Hi all,
I recently installed dealii on our school's cluster (which is not allowed
to access the internet).
*When I run step-2 I got the error "Segmentation fault (core dumped)".*
*The following is the warning I got when I run "make":*
-- 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
Some of these libraries may not be found correctly.
Call Stack (most recent call first):
CMakeLists.txt:39 (DEAL_II_INVOKE_AUTOPILOT)
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 runtime search path for target step-2 because files
in some directories may conflict with libraries in implicit directories:
runtime 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
runtime libr
*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
>
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/>...
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" 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
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();
Missing separate debuginfos, use: debuginfo-install
glibc-2.12-1.149.el6.x86_64 gsl-1.13-1.el6.x86_64
libudev-147-2.57.el6.x86_64 numactl-2.0.9-2.el6.x86_64
(gdb)
*In the last four lines of the error, it seems that it is the "tbb" that
leads to the error. *
*I dont understand this error, and any help will be appreciated.*
--
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