[Pw_forum] possible i/o bug in turbo_lanczos.x and turbo_davidson.x 5.3.0
Giuseppe Mattioli
giuseppe.mattioli at ism.cnr.it
Thu Feb 4 17:48:06 CET 2016
Dear Iurii
Thanks for your help.
> First thing to do, I think, is to check that you
> have enough space on the disc.
Yes, there is
> You may want to look in the routine TDDFPT/src/lr_solve_e.f90 at lines 110-138 where the code writes vectors to the disc in parallel.
I've checked that the lines are very similar (substantially identical?) in 5.3.0 and 5.1.1. So it is very strange that the latter works when the
former does not.
> Please make
> sure that the "outdir" is the same in PWscf and in Lanczos/Davidson (and don't specify wfcdir).
Done, I've also tried to place "outdir" in local or distributed filesystem: always same results
> If this does not solve the problem, could you
> report please also the output of Lanczos/Davidson (better Lanczos)?
Lanczos output attached
I'm sending the same test to the fermi at cineca bluegene machine to see if the xlf compilers like my scripts more than the intel compilers...
Best Wishes
Giuseppe
On Thursday, February 04, 2016 03:46:10 PM Timrov Iurii wrote:
> Dear Giuseppe,
>
> As far as I understand the code crashes when it tries to write the vectors "d0psi" to the disc. First thing to do, I think, is to check that you
> have enough space on the disc. If this is not the issue, then let's continue looking for a reason.
>
> You may want to look in the routine TDDFPT/src/lr_solve_e.f90 at lines 110-138 where the code writes vectors to the disc in parallel. Please make
> sure that the "outdir" is the same in PWscf and in Lanczos/Davidson (and don't specify wfcdir). If this does not solve the problem, could you
> report please also the output of Lanczos/Davidson (better Lanczos)?
>
> HTH
>
> Best regards,
> Iurii Timrov
> Post-doctoral researcher
> THEOS - École Polytechnique Fédérale de Lausanne
> Lausanne, Switzerland
>
>
> ________________________________________
> From: pw_forum-bounces at pwscf.org <pw_forum-bounces at pwscf.org> on behalf of Giuseppe Mattioli <giuseppe.mattioli at ism.cnr.it>
> Sent: Thursday, February 4, 2016 11:34 AM
> To: pw_forum at pwscf.org
> Subject: [Pw_forum] possible i/o bug in turbo_lanczos.x and turbo_davidson.x 5.3.0
>
> Dear All
> I'm having problems when performing nontrivial runs of turbo_davidson.x and turbo_lanczos.x with 5.2.1 and 5.3.0 versions of QE.
> Let me say first that "trivial" runs (CH4 molecule with same pseudopotentials and cutoffs but a smaller 30 a.u.^3 cubic cell) work fine with all the
> tested versions.
> However, the input files for a nontrivial case that leads to crash should run on a decent pc in about 1 hr, so they provide a significant but not
> huge test. *Note* that if I run the same input files with the 5.1.1 version (compiled against the very same environment) everything goes (more
> slowly but) fine! The 5.3.0 (and 5.2.1) crashes have been reproduced on two different machines (intel 8 cores 16GB RAM, amd 32 cores 64 GB RAM), so
> they should not be considered as erratic.
>
> here is the pw.x run. The PPs are quite old and can be found in the online library (or provided by me on demand).
