[CP2K-user] [CP2K:11766] CP2K+OMEN
Luca
luca.... at gmail.com
Wed May 22 07:07:41 UTC 2019
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
>
> 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>
>
> >
> >
> > 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>
>
> > > 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>
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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
> tiz... at chem.uzh.ch <javascript:>
>
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