See ldd.txt for the output of
$ ldd ./step-1
and gdb.txt for the output of
$ gdb ./step-1
Does this help?
Matthias Maier schrieb am Donnerstag, 22. Juni 2023 um 23:28:16 UTC+2:
> The most likely issue will be a "symbol clash" either due to ABI
> incompatible versions of the same external shared library linked into
> the executable, or due to the matlab shared library you are linking
> against containing these.
>
> Can you send us the output of $ ldd executable (for a faulty one)?
>
> Furthermore, have you tried running the startup in a debugger such as
> gdb? If possible, the stacktrace for the segfault will be very
> illuminating:
>
> $ gdb executable
> > run
> > bt
>
> Best,
> Matthias
>
>
>
> On Thu, Jun 22, 2023, at 14:46 CDT, Mathieu <mathi...@gmail.com> wrote:
>
> > Thanks Matthias for clarification.
> > But as I said, I do not have this problem using the default compiler on
> my
> > system.
> >
> > Since I have no experience with a debugger, I let valgrind run on the
> > program:
> > valgrind --tool=memcheck --leak-check=full --track-origins=yes ./step-1
> > (see the attachment for the output).
> >
> > From the memcheck, I can not deduce anything that would bring me closer
> to
> > the bottom.
> > Do you have any suggestions based on the memcheck?
> > I could imagine there is a mismatch between some deal.II dependencies
> (TBB
> > ?) and the
> > corresponding versions shipped with matlab.
> >
> > Best,
> > Math
> >
> >
> >
> > Matthias Maier schrieb am Donnerstag, 22. Juni 2023 um 20:14:02 UTC+2:
> >
> >
> > On Thu, Jun 22, 2023, at 04:13 CDT, Mathieu <mathi...@gmail.com> wrote:
> >
> >> Good point to narrow down the problem.
> >> I modified step-1 so that the main function only calls matlab via
> >> callFevalsqrt().
> >> This works fine, even if I use the mpi compiler mentioned in my
> original
> >> post.
> >> However, if I just add a second line in the main function,
> >> dealii::Triangulation<2> triangulation,
> >> I run again into the segfault.
> >
> > What happens when you include this statement in yourr main function is
> > that your main.cc compilation unit now contains a symbol to the deal.II
> > library. The linker will then keep libdeal_ii.so as a shared object
> > dependency. If you do not actually use any symbol from the deal.II
> > library itself then the linker might drop the shared object altogether
> > and the final result is as if you never linked to deal.II in the first
> > place. You can verify this by running "ldd" on the executable:
> >
> > $ ldd executable
> > libdeal_II.so.9999 => /usr/lib64/libdeal_II.so
> >
> > Best,
> > Matthias
>
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Reading symbols from ./step-1...
(gdb) r
Starting program: /opt/dealii-9.4.1/examples/step-1/step-1
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[New Thread 0x7fffbddff640 (LWP 455923)]
[New Thread 0x7fffbd5fe640 (LWP 455924)]
Thread 3 "step-1" received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7fffbd5fe640 (LWP 455924)]
0x00007fffc60cab83 in ?? () from /opt/MATLAB/R2023a/bin/glnxa64/libmwmvm.so
(gdb) r
The program being debugged has been started already.
Start it from the beginning? (y or n) n
Program not restarted.
(gdb) quit
A debugging session is active.
Inferior 1 [process 433269] will be killed.
