[Wien] The correct choice of mkl libraries to compile wien2k
Gavin Abo
gsabo at crimson.ua.edu
Sat May 23 03:41:40 CEST 2015
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
> <mailto: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
>> <mailto: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 <tel:%2B55%2075%2031618086>
>> http://www2.ecomp.uefs.br/ <http://www.uefs.br/portal>
>
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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
> http://www2.ecomp.uefs.br/ <http://www.uefs.br/portal>
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