[Pw_forum] "Lanczos.x with k-point algorithm"
Sajid Ali
Sajid.Ali at student.uts.edu.au
Mon Jan 18 01:05:40 CET 2016
Dear,
Iurii Timrov
i am Sorry, It was a typo, i meant QE-5.3.0.
SAJID ALI
Cell#+61449764974
Ph.D. Scholar
School of Mathematical and Physical Sciences
University of Technology, Sydney
Australia
________________________________________
From: Iurii Timrov <itimrov at sissa.it>
Sent: 17 January 2016 20:43
To: Sajid Ali
Cc: PWSCF Forum
Subject: Re: [Pw_forum] "Lanczos.x with k-point algorithm"
Dear Sajid Ali,
On 2016-01-17 00:40, Sajid Ali wrote:
> Dear,
> Iurii Timrov
> I have tried using QE-5.5.0 for both SCF and TDDFPT
This version does not exist...
> But i recieived
> similar kind of error in lanczos.x output
> i.e. "mpirun noticed that process rank 1 with PID 1046 on node ermdc06
> exited on signal 11 (Segmentation fault)".
> Cant find a way out of it....?
>
Do you perform a calculation for CH4 without any modifications? In your
test do you use gamma_only case or general k points algorithm?
Do you run your calculation on a cluster using some script? How many
cores did you use? How did you install QE? Could you ask your system
administrator to help you? Try to run the code on a local workstation
and see if it crashes.
Please provide more details (every step you do), because otherwise I
cannot help you.
> SAJID ALI
> Cell#+61449764974
> Ph.D. Scholar
> School of Mathematical and Physical Sciences
> University of Technology, Sydney
> Australia
>
>
Iurii Timrov
Postdoctoral Researcher
SISSA - International School for Advanced Studies
Condensed Matter Sector
Via Bonomea n. 265,
Trieste 34151, Italy
> ________________________________________
> From: Iurii Timrov <itimrov at sissa.it>
> Sent: 16 January 2016 14:01
> To: Sajid Ali
> Cc: PWSCF Forum
> Subject: Re: [Pw_forum] "Lanczos.x with k-point algorithm"
>
> Dear Sajid Ali,
>
> Why do you use now QE-5.2.1? Before you used QE-5.2.0. First of all,
> you
> should stick to one version, otherwise it is not possible to solve the
> problem. I suggest to use the latest official release, i.e. QE-5.3.0.
>
> On 2016-01-16 00:09, Sajid Ali wrote:
>> Dear,
>> Iurii Timrov
>> Thanks for your reply. I tried running default tests provided
>> with
>> the
>> TDDFPT code by command 'make', but did not succeed. I was returned
>> with the error message
>
> Try to run just one test:
>
> cd TDDFPT/Examples/CH4
> make
>
> Does this work for you?
>
>> "make[1]: Entering directory
>> `/panfs/panspermia/12108332/Programs/QE/espresso-5.2.1/TDDFPT/Examples/CH4'
>> Error reading bands from output file
>
> Do this:
>
> cd TDDFPT/Examples/CH4
> make clean
> make
>
> Does it work now?
>
>> Checking CH4.pw-out using CH4.pw-ref : make[1]: *** [small_test] Error
>> 5
>> make[1]: Leaving directory
>> `/panfs/panspermia/12108332/Programs/QE/espresso-5.2.1/TDDFPT/Examples/CH4'
>> make[1]: Entering directory
>> `/panfs/panspermia/12108332/Programs/QE/espresso-5.2.1/TDDFPT/Examples/SiH4'
>> mpirun -np 48 "../../../bin/turbo_lanczos.x" < SiH4.tddfpt-st-in >
>> SiH4.tddfpt-st-out
>
> 48 cores are too many. Try to use just 1 or 2 cores for testing.
