Re: [Wien] errors in lapw0 and lapw1 - parallel mode compilation

[McDermott Eamon John Gordon]

Google found some info here: 
https://software.intel.com/en-us/forums/topic/485528

You are mixing MKL libraries for the x86-64 target in R_LIB with MKL libraries 
targeting the Intel Phi (MIC) co-processor in RP_LIB (those in 
$MKLROOT/lib/mic/).

Are you really targeting the Intel Phi co-processor? If not, you need to remove 
/mic/ from your RP_LIB library paths. If yes, I suspect you need to make use of 
the MKL link line advisor 
(https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor) to set 
some more options (there is at least a -mmic compiler directive that you would 
need to set).

--
Eamon McDermott, M.Sc.
Institute of Materials Chemistry, TU Wien
eamon.mcderm...@tuwien.ac.at
Office: +43 (1) 58801-165304
Scheduling: http://doodle.com/eamon.mcdermott


On October 9, 2014 at 5:44:34 AM, Yocefu Hattori 
(yhattor...@gmail.com) wrote:

Dear Wien2k users,


I'm having problems during compilation of lapw0 and lapw1 in parallel mode. As 
you can see below there are errors in incompatibility with 32bit, but I 
installed the ifort (intel composer xe 2013 sp1)  compiler in 64 bit.


My settings:


MKLROOT=/opt/intel/composer_xe_2013_sp1.2.144/mkl

MKL_TARGET_ARCH=intel64

Compiler options: -I$(MKLROOT)/include -FR -mp1 -w -prec_div -pc80 -pad -ip 
-DINTEL_VML -traceback -assume buffered_io

F FFTW options: -DFFTW3 -I/opt/fftw3/include

L Linker Flags: $(FOPT) -L$(MKLROOT)/lib/intel64 -pthread

P Preprocessor flags '-DParallel'

R R_LIB (LAPACK+BLAS): -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread 
-lmkl_core -openmp -lpthread

FL FFTW_LIBS: /opt/fftw3/lib/libfftw3_mpi.a /opt/fftw3/lib/libfftw3.a

RP RP_LIB(SCALAPACK+PBLAS): $(MKLROOT)/lib/mic/libmkl_scalapack_lp64.a 
-Wl,--start-group $(MKLROOT)/lib/mic/libmkl_intel_lp64.a 
$(MKLROOT)/lib/mic/libmkl_core.a $(MKLROOT)/lib/mic/libmkl_sequential.a 
-Wl,--end-group $(MKLROOT)/lib/mic/libmkl_blacs_intelmpi_lp64.a -lpthread -lm

FP FPOPT(par.comp.options): -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML 
-traceback -assume buffered_io

MP MPIRUN commando : mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_


Compile Errors:


Compile time errors (if any) were:

SRC_lapw0/compile.msg:ld: k1om architecture of input file 
`/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_intel_lp64.a(dftierrorclass_lp64.o)'
 is incompatible with i386:x86-64 output

SRC_lapw0/compile.msg:ld: k1om architecture of input file 
`/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_intel_lp64.a(dfti_error_class_external.o)'
 is incompatible with i386:x86-64 output

SRC_lapw0/compile.msg:ld: k1om architecture of input file 
`/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_core.a(_knc_transfer_ipp_mkl_error.o)'
 is incompatible with i386:x86-64 output

SRC_lapw0/compile.msg:make[1]: *** [lapw0_mpi] Error 1

SRC_lapw0/compile.msg:make: *** [para] Error 2

SRC_lapw1/compile.msg:ld: k1om architecture of input file 
`/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_intel_lp64.a(vml_error_iface.o)'
 is incompatible with i386:x86-64 output

SRC_lapw1/compile.msg:ld: k1om architecture of input file 
`/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_core.a(vml_errors.o)' 
is incompatible with i386:x86-64 output

SRC_lapw1/compile.msg:make[1]: *** [lapw1_mpi] Error 1

SRC_lapw1/compile.msg:make: *** [rp] Error 2

SRC_lapw1/compile.msg:ld: k1om architecture of input file 
`/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_intel_lp64.a(vml_error_iface.o)'
 is incompatible with i386:x86-64 output

