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 ?
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