[DFTB-Plus-User] problem with installation
Ben Hourahine
benjamin.hourahine at strath.ac.uk
Sun Jun 23 00:32:55 CEST 2019
Hello Farzad,
The syntax for the arpack library should be
ARPACK_LIBS := /home/fmolani/ARPACK/libarpack.a
I'd also suggest building without MPI enabled if you want to use the
ARPACK library (or without ARPACK if you need MPI), so
WITH_MPI := 0
(see the comment next to that line in the make.config file you sent).
Undefined symbol errors mean the compilation was not successful.
After making the above changes, try
make distclean
make dftb+
Regards
Ben
On 22/06/2019 22:10, Farzad Molani wrote:
> Dear Ben,
> Actually, I don't understand what do you mean in the previous email.
> Although I changed ARPACK_NEEDS_LAPACK = from 0 to 1, the problem
> still persists.
> Also, I changed the following statement in*make.arch* to:
> # ScaLAPACK
> SCALAPACKDIR = /usr/lib
> LIB_SCALAPACK = -L/usr/lib -lscalapack
>
> # LAPACK/BLAS
> LIB_LAPACK = -L/usr/lib -llapack -lblas
>
> # Any other libraries to be linked
> OTHERLIBS = -lgomp -lpthread
> ARPACK_LIBS := -L/home/fmolani/ARPACK/libarpack.a .
>
> after making, I got the following error:
> .
> .
> .
> .
> /home/fmolani/DFTB+/dftbplus-18.2/_build/external/xmlf90/libxmlf90.a(m_io.o):
> In function `m_io_MP_find_eor_eof_':
> m_io.f90:(.text+0x3b3): undefined reference to `for_inquire'
> m_io.f90:(.text+0x3e9): undefined reference to `for_stop_core'
> m_io.f90:(.text+0x457): undefined reference to `for_open'
> m_io.f90:(.text+0x49b): undefined reference to `for_write_seq_lis'
> m_io.f90:(.text+0x4d7): undefined reference to `for_write_seq_lis'
> m_io.f90:(.text+0x4f9): undefined reference to `for_rewind'
> m_io.f90:(.text+0x55f): undefined reference to `for_read_seq_fmt'
> m_io.f90:(.text+0x597): undefined reference to `for_read_seq_lis'
> m_io.f90:(.text+0x5da): undefined reference to `for_close'
> m_io.f90:(.text+0x608): undefined reference to `for_stop_core'
> /home/fmolani/DFTB+/dftbplus-18.2/_build/external/xmlf90/libxmlf90.a(m_xml_error.o):
> In function `m_xml_error_MP_default_error_handler_':
> m_xml_error.f90:(.text+0x6e): undefined reference to `for_write_seq_fmt'
> m_xml_error.f90:(.text+0xbd): undefined reference to `for_write_seq_fmt'
> m_xml_error.f90:(.text+0xd9): undefined reference to `for_trim'
> m_xml_error.f90:(.text+0x11a): undefined reference to `for_write_seq_fmt'
> m_xml_error.f90:(.text+0x164): undefined reference to `for_write_seq_fmt'
> m_xml_error.f90:(.text+0x17f): undefined reference to
> `for_write_seq_fmt_xmit'
> m_xml_error.f90:(.text+0x1aa): undefined reference to
> `for_write_seq_fmt_xmit'
> m_xml_error.f90:(.text+0x1c8): undefined reference to
> `for_write_seq_fmt_xmit'
> m_xml_error.f90:(.text+0x212): undefined reference to `for_write_seq_fmt'
> m_xml_error.f90:(.text+0x244): undefined reference to `for_stop_core'
> m_xml_error.f90:(.text+0x29b): undefined reference to `for_write_seq_fmt'
> /home/fmolani/DFTB+/dftbplus-18.2/_build/external/xmlf90/libxmlf90.a(m_xml_error.o):
> In function `m_xml_error_MP_build_error_info_':
> m_xml_error.f90:(.text+0x2d9): undefined reference to `for_cpystr'
> m_xml_error.f90:(.text+0x2f9): undefined reference to `_intel_fast_memcpy'
> collect2: error: ld returned 1 exit status
> make[1]: *** [dftb+] Error 1
> make[1]: Leaving directory
> `/home/fmolani/DFTB+/dftbplus-18.2/_build/prog/dftb+'
> make: *** [dftb+] Error 2
>
> Is "undefined reference" normal message?
