[CP2K-user] [CP2K:11775] CP2K+OMEN
Luca
luca.... at gmail.com
Thu May 23 08:04:58 UTC 2019
Dear Tiziano
I thank you a lot for your help. I was able to compile the code although
new issues have turned up.
I did the two available tests: the former related to the graphene
transmission and the latter related to transport in a lithium chain.
The transmission calculation runs fine but it needs the same time both in
serial and in parallel with 2 mpi procs. It is, instead, much slower with
4 mpi processors.
With the other test, the Lithium chain, I get a segmentation fault. The
last lines printed are :
--------------------------------------------------------------------------------
KPOINTS| Number of kpoint groups
2
KPOINTS| Size of each kpoint group
1
KPOINTS| Number of kpoints per group
32
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= PID 29677 RUNNING AT node165
= EXIT CODE: 11
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault
(signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions
---------------------------------------------------------------------------------------------------------
Could you please give me other hints?
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>
>
> >
> >
> > 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>>
>
> >
> > >
> > >
> > > 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>
> > > > 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>
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> > Tiziano Müller
> > University of Zurich
> > Department of Chemistry
> > Winterthurerstrasse 190
> > CH-8057 Zürich
> >
> > Tel: +41 44 63 54234
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> Winterthurerstrasse 190
> CH-8057 Zürich
>
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> www.chem.uzh.ch
> tiz... at chem.uzh.ch <javascript:>
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