[CP2K-user] [CP2K:11777] CP2K+OMEN
Tiziano Müller
tiziano... at chem.uzh.ch
Wed May 22 17:45:31 UTC 2019
Hi Luca,
can you make sure that the order is actually "-lxcf03 -lxc" (and not the
other way round)?
Because the error message actually changed.
Best,
Tiziano
On 22.05.19 12:42, Luca wrote:
> Hi Tiziano
>
> I added -lxcf03 (-lxc was already there) to the .mk file, but this does
> not solve the issue.
>
> /CP2K-OMEN-GCC/cp2k/cp2k/tools/toolchain/install/libxc-4.0.3/lib/libxcf03.a(libxcf03_la-libxcf03.o):
> In function `__xc_f03_lib_m_MOD_xc_f03_functional_get_number':
> /CP2K-OMEN-GCC/cp2k/cp2k/tools/toolchain/build/libxc-4.0.3/src/./libxc_master.F03:694:
> undefined reference to `xc_functional_get_number'
> /CP2K-OMEN-GCC/cp2k/cp2k/tools/toolchain/install/libxc-4.0.3/lib/libxcf03.a(libxcf03_la-libxcf03.o):
> In function `__xc_f03_lib_m_MOD_xc_f03_functional_get_name':
> /CP2K-OMEN-GCC/cp2k/cp2k/tools/toolchain/build/libxc-4.0.3/src/./libxc_master.F03:687:
> undefined reference to `xc_functional_get_name'
> /CP2K-OMEN-GCC/cp2k/cp2k/tools/toolchain/install/libxc-4.0.3/lib/libxcf03.a(libxcf03_la-libxcf03.o):
> In function `__xc_f03_lib_m_MOD_xc_f03_func_get_info':
> /CP2K-OMEN-GCC/cp2k/cp2k/tools/toolchain/build/libxc-4.0.3/src/./libxc_master.F03:680:
> undefined reference to `xc_func_get_info'
> /CP2K-OMEN-GCC/cp2k/cp2k/tools/toolchain/install/libxc-4.0.3/lib/libxcf03.a(libxcf03_la-libxcf03.o):
> In function `__xc_f03_lib_m_MOD_xc_f03_func_end':
>
>
> Bests
> Luca
>
>
> On Wednesday, May 22, 2019 at 9:31:21 AM UTC+2, Tiziano Müller wrote:
>
> Hi Luca,
>
> I guess one or both of
>
> -lxcf03 -lxc
>
> are missing from the linker line.
>
> Best regards,
> Tiziano
>
> On 22.05.19 09:07, Luca wrote:
> > Dear Tiziano
> >
> > yes, I forgot to source the setup. However, setting the
> environment does
> > not seem to be enough for compiling omen.
> > The installer gets stuck now with:
> >
> > DHAVE_MUMPS -DHAVE_PEXSI -lrt -ldl -lstdc++ -lgfortran -lmpifort
> > -lopenblas
> > /CP2K-OMEN-GCC/cp2k/cp2k/lib/local/popt/libcp2k.a(xc_libxc.o): In
> > function `__xc_libxc_MOD_libxc_lsd_eval':
> > /CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:631: undefined
> reference to
> > `__xc_f03_lib_m_MOD_xc_f03_func_init'
> > /CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:632: undefined
> reference to
> > `__xc_f03_lib_m_MOD_xc_f03_func_get_info'
> > /CP2K-OMEN-GCC/cp2k/cp2k/lib/local/popt/libcp2k.a(xc_libxc.o): In
> > function `libxc_lsd_calc':
> > /CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:1621: undefined
> reference to
> > `__xc_f03_lib_m_MOD_xc_f03_func_init'
> > /CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:1622: undefined
> reference to
> > `__xc_f03_lib_m_MOD_xc_f03_func_get_info'
> > /CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:2281: undefined
> reference to
> > `__xc_f03_lib_m_MOD_xc_f03_func_info_get_family'
> > /CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:1962: undefined
> reference to
> > `__xc_f03_lib_m_MOD_xc_f03_mgga_exc'
> > /CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:1962: undefined
> reference to
> > `__xc_f03_lib_m_MOD_xc_f03_mgga_exc'
> > /CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:1759: undefined
> reference to
> > `__xc_f03_lib_m_MOD_xc_f03_gga_exc'
> > /CP2K-OMEN-GCC/cp2k/cp2k/src/xc/xc_libxc.F:1759: undefined
> reference to
> > `__xc_f03_lib_m_MOD_xc_f03_gga_exc'
> >
> >
> > Could you please help me again?