> How can I solve the problem?
> make.config and make.arch have been attached.
> Best regards, Farzad
>
>
> On Sat, Jun 22, 2019 at 11:50 PM Ben Hourahine
> <benjamin.hourahine at strath.ac.uk
> <mailto:benjamin.hourahine at strath.ac.uk>> wrote:
>
> Hello Farzad,
>
> Try over-riding
>
> # Whether ARPACK depends on the external LAPACK and BLAS libraries
> ARPACK_NEEDS_LAPACK = 0
>
> in make.arch, as that is a lapack dependency error from arpack.
>
> Regards
>
> Ben
>
> On 22/06/2019 20:12, Farzad Molani wrote:
>> Hello Ben,
>> To compile arpack, I used the following commands:
>> wget -O - http://www.caam.rice.edu/software/ARPACK/SRC/arpack96.tar.gz | tar xzvf -
>> wget -O - http://www.caam.rice.edu/software/ARPACK/SRC/patch.tar.gz | tar xzvf -
>> cd ARPACK
>> make FC=gfortran FFLAGS= MAKE=/usr/bin/make ARPACKLIB=$MYDIRECTORY/ARPACK/libarpack.a lib
>> Then, ARPACK_LIB= -L$MYDIRECTORY/ARPACK/libarpack.a lib copied
>> into make.config and make.arch. But still I've got the following
>> error:
>>
>> zlarf.f:(.text+0x192): undefined reference to `ilazlc_'
>> zlarf.f:(.text+0x2a9): undefined reference to `ilazlr_'
>> collect2: error: ld returned 1 exit status
>> make[1]: *** [dftb+] Error 1
>> make[1]: Leaving directory
>> `/home/fmolani/DFTB+/dftbplus-18.2/_build/prog/dftb+'
>> make: *** [dftb+] Error 2
>> please find make.config and make.arch for further information.
>> Best regards, Farzad
>>
>>
>> On Sat, Jun 22, 2019 at 6:29 PM Ben Hourahine
>> <benjamin.hourahine at strath.ac.uk
>> <mailto:benjamin.hourahine at strath.ac.uk>> wrote:
>>
>> Hello Farzad,
>>
>> do you need excited state calculations? If not disable
>> WITH_ARPACK := 0 in make.config.
>>
>> Otherwise, you can compile arpack yourself, then (if its a
>> static .a file) tell the DFTB+ build to use its location in
>> make.arch :
>>
>> ARPACK_LIBS = -L/your/path/to/library -larpack
>>
>> if its a dynamic arpack build (.so) you need to also include
>> its location in your LDPATH variable (and keep the library,
>> as it will load every time you run).
>>
>> Regards
>>
>> Ben
>>
>> On 22/06/2019 14:42, Farzad Molani wrote:
>>> I know, but I don't know how can I unstall arpack?
>>> The package downloaded and now I need help to install it.
>>> Please note that, I don't permit to login as a root.
>>>
>>> On Saturday, June 22, 2019, RICCARDO ROZZA
>>> <rozza.riccardo at studium.unict.it
>>> <mailto:rozza.riccardo at studium.unict.it>> wrote:
>>>
>>> Dear Farzad,
>>>
>>> It seems that you need to install the arpack library
>>> (ld: cannot find -larpack).
>>> All the best,
>>>
>>> Riccardo.
