoles:no
  Using G-space approach :yes
  Using R-space approach :no
  Direct v evaluation    :no
  Field momentum norm    :0.10000E-4
  Wavefunctions          :Perdew, Burke & Ernzerhof(X)+Perdew, Burke & Ernzerhof(C)
 - S/N 002163 -------------------------- v.04.02.01 r.00110 -


it creates a big empty core.XXXX file but writes nothing in the corresponding LOG file

Code: Select all
 <01s> P0010: Reading dip_iR_and_P_fragment_10
 <01s> P0010: Reading dip_iR_and_P_fragment_11
 <01s> P0010: Reading dip_iR_and_P_fragment_12
 <01s> P0010: Reading dip_iR_and_P_fragment_13
 <01s> P0010: Reading dip_iR_and_P_fragment_14
 <01s> P0010: Reading dip_iR_and_P_fragment_15


in the cluster error file it complains that a file is missing (but the file is there and it works when I run yambo interactively)
Code: Select all
[ERROR] STOP signal received while in :[04] Optics
[ERROR] File ; Variable DIP_iR_k_0274_spin_0001; NetCDF: Not a valid ID


is there something to do when using bash/pbs to run yambo non-interactively?

Thanks in advance for your help!

Chris

Code: Select all
for smear in $(seq 0.001 0.05 0.5); do

cat >yambo.in <<EOF
# GPL Version 4.2.1 Revision 110. (Based on r.14778 h.7b4dc3
#                        MPI Build                         
#                http://www.yambo-code.org                 
#
optics                         # [R OPT] Optics
chi                            # [R CHI] Dyson equation for Chi.
Chimod= "IP"                   # [X] IP/Hartree/ALDA/LRC/BSfxc
NGsBlkXd= 1            Ry      # [Xd] Response block size
% QpntsRXd
    1 |  1 |                 # [Xd] Transferred momenta
%
% BndsRnXd
   1 |  60 |                   # [Xd] Polarization function bands
%
% EnRngeXd
  0.00000 | 5.00000 | eV      # [Xd] Energy range
%
% DmRngeXd
  $smear |  $smear | eV      # [Xd] Damping range
%
ETStpsXd= 1000                  # [Xd] Total Energy steps
% LongDrXd
 0.000000 | 0.000000 | 1.000000 |        # [Xd] [cc] Electric Field
%
EOF


mpirun -machinefile $PBS_NODEFILE -np $NCORE /usr/local/qe-6.3/yambo-devel/bin/yambo -J smear-$smear

done
Christoph Wolf

Postech university, South Korea
chwolf@postech.ac.kr
chwolf
 
Posts: 12
Joined: Mon Jul 11, 2016 2:11 pm
Location: South Korea

Re: strange crashes when using "heredocs" for convergence te

Postby Daniele Varsano » Tue Jan 01, 2019 5:27 pm

Dear Christoph,
is there something to do when using bash/pbs to run yambo non-interactively?

I would say no. T
The same, or similar problem was reported here:
viewtopic.php?f=13&t=1493&p=7127&hilit=NetCDF%3A+Not+a+valid+ID#p7127
I do not remember exactly what was the source of the error, anyway, it was fixed in the more recent releases. I suggest you to update to a more recent
release.

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/
User avatar
Daniele Varsano
 
Posts: 1950
Joined: Tue Mar 17, 2009 2:23 pm

Re: strange crashes when using "heredocs" for convergence te

Postby chwolf » Thu Jan 03, 2019 2:14 pm

Thanks Daniele,

it seems to be working now!
Christoph Wolf

Postech university, South Korea
chwolf@postech.ac.kr
chwolf
 
Posts: 12
Joined: Mon Jul 11, 2016 2:11 pm
Location: South Korea


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