> >
> > Bests
> > Luca
> >
> >
> >
> >
> >
> > On Tuesday, May 21, 2019 at 1:05:50 PM UTC+2, Tiziano Müller wrote:
> >
> > Hi Luca,
> >
> > this means that the linker is unable to find the mentioned
> libraries
> > [1].
> >
> > Make sure you source the `setup` file from the toolchain (as
> instructed
> > by the toolchain script):
> >
> > source [...]/cp2k/tools/toolchain/install/setup
> >
> > which adds the library paths to the variable
> `$LD_LIBRARY_PATH` from
> > where the linker should pick them up.
> >
> > Best regards,
> > Tiziano
> >
> > [1]
> >
> https://stackoverflow.com/questions/16710047/usr-bin-ld-cannot-find-lnameofthelibrary
> <https://stackoverflow.com/questions/16710047/usr-bin-ld-cannot-find-lnameofthelibrary>
>
> >
> <https://stackoverflow.com/questions/16710047/usr-bin-ld-cannot-find-lnameofthelibrary
> <https://stackoverflow.com/questions/16710047/usr-bin-ld-cannot-find-lnameofthelibrary>>
>
> >
> >
> > On 21.05.19 11:09, Luca wrote:
> > > Dear Tiziano
> > >
> > > I was able to compile libcp2k, but I was less lucky with
> omen.
> > >
> > > I get the errors
> > >
> > > /usr/bin/ld: cannot find -lxsmmf
> > > /usr/bin/ld: cannot find -lxsmm
> > > /usr/bin/ld: cannot find -lderiv
> > > /usr/bin/ld: cannot find -lint
> > > /usr/bin/ld: cannot find -lxcf90
> > > /usr/bin/ld: cannot find -lxc
> > > /usr/bin/ld: cannot find -lfftw3
> > > /usr/bin/ld: cannot find -lmpifort
> > > /usr/bin/ld: cannot find -lopenblas
> > >
> > > Could you please help me with this?
> > >
> > > Bests
> > > Luca
> > >
> > >
> > > On Monday, May 20, 2019 at 12:48:24 PM UTC+2, Tiziano
> Müller wrote:
> > >
> > > Hi Luca,
> > >
> > > On 20.05.19 10:21, Luca wrote:
> > > > Dear Tiziano
> > > >
> > > > thank you for your answer. Unfortunately, your
> hints do
> > not fix the
> > > > issue. The path to the cp2k sources is
> > > .../CP2K-OMEN/cp2k/cp2k/src. > I believe the reason is
> that the
> > > script package_versions.sh do not exist
> > > > in the dir ../script.
> > > > Furthermore, that script is not even present in the
> entire
> > cp2k dir.
> > > > Does anyone know the reason for that? Which is the
> cp2k
> > release I
> > > have
> > > > to use with OMEN? I am using the 6.1
> > >
> > > in v6.1 the script should still be there:
> > >
> > >
> >
> https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh
> <https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh>
>
> >
> <https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh
> <https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh>>
>
> >
> > >
> >
> <https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh
> <https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh>
>
> >
> <https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh
> <https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh>>>
>
> >
> > >
> > >
> > > But it seems that the script by default pulls from old
> SVN
> > trunk which
> > > is already missing the `package_versions.sh`.
> > >
> > > You can proceed by either commenting out the SVN checkout
> > part in
> > > OMEN's
> > > `installer.sh` and make sure it uses the CP2K sources you
> > provide or
> > > change
> > >
> > > cp2kTRUNKorRELEASE="trunk"
> > > cp2kRELEASEVER="4_1"
> > >
> > > to
> > >
> > > cp2kTRUNKorRELEASE="release"
> > > cp2kRELEASEVER="6_1"
> > >
> > > which should make the script pull version 6.1 from the
> old
> > SVN (both
> > > methods not tested by me).
> > > In any what it seems you need some manual work to make
> the
> > > `installer.sh` work again.