>>>
>>>> On 22 Jun 2019, at 10:01, Farzad Molani
>>>> <f.molani at gmail.com <mailto:f.molani at gmail.com>> wrote:
>>>>
>>>>
>>>> Dear DFTB users,
>>>> I want to install the newest version of DFTB+. The
>>>> source and executable files
>>>> from http://www.dftbplus.org/download/dftb-stable/
>>>> have been downloaded and untarred. I try to install the
>>>> software based on instructions on INSTALL.rst, but I
>>>> got the following error after the make.
>>>> .
>>>> .
>>>> .
>>>> .
>>>> w.o dispuffdata.o inputdata.o pmlocalisation.o
>>>> repcont.o repspline.o reppoly.o xlbomd.o
>>>> extlagrangian.o linresp.o linrespgrad.o qm.o
>>>> linrespcommon.o arpack.o eigensolver.o typegeometry.o
>>>> simplemixer.o numderivs2.o potentials.o thirdorder.o
>>>> charges.o dftbplusu.o geoopt.o steepdesc.o gdiis.o
>>>> orbitalequiv.o broydenmixer.o stress.o etemp.o
>>>> hermite.o factorial.o intrinsicpr.o mixer.o
>>>> andersonmixer.o elecconstraints.o angmomentum.o
>>>> eigenvects.o parser.o hsdutils2.o unitconversion.o
>>>> oldcompat.o typegeometryhsd.o oldskdata.o
>>>> densitymatrix.o populations.o repulsive.o spinorbit.o
>>>> forces.o
>>>> -L/home/fmolani/DFTB+/dftbplus-18.2/_build/external/xmlf90
>>>> -lxmlf90
>>>> -L/home/fmolani/DFTB+/dftbplus-18.2/_build/external/fsockets
>>>> -lfsockets
>>>> -L/apps/intel/2015/composer_xe_2015.3.187/mkl/lib/intel64
>>>> -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
>>>> -larpack -liomp5
>>>> ld: cannot find -larpack
>>>> make[1]: *** [dftb+] Error 1
>>>> make[1]: Leaving directory
>>>> `/home/fmolani/DFTB+/dftbplus-18.2/_build/prog/dftb+'
>>>> make: *** [dftb+] Error 2
>>>>
>>>> I would appreciate to help me to solve the problem.
>>>> Best regards, Farzad
>>>> --
>>>> Farzad Molani
>>>> Postdoctoral Research Fellow
>>>> School of Pharmaceutical Science and Technology
>>>> Tianjin University
>>>> Building 24, Room A205
>>>> 92 Weijin Road, Nankai District
>>>> <https://www.google.com/maps/search/92+Weijin+Road,+Nankai+District+%0D%0A+P.+R.+China?entry=gmail&source=g>
>>>> P. R. China
>>>> <https://www.google.com/maps/search/92+Weijin+Road,+Nankai+District+%0D%0A+P.+R.+China?entry=gmail&source=g>
>>>> Tel.: +8617526526420
>>>> Email: f.molani at gmail.com
>>>> <mailto:f.molani at gmail.com> and f.molani at tju.edu.cn
>>>> <mailto:fmolani at dena.kntu.ac.ir>
>>>>
>>>>
>>>> --
>>>> Farzad Molani
>>>> Postdoctoral Research Fellow
>>>> School of Pharmaceutical Science and Technology
>>>> Tianjin University
>>>> Building 24, Room A205
>>>> 92 Weijin Road, Nankai District
>>>> <https://www.google.com/maps/search/92+Weijin+Road,+Nankai+District+%0D%0A+P.+R.+China?entry=gmail&source=g>
>>>> P. R. China
>>>> <https://www.google.com/maps/search/92+Weijin+Road,+Nankai+District+%0D%0A+P.+R.+China?entry=gmail&source=g>
>>>> Tel.: +8617526526420
>>>> Email: f.molani at gmail.com
>>>> <mailto:f.molani at gmail.com> and f.molani at tju.edu.cn
>>>> <mailto:fmolani at dena.kntu.ac.ir>
>>>> _______________________________________________
>>>> DFTB-Plus-User mailing list
>>>> DFTB-Plus-User at mailman.zfn.uni-bremen.de
>>>> <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
>>>> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>>>
>>>
>>>
>>> --
>>> Farzad Molani
>>> Postdoctoral Research Fellow
>>> School of Pharmaceutical Science and Technology
>>> Tianjin University
>>> Building 24, Room A205
>>> 92 Weijin Road, Nankai District
>>> P. R. China
>>> Tel.: +8617526526420
>>> Email: f.molani at gmail.com
>>> <mailto:f.molani at gmail.com> and f.molani at tju.edu.cn
>>> <mailto:fmolani at dena.kntu.ac.ir>
>>>
>>>
>>> _______________________________________________
>>> DFTB-Plus-User mailing list
>>> DFTB-Plus-User at mailman.zfn.uni-bremen.de <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
>>> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>>
>> --
>> Dr. B. Hourahine, Senior lecturer
>> SUPA, Department of Physics,
>> University of Strathclyde,
>> John Anderson Building,
>> 107 Rottenrow, Glasgow G4 0NG, UK.
