Re: [Wien] Running parallel job with Slurm+intel mpi

[Gavin Abo]

SIGSEGV errors can be not easy to solve, because they can have many 
possible causes:


http://www.democritos.it/pipermail/pw_forum/2005-March/002272.html
http://software.intel.com/en-us/articles/determining-root-cause-of-sigsegv-or-sigbus-errors/

However, maybe the cause is the same as a similar case that occurred 
before where the error occurred when -lmkl_blacs_lp64 was used when 
-lmkl_blacs_openmpi_lp64 should have been used instead for Open MPI [ 
http://www.mail-archive.com/wien%40zeus.theochem.tuwien.ac.at/msg12746.html 
].


What blacs did you use in your parallel compiler options (for RP_LIB) 
when you compiled WIEN2k using Open MPI?


On 6/22/2016 7:30 AM, Md. Fhokrul Islam wrote:


Hi Prof Blaha,


I have compiled MPI version of Wien2k_14.2 with OpenMPI and have 
got all MPI executables.


But when I run a test calculation using 4 cores, I get the the 
following error message. Could you


please let me know what should I do to fix this problem.


case.dayfile


   start   (Tue Jun 21 20:57:01 CEST 2016) with lapw0 (100/99 to go)

cycle 1 (Tue Jun 21 20:57:01 CEST 2016) (100/99 to go)

>   lapw0 -p(20:57:01) starting parallel lapw0 at Tue Jun 21 
20:57:02 CEST 2016

 .machine0 : 4 processors
4.684u 0.733s 0:04.50 120.2%0+0k 220432+4688io 78pf+0w
>   lapw1  -up -p-c (20:57:06) starting parallel lapw1 at 
Tue Jun 21 20:57:06 CEST 2016

->  starting parallel LAPW1 jobs at Tue Jun 21 20:57:06 CEST 2016
running LAPW1 in parallel mode (using .machines)
1 number_of_parallel_jobs
 au063 au063 au063 au063(47)  Child id   3 SIGSEGV
 Child id   0 SIGSEGV
 Child id   1 SIGSEGV
 Child id   2 SIGSEGV
--
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1543169252.


Error file:


LAPW0 END
w2k_dispatch_signal(): received: Segmentation fault
w2k_dispatch_signal(): received: Segmentation fault
w2k_dispatch_signal(): received: Segmentation fault
w2k_dispatch_signal(): received: Segmentation fault
[au063:29993] 3 more processes have sent help message help-mpi-api.txt 
/ mpi-abort
[au063:29993] Set MCA parameter "orte_base_help_aggregate" to 0 to see 
all help / error messages



Thanks,

Fhokrul






*From:* Wien  on behalf of 
Peter Blaha 

*Sent:* Monday, June 13, 2016 8:54 AM
*To:* A Mailing list for WIEN2k users
*Subject:* Re: [Wien] Running parallel job with Slurm+intel mpi
No, the srun command cannot work with these options, but need other
switches.
Most likely in WIEN2k_14.2 you will have to use mpirun, or try:

srun -n_NP_   (i.e. without the blank between n and _NP_)


In the next version, we will have support for srun, but at least for
mixed k-point+mpi-support it requires also a small change in the
lapw*para scripts.



On 06/09/2016 04:29 PM, Md. Fhokrul Islam wrote:
> Dear Wien2k users,
>
>
>   I am trying to do some calculation with a large system with mpi
> version but having problem with
>
> running the job. I have compiled Wien2k 14.2 with intel libraries and
> have generated all mpi executables.
>
> But our system requires us to use srun instead of mpirun. So I have
> changed parallel options to
>
>
> srun -n _NP_ -machinefile _HOSTS_ _EXEC_.
>
>
> I also have tried other options that I saw in the mailing list
>
>
>  srun -n _NP_
>
>
> but that didn't work. No new files are created and the dayfile is stuck
>
> in lapw0.
>
>
> case.dayfile:
> --
> Calculating GaAs in /lunarc/nobackup/users/eishfh/WIEN2k/test/GaAs
> on au054 with PID 189944
> using WIEN2k_14.2 (Release 15/10/2014) in
> /lunarc/nobackup/users/eishfh/SRC/Wien2k14.2-mpi
>
>
>  start   (Thu Jun  9 13:14:39 CEST 2016) with lapw0 (100/99 
to go)

>
>  cycle 1 (Thu Jun  9 13:14:39 CEST 2016) (100/99 to go)
>
>  >   lapw0 -p(13:14:39) starting parallel lapw0 at Thu Jun  9
> 13:14:39 CEST 2016
>  .machine0 : 4 processors
> ---
>
>
> I understood from the userguide that the -p option in runsp_lapw 
picks up

>
> mpi version depending on the form of the .machines file. Here is the
>
> .machines file that I have used for this test calculation.
>
>
> #
> lapw0:au165 au165 au165 au165
> 1:au165 au165 au165 au165
> granularity:1
> extrafine:1
> lapw2_vector_split:2
>
> So I am wondering if anyone can tell me how can I fix the problem.
>
> Thanks,
>
> Fhokrul
>
>
>
>
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A Mailing list for WIEN2k users. Please post questions, suggestions or 
comments about 

[Wien] (no subject)

[Jyoti Krishna]

Hello Prof. Blaha ,

Could you please suggest me that in Wien2k, how can I get Fermi
surface plot in Xcrysden by taking spin-orbit (SO) and ORB into
consideration?

