[Wien] job is crashing [lapw2] on cluster

[Dr. K. C. Bhamu]

Dear Prof. Peter and experts

Greetings!!!

This is error is severely reported previously but I could not find a
solution.
The error occurs after several scf cycles in 2Doptimization case for
hexagonal structure


**
in cycle 17ETEST: .0626   CTEST: -.97
Fallback to compatibility mode with "old" save_lapw

 for shortening the email

starting parallel dstart at Wed Jan 18 11:41:59 IST 2017
 .machine0 : processors
running dstart in single mode
3.028u 0.067s 0:03.17 97.1% 0+0k 0+1056io 0pf+0w
0.028u 0.025s 0:00.06 66.6% 0+0k 0+920io 0pf+0w
clmextrapol_lapw has generated a new CuGaO2_993.clm
in cycle 12ETEST: .20715000   CTEST: .000134

>   stop error
>>> (min) status after runsp_c_lapw -I -p -orb -ec 0.1 -cc 0.0001 -fc
1.0 -i 120\: 9 -> exit
ERROR status in 2D_V_-6.0_COA_-4.0

[kcbhamu@gu CuGaO2_993]$ cat *.dayfile


>   stop
Fallback to compatibility mode with "old" save_lapw


>   lapw2 -up -p   -orb (11:49:42) running LAPW2 in parallel mode
**  LAPW2 crashed!
0.063u 0.262s 0:00.66 48.4% 0+0k 0+216io 1pf+0w
error: command   /home/kcbhamu/Wien2k_16/lapw2para -up uplapw2.def   failed

>   stop error
[kcbhamu@gu CuGaO2_993]$


The job.err files tells about cluster connection problem,

ssh: Could not resolve hostname compute-11-20: Name or service not known
ssh: Could not resolve hostname compute-11-20: Name or service not known
ssh: Could not resolve hostname compute-11-20: Name or service not known
 LAPW1 END
 LAPW1 END
 LAPW1 END
 LAPW1 END
 LAPW1 END
FERMI - Error
cp: cannot stat `.in.tmp': No such file or directory
[kcbhamu@gu CuGaO2_993]$


I guess that it is cluster issue but when I saw the node in question, it
looks fine.


Could you please suggest me any possible solution?


Sincerely

Bhamu
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Re: [Wien] WARNING: K-list has changed

[Dr. K. C. Bhamu]

Thank you Gavin for quick reply,

I think you mentioned that this was for a 2D optimization.  I don't think
> you provided the optimize.job file.  Did you perhaps have -NI on
> run[sp]_lapw in it?  The -NI will not remove the case.broyd* files.  Not
> sure, but perhaps keeping those files could lead to the WARNINGs.
>



Yes, it was the -NI problem now "case.scf: :WARNING: K-list has change"
warning has gone but the remaining warning still persists:
"case.scf: :WARNING: Density Matrix or Orbital Potential has changed".




>
> In what ITERATION in case.scf did the WARNINGs occur?


>From begging.


> The output you showed from "grep :WARN *.scf" looked like it had only one
> occurrence of the WARNINGs or you did you remove the other repeating
> occurrences to shorten your email?


Yes, I removed the repeating occurrences for shorten the email.


> If they only happened in the first cycle (iteration), then it might be
> safe to ignore the WARNINGs.
>


No, I am getting ""case.scf: :WARNING: Density Matrix or Orbital Potential
has changed" in each scf cycle.



Hope someone other will look for the remaining warning message.



Sincerely
Bhamu


>
> On 1/17/2017 2:06 PM, Dr. K. C. Bhamu wrote:
>
>> Dear Gavin
>>
>> I am facing same problem
>>
>> case.scf: :WARNING: Density Matrix or Orbital Potential has changed
>> case.scf: :WARNING: K-list has change
>>
>>  that you answered in your previous email:
>>
>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13758.html
>>
>> and Prof. Marks
>>
>> mentioned that this patch will be incorporated in next release (Wie2k_16).
>>
>>
>> So, could I know if the patch has already incorporated in the Wien2k_16
>> or if I have made some mistake?
>>
>> Sincerely
>>
>> Bhamu
>>
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Re: [Wien] How to use the LIBXC library?

