[Wien] The correct choice of mkl libraries to compile wien2k

Sat May 23 21:40:24 CEST 2015

Dear Gavin, more one time, thanks a lot for the great help. Yes, I am using
rocks and I didn't knew about the kgen.py. I fix the problem in a soft way:
I change the line 494 in init_lapw to kgen_lapw, where kgen_lapw is a soft
link to kgen. It's works very well.
Best regards,
Nilton

2015-05-22 22:41 GMT-03:00 Gavin Abo <gsabo at crimson.ua.edu>:

>  Regarding "WARNING: R0=0.000100 for atom   -1 Z= 83.00 too big. Use
> 0.00005", if you want to remove this warning, create/load and save
> case.struct with StructGen so that it generates R0=0.00005000 for Atom 1 or
> you could edit case.struct in a text editor and change R0=0.00010000 to
> R0=0.00005000 for Atom 1 (note: Make sure you maintain the same number of
> digits; so use for example 0.00005000 and not 0.00005.).
>
> Regarding "kgen XML parse exception: <unknown>:1:1: syntax error", I think
> you might be using a Rocks cluster that has a python file called kgen.py [
> https://searchcode.com/codesearch/view/96513148/ ].  So I think the error
> might be because it is running kgen.py instead of the kgen executable of
> WIEN2k.  Talk to the administrator of your cluster, maybe they can rename
> kgen.py to something else.  If they will not do that, then changing the
> WIEN2k kgen filename, using a symbolic link to WIEN2k kgen, or specifying
> the full path to the WIEN2k kgen executable might be other ways in which to
> solve the problem.
>
>
> On 5/22/2015 2:14 PM, Nilton wrote:
>
> Dear Gavin, is I fixed my mistake and now it is works. Thanks a lot. But
> now I still have another issue, I am trying to use the init_lapw with -bath
> key, like this:
> init_lapw -b -vxc 13 -ecut -6.0 -rkmax 7.0 -numk 1000. The last switch is
> about kgen program. Then I got that message:
>
>  LSTART ENDS
> WARNING: R0=0.000100 for atom   -1 Z= 83.00 too big. Use 0.00005
> WARNING: R0=0.000100 for atom   -2 Z= 53.00 too big. Use 0.00005
> WARNING: R0=0.000100 for atom   -3 Z= 53.00 too big. Use 0.00005
> >   inputfiles prepared (16:59:41)
>  inputfiles prepared
>  next is kgen
> kgen XML parse exception: <unknown>:1:1: syntax error
>
>  So, I change the comand to kgen kgen.def and I got the same error
> message:
>
>  [nilton at bodesking case]$ kgen kgen.def << OEF
> > -numk 500
> > OEF
> kgen XML parse exception: <unknown>:1:1: syntax error
>
>  This show me the problem is in kgen.
> Any  clue?
> Thanks in  advance,
> Nilton
>
> 2015-05-21 19:07 GMT-03:00 Gavin Abo <gsabo at crimson.ua.edu>:
>
>>  Regarding the error:
>>
>> atpar_tmp_.F:(.text+0x157e): undefined reference to `outwinb_'
>>
>>  It looks like you are missing the outwinb object file (outwinb.o) in the
>> link stage.
>>
>> Check in the SRC_lapw1 directory.  Do you have outwinb.f?  After you
>> compile, does it create outwinb.o?
>>
>>
>> On 5/21/2015 12:42 PM, Nilton wrote:
>>
>> Dear Gavin, first of all, thanks a lot for the help. I follow yours