>
>> /bin/sh: mpirun: command not found
>> make[1]: *** [SiH4.tddfpt-st-out] Error 127
>> make[1]: Leaving directory
>> `/panfs/panspermia/12108332/Programs/QE/espresso-5.2.1/TDDFPT/Examples/SiH4'
>> make[1]: Entering directory
>> `/panfs/panspermia/12108332/Programs/QE/espresso-5.2.1/TDDFPT/Examples/Benzene'
>> Checking Benzene.pw-out using Benzene.pw-ref : [OK]
>> Checking Benzene.tddfpt-st-out using Benzene.tddfpt-st-ref : [NOT OK]
>> Different number of norms in files
>> make[1]: *** [small_test] Error 5
>> make[1]: Leaving directory
>> `/panfs/panspermia/12108332/Programs/QE/espresso-5.2.1/TDDFPT/Examples/Benzene'
>> make: *** [small_test] Error 2
>> -bash-4.1$ Different number of norms in files
>> -bash: Different: command not found
>> -bash-4.1$ make[1]: *** [small_test] Error 5
>> -bash: make[1]:: command not found"
>>
>> As you suggested me to provide the input files for PWscf and TDDFPT
>> for my own calculations. so i am pasting them here respectively, I
>> will be thankful for any help you can provide to me as it is really
>> important for me....
>> For SCF input file is
>> "&CONTROL
>> calculation = 'scf'
>> prefix='BN'
>> pseudo_dir = './'
>> outdir='./'
>> tstress=.true.
>> tprnfor = .true.
>> forc_conv_thr=1.0d-4
>> nstep=200
>> /
>
> For 'scf' you don't need 'forc_conv_thr' and 'nstep'.
>
>> &SYSTEM
>> ibrav=0
>> celldm(1)=1.889726
>> nat=2
>> ntyp=2
>> ecutwfc=50.0
>> nosym = .true.,
>> nosym_evc= .true.,
>> /
>
> Are you sure that you need to set 'nosym = .true.' and 'nosym_evc=
> .true.'? For HGH norm-conserving pseudopotentials the cutoff of 50 Ry
> is
> probably too low (others probably can comment more on this issue).
> Check
> the convergence wrt ecutwfc.
>
>> &ELECTRONS
>> mixing_beta=0.7
>> conv_thr = 1.0d-8
>> electron_maxstep=200
>> /
>
> The default value for 'electron_maxstep' should be fine.
>
>> &IONS
>> trust_radius_max=0.2
>> /
>> &CELL
>> cell_dynamics='bfgs'
>> /
>
> The cards "ions" and "cell" are not needed for the SCF calculation.
>
>> ATOMIC_SPECIES
>> N 14.0067 N.pbe-hgh.UPF
>> B 10.8110 B.pbe-hgh.UPF
>>
>> CELL_PARAMETERS (alat= 1.88972600)
>> 2.509073557 -0.002024330 0.000000000
>> 1.252797201 2.173934109 0.000000000
>> -0.000000000 -0.000000000 29.979498417
>>
>> ATOMIC_POSITIONS (crystal)
>> B -0.000266196 -0.000266358 -0.000000000
>> N 0.333599496 0.333599658 0.000000000
>>
>> K_POINTS {automatic}
>> 4 4 1 0 0 0 "
>> For Lanczos the input file is
>> "&lr_input
>> prefix = 'BN',
>> outdir = './',
>> restart=.false.,
>> restart_step=500
>> /
>> &lr_control
>> itermax = 500,
>> ipol = 1,
>> /
>> [ &lr_post
>> epsil = 0.0004d0
>> ]
>> /"
>>
>
> The input for the turbo_lanczos.x code seems to be fine.
