Re: [Wien] [please pay attention] query for mpi job file

[Lyudmila Dobysheva]

18.01.2017 22:35, Dr. K. C. Bhamu wrote:
> On Tue, Jan 17, 2017 at 10:50 PM, Dr. K. C. Bhamu 
 > wrote:


I do not use mpi, only simple parallelization over k-points, so I will 
answer only some of your questions.
> (1) is it ok with mpiifort or mpicc or it should have mpifort or 
mpicc??


I do not know and I even do not understand the question.

> (2) how to know that job is running with mpi parallelization?

IMHO, the simplest way is from dayfile:
cycle 1 (Ср. сент. 21 21:59:09 SAMT 2016)   (60/99 to go)
>   lapw0 -p(21:59:09) starting parallel lapw0 at Ср. сент. 21 
21:59:09 SAMT 2016

 .machine0 : processors
running lapw0 in single mode  <-***this is no mpi--)
10.221u 0.064s 0:10.35 99.3%0+0k 0+28016io 0pf+0w
>   lapw1  -up -p-c (21:59:19) starting parallel lapw1 at 
Ср. сент. 21 21:59:19 SAMT 2016

->  starting parallel LAPW1 jobs at Ср. сент. 21 21:59:19 SAMT 2016
running LAPW1 in parallel mode (using .machines) <---***this is k-point 
parallel.--)

9 number_of_parallel_jobs <-***this is k-point parallel.--)
localhost(12) 131.805u 1.038s 2:13.24 99.6% 0+0k 0+94072io 0pf+0w
...
localhost(12) 122.034u 1.234s 2:03.67 99.6% 0+0k 0+81472io 0pf+0w
   Summary of lapw1para: <--***this is k-point parallel.--)

> the *.err file seems as:

cp: cannot stat `CuGaO2.scfdmup': No such file or directory  >>>
why this is error? I want to overcome this.


I don't know, and I am afraid nobody knows without info


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


log file gives in my case (k-points parallel.!, do not know with mpi):
">   (runsp_lapw) options: -cc 0.005 -i 60 -p
Mond. Sept 19 15:10:18 SAMT 2016> (x) lapw0 -p
Mond. Sept 19 15:10:29 SAMT 2016> (x) lapw1 -up -p -c
Mond. Sept 19 15:12:52 SAMT 2016> (x) lapw1 -dn -p -c
Mond. Sept 19 15:15:09 SAMT 2016> (x) lapw2 -up -p -c ...
"


(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???


I don't know.


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


From your log file it looks like you do not have any parallelization, 
so in both cases you have equal time.


Best wishes
  Lyudmila Dobysheva
--
Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci.
426001 Izhevsk, ul.Kirova 132
RUSSIA
--
Tel.:7(3412) 432045(office), 722529(Fax)
E-mail: l...@ftiudm.ru, lyuk...@mail.ru (office)
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Re: [Wien] How to use the LIBXC library?

[Abderrahmane Reggad]

Thanks Dr gavin for all

I still get the old version , I don't know why

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] [not solved] WARNING: K-list has changed

[Dr. K. C. Bhamu]

Dear Gavin and Prof Marks

The problem reported in this thread was still persists.

As you suggested the ""case.scf: :WARNING: K-list has change" warning may
be due to -NI switch in job script but it is not so.
Previously I resubmit the job without -NI switch and the above warning has
gone but I just double checked that it does not depend on -NI switch.
Could you please guide me to remove this warning message.

The other warning "case.scf: :WARNING: Density Matrix or Orbital Potential
has changed" might be occurring for higher value of volume and c/a
reduction and now the volume and c/a ration values are 0 and +4 and this
warning is not occurring now.
What may be possible reason for this warning message.


Sincerely
Bhamu


On Wed, Jan 18, 2017 at 11:12 AM, Dr. K. C. Bhamu 
wrote:

> 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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>> e...@zeus.theochem.tuwien.ac.at/index.html
>>
>
>
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Re: [Wien] [please pay attention] query for mpi job file

[Dr. K. C. Bhamu]

Dear Experts,

Could someone please help me in running mpi job for below query:

Sincerely
Bhamu
On Tue, Jan 17, 2017 at 10:50 PM, Dr. K. C. Bhamu 
wrote:

> 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/include/lib  +  
> -DFFTW3 -I/usr/include/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] Broadening error in TELNES3

[MCDERMOTT Eamon 250772]

In a slightly related bug, my telnes3 isn't writing an E0 parameter when it
overwrites the case.inb file, which is now required. A. Yamaguchi below has
a valid case.inb, but I imagine it is adapted from SRC_templates after
telnes is run. 

This results in an error in 'broadening.error':

'BROADE' - input file  has wrong format or is corrupt!