>
> &control
> calculation = 'scf'
> restart_mode='from_scratch',
> prefix='l0-5.3.0',
> pseudo_dir = '/home/mattioligi/PP_UPF/',
> outdir='/home/mattioligi/cocat/test_tddft/5.2.1/l0/5.3.0/run/tmp/',
> nstep=300,
> max_seconds=80000,
> disk_io='low',
> tprnfor=.true.,
> /
> &system
> ibrav=1, celldm(1)=40.000000,
> nat=42, ntyp=4, nbnd=75,
> ecutwfc = 40.0,
> ecutrho = 320.0,
> nspin=1,
> /
> &electrons
> diagonalization='david',
> mixing_mode='plain'
> mixing_beta=0.1
> conv_thr=1.0d-8
> electron_maxstep=100
> /
> &ions
> /
> ATOMIC_SPECIES
> O 15.999 O_pbe.van.UPF
> N 14.007 N.pbe-van_bm.UPF
> C 12.011 C_pbe.van.UPF
> H 1.008 H_pbe.van.UPF
> ATOMIC_POSITIONS {angstrom}
> C 4.815369179 12.355337788 8.111406911
> C 5.639537337 12.072210478 7.018248617
> C 6.373883049 10.886794669 6.974735758
> H 5.707874252 12.778745273 6.179910928
> C 4.734413944 11.441350355 9.166316558
> H 4.235443595 13.287281698 8.140567718
> C 6.304598307 9.977077773 8.041477142
> H 7.012644682 10.659891408 6.111132336
> C 5.477180541 10.260422385 9.138835842
> H 4.092409998 11.653694694 10.031778418
> H 5.418528381 9.546881383 9.971310698
> N 7.058612774 8.759574945 8.006208499
> C 6.384981399 7.544139013 8.340645249
> C 6.997532612 6.588483316 9.168188787
> C 5.084708421 7.308024697 7.864810575
> C 6.325550737 5.410241765 9.493833204
> H 8.006262126 6.776794433 9.557919083
> C 4.414663626 6.134355690 8.210976959
> H 4.597637090 8.055249046 7.224770074
> C 5.030975670 5.176070562 9.020776666
> H 6.819890970 4.670618768 10.138154855
> H 3.397721512 5.964689741 7.832306200
> H 4.503298572 4.249946635 9.284425745
> C 8.412602212 8.773905175 7.652414992
> C 9.197305040 9.938168667 7.841458619
> C 9.043381168 7.634703664 7.098599788
> C 10.533008285 9.972397555 7.486007356
> H 8.740413757 10.828552107 8.290447985
> C 10.383506998 7.674400214 6.758021800
> H 8.466388332 6.717306584 6.931252215
> C 11.175184928 8.838234071 6.927523312
> H 11.098162573 10.894629696 7.663657304
> H 10.849606517 6.778483121 6.322529487
> C 12.554045113 8.768090174 6.529797787
> C 13.538745611 9.729179498 6.474718127
> H 12.882286114 7.769870632 6.203237321
> C 13.338246843 11.096686263 6.810664645
> N 13.160471613 12.223162736 7.083088078
> C 14.914360413 9.407055683 6.034105289
> O 15.832284936 10.221452163 5.956798921
> O 15.091537629 8.085358800 5.710801225
> H 16.043983143 8.016066678 5.436328923
> K_POINTS {gamma}
>
> And here are the turbo_lanczos.x and turbo davidson.x input files
>
> lanczos
>
> &lr_input
> prefix="l0-5.3.0",
> outdir='/state/partition1/mattioligi/34339',
> wfcdir='/state/partition1/mattioligi/34339',
> restart_step=6,
> restart=.false.
> /
> &lr_control
> itermax=12,
> ipol=4,
> /
>
> davidson
>
> &lr_input
> prefix="l0-5.3.0",
> outdir='/state/partition1/mattioligi/34340',
> restart=.false.
> /
> &lr_dav
> num_eign=2
> num_init=4
> num_basis_max=10
> residue_conv_thr=1.0E-4
> start=0.1
> finish=1.5
> step=0.0002
> broadening=0.005
> reference=0.2
> p_nbnd_occ=5
> p_nbnd_virt=5
> poor_of_ram=.false.
> poor_of_ram2=.false.
> /
>
> In both cases and on both machines the CRASH report is something like
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> task # 1
> from davcio : error # 20
> error while writing from file "/state/partition1/mattioligi/34340/l0-5.3.0.d0psi.32"
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> I suppose that it is some kind of I/O error, but I warmly require your opinion...:-)
> Thank you in advance
> Giuseppe
>
> ********************************************************
> - Article premier - Les hommes naissent et demeurent
> libres et égaux en droits. Les distinctions sociales
> ne peuvent être fondées que sur l'utilité commune
> - Article 2 - Le but de toute association politique
> est la conservation des droits naturels et
> imprescriptibles de l'homme. Ces droits sont la liberté,
> la propriété, la sûreté et la résistance à l'oppression.