>
>> SAJID ALI
>> Cell#+61449764974
>> Ph.D. Scholar
>> School of Mathematical and Physical Sciences
>> University of Technology, Sydney
>> Australia
>>
>
> HTH
>
> Iurii Timrov
> Postdoctoral Researcher
> SISSA - International School for Advanced Studies
> Condensed Matter Sector
> Via Bonomea n. 265,
> Trieste, Italy
>
>
>>
>> ________________________________________
>> From: Iurii Timrov <itimrov at sissa.it>
>> Sent: 15 January 2016 17:10
>> To: PWSCF Forum
>> Cc: Sajid Ali
>> Subject: Re: [Pw_forum] "Lanczos.x with k-point algorithm"
>>
>> Dear Sajid Ali,
>>
>> I made a test using QE-5.3.0 (the latest release) and QE-5.2.0 (the
>> one
>> which you use apparently) for the example TDDFPT/Examples/CH4 using
>> the
>> general k-points implementation of TDDFPT. My calculations didn't
>> crash
>> (neither in serial nor in parallel). Could you repeat these tests too?
>>
>> In order to understand what is the problem with your calculations, you
>> should provide here the input data for PWscf and TDDFPT. Otherwise we
>> cannot help you. But before that try the default tests provided with
>> the
>> TDDFPT code, which I mentioned above.
>>
>> Please note, even if you solve your problem, remember that the general
>> k-points implementation of TDDFPT was not benchmarked, and hence it
>> can
>> give completely wrong results. This is why it is disabled in the code.
>>
>> HTH
>>
>> Iurii Timrov
>>
>>
>> On 2016-01-15 00:52, Sajid Ali wrote:
>>> Dear,
>>>
>>> All,
>>>
>>> i am trying to do some TDDFPT calculations with K-point algorithm. I
>>> did comment the line ''IF ( .NOT. gamma_only ) && CALL errore('
>>> iosys', 'k-point algorithm is not tested yet',1)" in
>>> espresso/TDDFPT/src/lr_readin.f90 as was suggested by "Iurii Timrov".
>>> K point algorithm is implemented. But still i am returned the
>>> following error message in Lanczos.x output.[i am pasting the entire
>>> output file]..Can somebody help me out of this? It will be greatly
>>> appreciated.
>>>
>>> Program turboTDDFT v.5.2.0 starts on 15Jan2016 at 10:32:10
>>> 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 24 processors
>>> R & G space division: proc/nbgrp/npool/nimage = 24
>>> Reading data from directory:
>>> ./BN.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-PBX-PBC ( 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 13 13 3 2189 2189 339
>>> Max 14 14 4 2219 2219 394
>>> Sum 313 313 91 52939 52939 8919
>>> Subspace diagonalization in iterative solution of the eigenvalue
>>> problem:
>>> a serial algorithm will be used
>>> Normal read
>>> WARNING: Generalised k-points algorithm
>>> LANCZOS LINEAR-RESPONSE SPECTRUM CALCULATION
>>> Number of Lanczos iterations = 1500
>>> Starting Lanczos loop 2
>>> Lanczos iteration: 1 Pol:1
>>> lr_apply_liouvillian: not applying interaction
>>> alpha(00000001)= 0.000000
>>> beta (00000001)= 2.374383
>>> gamma(00000001)= 2.374383
>>> z1= 1 0.000000000000000E+00 0.000000000000000E+00
>>> Lanczos iteration: 2 Pol:1
>>> --------------------------------------------------------------------------
>>>
>>> mpirun noticed that process rank 20 with PID 62359 on node c3node01
>>> exited on signal 11 (Segmentation fault).
>>> --------------------------------------------------------------------------
>>>
>>>
>>> SAJID ALI
>>>
>>> Cell#+61449764974
>>>
>>> Ph.D. Scholar
>>>
>>> School of Mathematical and Physical Sciences
>>>
>>> University of Technology, Sydney
>>>
>>> Australia
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>> --
>> Dr. Iurii TIMROV
>> Postdoctoral Researcher
>> SISSA - International School for Advanced Studies
>> Condensed Matter Sector
>> Via Bonomea n. 265,
>> Trieste 34151, Italy
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