SRC_lapw1/compile.msg:ld: k1om architecture of input file 
`/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_core.a(vml_errors.o)' 
is incompatible with i386:x86-64 output

SRC_lapw1/compile.msg:make[1]: *** [lapw1c_mpi] Error 1

SRC_lapw1/compile.msg:make: *** [cp] Error 2


I had those messages to:


fft_modules.o: In function `fftw_parallel_mp_prepare_parallel_ffts_':

fft_modules.F:(.text+0x41): undefined reference to `fftw_mpi_init'

fft_modules.F:(.text+0xbe): undefined reference to `fftw_mpi_local_size_3d_f03'

fft_modules.F:(.text+0xcd): undefined reference to `fftw_alloc_complex'

fft_modules.o: In function `fftw_parallel_mp_c3fft_':

fft_modules.F:(.text+0x11d4): undefined reference to `fftw_mpi_execute_dft'

fft_modules.F:(.text+0x2523): undefined reference to `fftw_mpi_execute_dft'

fft_modules.F:(.text+0x46f1): undefined reference to `fftw_mpi_plan_dft_3d_f03'

fft_modules.F:(.text+0x5195): undefined reference to `fftw_mpi_plan_dft_3d_f03'

ld: 
/opt/intel/composer_xe_2013_sp1.2.144/mkl/lib/mic/libmkl_core.a(_knc_Iotensor.o)(.text+0xb99):
 unresolvable R_X86_64_PLT32 relocation against symbol `fflush@@GLIBC_2.2.5'

ld: final link failed: Nonrepresentable section on output

make[1]: *** [lapw0_mpi] Error 1

make[1]: Leaving directory `/home/yhattori/WIEN2k_13/SRC_lapw0'

make: *** [para] Error 2

Copying programs

SRC_lapw0/lapw0

done.


For fftw3 (3.3.3) installation I used configure --prefix=/opt/

Re: [Wien] QTL-B error for Zn K-edge ELNES

[McDermott Eamon John Gordon]

You should use an "extra electron charge" of 1.0 in case.inm when
removing a core electron, not -1.0 as you have. Currently you are
effectively removing two electrons from the system (the core and a
background charge).

I would also recommend using a supercell when doing a core hole
calculation. I have had experience in the past with QTL-B errors when a
core hole is not sufficiently isolated.

Regards,

-- 
Eamon McDermott, M.Sc.
Institute of Materials Chemistry, TU Wien
eamon.mcderm...@tuwien.ac.at
Office: +43 (1) 58801-165304
Scheduling: http://doodle.com/eamon.mcdermott