As read from the previous archives, I had done Fermi surface plot for
GGA+U+SO  by  first doing cp case.outputso case.output1 .
But, its still showing erroneous results. Is there any other method?

Thanks

Jyoti Krishna
Research Scholar
Department of Physics
Indian Institute of Technology Roorkee,
Roorkee,
Uttrakhand.
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Re: [Wien] Reg: Calculation of McMillan-Hopfield parameter

[Peram sreenivasa reddy]

Dear Blaha sir,

Thank you very much for your replay.

Here the problem comes in the calculation of , square of the
electron-phonon matrix averaged over the Fermi surface. Here my questions
are:

1. To get alone  value do we need to use the rigid muffin-tin
approximation(RMTA)?
2. Is there any package or code available which can be used the WIEN2k
files as input files?


Thanking you.


On Wed, Jun 22, 2016 at 6:39 PM, Peter Blaha 
wrote:

> No, it is not "printed".
>
> But all the required quantities can be derived from a band structure
> calculation and the rigid-muffin-tin approx.
>
> On 06/22/2016 05:53 AM, Peram sreenivasa reddy wrote:
>
>> Dear WIEN2k,
>>
>> Is it possible to calculate McMillan-Hopfield parameter directly with
>> WIEN2k, which is used to calculate electron-phonon coupling  of a
>> particular superconducting material as given in PHYSICAL REVIEW B 74,
>> 184519 (2006).
>>
>> I searched in the user guide. But there is no use.
>>
>> Thanking you ..
>>
>>
>>
>>
>> --
>> /P.V.SREENIVASA REDDY/
>> /Research Scholar
>> Department of Physics/
>> /Indian Institute of Technology/
>> /Hyderabad/
>>
>>
>> ___
>> Wien mailing list
>> Wien@zeus.theochem.tuwien.ac.at
>> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>> SEARCH the MAILING-LIST at:
>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>
>>
> --
>
>   P.Blaha
> --
> Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
> Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
> WWW:   http://www.imc.tuwien.ac.at/staff/tc_group_e.php
> --
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>



-- 
*P.V.SREENIVASA REDDY*

*Research ScholarDepartment of Physics *
*Indian Institute of Technology*
*Hyderabad*
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Re: [Wien] Reg: Calculation of McMillan-Hopfield parameter

[Peter Blaha]

No, it is not "printed".

But all the required quantities can be derived from a band structure 
calculation and the rigid-muffin-tin approx.


On 06/22/2016 05:53 AM, Peram sreenivasa reddy wrote:

Dear WIEN2k,

Is it possible to calculate McMillan-Hopfield parameter directly with
WIEN2k, which is used to calculate electron-phonon coupling  of a
particular superconducting material as given in PHYSICAL REVIEW B 74,
184519 (2006).

I searched in the user guide. But there is no use.

Thanking you ..




--
/P.V.SREENIVASA REDDY/
/Research Scholar
Department of Physics/
/Indian Institute of Technology/
/Hyderabad/


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--

  P.Blaha
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW:   http://www.imc.tuwien.ac.at/staff/tc_group_e.php
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Re: [Wien] optic-tetra value

[Peter Blaha]

It will not matter too much, but in principle for metals and half-metals 
101 is more "save", because with the Blöchl-correction "negative 
occupation numbers" could occur, leading to a "negative eps-2".


On 06/22/2016 12:34 PM, emami seyyed amir abbas wrote:

Dear users.

I am trying to obtain optical properties of a half-metal compound. As i
know for metallic systems we should put tetra/with value=101. But in
half-metal systems one spin channel has metallic behavior and other has
insulator or semiconductor behavior. Accordingly, which value will be
appropriated for this input.

Thank you in advance for your attention to this matter


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--

  P.Blaha
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
Email: bl...@theochem.tuwien.ac.atWIEN2k: http://www.wien2k.at
WWW:   http://www.imc.tuwien.ac.at/staff/tc_group_e.php
--
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[Wien] optic-tetra value

[emami seyyed amir abbas]

Dear users.

I  am trying to obtain optical properties of a half-metal compound. As i  know 
for metallic systems we should put tetra/with value=101. But in  half-metal 
systems one spin channel has metallic behavior and other has  insulator or 
semiconductor behavior. Accordingly, which value will be  appropriated for this 
input.
 