> ********************************************************
>
> Giuseppe Mattioli
> CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
> v. Salaria Km 29,300 - C.P. 10
> I 00015 - Monterotondo Stazione (RM), Italy
> Tel + 39 06 90672836 - Fax +39 06 90672316
> E-mail: <giuseppe.mattioli at ism.cnr.it>
> http://www.ism.cnr.it/english/staff/mattiolig
> ResearcherID: F-6308-2012
>
> _______________________________________________
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********************************************************
- Article premier - Les hommes naissent et demeurent
libres et égaux en droits. Les distinctions sociales
ne peuvent être fondées que sur l'utilité commune
- Article 2 - Le but de toute association politique
est la conservation des droits naturels et
imprescriptibles de l'homme. Ces droits sont la liberté,
la propriété, la sûreté et la résistance à l'oppression.
********************************************************
Giuseppe Mattioli
CNR - ISTITUTO DI STRUTTURA DELLA MATERIA
v. Salaria Km 29,300 - C.P. 10
I 00015 - Monterotondo Stazione (RM), Italy
Tel + 39 06 90672836 - Fax +39 06 90672316
E-mail: <giuseppe.mattioli at ism.cnr.it>
http://www.ism.cnr.it/english/staff/mattiolig
ResearcherID: F-6308-2012
-------------- next part --------------
Program turboTDDFT v.5.3.0 (svn rev. 11974) starts on 3Feb2016 at 11: 6:53
This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote
Parallel version (MPI), running on 8 processors
R & G space division: proc/nbgrp/npool/nimage = 8
Reading data from directory:
/tmp/mattioli/107868.blade-07.sic.rm.cnr.it/l0-5.3.0.save
Info: using nr1, nr2, nr3 values from input
Info: using nr1, nr2, nr3 values from input
IMPORTANT: XC functional enforced from input :
Exchange-correlation = SLA PW PBE PBE ( 1 4 3 4 0 0)
Any further DFT definition will be discarded
Please, verify this is what you really want
Parallelization info
--------------------
sticks: dense smooth PW G-vecs: dense smooth PW
Min 5090 2546 636 773298 273310 34176
Max 5092 2547 638 773308 273399 34182
Sum 40733 20369 5097 6186431 2186841 273425
Tot 20367 10185 2549
negative rho (up, down): 9.597E-02 0.000E+00
Subspace diagonalization in iterative solution of the eigenvalue problem:
one sub-group per k-point group (pool) will be used
scalapack distributed-memory algorithm (size of sub-group: 2* 2 procs)
Warning: There are virtual states in the input file, trying to disregard in response calculation
Ultrasoft (Vanderbilt) Pseudopotentials
Normal read
Gamma point algorithm
LANCZOS LINEAR-RESPONSE SPECTRUM CALCULATION
Number of Lanczos iterations = 12
Starting Lanczos loop 1
Lanczos iteration: 1 Pol:1
lr_apply_liouvillian: not applying interaction
alpha(00000001)= 0.000000
beta (00000001)= 8.601483
gamma(00000001)= 8.601483
z1= 1 0.000000000000000E+00 0.000000000000000E+00
z1= 2 0.000000000000000E+00 0.000000000000000E+00
z1= 3 0.000000000000000E+00 0.000000000000000E+00
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine davcio (22):
error while writing from file "/tmp/mattioli/107868.blade-07.sic.rm.cnr.it/l0-5.3.0.restart_lanczos.11"
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine davcio (22):
error while writing from file "/tmp/mattioli/107868.blade-07.sic.rm.cnr.it/l0-5.3.0.restart_lanczos.15"
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine davcio (22):
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine davcio (22):
error while writing from file "/tmp/mattioli/107868.blade-07.sic.rm.cnr.it/l0-5.3.0.restart_lanczos.13"
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine davcio (22):
error while writing from file "/tmp/mattioli/107868.blade-07.sic.rm.cnr.it/l0-5.3.0.restart_lanczos.17"
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
Error in routine davcio (22):
error while writing from file "/tmp/mattioli/107868.blade-07.sic.rm.cnr.it/l0-5.3.0.restart_lanczos.14"
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
error while writing from file "/tmp/mattioli/107868.blade-07.sic.rm.cnr.it/l0-5.3.0.restart_lanczos.18"
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
Error in routine davcio (22):
error while writing from file "/tmp/mattioli/107868.blade-07.sic.rm.cnr.it/l0-5.3.0.restart_lanczos.12"
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Error in routine davcio (22):
error while writing from file "/tmp/mattioli/107868.blade-07.sic.rm.cnr.it/l0-5.3.0.restart_lanczos.16"
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
stopping ...
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