 The attached patch for SRC_telnes3 will have it write the old default of E0
= 0, though you may instead want E0=8.00  as in the new case.inb, or to have
a value read out of case.innes or w2web

--
Eamon McDERMOTT
Postdoc – EELS spectra simulation
Département des Technologies Silicium
Laboratoire d’Electronique et de Technologie de l’Information 
eamon.mcderm...@cea.fr

Leti, technology research institute 
Commissariat à l’énergie atomique et aux énergies alternatives
T. +33 4 38 78 18 48 F. +33 4 38 78 52 73 M. +33 7 68 32 93 52
www.leti.fr  | Leti is a member of the Carnot Institutes network

-Original Message-
From: Wien [mailto:wien-boun...@zeus.theochem.tuwien.ac.at] On Behalf Of
Peter Blaha
Sent: Tuesday, January 10, 2017 14:01
To: A Mailing list for WIEN2k users 
Subject: Re: [Wien] Broadening error in TELNES3

Yes, there is a severe bug in broadening.f of WIEN2k_16/SRC_broadening:
The corrected part of the code should look like:



! *** READING THE SPECTRUM




 




  
  



! first scan the file to count the header lines :
   nimax=0
   header=0
   1   read(47,'(a11)',end=2) status
   if (status(1:1).eq.'#'.or.status(2:2).eq.'#'.or.status.eq.' 
 ') then


In the last line  status has been changed against modus.

I'm reading now the variable  "status", and thus we need to check the
content of "status and not of "modus".

Thanks for the report and the fix.

Regards

I'm reading now into the
On 01/10/2017 08:04 AM, Gavin Abo wrote:
> Caused by a bug in SRC_broadening/broadening.f?
>
> The read statement on line 163 has status (a CHARACTER *11), but 
> previous WIEN2k 14.2 had modus (a CHARACTER *4).
>
> On line 164, there is:
>
>   if (modus(1:1).eq.'#'.or.modus(2:2).eq.'#'.or.modus.eq.'   ')
then
>
> The WIEN2k update page [
> http://susi.theochem.tuwien.ac.at/reg_user/updates/ ] says:
>
> SRC_broadening: broadening.f (better recognition of comment lines
>
> My guess is that the number of characters the input file could handle 
> was increased from 4 to 11 characters, but the check for the header 
> counter wasn't changed to:
>
>   if (status(1:1).eq.'#'.or.status(2:2).eq.'#'.or.status.eq.'
> ') then
>
> Thus, the '0  lines' for the number of header lines in your output, 
> which is likely not the case when you check STO-test.elnes.
>
> On 1/5/2017 1:23 AM, Atsushi Yamaguchi wrote:
>>
>> Dear WIEN2k users,
>>
>>
>>
>> An error occurs in x broadening of TELNES3 in WIEN2k_16.1.
>>
>> The details of the error are as follows.
>>
>>
>>
>>0  lines1014  lines
>>
>> forrtl: severe (59): list-directed I/O syntax error, unit 47, file 
>> /net/h86/WIEN2k/STO-test/STO-test.elnes
>>
>> Image  PCRoutineLine
>> Source
>>
>> broadening 0042A94A  Unknown   Unknown
>> Unknown
>>
>> broadening 00428547  Unknown   Unknown
>> Unknown
>>
>> broadening 00404B9B  MAIN__201
>> broadening.f
>>
>> broadening 00403156  Unknown   Unknown
>> Unknown
>>
>> libc.so.6  00321B41ED1D  Unknown   Unknown
>> Unknown
>>
>> broadening 00403059  Unknown   Unknown
>> Unknown
>>
>> 0.000u 0.012s 0:00.01 100.0%0+0k 0+16io 0pf+0w
>>
>> error: command   /net/h86/home/wien16/WIEN/broadening broadening.def
>> failed
>>
>>
>>
>> The case.inb file is as follows.
>>
>>
>>
>> O-K edge of STO
>>
>> ELNES
>>
>> 1 1 0
>>
>> 0.0 1.0 0.0
>>
>> 0.1558639190 0.1558639190
>>
>> 1   0.00
>>
>> 0.1
>>
>> dummy
>>
>> 0.00
>>
>> 0.000
>>
>> 0.0
>>
>>
>>
>> Note that x telnes3 is executed successfully, and the ELNES spectrum 
>> of unbroaded appears in the plot.
>>
>> What causes an error?
>>
>> Thank you.
>>
>>
>>
>> A. Yamaguchi
>>
>
>
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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
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--

Re: [Wien] How to use the LIBXC library?

[Gavin Abo]

http://susi.theochem.tuwien.ac.at/reg_user/textbooks/usersguide.pdf - 
When a new WIEN2k version is released, the file at that link gets updated.


At least for me, when I enter that link today (January 18, 2017) into my 
web browser, it is showing me on the cover page:


User’s Guide, WIEN2k 16.1 (Release 12/12/2016)

On 1/18/2017 3:11 AM, Abderrahmane Reggad wrote:

Thank you Dr for your detailed explanation as usual.

Now, It becomes clear to me

But the link of the userguide is for that of WIEN2k 14.2 version.

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] How to use the LIBXC library?

[Abderrahmane Reggad]

Thank you Dr for your detailed explanation as usual.

Now, It becomes clear to me

But the link of the userguide is for that of WIEN2k 14.2 version.

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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