On Tue, 2014-08-26 at 04:12 -0700, Hajar Nejati wrote:
> Dear Dr. Jorissen
> I attached zno.strcuct, zno.in1c, zno.in2c, zno.inc and zno.inm for
> corehole in the unit-cell.
> Can you cheak my input files and help what is wrong?
> Thank you for your help
> 
> 
> 
> __
> From: Kevin Jorissen 
> To: A Mailing list for WIEN2k users  
> Sent: Tuesday, August 26, 2014 1:20 AM
> Subject: Re: [Wien] QTL-B error for Zn K-edge ELNES
> 
> 
> In recent versions of WIEN such a large version of QTL-B almost always
> indicates an error in the input files.  Case.struct is likely fine
> since the ground-state calculation works fine.  There may be a problem
> with the core hole?  Are you sure that case.struct, case.inc, and
> case.in2(c) match?  
> 
> 
> Cheers,
> 
> 
> 
> 
> Kevin Jorissen
> 
> 
> 
> 
> On Mon, Aug 25, 2014 at 6:20 AM, Hajar Nejati
>  wrote:
> 
> 
> 
> 
> 
> 
> Dear wien2k users and developers
> 
> 
> I want to calculate Zn K-edge ELNES of the bulk wurtzite ZnO.
> For calculating the ELNES of bulk without core-hole
> approximation, I have no problem. The scf run succesfully as
> well as ELNES.
> for core-hole, I set in the structure:
> 
> 
> spacegroup=156 (P3m1)
> Zn1 1/3 2/3 0 RMT=2.2
> Zn 2/3 1/3 0.5 RMT=2.2
> O 1/3 2/3 0.383 RMT=1.3
> O 2/3 1/3 0.883 RMT=1.3
> ---
> I labled one of the Zn atoms to 1, for core-hole calc.
> spacegroup changes from 186(p63mc) to 156 (p3m1)
> ---
> 
> 
> When I want to use corehole approximation (for Zn 1s ELNES) in
> the bulk of wurtzite ZnO, the L2main - QTL-B Error appears.
> All recommendations about the solve of this error listed in
> mailing list and FAQ could not solve this error in my case!!!
> such as reducing the mixing factor, removing the local orbital
> in zno.in1c, or using the switch -in1new.
> 
> 
> I listed zno.scf2 and zno.scf1 in below:
> 
> 
> zno.scf2:
> 
> 
> 
> QTL-B VALUE .EQ. 62.71953 in Band of energy -0.42747 ATOM= 1
> L= 0
> Check for ghostbands or EIGENVALUES BELOW XX messages
> Adjust your Energy-parameters for this ATOM and L (or use
> -in1new switch), check RMTs !!!
> 
> 
> 
> 
> :WARN : QTL-B value eq. 62.72 in Band of energy -0.42747 ATOM=
> 1 L= 0
> :WARN : You should change the E-parameter for this atom and
> L-value in cas
> 
> 
> 
> 
> 
> zno.scf1
> 
> 
> 
> 
> 
> ATOMIC SPHERE DEPENDENT PARAMETERS FOR ATOM Zn1 
> :e__0001: OVERALL ENERGY PARAMETER IS 0.9383
> OVERALL BASIS SET ON ATOM IS LAPW
> :E2_0001: E( 2)= 0.9383 E(BOTTOM)= 0.405 E(TOP)= -200.000 1 -1
> 113
> APW+lo
> :E0_0001: E( 0)= 0.9383
> APW+lo
> 
> 
> ATOMIC SPHERE DEPENDENT PARAMETERS FOR ATOM Zn 
> :e__0002: OVERALL ENERGY PARAMETER IS 0.9383
> OVERALL BASIS SET ON ATOM IS LAPW
> :E2_0002: E( 2)= 0.0971 E(BOTTOM)= 0.012 E(TOP)= 0.182 0 0 189
> APW+lo
> :E0_0002: E( 0)= 0.9383
> APW+lo
> 
> 
> ATOMIC SPHERE DEPENDENT PARAMETERS FOR ATOM O 
> :e__0003: OVERALL ENERGY PARAMETER IS 0.9383
> OVERALL BASIS SET ON ATOM IS LAPW
> :E0_0003: E( 0)= -1.4600 E(BOTTOM)= -3.138 E(TOP)= -200.000 1
> -1 285
> APW+lo
> :E0_0003: E( 0)= 0.9383
> LOCAL ORBITAL
> :E1_0003: E( 1)= 0.9383
> APW+lo
> ...and so on
> 
> 
> 
> 
> 
> by attention to the WIEN2k-FAQ: QTL-B page, seems that error
> is concerned to the Zn 1s orbital (Atom 1 L 0) that I want to
> calculate its ELNES!!
> 
> 
> Please help me for this error
>

Re: [Wien] lapw2 error

[McDermott Eamon John Gordon]

You must run add -up and -dn to your command. 

Regards,

--
Eamon

> On Mar 28, 2014, at 10:15 AM, "ben amara imen"  
> wrote:
> 
> Hello, 
> 
> I'm working on a  magnetic compound . I do the SCF (runsp_lapw) and it went 
> well. Then to calculate the DOS, I executed the command ''x lapw2-qtl'' but I 
> have this error in lapw2 !! :
> 
> Error in LAPW2
>'LAPW2'  -can't open unit 18
>   'LAPW2'filename :  case.vsp
>   'LAPW2' Status: old  form : formatted   
>  
> 
> what can I do to overcome my probleme , can someone helps me please and 
> Thanks in advance
> 
> Best  Regards
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Re: [Wien] Bi2Se3 atomic positions in wien2k structure file.

