Segmentation fault in `H5FL.c`

[dschwoerer]

Describe the bug
While testing python-xbout I got some segfaults from python.
While the error is only seemingly random, it always in hdf5 code, in H5FL.c

Here are some backtraces:

xbout/tests/test_grid.py::TestOpenGrid::test_open_grid_chunks 
Thread 4 "python3" received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7fffd5f506c0 (LWP 809)]
H5FL_reg_malloc (head=0x7fffe10608e0 <H5_H5SL_node_t_reg_free_list.lto_priv.0>) at ../../src/H5FL.c:345
345	        head->list = head->list->next;
#0  H5FL_reg_malloc (head=0x7fffe10608e0 <H5_H5SL_node_t_reg_free_list.lto_priv.0>) at ../../src/H5FL.c:345
#1  0x00007fffe0e71e6d in H5SL__new_node (item=0x555555db3bd0, key=0x555555db3bd0, hashval=1249207996) at ../../src/H5SL.c:633
#2  0x00007fffe0e73d4b in H5SL__insert_common (slist=<optimized out>, item=0x555555db3bd0, key=0x555555db3bd0) at ../../src/H5SL.c:742
#3  0x00007fffe0e7438d in H5SL_insert (slist=<optimized out>, item=<optimized out>, key=<optimized out>) at ../../src/H5SL.c:1035
#4  0x00007fffe0e409f8 in H5P__create (pclass=<optimized out>) at ../../src/H5Pint.c:1881
#5  H5P_create_id (pclass=<optimized out>, app_ref=true) at ../../src/H5Pint.c:1967
#6  0x00007fffe0e16971 in H5Pcreate (cls_id=720575940379279371) at ../../src/H5P.c:237
#7  0x00007fffe11259e2 in NC4_get_vars (ncid=720896, varid=<optimized out>, startp=<optimized out>, countp=<optimized out>, stridep=stridep@entry=0x0, data=0x7fffd00e9d00, mem_nc_type=<optimized out>) at ../libhdf5/../../libhdf5/hdf5var.c:2091
#8  0x00007fffe11261d9 in NC4_get_vara (ncid=<optimized out>, varid=<optimized out>, startp=<optimized out>, countp=<optimized out>, ip=<optimized out>, memtype=<optimized out>) at ../libhdf5/../../libhdf5/hdf5var.c:1402
#9  0x00007fffe10d2bd2 in NC_get_vara (ncid=ncid@entry=720896, varid=varid@entry=1, start=start@entry=0x7fffd00046a0, edges=edges@entry=0x7fffd0026c80, value=value@entry=0x7fffd00e9d00, memtype=6) at ../libdispatch/../../libdispatch/dvarget.c:104
#10 0x00007fffe10d2ce1 in nc_get_vara (ncid=720896, varid=1, startp=startp@entry=0x7fffd00046a0, countp=countp@entry=0x7fffd0026c80, ip=0x7fffd00e9d00) at ../libdispatch/../../libdispatch/dvarget.c:750
#11 0x00007fffe13c7302 in __pyx_pf_7netCDF4_8_netCDF4_8Variable_84_get (__pyx_v_self=0x7fffd69481e0, __pyx_v_start=<optimized out>, __pyx_v_count=<optimized out>, __pyx_v_stride=<optimized out>) at src/netCDF4/_netCDF4.c:80071
#12 __pyx_pw_7netCDF4_8_netCDF4_8Variable_85_get (__pyx_v_self=<netCDF4._netCDF4.Variable at remote 0x7fffd69481e0>, __pyx_args=<optimized out>, __pyx_nargs=<optimized out>, __pyx_kwds=<optimized out>) at src/netCDF4/_netCDF4.c:79403
#13 0x00007fffe13f9ed8 in __pyx_pf_7netCDF4_8_netCDF4_8Variable_50__getitem__ (__pyx_v_self=<optimized out>, __pyx_v_elem=<optimized out>) at src/netCDF4/_netCDF4.c:66013
#14 0x00007ffff7b55fd7 in _PyEval_EvalFrameDefault (tstate=<optimized out>, frame=<optimized out>, throwflag=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Python/generated_cases.c.h:1167
#15 0x00007ffff7bd5d9f in _PyEval_EvalFrame (tstate=0x555555faa340, frame=0x7ffff732e7f0, throwflag=0) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Include/internal/pycore_ceval.h:119
#16 _PyEval_Vector (tstate=0x555555faa340, func=0x7fffdc9087c0, locals=0x0, args=<optimized out>, argcount=<optimized out>, kwnames=0x0) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Python/ceval.c:1806