Thank you in advance for your attention to this matter  ___
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Re: [Wien] DFTD3 h-BN testing

[tran]

Hi,

The intralayer lattice constant was kept fixed at about
a=2.503 Angstrom (it would not really make sense to fix the volume
for such a plot). The interlayer distance corresponds to half of the
lattice constant c. I attached the struct file of hBN that I used.

F. Tran

On Tuesday 2016-06-21 21:14, Tristan de Boer wrote:


Date: Tue, 21 Jun 2016 21:14:50
From: Tristan de Boer 
Reply-To: A Mailing list for WIEN2k users 
To: wien@zeus.theochem.tuwien.ac.at
Subject: [Wien] DFTD3 h-BN testing

Hi,
I've installed DFTD3 and am attempting to make sure it's installed correctly, 
so I've been attempting to reproduce slide 20 of F. Tran's 2015 WIEN2k 
workshop. Are the cells in this slide held to a constant volume as the 
interlayer distance is changed, or is the unit cell volume changing as well? 
I've tried calculations with the PBE functional both ways, with and without 
DFTD3, I can't reproduce this figure.


If I hold the volume constant and change the interlayer spacing, I get 
something resembling the PBE+D3 line in total energy, with and without DFTD3 
(assuming :ENE = :ENE(no dispersion corrections) + :EDFTD3). If I simply 
change the interlayer spacing I get a monotonic decrease in total unit cell 
energy with increasing spacing without the minimum shown in the slide both 
with and without :EDFTD3. For both cases, :EDFTD3 is about -0.03 -- -0.04 Ry.


Alternatively, since :EDFTD3 matches the output in case.scfdftd3, should I 
simply ignore the issue and assume things are working well?

Regards,
Tristan
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hBN
H   LATTICE,NONEQUIV.ATOMS:  2 194 P63/mmc 
 RELA  
  4.729984  4.729984 13.00 90.00 90.00120.00   
ATOM  -1: X=0.3334 Y=0. Z=0.7500
  MULT= 2  ISPLIT= 4
  -1: X=0. Y=0.3334 Z=0.2500
B 1NPT=  781  R0=0.0001 RMT= 1.29Z:  5.0   
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
ATOM  -2: X=0.3334 Y=0. Z=0.2500
  MULT= 2  ISPLIT= 4
  -2: X=0. Y=0.3334 Z=0.7500
N 1NPT=  781  R0=0.0001 RMT= 1.43Z:  7.0   
LOCAL ROT MATRIX:1.000 0.000 0.000
 0.000 1.000 0.000
 0.000 0.000 1.000
  24  NUMBER OF SYMMETRY OPERATIONS
-1 0 0 0.
-1 1 0 0.0002
 0 0-1 0.
   1
-1 1 0 0.0002
-1 0 0 0.
 0 0 1 0.
   2
-1 0 0 0.
 0-1 0 0.
 0 0-1 0.
   3
-1 1 0 0.0002
 0 1 0 0.
 0 0 1 0.
   4
 0-1 0 0.
-1 0 0 0.
 0 0 1 0.
   5
 0 1 0 0.
-1 1 0 0.0002
 0 0-1 0.
   6
 0-1 0 0.
 1-1 0-0.0002
 0 0 1 0.
   7
 0 1 0 0.
 1 0 0-0.
 0 0-1 0.
   8
 1-1 0-0.0002
 0-1 0 0.
 0 0-1 0.
   9
 1 0 0 0.
 0 1 0 0.
 0 0 1 0.
  10
 1-1 0-0.0002
 1 0 0-0.
 0 0-1 0.
  11
 1 0 0 0.
 1-1 0-0.0002
 0 0 1 0.
  12
 0 1 0 0.
-1 1 0 0.0002
 0 0 1 0.5000
  13
 0-1 0 0.
 1-1 0-0.0002
 0 0-1 0.5000
  14
-1 1 0 0.0002
 0 1 0 0.
 0 0-1 0.5000
  15
-1 0 0 0.
-1 1 0 0.0002
 0 0 1 0.5000
  16
 0 1 0 0.
 1 0 0-0.
 0 0 1 0.5000
  17
 0-1 0 0.
-1 0 0 0.
 0 0-1 0.5000
  18
 1-1 0-0.0002
 0-1 0 0.
 0 0 1 0.5000
  19
 1 0 0 0.
 0 1 0 0.
 0 0-1 0.5000
  20
-1 1 0 0.0002
-1 0 0 0.
 0 0-1 0.5000
  21
-1 0 0 0.
 0-1 0 0.
 0 0 1 0.5000
  22
 1-1 0-0.0002
 1 0 0-0.
 0 0 1 0.5000
  23
 1 0 0 0.
 1-1 0-0.0002
 0 0-1 0.5000
  24
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