[McDermott Eamon John Gordon]

Crystallography.net appears to have the structure 
you want: http://www.crystallography.net/9011965.html

Simply download the .CIF file and use 'cif2struct'.

Regards,

--
Eamon McDermott, M.Sc.
Institute of Materials Chemistry, TU Wien
eamon.mcderm...@tuwien.ac.at
Office: +43 (1) 58801-165304
Scheduling: http://doodle.com/eamon.mcdermott

On Feb 6, 2014, at 3:35 PM, Naseem Hassan 
mailto:rahesk...@gmail.com>> wrote:

Dear Users,

This is strange but what else I can do except reporting it. I am unable to 
download the attachment from the fallowing email which is in the archive 
(probably never attached).

http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg08497.html

Kindly suggest me how can I make Bi2Se3 structure file ? The space group is

space group R3m (166)and structure is hexagonal. But I do not know how many 
atoms should

I generate for structure file and what are the positions for respective

atoms ? I would appreciate if some one help how to find position



from the official link below, in this way I will learn alot.

http://cryst.ehu.es/cgi-bin/cryst/programs/nph-wp-list?gnum=166&grha=hexagonal



Best wishes

Naseem (A beginner in wien2k code)

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Re: [Wien] mbj error

[McDermott Eamon John Gordon]

Then the problem is exactly as Tomas has described it. If lapw1 is searching 
for a .vsp file (and not .vspup/.vspdn) then you are running 'run_lapw' when 
you have initialized for a spin-polarized case.

I agree that you should re-start your calculation from a clean directory with 
only the struct file, and make sure to use 'runsp_lapw' if starting your SCF 
cycle from the command line.

Regards,

--
Eamon McDermott
PhD student
Institute for Materials Chemistry,
TU Wien
eamon.mcderm...@tuwien.ac.at

On 2013-08-01, at 8:57 PM, "mourad boujnah" 
mailto:boujnah.mou...@gmail.com>> wrote:

Dear Gavin and Tomas,

this is the error in lapw1.error
Error in LAPW1
 'INILPW' - can't open unit:  18
 'INILPW' -filename: ZrO2-Fe.vsp
 'INILPW' -  status: old  form: formatted
 'LAPW1' - INILPW aborted unsuccessfully.

and this calculation with spin polarized


2013/8/1 Tomas Kana mailto:k...@seznam.cz>>

Dear Mourad Boujnah,

Just a guess: Do you perform a non-magnetic or a spin polarized calculation?

(in your directory you have Ferro-dos)

If you initialized your structure as spin-polarized, you should use runsp_lapw 
instead of run_lapw

If this is really the cause of your problem, I would erase everything except 
struct file

and initialize again and then run runsp_lapw

Tomas


-- Původní zpráva --
Od: mourad boujnah mailto:boujnah.mou...@gmail.com>>
Datum: 1. 8. 2013
Předmět: [Wien] mbj error

Dear Wien2k Users,

I am using Wien2k 13 version and i am performing mBj calculations.
In the firt step when I give the command
run_lapw -i 1 -NI
The following error appeared.
oujnah@boujnah:~/WIEN2k/Boujnah/TM-ZrO2/Ferro-dos/ZrO2-Fe$ run_lapw -i 1 -NI
hup: Command not found.
 LAPW0 END
LAPW1 - Error

>   stop error
Please can you help me to overcome this problem .?

Cordialy

--
Mourad BOUJNAH
PhD Student in laboratory of magnetism and physics of high energy
Faculty of Sciences in Rabat - Morocco
Tel: +212 677316706
Email: boujnah.mou...@gmail.com
"Research is to see what everybody else has seen, and to think what nobody else 
has thought"

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--
Mourad BOUJNAH
PhD Student in laboratory of magnetism and physics of high energy
Faculty of Sciences in Rabat - Morocco
Tel: +212 677316706
Email: boujnah.mou...@gmail.com
"Research is to see what everybody else has seen, and to think what nobody else 
has thought"
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Re: [Wien] "no space left on device?"

[McDermott Eamon John Gordon]

I would suggest talking to your system administrator or IT support
person, or perhaps deleting some unused files in your home directory.
This is not a Wien2k problem but a system issue.

