[DFTB-Plus-User] problem with installation

Farzad Molani f.molani at gmail.com
Sat Jun 22 23:10:31 CEST 2019 

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> 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> 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> 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> 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 and f.molani at tju.edu.cn
>>> <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 and f.molani at tju.edu.cn
>>> <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
>>>
>>>
>>>
>>
>> --
>> 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 and f.molani at tju.edu.cn
>> <fmolani at dena.kntu.ac.ir>
>>
>>
>> _______________________________________________
>> DFTB-Plus-User mailing listDFTB-Plus-User at mailman.zfn.uni-bremen.dehttps://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
>>
>> _______________________________________________
>> 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
>
>
>
> --
> 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 and f.molani at tju.edu.cn
> <fmolani at dena.kntu.ac.ir>
>
> _______________________________________________
> DFTB-Plus-User mailing listDFTB-Plus-User at mailman.zfn.uni-bremen.dehttps://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
>
> _______________________________________________
> 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



-- 
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 and f.molani at tju.edu.cn <fmolani at dena.kntu.ac.ir>
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