>> suggestions and this is the config of Makefile for lapw1 (please, just look
>> at R_LIBS):
>>
>>  SHELL = /bin/sh
>> FC = ifort
>> MPF = mpif90
>> CC = cc
>> FOPT =  -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback
>> -I$(MKLROOT)/include/intel64/lp64 -I$(MKLROOT)/include
>> FPOPT = -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback
>> DParallel = '-DParallel'
>> FGEN = $(PARALLEL)
>> LDFLAGS = $(FOPT) -L$(MKLROOT)/lib/intel64 -static -pthread
>> R_LIBS = $(MKLROOT)/lib/intel64/libmkl_blas95_lp64.a
>> $(MKLROOT)/lib/intel64/libmkl_lapack95_lp64.a
>> $(MKLROOT)/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group
>> $(MKLROOT)/lib/intel64/libmkl_cdft_core.a
>> $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a
>> $(MKLROOT)/lib/intel64/libmkl_intel_thread.a
>> $(MKLROOT)/lib/intel64/libmkl_core.a
>> $(MKLROOT)/lib/intel64/libmkl_blacs_lp64.a -Wl,--end-group -openmp
>> -lpthread -lm
>> C_LIBS = $(R_LIBS)
>> RP_LIBS =  /usr/local/fftw/lib/libfftw_mpi.a
>> /usr/local/fftw/lib/libfftw.a /home/nilton/mpich-1.2.7p1/lib/libmpich.a
>> $(R_LIBS)
>> CP_LIBS = $(RP_LIBS)
>>
>>  And this is the erros I got at final of compilation:
>>
>>  ifort  -o ./lapw1 abc.o atpar.o bandv1.o calkpt.o cbcomb.o coors.o
>> cputim.o dblr2k.o dgeqrl.o dgewy.o dgewyg.o dlbrfg.o dsbein1.o dscgst.o
>> dstebz2.o dsyevx2.o dsyr2m.o dsyrb4.o dsyrb5l.o dsyrdt4.o dsywyv.o
>> dsyxev4.o dvbes1.o eisps.o errclr.o errflg.o forfhs.o gaunt1.o gaunt2.o
>> gbass.o gtfnam.o hamilt.o hns.o horb.o inikpt.o inilpw.o lapw1.o latgen.o
>> lmsort.o locdef.o lohns.o lopw.o matmm.o modules.o nn.o outerr.o outwin.o
>> prtkpt.o prtres.o pzheevx16.o rdswar.o rint13.o rotate.o rotdef.o seclit.o
>> seclr4.o seclr5.o select.o service.o setkpt.o setwar.o sphbes.o stern.o
>> tapewf.o ustphx.o vectf.o warpin.o wfpnt.o wfpnt1.o ylm.o zhcgst.o
>> zheevx2.o zher2m.o jacdavblock.o make_albl.o global2local.o par_syrk.o
>> my_dsygst.o refblas_dtrsm.o seclit_par.o pdsyevx17.o pdstebz17.o
>> pdgetri_my.o pzgetri_my.o W2kutils.o W2kinit.o -FR -mp1 -w -prec_div -pc80
>> -pad -ip -DINTEL_VML -traceback
>> -I/opt/intel/composerxe-2011.2.137/mkl/include/intel64/lp64
>> -I/opt/intel/composerxe-2011.2.137/mkl/include
>> -L/opt/intel/composerxe-2011.2.137/mkl/lib/intel64 -static -pthread
>> /opt/intel/composerxe-2011.2.137/mkl/lib/intel64/libmkl_blas95_lp64.a
>> /opt/intel/composerxe-2011.2.137/mkl/lib/intel64/libmkl_lapack95_lp64.a
>> /opt/intel/composerxe-2011.2.137/mkl/lib/intel64/libmkl_scalapack_lp64.a
>> -Wl,--start-group
>> /opt/intel/composerxe-2011.2.137/mkl/lib/intel64/libmkl_cdft_core.a
>> /opt/intel/composerxe-2011.2.137/mkl/lib/intel64/libmkl_intel_lp64.a
>> /opt/intel/composerxe-2011.2.137/mkl/lib/intel64/libmkl_intel_thread.a
>> /opt/intel/composerxe-2011.2.137/mkl/lib/intel64/libmkl_core.a
>> /opt/intel/composerxe-2011.2.137/mkl/lib/intel64/libmkl_blacs_lp64.a
>> -Wl,--end-group -openmp -lpthread -lm
>> atpar.o: In function `atpar_':
>> atpar_tmp_.F:(.text+0x157e): undefined reference to `outwinb_'
>> atpar_tmp_.F:(.text+0x19fa): undefined reference to `outwinb_'
