Pai,
> -- Configuring done > CMake Warning at > /public/home/ZK/opt/dealii/deal.II-v9.1.1/share/deal.II/macros/macro_deal_ii_invoke_autopilot.cmake:54 > > (ADD_EXECUTABLE): > Cannot generate a safe linker search path for target step-2 because files > in some directories may conflict with libraries in implicit directories: > > link library [libmkl_gf_lp64.so] in > /public/software/compiler/intel/composer_xe_2018.u2/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64_lin > > may be hidden by files in: > /public/software/compiler/intel/composer_xe_2018.u2/mkl/lib/intel64 > link library [libmkl_intel_lp64.so] in > /public/software/compiler/intel/composer_xe_2018.u2/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64_lin > > may be hidden by files in: > /public/software/compiler/intel/composer_xe_2018.u2/mkl/lib/intel64 > link library [libmkl_intel_thread.so] in > /public/software/compiler/intel/composer_xe_2018.u2/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64_lin > > may be hidden by files in: > /public/software/compiler/intel/composer_xe_2018.u2/mkl/lib/intel64 > link library [libmkl_core.so] in > /public/software/compiler/intel/composer_xe_2018.u2/compilers_and_libraries_2018.2.199/linux/mkl/lib/intel64_lin > > may be hidden by files in: > /public/software/compiler/intel/composer_xe_2018.u2/mkl/lib/intel64 This is concerning. Do you have two different versions of the MKL installed? That is generally not useful nor, as the warning says, safe. > *And the following is the error I got when I run step-2 by "gdb ./step-2":* > GNU gdb (GDB) Red Hat Enterprise Linux (7.2-75.el6) > Copyright (C) 2010 Free Software Foundation, Inc. > License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html > <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fgnu.org%2Flicenses%2Fgpl.html&data=02%7C01%7CWolfgang.Bangerth%40colostate.edu%7Cade479cf246a4a6b7f4d08d76cbb5c3f%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C637097424282089100&sdata=aJonaqKT57ko5fmt%2FA3R9eLXN3fvkkFblACqYpRJvSc%3D&reserved=0>> > This is free software: you are free to change and redistribute it. > There is NO WARRANTY, to the extent permitted by law. Type "show copying" > and "show warranty" for details. > This GDB was configured as "x86_64-redhat-linux-gnu". > For bug reporting instructions, please see: > <http://www.gnu.org/software/gdb/bugs/ > <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.gnu.org%2Fsoftware%2Fgdb%2Fbugs%2F&data=02%7C01%7CWolfgang.Bangerth%40colostate.edu%7Cade479cf246a4a6b7f4d08d76cbb5c3f%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C637097424282099098&sdata=u6pGrXw22F%2FzJ2WEL7sUUePxe45EpfGKAUnrTnMJAjs%3D&reserved=0>>... > Reading symbols from > /public/home/ZK/opt/dealii/deal.II-v9.1.1/examples/step-2/step-2...done. > (gdb) r > Starting program: > /public/home/ZK/opt/dealii/deal.II-v9.1.1/examples/step-2/step-2 > [Thread debugging using libthread_db enabled] > warning: File > "/public/software/compiler/gcc/5.4.0/lib64/libstdc++.so.6.0.21-gdb.py > <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fso.6.0.21-gdb.py&data=02%7C01%7CWolfgang.Bangerth%40colostate.edu%7Cade479cf246a4a6b7f4d08d76cbb5c3f%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C637097424282099098&sdata=n3rGTmQSOqmR6lK49fkaVagN8A%2Bf5ISwKgYZ%2FYd1YpI%3D&reserved=0>" > > auto-loading has been declined by your `auto-load safe-path' set to > "/usr/share/gdb/auto-load:/usr/lib/debug:/usr/bin/mono-gdb.py". > To enable execution of this file add > add-auto-load-safe-path > /public/software/compiler/gcc/5.4.0/lib64/libstdc++.so.6.0.21-gdb.py > <https://nam01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fso.6.0.21-gdb.py&data=02%7C01%7CWolfgang.Bangerth%40colostate.edu%7Cade479cf246a4a6b7f4d08d76cbb5c3f%7Cafb58802ff7a4bb1ab21367ff2ecfc8b%7C0%7C0%7C637097424282099098&sdata=n3rGTmQSOqmR6lK49fkaVagN8A%2Bf5ISwKgYZ%2FYd1YpI%3D&reserved=0> > line to your configuration file "/public/home/ZK/.gdbinit". > To completely disable this security protection add > set auto-load safe-path / > line to your configuration file "/public/home/ZK/.gdbinit". > For more information about this security protection see the > "Auto-loading safe path" section in the GDB manual. E.g., run from the shell: > info "(gdb)Auto-loading safe path" > > Program received signal SIGSEGV, Segmentation fault. > 0x00007fffe9760615 in tbb::interface9::global_control::active_value(int) () > at > /public/home/ZK/opt/dealii/tmp/unpack/deal.II-v9.1.1/bundled/tbb-2018_U2/src/tbb/tbb_main.cpp:563 > 563 return controls[param]->active_value(); I have to admit that I don't know what this refers to. The place where I've seen these kinds of errors is if there are multiple versions of the Threading Building Blocks installed and/or if you compiled on our hardware platform and then run on a different hardware platform. I have a suspicion that it is related to the error you show: deal.II is compiled agains the version of the TBB that is bundled with deal.II, but then linked against the one on your system. Best W. -- ------------------------------------------------------------------------ Wolfgang Bangerth email: [email protected] www: http://www.math.colostate.edu/~bangerth/ -- The deal.II project is located at http://www.dealii.org/ For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en --- You received this message because you are subscribed to the Google Groups "deal.II User Group" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/26e01a8b-77cb-c396-a6d3-1858cbf868a7%40colostate.edu.