Quit anyway? (y or n) y
linux-vdso.so.1 (0x00007ffc1654b000)
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libgomp.so.1 => /lib/x86_64-linux-gnu/libgomp.so.1 (0x00007fe8a8654000)
libgaleri-epetra.so.13 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/trilinos-13.0.1-d2lx23wgf5vqrb3zqj5hs4e36lcws545/lib/libgaleri-epetra.so.13
(0x00007fe8a83bf000)
libtrilinosss.so.13 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/trilinos-13.0.1-d2lx23wgf5vqrb3zqj5hs4e36lcws545/lib/libtrilinosss.so.13
(0x00007fe8a838d000)
libteuchosremainder.so.13 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/trilinos-13.0.1-d2lx23wgf5vqrb3zqj5hs4e36lcws545/lib/libteuchosremainder.so.13
(0x00007fe8ab1c4000)
libteuchosnumerics.so.13 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/trilinos-13.0.1-d2lx23wgf5vqrb3zqj5hs4e36lcws545/lib/libteuchosnumerics.so.13
(0x00007fe8a8bc4000)
libtriutils.so.13 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/trilinos-13.0.1-d2lx23wgf5vqrb3zqj5hs4e36lcws545/lib/libtriutils.so.13
(0x00007fe8a8339000)
libteuchosparser.so.13 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/trilinos-13.0.1-d2lx23wgf5vqrb3zqj5hs4e36lcws545/lib/libteuchosparser.so.13
(0x00007fe8a7d80000)
libamd.so.2 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/suite-sparse-5.10.1-q3ash3yons2suh3544kqmtjqy47vg4xl/lib/libamd.so.2
(0x00007fe8aa6a0000)
libsuitesparseconfig.so.5 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/suite-sparse-5.10.1-q3ash3yons2suh3544kqmtjqy47vg4xl/lib/libsuitesparseconfig.so.5
(0x00007fe8aba0e000)
libcholmod.so.3 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/suite-sparse-5.10.1-q3ash3yons2suh3544kqmtjqy47vg4xl/lib/libcholmod.so.3
(0x00007fe8a72ef000)
libfltk_images.so.1.3 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/fltk-1.3.7-st53jbl2mo2mms2b75xgxqhdsmqmrtax/lib/libfltk_images.so.1.3
(0x00007fe8a7d3f000)
libfltk_gl.so.1.3 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/fltk-1.3.7-st53jbl2mo2mms2b75xgxqhdsmqmrtax/lib/libfltk_gl.so.1.3
(0x00007fe8a7d1e000)
libGL.so.1 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/mesa-22.0.2-lvmqk5krmommt2v6fqfjtvkbmj55iaq4/lib/libGL.so.1
(0x00007fe89ee00000)
libfltk.so.1.3 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/fltk-1.3.7-st53jbl2mo2mms2b75xgxqhdsmqmrtax/lib/libfltk.so.1.3
(0x00007fe8a6efe000)
libX11.so.6 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/libx11-1.7.0-gehg3dnkswgtu5kgdqq5giao2w5ghljw/lib/libX11.so.6
(0x00007fe8a6abb000)
libmmg.so.5 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/mmg-5.6.0-lohn2xxn52kkunhq3tjc2ddqcqggrghx/lib/libmmg.so.5
(0x00007fe8a1ea8000)
libcgns.so.4.3 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/cgns-4.3.0-mnjwjpsdgveyzgvgz2w2li5odb7wz4iy/lib/libcgns.so.4.3
(0x00007fe8a672f000)
libTKOffset.so.11 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/oce-0.18.3-ecsmaa46gxbflztayfsqannu7m66vwcb/lib/libTKOffset.so.11
(0x00007fe8a62d1000)
libTKFillet.so.11 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/oce-0.18.3-ecsmaa46gxbflztayfsqannu7m66vwcb/lib/libTKFillet.so.11
(0x00007fe89ea00000)
libTKBO.so.11 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/oce-0.18.3-ecsmaa46gxbflztayfsqannu7m66vwcb/lib/libTKBO.so.11