> > >
> > > Best regards,
> > > Tiziano
> > >
> > > >
> > > > Best Regards.
> > > > Luca
> > > >
> > > > On Monday, May 20, 2019 at 9:22:00 AM UTC+2, Tiziano
> > Müller wrote:
> > > >
> > > > Hi Luca,
> > > >
> > > > the dft-transport code seems to be assuming the
> old CP2K
> > > directory
> > > > layout from when we were still using Subversion.
> > > >
> > > > It might be enough to correct line 111 in the
> > installer.sh to
> > > >
> > > > cp2k_toolchainDIR=${cp2kDIR}/tools/toolchain
> > > >
> > > > ... and in lines 121, 130, 403 remove the
> `cp2k/` as
> > well.
> > > >
> > > > Best regards,
> > > > Tiziano
> > > >
> > > > On 19.05.19 21:57, Luca wrote:
> > > > > Dear developers
> > > > >
> > > > > I am trying to install CP2K+OMEN by using the
> > installer.sh
> > > script
> > > > > provided with the dft-transport sources.
> > > > > Unfortunately, the installer does not finish
> his work
> > > since it
> > > > crashes
> > > > > with the error:
> > > > >
> > > > >
> > > >
> > >
> >
> --------------------------------------------------------------------------------------------------------
>
> >
> > >
> > > >
> > > > > build CP2K you should change directory:
> > > > > cd cp2k/makefiles/
> > > > > make -j 16 ARCH=local VERSION="sopt sdbg
> ssmp
> > popt pdbg
> > > psmp"
> > > > >
> > > > > arch files for GPU enabled CUDA versions are
> named
> > > "local_cuda.*"
> > > > > arch files for valgrind versions are named
> > "local_valgrind.*"
> > > > > arch files for coverage versions are named
> > "local_coverage.*"
> > > > > ./installer.sh: line 141:
> > > > >
> > > >
> > >
> >
> .../CP2K-OMEN/cp2k/cp2k/tools/toolchain/scripts/package_versions.sh: No
> > > > > such file or directory
> > > > >
> > > >
> > >
> >
> --------------------------------------------------------------------------------------------------------
>
> >
> > >
> > > >
> > > > >
> > > > > Could you please help me to overcome this
> issue?
> > > > > Best Regards.
> > > > >
> > > > > Luca
> > > > >
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> > > >
> > > > --
> > > > Tiziano Müller
> > > > University of Zurich
> > > > Department of Chemistry
> > > > Winterthurerstrasse 190
> > > > CH-8057 Zürich
> > > >
> > > > Tel: +41 44 63 54234
> > > > www.chem.uzh.ch <http://www.chem.uzh.ch>
> <http://www.chem.uzh.ch>
> > <http://www.chem.uzh.ch> <http://www.chem.uzh.ch>
> > > > tiz... at chem.uzh.ch <javascript:>
> > > >
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> > >
> > > --
> > > Tiziano Müller
> > > University of Zurich
> > > Department of Chemistry
> > > Winterthurerstrasse 190
> > > CH-8057 Zürich
> > >
> > > Tel: +41 44 63 54234
> > > www.chem.uzh.ch <http://www.chem.uzh.ch>
> <http://www.chem.uzh.ch> <http://www.chem.uzh.ch>
> > > tiz... at chem.uzh.ch
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> >
> > --
> > Tiziano Müller
> > University of Zurich
> > Department of Chemistry
> > Winterthurerstrasse 190
> > CH-8057 Zürich
> >
> > Tel: +41 44 63 54234
> > www.chem.uzh.ch <http://www.chem.uzh.ch> <http://www.chem.uzh.ch>
> > tiz... at chem.uzh.ch <javascript:>
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> --
> Tiziano Müller
> University of Zurich
> Department of Chemistry
> Winterthurerstrasse 190
> CH-8057 Zürich
>
> Tel: +41 44 63 54234
> www.chem.uzh.ch <http://www.chem.uzh.ch>
> tiz... at chem.uzh.ch <javascript:>
>
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--
Tiziano Müller
University of Zurich
Department of Chemistry
Winterthurerstrasse 190
CH-8057 Zürich
Tel: +41 44 63 54234
www.chem.uzh.ch
tiziano... at chem.uzh.ch
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