dealii example error on school's cluster

[Pai Liu]

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.

[Wolfgang Bangerth]

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: bang...@colostate.edu
www: http://www.math.colostate.edu/~bangerth/