Received signal SIGSEGV, Segmentation fault

[Smith Jack]

Hello, I am trying to compile DEAL.II on a server. There is no error in the compilation, but when I try to run an example, segmentation fault occurs.

I create a environment by conda, in this environment, I installed 

gcc, gxx， gfortan, make, cmake, lapack, blas, scalapack, petsc, symengine

I also compiled SUNDIALS, Trilinos, p4est by myself. Trilinos depends on two others libraries, NETCDF and MATIO, I also compiled them by myself. Everything seemed to be fine. But when I run the example, I got the error:

(gdb) r
Starting program: /work5/luandong/softwares/dealii-9.5.1/examples/step-1/step-1.debug
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
[New Thread 0x2aaaf6efd700 (LWP 100087)]
[New Thread 0x2aaaf70fe700 (LWP 100088)]
[New Thread 0x2aaaff2ff700 (LWP 100089)]
[New Thread 0x2aab0f500700 (LWP 100090)]
[New Thread 0x2aab0f701700 (LWP 100091)]
[New Thread 0x2aab1f902700 (LWP 100092)]
[New Thread 0x2aab27b03700 (LWP 100093)]

Thread 1 "step-1.debug" received signal SIGSEGV, Segmentation fault.
0x00002aaac5a3089f in __static_initialization_and_destruction_0 () at /home/luandong/data-copy/download/dealii-9.5.1/include/deal.II/base/mpi.h:1732
1732          mpi_type_id_for_type = internal::MPIDataTypes::mpi_type_id(
(gdb) q
A debugging session is active.

        Inferior 1 [process 99962] will be killed.

Quit anyway? (y or n) y

Is that because the program use the library "libthread_db.so" ? 

If I use ldd program to see which *so libraries are linked to the program, I get 

ldd ./step-1.debug | grep lib64 | grep -v Trilinos | grep -v sundials
        libdl.so.2 => /lib64/libdl.so.2 (0x00002b026da10000)
        librt.so.1 => /lib64/librt.so.1 (0x00002b028782e000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b028871f000)
        libm.so.6 => /lib64/libm.so.6 (0x00002b0288964000)
        libc.so.6 => /lib64/libc.so.6 (0x00002b028fd1d000)
        /lib64/ld-linux-x86-64.so.2 (0x00002b0246f78000)
        libresolv.so.2 => /lib64/libresolv.so.2 (0x00002b0292e89000)

There are some libraries which are the default libraries of the linux. Do I have to install them in my conda environment ?

[Wolfgang Bangerth]

Jack:
I don't know what is causing the problem, but will say that what you are doing
is just too complicated -- building everything in a conda environment by hand.
From where the error appears, one might suspect that you are mixing the MPI
implementation used inside conda with the one that's available on the system.

My suggestion is to either install deal.II via one of the packages available
for a number of operating systems, or to use the candi installer. Both are
available from
https://dealii.org/download.html
and will vastly simplify your life.

Best
W.


On 12/29/23 17:47, Smith Jack wrote:
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Wolfgang Bangerth email: bang...@colostate.edu
www: http://www.math.colostate.edu/~bangerth/