<div dir="ltr"><div>Dear Tiziano</div><div> </div><div>I thank you a lot for your help. I was able to compile the code although new issues have turned up.</div><div>I did the two available tests: the former related to the graphene transmission and the latter related to transport in a lithium chain.</div><div>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. </div><div>With the other test, the Lithium chain, I get a segmentation fault. The last lines printed are :</div><div> </div><div> </div><div>--------------------------------------------------------------------------------</div><div> KPOINTS| Number of kpoint groups 2</div><div> KPOINTS| Size of each kpoint group 1</div><div> KPOINTS| Number of kpoints per group 32</div><div> </div><div>===================================================================================</div><div>= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES</div><div>= PID 29677 RUNNING AT node165</div><div>= EXIT CODE: 11</div><div>= CLEANING UP REMAINING PROCESSES</div><div>= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES</div><div>===================================================================================</div><div>YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)</div><div>This typically refers to a problem with your application.</div><div>Please see the FAQ page for debugging suggestions</div><div>---------------------------------------------------------------------------------------------------------</div><div> </div><div> </div><div>Could you please give me other hints?</div><div> </div><div>Bests</div><div>Luca </div><div> </div><div> On Wednesday, May 22, 2019 at 9:31:21 AM UTC+2, Tiziano Müller wrote:<blockquote class="gmail_quote" style="margin: 0;margin-left: 0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">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] > <a href="https://stackoverflow.com/questions/16710047/usr-bin-ld-cannot-find-lnameofthelibrary" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fstackoverflow.com%2Fquestions%2F16710047%2Fusr-bin-ld-cannot-find-lnameofthelibrary\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHdvNRAZFk1wk9_xsYGhuJIpzsz4A';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fstackoverflow.com%2Fquestions%2F16710047%2Fusr-bin-ld-cannot-find-lnameofthelibrary\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHdvNRAZFk1wk9_xsYGhuJIpzsz4A';return true;">https://stackoverflow.com/questions/16710047/usr-bin-ld-cannot-find-lnameofthelibrary</a> > <<a href="https://stackoverflow.com/questions/16710047/usr-bin-ld-cannot-find-lnameofthelibrary" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fstackoverflow.com%2Fquestions%2F16710047%2Fusr-bin-ld-cannot-find-lnameofthelibrary\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHdvNRAZFk1wk9_xsYGhuJIpzsz4A';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fstackoverflow.com%2Fquestions%2F16710047%2Fusr-bin-ld-cannot-find-lnameofthelibrary\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHdvNRAZFk1wk9_xsYGhuJIpzsz4A';return true;">https://stackoverflow.com/questions/16710047/usr-bin-ld-cannot-find-lnameofthelibrary</a>> > > > 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: > > > > > <a href="https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fcp2k%2Fcp2k%2Fblob%2Fv6.1.0%2Ftools%2Ftoolchain%2Fscripts%2Fpackage_versions.sh\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGUTi-C-6QBhBvhe88tc8k4iVul3A';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fcp2k%2Fcp2k%2Fblob%2Fv6.1.0%2Ftools%2Ftoolchain%2Fscripts%2Fpackage_versions.sh\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGUTi-C-6QBhBvhe88tc8k4iVul3A';return true;">https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh</a> > <<a href="https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fcp2k%2Fcp2k%2Fblob%2Fv6.1.0%2Ftools%2Ftoolchain%2Fscripts%2Fpackage_versions.sh\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGUTi-C-6QBhBvhe88tc8k4iVul3A';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fcp2k%2Fcp2k%2Fblob%2Fv6.1.0%2Ftools%2Ftoolchain%2Fscripts%2Fpackage_versions.sh\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGUTi-C-6QBhBvhe88tc8k4iVul3A';return true;">https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh</a>> > > > > <<a href="https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fcp2k%2Fcp2k%2Fblob%2Fv6.1.0%2Ftools%2Ftoolchain%2Fscripts%2Fpackage_versions.sh\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGUTi-C-6QBhBvhe88tc8k4iVul3A';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fcp2k%2Fcp2k%2Fblob%2Fv6.1.0%2Ftools%2Ftoolchain%2Fscripts%2Fpackage_versions.sh\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGUTi-C-6QBhBvhe88tc8k4iVul3A';return true;">https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh</a> > <<a href="https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh" target="_blank" rel="nofollow" onmousedown="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fcp2k%2Fcp2k%2Fblob%2Fv6.1.0%2Ftools%2Ftoolchain%2Fscripts%2Fpackage_versions.sh\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGUTi-C-6QBhBvhe88tc8k4iVul3A';return true;" onclick="this.href='https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2Fcp2k%2Fcp2k%2Fblob%2Fv6.1.0%2Ftools%2Ftoolchain%2Fscripts%2Fpackage_versions.sh\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGUTi-C-6QBhBvhe88tc8k4iVul3A';return true;">https://github.com/cp2k/cp2k/blob/v6.1.0/tools/toolchain/scripts/package_versions.sh</a>>> > > > > > > > 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 > > > > > > > > -- > > > > You received this message because you are > subscribed to > > the Google > > > > Groups "cp2k" group. > > > > To unsubscribe from this group and stop receiving > emails > > from it, > > > send > > > > an email to <a>c...@googlegroups.com</a> <javascript:> > > > > <mailto:<a>c...@googlegroups.com</a> <javascript:>>. > > > > To post to this group, send email to > <a>c...@googlegroups.com</a> > > > <javascript:> 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Winterthurerstrasse 190 > > > CH-8057 Zürich > > > > > > Tel: +41 44 63 54234 > > > <a href="http://www.chem.uzh.ch" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.chem.uzh.ch\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEaSd80M-dQwlA8q5GEKkKY5wRCiQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.chem.uzh.ch\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEaSd80M-dQwlA8q5GEKkKY5wRCiQ';return true;">www.chem.uzh.ch</a> <<a href="http://www.chem.uzh.ch" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.chem.uzh.ch\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEaSd80M-dQwlA8q5GEKkKY5wRCiQ';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.chem.uzh.ch\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEaSd80M-dQwlA8q5GEKkKY5wRCiQ';return true;">http://www.chem.uzh.ch</a>> > <<a href="http://www.chem.uzh.ch" target="_blank" rel="nofollow" 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