segfault running adios_reorganize to convert to hdf5
Created by: jhidding
Describe the bug
Running the example line: adios_reorganize sim.bp sim.h5 BPFile "" HDF5 "" from the documentation creates a segmentation fault. Both with and without the mpirun bit.
To Reproduce
- have a .bp file (in this case created with the OpenFOAM Adios writer)
- run
adios_reorganize, doesn't matter which output back-end is used
Expected behavior no segfault
Desktop (please complete the following information):
- OS/Platform: Fedora 31
- Build: gcc 9.2.1
Additional context The same bp file seems to read fine using the Python module.
printed backtrace:
[ESLT0107:12052:0:12052] Caught signal 11 (Segmentation fault: address not mapped to object at address (nil))
==== backtrace ====
0 /lib64/libucs.so.0(+0x1b25f) [0x7f40e808525f]
1 /lib64/libucs.so.0(+0x1b42a) [0x7f40e808542a]
2 /lib64/libc.so.6(cfree+0x52) [0x7f40ea63b7e2]
3 /home/johannes/.local/lib/libadios2.so.2(_ZN6adios26format15BP3Deserializer12PostDataReadIdEEvRNS_4core8VariableIT_EERNS6_4InfoERKNS_6helper16SubStreamBoxInfoEbm+0x265) [0x7f40eb02e945]
4 /home/johannes/.local/lib/libadios2.so.2(_ZN6adios24core6engine9BP3Reader18ReadVariableBlocksIdEEvRNS0_8VariableIT_EE+0x19e) [0x7f40eaf3e84e]
5 /home/johannes/.local/lib/libadios2.so.2(_ZN6adios24core6engine9BP3Reader9DoGetSyncERNS0_8VariableIdEEPd+0x86) [0x7f40eaf378a6]
6 /home/johannes/.local/lib/libadios2.so.2(_ZN6adios24core6Engine3GetIdEEvRNS0_8VariableIT_EEPS4_NS_4ModeE+0x19b) [0x7f40eae9215b]
7 /home/johannes/.local/lib/libadios2.so.2(_ZN6adios24core6Engine3GetIdEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPT_NS_4ModeE+0x64) [0x7f40eae922e4]
8 adios_reorganize() [0x409232]
9 adios_reorganize() [0x40cfd7]
10 adios_reorganize() [0x405f2a]
11 /lib64/libc.so.6(__libc_start_main+0xf3) [0x7f40ea5d61a3]
12 adios_reorganize() [0x4061be]
===================follow up Let me know if you need me to repeat this with ADIOS2 built with build-type set to Debug