[Gavin Abo]

The new version of wien2k is arrived but there is no sufficient 
information on how to use the new library LIBXC implemented


Section 7.1.3 on page 112 of the WIEN2k 16.1 usersguide [ 
http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf ] has:


Example for PBE with the
- global keyword : XC_PBE
- LIBXC-keywords : XC_GGA_X_PBE XC_GGA_C_PBE

The first line of case.in0 on page 110 uses the WIEN2k PBE implementation:

TOT  XC_PBE

To use the LIBXC implementation, I followed the above given example and 
changed the first line in case.in0 to:


TOT  XC_GGA_X_PBE XC_GGA_C_PBE

On page 112, it has:

Keywords to use functionals from the library of exchange and correlation 
functionals LIBXC 
(http://www.tddft.org/programs/octopus/wiki/index.php/Libxc).


Say one is interested in a GGA PW91 calculation.  So went to that page 
of the LIBXC website, clicked on the "Version 3.0" link, which directs to:


http://octopus-code.org/wiki/Libxc_3.0_functionals

There in the list for GGA PW91 is:

GGA_X_PW91
GGA_C_PW91

Also, in the list, GGA PBE is:

GGA_X_PBE
GGA_C_PBE

From the example, it can be seen that XC_ was added to the beginning of 
it.  So first line in case.in0 for a LIBXC GGA PW91 calculation becomes:


TOT  XC_GGA_X_PW91 XC_GGA_C_PW91

and how to combine the different functionals for exchange and 
correlation to get a result close to the experimental one.


In the list at http://octopus-code.org/wiki/Libxc_3.0_functionals, it 
looks like there are like 50+ articles.  Each functional is usually 
designed to solve a "specific" problem or application.  So you have to 
read articles and choose an appropriate one for your application.  So 
each of those articles are basically giving their own answer to your 
question.  Also, that may also be the reason for the LIBXC library, 
nobody probably has the answer to the question for the new combinations, 
which gives researchers something new to study.

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Re: [Wien] WARNING: K-list has changed

[Gavin Abo]

Yes, the patch to fix the problem in the post at that link was 
incorporated in WIEN2k 16.1.


The patch was to remove the following error when WIEN2k was compiled 
with gfortran:


At line 1015 of file mixer.F (unit = 22, file = 'S.scf')
Fortran runtime error: Sequential READ or WRITE not allowed after EOF 
marker, possibly use REWIND or BACKSPACE


So that patch is not going to remove those WARNINGs.

I don't know whether it is safe to ignore those WARNINGs or not. Someone 
like Prof. Marks might have better advice about that.


What I can say about it is:

You reported other problems that proceeded those WARNINGs.  So they 
might go away when you fix the other problems.


I think you mentioned that this was for a 2D optimization.  I don't 
think you provided the optimize.job file.  Did you perhaps have -NI on 
run[sp]_lapw in it?  The -NI will not remove the case.broyd* files.  Not 
sure, but perhaps keeping those files could lead to the WARNINGs.


In what ITERATION in case.scf did the WARNINGs occur?  The output you 
showed from "grep :WARN *.scf" looked like it had only one occurrence of 
the WARNINGs or you did you remove the other repeating occurrences to 
shorten your email?  If they only happened in the first cycle 
(iteration), then it might be safe to ignore the WARNINGs.


On 1/17/2017 2:06 PM, Dr. K. C. Bhamu wrote:

Dear Gavin

I am facing same problem

case.scf: :WARNING: Density Matrix or Orbital Potential has changed
case.scf: :WARNING: K-list has change

 that you answered in your previous email:

http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13758.html

and Prof. Marks

mentioned that this patch will be incorporated in next release (Wie2k_16).


So, could I know if the patch has already incorporated in the 
Wien2k_16 or if I have made some mistake?


Sincerely

Bhamu

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[Wien] How to use the LIBXC library?

[Abderrahmane Reggad]

Dear wien developpers

The new version of wien2k is arrived but there is no sufficient information
on how to use the new library LIBXC implemented and how to combine the
different functionals for exchange and correlation to get a result close to
the experimental one.