(0x00007fe89e600000)
libTKPrim.so.11 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/oce-0.18.3-ecsmaa46gxbflztayfsqannu7m66vwcb/lib/libTKPrim.so.11
(0x00007fe8a6ea7000)
libTKG2d.so.11 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/oce-0.18.3-ecsmaa46gxbflztayfsqannu7m66vwcb/lib/libTKG2d.so.11
(0x00007fe8a66b4000)
libGLU.so.1 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/mesa-glu-9.0.2-jo53cx2abfku4pdtbo2oc4oey2ftud5w/lib/libGLU.so.1
(0x00007fe8a598b000)
libtbbmalloc.so.2 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/intel-tbb-2020.3-ulfjl2ollhdkou6aoriwp27nlydyzuvj/lib/libtbbmalloc.so.2
(0x00007fe8a72ac000)
libtbb.so.2 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/intel-tbb-2020.3-ulfjl2ollhdkou6aoriwp27nlydyzuvj/lib/libtbb.so.2
(0x00007fe8a6e60000)
libTKSTEPAttr.so.11 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/oce-0.18.3-ecsmaa46gxbflztayfsqannu7m66vwcb/lib/libTKSTEPAttr.so.11
(0x00007fe8a5552000)
libTKSTEP209.so.11 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/oce-0.18.3-ecsmaa46gxbflztayfsqannu7m66vwcb/lib/libTKSTEP209.so.11
(0x00007fe8a2f38000)
libTKSTEPBase.so.11 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/oce-0.18.3-ecsmaa46gxbflztayfsqannu7m66vwcb/lib/libTKSTEPBase.so.11
(0x00007fe89e200000)
libgfortran.so.5 => /lib/x86_64-linux-gnu/libgfortran.so.5
(0x00007fe89de00000)
libparpack.so.2 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/arpack-ng-3.8.0-rnfwee67o4c2plbz5i7j2iqnmuky6k7f/lib/libparpack.so.2
(0x00007fe8a5fb9000)
libHYPRE-2.24.0.so =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/hypre-2.24.0-iw5kk4gesmb6uhsx4fuhkgy6owyh4uvp/lib/libHYPRE-2.24.0.so
(0x00007fe89da00000)
libsuperlu_dist.so.7 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/superlu-dist-7.2.0-2zzvm6zshyz5xliym7gse244rzeuotae/lib/libsuperlu_dist.so.7
(0x00007fe8a2500000)
libparmetis.so =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/parmetis-4.0.3-5ryxr7emwfu7eyykoe2cpdk4i2csi63c/lib/libparmetis.so
(0x00007fe8a6293000)
libmetis.so =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/metis-5.1.0-37lsyz4qnw3cdthyiztiumiksod2vq75/lib/libmetis.so
(0x00007fe8a54dd000)
libmpi_mpifh.so.40 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/openmpi-4.1.3-gtd2oilryfrlklfhop45kp67vtzmahzb/lib/libmpi_mpifh.so.40
(0x00007fe8a2b98000)
libopen-rte.so.40 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/openmpi-4.1.3-gtd2oilryfrlklfhop45kp67vtzmahzb/lib/libopen-rte.so.40
(0x00007fe89ecdc000)
libopen-pal.so.40 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/openmpi-4.1.3-gtd2oilryfrlklfhop45kp67vtzmahzb/lib/libopen-pal.so.40
(0x00007fe89e8f7000)
libhwloc.so.15 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/hwloc-2.7.1-axxuldgfjlb2zgvxj5fimam7spvcvtk6/lib/libhwloc.so.15
(0x00007fe8a3fa1000)
libcolamd.so.2 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/suite-sparse-5.10.1-q3ash3yons2suh3544kqmtjqy47vg4xl/lib/libcolamd.so.2
(0x00007fe8a8eda000)
libccolamd.so.2 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/suite-sparse-5.10.1-q3ash3yons2suh3544kqmtjqy47vg4xl/lib/libccolamd.so.2
(0x00007fe8a8ecc000)
libcamd.so.2 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/suite-sparse-5.10.1-q3ash3yons2suh3544kqmtjqy47vg4xl/lib/libcamd.so.2