>> +44 141 548 2325, benjamin.hourahine at strath.ac.uk <mailto:benjamin.hourahine at strath.ac.uk>
>>
>> The Department is a partner in SUPA, the Scottish
>> Universities Physics Alliance
>>
>> The University of Strathclyde is a charitable body,
>> registered in Scotland, number SC015263
>>
>> _______________________________________________
>> DFTB-Plus-User mailing list
>> DFTB-Plus-User at mailman.zfn.uni-bremen.de
>> <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
>> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>>
>>
>>
>> --
>> Farzad Molani
>> Postdoctoral Research Fellow
>> School of Pharmaceutical Science and Technology
>> Tianjin University
>> Building 24, Room A205
>> 92 Weijin Road, Nankai District
>> P. R. China
>> Tel.: +8617526526420
>> Email: f.molani at gmail.com
>> <mailto:f.molani at gmail.com> and f.molani at tju.edu.cn
>> <mailto:fmolani at dena.kntu.ac.ir>
>>
>> _______________________________________________
>> DFTB-Plus-User mailing list
>> DFTB-Plus-User at mailman.zfn.uni-bremen.de <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
>> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>
> --
> Dr. B. Hourahine, Senior lecturer
> SUPA, Department of Physics,
> University of Strathclyde,
> John Anderson Building,
> 107 Rottenrow, Glasgow G4 0NG, UK.
> +44 141 548 2325, benjamin.hourahine at strath.ac.uk <mailto:benjamin.hourahine at strath.ac.uk>
>
> The Department is a partner in SUPA, the Scottish
> Universities Physics Alliance
>
> The University of Strathclyde is a charitable body,
> registered in Scotland, number SC015263
>
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at mailman.zfn.uni-bremen.de
> <mailto:DFTB-Plus-User at mailman.zfn.uni-bremen.de>
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
>
>
>
> --
> Farzad Molani
> Postdoctoral Research Fellow
> School of Pharmaceutical Science and Technology
> Tianjin University
> Building 24, Room A205
> 92 Weijin Road, Nankai District
> P. R. China
> Tel.: +8617526526420
> Email: f.molani at gmail.com
> <mailto:f.molani at gmail.com> and f.molani at tju.edu.cn
> <mailto:fmolani at dena.kntu.ac.ir>
>
> _______________________________________________
> DFTB-Plus-User mailing list
> DFTB-Plus-User at mailman.zfn.uni-bremen.de
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
--
Dr. B. Hourahine, Senior lecturer
SUPA, Department of Physics,
University of Strathclyde,
John Anderson Building,
107 Rottenrow, Glasgow G4 0NG, UK.
+44 141 548 2325, benjamin.hourahine at strath.ac.uk
The Department is a partner in SUPA, the Scottish
Universities Physics Alliance
The University of Strathclyde is a charitable body,
registered in Scotland, number SC015263
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