Best regards

-- 
Mr: A.Reggad
Laboratoire de Génie Physique
Université Ibn Khaldoun - Tiaret
Adresse: BP 144 AL ATTAF AIN DEFLA
Tel: +213(0)561861963
Algerie
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[Wien] WARNING: K-list has changed

[Dr. K. C. Bhamu]

Dear Gavin

I am facing same problem

case.scf: :WARNING: Density Matrix or Orbital Potential has changed
case.scf: :WARNING: K-list has change

 that you answered in your previous email:

http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg13758.html

and Prof. Marks

mentioned that this patch will be incorporated in next release (Wie2k_16).


So, could I know if the patch has already incorporated in the Wien2k_16 or
if I have made some mistake?

Sincerely

Bhamu
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Re: [Wien] How to calculate Band structure and DOS by the onsite hybrid method

[Abderrahmane Reggad]

Thanks again Dr Gavin

* I see that the procedure in w2web is different from that of terminal

* I couldn't understand why

use x lapw1 -band -dn -orb  when up is selected

and

use x lapw1 -band -up -orb  when dn is selected

* Do we make one plot for both spins or one plot for every spin?

Best regards

 --
Mr: A.Reggad
Laboratoire de Génie Physique
Université Ibn Khaldoun - Tiaret
Adresse: BP 144 AL ATTAF AIN DEFLA
Tel: +213(0)561861963
Algerie
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Re: [Wien] [almost solved but some warning messages are there] problem in 2Doptimize.job or in my method ...

[Dr. K. C. Bhamu]

Dear Prof. Gerhard
I could solve the nn problem and for the same I send a detailed email which
is pending with admin for approval as it is more than 40kb.

In brief, what I did is

just shifted the principal O(Z) position to 0.011 towards x-y plane (from
0.089*** to 0.078) and then there was no nn distance error.
I used the following environment:
http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15348.html

Now the job is running  but I observed few warnings in scf:

 :WARNING: Step size reduced due to overlapping spheres -- check RMT
  >>> in initialisation it was not occurred.
[bhamu@gu CuGaO2]$ grep :WARN *.scf
CuGaO2_1.scf: :WARNING: Density Matrix or Orbital Potential has changed
CuGaO2_1.scf: :WARNING: K-list has changed
[bhamu@gu CuGaO2]$

After 5% rmt reduction I shifted O(Z) position.


Kindly comment on the queries of this email and on the link mentioned above.


Sincerely
Bhamu



On Thu, Jan 12, 2017 at 1:29 PM, Fecher, Gerhard 
wrote:

> It seems you still do not know what the nn error is telling you.
>
> How much is the nearest neighbour distance reduced when you reduce from
> the initial structure the volume by 15 % and afterwards c/a by 9%
> (My guess would be more than 10%)
> (in addition what happens if you shift the atom with the free parameter)
>
> Try to initialize the calculation for the structure that causes the nn
> error and see what happens.
> (also try to initialize the structure with the largest volume and c/a
> reduction.)
>
> Which atom is affected when you use min ?
> How does this influence the nearest neighbour distances (which ones) ?
>
> What do you finally conclude for your RMT settings ?
>
> Ciao
> Gerhard
>
> DEEP THOUGHT in D. Adams; Hitchhikers Guide to the Galaxy:
> "I think the problem, to be quite honest with you,
> is that you have never actually known what the question is."
>
> 
> Dr. Gerhard H. Fecher
> Institut of Inorganic and Analytical Chemistry
> Johannes Gutenberg - University
> 55099 Mainz
> and
> Max Planck Institute for Chemical Physics of Solids
> 01187 Dresden
> 
>
>
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[Wien] query for mpi job file

[Dr. K. C. Bhamu]

Dear Experts

I just installed Wien2k_16 on a sge cluster (linuxifc) with 40 nodes with
each node having 16 core and each core has 4GB RAM (~2GB/ processor), 40
Gbps Infiniband interconnect. I used "mpiifort" and "mpiicc"   compiler
with scalapck, blas, fftd3 and blacs library (without ELPA and
LIBXC-3.0.0). I also specified number of core (16) during configuration for
each node (the compiler options are specified at the bottom or email).

Now I have submitted the job using the sge script:

http://susi.theochem.tuwien.ac.at/reg_user/faq/sge.job

with set mpijob=2 instead of set mpijob=1.