>> atpar_tmp_.F:(.text+0x1fc0): undefined reference to `outwinb_'
>> atpar_tmp_.F:(.text+0x3a15): undefined reference to `outwinb_'
>> inilpw.o: In function `inilpw_':
>> inilpw.f:(.text+0x4e7): undefined reference to `find_nloat_'
>> inilpw.f:(.text+0x18f1): undefined reference to `symmrot_'
>> select.o: In function `select_':
>> select.f:(.text+0x28a): undefined reference to `outwinb_'
>> select.f:(.text+0x375): undefined reference to `outwinb_'
>> select.f:(.text+0x48c): undefined reference to `outwinb_'
>> select.f:(.text+0x630): undefined reference to `outwinb_'
>> select.f:(.text+0x6f1): undefined reference to `outwinb_'
>> select.o:select.f:(.text+0x7d1): more undefined references to `outwinb_'
>> follow
>> make[1]: ** [lapw1] Erro 1
>> make[1]: Saindo do diretório `/home/nilton/wien2k_14.2/SRC_lapw1'
>> make: ** [real] Erro 2
>>
>>  As you can see above the problem is in the link stage. Curiously, the
>> Makefile works very well on wien2k_10.1
>>
>> 2015-05-20 20:37 GMT-03:00 Gavin Abo <gsabo at crimson.ua.edu>:
>>
>>>  Sorry, there is a mistake in my previous post. The "-Wl,--end-group"
>>> should go after libmkl_core.a.  The corrected settings are given below:
>>>
>>> current:R_LIBS:$(MKLROOT)/lib/intel64/libmkl_lapack95_lp64.a
>>> -Wl,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64.a
>>> $(MKLROOT)/lib/intel64/libmkl_intel_thread.a
>>> $(MKLROOT)/lib/intel64/libmkl_core.a -Wl,--end-group -openmp -lpthread
>>> -lm
>>>
>>> _______________________________________________
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>>>
>>
>>
>>  --
>> Nilton S. Dantas
>> Diretor do Núcleo de Inovação Tecnológica
>> Universidade Estadual de Feira de Santana
>> Departamento de Ciências Exatas
>> Área de Informática
>> Av. Transnordestina, S/N, Bairro Novo Horizonte
>> CEP 44036900 - Feira de Santana, Bahia, Brasil
>> Tel./Fax +55 75 31618086 <%2B55%2075%2031618086>
>> http://www2.ecomp.uefs.br/ <http://www.uefs.br/portal>
>>
>>
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>> SEARCH the MAILING-LIST at:
>> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>>
>>
>
>
>  --
> Nilton S. Dantas
> Diretor do Núcleo de Inovação Tecnológica
> Universidade Estadual de Feira de Santana
> Departamento de Ciências Exatas
> Área de Informática
> Av. Transnordestina, S/N, Bairro Novo Horizonte
> CEP 44036900 - Feira de Santana, Bahia, Brasil
> Tel./Fax +55 75 31618086
> http://www2.ecomp.uefs.br/ <http://www.uefs.br/portal>
>
>
> _______________________________________________
> Wien mailing list
> Wien at 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
>
>

-- 
Nilton S. Dantas
Diretor do Núcleo de Inovação Tecnológica
Universidade Estadual de Feira de Santana
Departamento de Ciências Exatas
Área de Informática
Av. Transnordestina, S/N, Bairro Novo Horizonte
CEP 44036900 - Feira de Santana, Bahia, Brasil
Tel./Fax +55 75 31618086
http://www2.ecomp.uefs.br/ <http://www.uefs.br/portal>
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