(0x00007fe8a8bb5000)
libglapi.so.0 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/mesa-22.0.2-lvmqk5krmommt2v6fqfjtvkbmj55iaq4/lib/libglapi.so.0
(0x00007fe8a2b5c000)
libunwind.so.8 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/libunwind-1.6.2-2cu47c42zfoywg4dii6v26ijg4frxqin/lib/libunwind.so.8
(0x00007fe8a7d04000)
libtinfo.so.6 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/ncurses-6.2-fa7yup4glvpmb3hyzxibos6aisfeq6wt/lib/libtinfo.so.6
(0x00007fe8a2b1e000)
libXext.so.6 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/libxext-1.3.3-tpygehuciekjrxze4bx6n3uqdb6jv6qw/lib/libXext.so.6
(0x00007fe8a863f000)
libXrender.so.1 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/libxrender-0.9.10-oxmtflryiw6afks3gzj2zt3pb7vkba2h/lib/libXrender.so.1
(0x00007fe8a832c000)
libxcb.so.1 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/libxcb-1.14-y2ut3iyxnfgflkldizyzmsyug7rkl7bg/lib/libxcb.so.1
(0x00007fe8a77d5000)
libscotch.so.7.0.1 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/scotch-7.0.1-klik7fo67xo26ajpu4zn77ugnfa74tv3/lib/libscotch.so.7.0.1
(0x00007fe89e864000)
libscotcherrexit.so =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/scotch-7.0.1-klik7fo67xo26ajpu4zn77ugnfa74tv3/lib/libscotcherrexit.so
(0x00007fe8a8326000)
libquadmath.so.0 => /lib/x86_64-linux-gnu/libquadmath.so.0
(0x00007fe8a24b8000)
libarpack.so.2 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/arpack-ng-3.8.0-rnfwee67o4c2plbz5i7j2iqnmuky6k7f/lib/libarpack.so.2
(0x00007fe89e81d000)
libevent_core-2.1.so.7 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/libevent-2.1.12-4jxqzv7nl6j4jbewoqzso3p3ijxomxss/lib/libevent_core-2.1.so.7
(0x00007fe8a1e6f000)
libpmix.so.2 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/pmix-4.1.2-cmh4mijo5za6i7wiysxpd4fkqtrvr3qv/lib/libpmix.so.2
(0x00007fe89d802000)
libevent_pthreads-2.1.so.7 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/libevent-2.1.12-4jxqzv7nl6j4jbewoqzso3p3ijxomxss/lib/libevent_pthreads-2.1.so.7
(0x00007fe8a7cff000)
libpciaccess.so.0 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/libpciaccess-0.16-xq5a55i6t2rpuupcakcb7zqui6w6q4hj/lib/libpciaccess.so.0
(0x00007fe8a7cf1000)
libxml2.so.2 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/libxml2-2.9.13-rcxrm6tp4yfmmm3fiez32lhxydg4x4ha/lib/libxml2.so.2
(0x00007fe89d694000)
libXau.so.6 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/libxau-1.0.8-lyspqelpgyipptq3oytkg3ukuf6brrn7/lib/libXau.so.6
(0x00007fe8a7ceb000)
libXdmcp.so.6 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/libxdmcp-1.1.2-i44y5lf2y6buvwc5q2butkfgefztajzf/lib/libXdmcp.so.6
(0x00007fe8a72a2000)
liblzma.so.5 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/xz-5.2.5-xnx2rm7camnar3gas3odzt6jiz5jlj6f/lib/liblzma.so.5
(0x00007fe8a5962000)
libiconv.so.2 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/libiconv-1.16-p6h4mctf7w33phvkcpl7ai4x5pwlffuk/lib/libiconv.so.2
(0x00007fe89e502000)
libbsd.so.0 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/libbsd-0.11.5-nmsykvfflb54lxssowzpwvkjt7bhdkrd/lib/libbsd.so.0
(0x00007fe8a6aa3000)
libmd.so.0 =>
/dealii-9.3.2/opt/spack/linux-ubuntu22.04-skylake/gcc-12.1.0/libmd-1.0.4-rhpchybp5opz2i7ji4wh3hbw3fs54aiq/lib/libmd.so.0
(0x00007fe8a6a95000)