I spacified
  PARAMETER  (NMATMAX=   19000)
  PARAMETER  (NUME=   6000)

Now I have few queries:
(1) is it ok with mpiifort or mpicc or it should have mpifort or mpicc??
(2) how to know that job is running with mpi parallelization?


the basic outputs are:

[bhamu@gu CuGaO2]$ testpara1_lapw
.processes: No such file or directory.
(standard_in) 1: syntax error

#
# TESTPARA1 #
#

Tue Jan 17 22:14:57 IST 2017

   lapw1para was not yet executed

the *.err file seems as:
LAPW0 END
 ORB   END
 ORB   END
 LAPW1 END
 LAPW2 END
cp: cannot stat `CuGaO2.scfdmup': No such file or directory  >>> why
this is error? I want to overcome this.
 CORE  END
 CORE  END
 MIXER END

The :log file

Tue Jan 17 22:16:14 IST 2017> (x) lapw0
Tue Jan 17 22:16:17 IST 2017> (x) orb -up
Tue Jan 17 22:16:17 IST 2017> (x) orb -dn
Tue Jan 17 22:16:17 IST 2017> (x) lapw1 -up -orb
Tue Jan 17 22:17:26 IST 2017> (x) lapw2 -up -orb
Tue Jan 17 22:17:44 IST 2017> (x) lcore -up
Tue Jan 17 22:17:44 IST 2017> (x) lcore -dn
Tue Jan 17 22:17:45 IST 2017> (x) mixer -orb


(3) I want to know how to change below variable in the job file so that I
can run more effectively mpi run

# the following number / 4 = number of nodes
#$ -pe mpich 32
set mpijob=1??
set jobs_per_node=4??

 the definition above requests 32 cores and we have 4 cores /node.
 We request only k-point parallel, thus mpijob=1
 the resulting machines names are in $TMPDIR/machines

setenv OMP_NUM_THREADS 1???


(4) The job with 32 core and with 64 core (with "set mpijob=2") taking
~equal time for scf cycles.



The other compilers options set as:


   Recommended options for system linuxifc are:

 RP_LIB(SCALAPACK+PBLAS): -lmkl_scalapack_lp64
-lmkl_blacs_intelmpi_lp64 $(R_LIBS)
 FPOPT(par.comp.options): -O1 -FR -mp1 -w -prec_div -pc80 -pad
-ip -DINTEL_VML -traceback -assume buffered_io -I$(MKLROOT)/include
 MPIRUN command : mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_

   Current settings:

 FFTW_LIB + FFTW_OPT: -lfftw3_mpi -lfftw3 -L/usr/local/lib
 +  -DFFTW3 -I/usr/local/include (already set)
 ELPA_LIB + ELPA_OPT:   +   (already set)
 RP  RP_LIB(SCALAPACK+PBLAS): -lmkl_scalapack_lp64
-lmkl_blacs_intelmpi_lp64 $(R_LIBS)
 FP  FPOPT(par.comp.options): -O1 -FR -mp1 -w -prec_div -pc80 -pad
-ip -DINTEL_VML -traceback -assume buffered_io -I$(MKLROOT)/include
 MP  MPIRUN command : mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_
 CN  CORES_PER_NODE : 16


For any other supporting information please let me know.


Sincerely

Bhamu
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Re: [Wien] The correlation and exchange formulas of potential and energy for PBE functional

[Abderrahmane Reggad]

Thanks again Dr Gavin for the explanation

Since the total potential Vt is calculated by the program lapw0, we can
find in the repertory SRC_lapw0 how the diiferent parts are implemented and
their formulas.



-- 
Mr: A.Reggad
Laboratoire de Génie Physique
Université Ibn Khaldoun - Tiaret
Adresse: BP 144 AL ATTAF AIN DEFLA
Tel: +213(0)561861963 <+213%20561%2086%2019%2063>
Algerie
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Re: [Wien] The correlation and exchange formulas of potential and energy for PBE functional

[Abderrahmane Reggad]

Thanks again Dr Gavin for the explanation

Since the total potential Vt is calculated by the program lapw0, we can
find in the repertory SRC_lapw0 how the diiferent parts are implemented and
their formulas.

On other side, I think the new library LIBXC contains all the formulas of
the didderent parts for energy and potential.

Best regards

-- 
Mr: A.Reggad
Laboratoire de Génie Physique
Université Ibn Khaldoun - Tiaret
Adresse: BP 144 AL ATTAF AIN DEFLA
Tel: +213(0)561861963
Algerie
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