Best regards,

-- 
Eamon McDermott, M.Sc.
Institute of Materials Chemistry, TU Wien
eamon.mcderm...@tuwien.ac.at
Office: +43 (1) 58801-165304
Scheduling: http://doodle.com/eamon.mcdermott


On Mon, 2013-04-08 at 09:50 +0100, ben abdallah houda wrote:
> 
> 
> Dear users,
> 
> 
> I already sent an email regarding my problem that I encountered during
> the execution of x opticc. the error is found "no space left on
> device". Someone can  help me to solve? I'll be very grateful. This is
> very urgent.
> thank you for your cooperation.
> 
> 
> Dr Houda Ben Abdallah
> Laboratory of condensed matter. Departement of Physics.
> Faculty of Sciences, Tunis. Tunisia
> 
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Re: [Wien] error in running the x opticc

[McDermott Eamon John Gordon]

no space left on device

You have run out of disk space on the device containing your output directory, 
or for some other reason the process is unable to write to the disk (such as 
NFS issues).

Best regards,

--
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Institute of Materials Chemistry, TU Wien
eamon.mcderm...@tuwien.ac.at
Office: +43 (1) 58801-165304
Scheduling: http://doodle.com/eamon.mcdermott

On 2013-04-07, at 12:08 PM, ben abdallah houda 
mailto:bhoud...@yahoo.fr>>
 wrote:

Dear Wien2k users,

I am trying to calculate the magneto-optical properties of GaMnAsP. For this I 
have done in the first step the calculation SO then I completed all the steps 
to start the stage optics, using the "x opticc -so -up." This step has been 
discontinued and I found the following message:

forrtl: no space left on device
forrtl: severe (38): error during write, unit 3, file /home/houda/WIEN2K/ 
GaMnAsP.symmatup
error: command /homr/houda/wien2kpackages/ opticc upoptic.def failed

 I want to know:  what this message means and how I can fix this error. I 
really need to solve this as I am in the final stage of my work.
Thank you for your answer in advance. I am very grateful

Dr. Houda Ben Abdallah.
Departement of Physics, Laboratory of Condensed Matter (LPMC).
Faculty of Sciences, Tunis. Tunisia

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[Wien] error in lapw2 - parallel

[McDermott Eamon John Gordon]

I recommend checking for NaN's in your Cu.scf0 file.

This behaviour looks similar to what I've seen before in some cases when
using the broken FFT library in the early 12.1 release. It can be fixed
for the serial mode lapw0 by adding -DFFTW3 or -DFFTW2 to FOPT and
linking to an fftw in R_LIBS. 

-- 
Eamon McDermott, M.Sc.
Institute of Materials Chemistry, TU Wien
eamon.mcdermott at tuwien.ac.at
Office: +43 (1) 58801-165304
Scheduling: http://doodle.com/eamon.mcdermott


On Fri, 2013-03-22 at 08:41 -0400, Mathrubutham Rajagopalan wrote:
> I am waiting for your reply
> Raja
> 
> Sent from my iPad
> 
> On Mar 22, 2013, at 5:21 AM, Lyudmila Dobysheva  wrote:
> 
> > The order of your actions should be another:
> > 1. Make a fresh directory.
> >
> > 2. Make in terminal the commands by hand
> > x lapw0
> > x lapw1 -c -p
> > x lapw2 -c -p
> >
> > and send us the output in terminal and error files if nonzero
> >
> > 3. Check the output of lapw1: *.scf1 and *.output1
> >
> > Best wishes
> >  Lyudmila Dobysheva
> > --
> > Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci.
> > 426001 Izhevsk, ul.Kirova 132
> > RUSSIA
> > --
> > Tel.:7(3412) 442118 (home), 218988(office), 722529(Fax)
> > E-mail: lyu at ftiudm.ru
> >lyuka17 at mail.ru (office) lyuka17 at gmail.com (home)
> > Skype:  lyuka17 (home), lyuka18 (office)
> > http://fti.udm.ru/content/view/25/103/lang,english/
> > --
> >
> >
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