and

[Switching to Thread 0x7fffd574f6c0 (LWP 767)]
0x00007fffe0d7c6c9 in H5FL_fac_free (head=0x31, obj=0x55555e055930) at ../../src/H5FL.c:1774
1774	    head->onlist++;
#0  0x00007fffe0d7c6c9 in H5FL_fac_free (head=0x31, obj=0x55555e055930) at ../../src/H5FL.c:1774
#1  0x00007fffe0e72ef3 in H5SL__insert_common (slist=0x55555f4f2dd0, item=0x555555db3060, key=0x555555db3060) at ../../src/H5SL.c:705
#2  0x00007fffe0e7438d in H5SL_insert (slist=<optimized out>, item=<optimized out>, key=<optimized out>) at ../../src/H5SL.c:1035
#3  0x00007fffe0e4075f in H5P_close (plist=0x5555603d3a20) at ../../src/H5Pint.c:5218
#4  0x00007fffe0e3a88d in H5P__close_list_cb (_plist=<optimized out>, request=<optimized out>) at ../../src/H5Pint.c:730
#5  0x00007fffe0dc1c5b in H5I__dec_ref (id=792633534417612735, request=request@entry=0x0) at ../../src/H5Iint.c:970
#6  0x00007fffe0dc1d0f in H5I_dec_ref (id=<optimized out>) at ../../src/H5Iint.c:1009
#7  0x00007fffe0d0e6aa in H5D_close (dataset=0x55555ffd68b0) at ../../src/H5Dint.c:2020
#8  0x00007fffe0f386ed in H5VL__native_dataset_close (dset=<optimized out>, dxpl_id=<optimized out>, req=<optimized out>) at ../../src/H5VLnative_dataset.c:826
#9  0x00007fffe0f5b628 in H5VL__dataset_close.isra.0 (obj=<optimized out>, dxpl_id=<optimized out>, req=<optimized out>, cls=<optimized out>) at ../../src/H5VLcallback.c:2619
#10 0x00007fffe0f2717f in H5VL_dataset_close (vol_obj=0x55555a766650, dxpl_id=792633534417207304, req=0x0) at ../../src/H5VLcallback.c:2656
#11 0x00007fffe0d0b327 in H5D__close_cb (dset_vol_obj=0x55555a766650, request=<optimized out>) at ../../src/H5Dint.c:298
#12 0x00007fffe0dc1c5b in H5I__dec_ref (id=id@entry=360287970189864103, request=request@entry=0x0) at ../../src/H5Iint.c:970
#13 0x00007fffe0dc1d71 in H5I__dec_app_ref (id=id@entry=360287970189864103, request=request@entry=0x0) at ../../src/H5Iint.c:1041
#14 0x00007fffe0dc1f8b in H5I__dec_app_ref_always_close (id=360287970189864103, request=0x0) at ../../src/H5Iint.c:1150
#15 H5I_dec_app_ref_always_close (id=360287970189864103) at ../../src/H5Iint.c:1191

And here is another one:

xbout/tests/test_load.py::TestOpen::test_combine_along_t SKIPPED         [ 30%]
xbout/tests/test_load.py::TestOpen::test_combine_along_xy[lengths0-False-False] 
Thread 1 "python3" received signal SIGSEGV, Segmentation fault.
0x00007fffe0d72503 in H5FL__reg_gc_list (head=0x7fffe105dde0 <H5_H5CX_node_t_reg_free_list.lto_priv.0>) at ../../src/H5FL.c:420
420	        tmp = free_list->next;
#0  0x00007fffe0d72503 in H5FL__reg_gc_list (head=0x7fffe105dde0 <H5_H5CX_node_t_reg_free_list.lto_priv.0>) at ../../src/H5FL.c:420
#1  H5FL__reg_gc () at ../../src/H5FL.c:464
#2  H5FL_reg_free (head=<optimized out>, obj=<optimized out>) at ../../src/H5FL.c:307
#3  H5FL_reg_free (head=<optimized out>, obj=<optimized out>) at ../../src/H5FL.c:268
#4  0x00007fffe0dae0a9 in H5HF__hdr_free (hdr=0x555557feb7b0) at ../../src/H5HFhdr.c:1330
#5  0x00007fffe0da557d in H5HF__cache_hdr_free_icr (_thing=<optimized out>) at ../../src/H5HFcache.c:816
#6  0x00007fffe0cd50fd in H5C__flush_single_entry (f=0x55555ba73640, entry_ptr=0x555557feb7b0, flags=24592) at ../../src/H5Centry.c:861
#7  0x00007fffe0ce20df in H5C__flush_invalidate_ring (f=<optimized out>, ring=1, flags=<optimized out>) at ../../src/H5Cint.c:1453
#8  H5C__flush_invalidate_cache (f=0x55555ba73640, flags=<optimized out>) at ../../src/H5Cint.c:1051
#9  0x00007fffe0cd9d24 in H5C_dest (f=0x55555ba73640) at ../../src/H5C.c:501
#10 0x00007fffe0cb5d0f in H5AC_dest (f=0x55555ba73640) at ../../src/H5AC.c:476
#11 0x00007fffe0d49388 in H5F__dest (f=f@entry=0x55555ba73640, flush=flush@entry=true, free_on_failure=free_on_failure@entry=false) at ../../src/H5Fint.c:1536
#12 0x00007fffe0d4c6d4 in H5F_try_close (f=0x55555ba73640, was_closed=was_closed@entry=0x0) at ../../src/H5Fint.c:2653
#13 0x00007fffe0d4ca91 in H5F__close (f=<optimized out>) at ../../src/H5Fint.c:2455
#14 0x00007fffe0f3a36d in H5VL__native_file_close (file=0x55555ba73640, dxpl_id=<optimized out>, req=<optimized out>) at ../../src/H5VLnative_file.c:777
#15 0x00007fffe0f5aeb8 in H5VL__file_close.isra.0 (obj=<optimized out>, dxpl_id=<optimized out>, req=<optimized out>, cls=<optimized out>) at ../../src/H5VLcallback.c:4121
#16 0x00007fffe0f30dcf in H5VL_file_close (vol_obj=0x5555586924f0, dxpl_id=792633534417207304, req=0x0) at ../../src/H5VLcallback.c:4152
#17 0x00007fffe0d45d52 in H5F__close_cb (file_vol_obj=0x5555586924f0, request=<optimized out>) at ../../src/H5Fint.c:217
#18 0x00007fffe0dc1c5b in H5I__dec_ref (id=id@entry=72057594037929534, request=request@entry=0x0) at ../../src/H5Iint.c:970
#19 0x00007fffe0dc1d71 in H5I__dec_app_ref (id=72057594037929534, request=request@entry=0x0) at ../../src/H5Iint.c:1041
#20 0x00007fffe0dc1e2f in H5I_dec_app_ref (id=<optimized out>) at ../../src/H5Iint.c:1086
#21 0x00007fffe0d3f2f8 in H5Fclose (file_id=72057594037929534) at ../../src/H5F.c:1046
#22 0x00007fffe111b835 in nc4_close_netcdf4_file (h5=0x55555cc048e0, abort=0, memio=0x0) at ../libhdf5/../../libhdf5/hdf5file.c:233
#23 0x00007fffe1120138 in NC4_close (ncid=<optimized out>, params=<optimized out>) at ../libhdf5/../../libhdf5/hdf5file.c:633
#24 0x00007fffe10d806b in nc_close (ncid=131072) at ../libdispatch/../../libdispatch/dfile.c:1308
#25 0x00007fffe132421e in __pyx_pf_7netCDF4_8_netCDF4_7Dataset_14_close (__pyx_v_self=0x7fffd8be6240, __pyx_v_check_err=True) at src/netCDF4/_netCDF4.c:30377
#26 __pyx_pw_7netCDF4_8_netCDF4_7Dataset_15_close (__pyx_v_self=<netCDF4._netCDF4.Dataset at remote 0x7fffd8be6240>, __pyx_args=<optimized out>, __pyx_nargs=1, __pyx_kwds=<optimized out>) at src/netCDF4/_netCDF4.c:30326
#27 0x00007fffe1323853 in __pyx_pf_7netCDF4_8_netCDF4_7Dataset_18close (__pyx_v_self=<optimized out>) at src/netCDF4/_netCDF4.c:30925
#28 __pyx_pw_7netCDF4_8_netCDF4_7Dataset_19close (__pyx_v_self=<optimized out>, __pyx_args=<optimized out>, __pyx_nargs=<optimized out>, __pyx_kwds=<optimized out>) at src/netCDF4/_netCDF4.c:30813
#29 0x00007ffff7b42fd7 in _PyObject_VectorcallTstate (tstate=0x7ffff7f41860 <_PyRuntime+282976>, callable=<_cython_3_0_11.cython_function_or_method at remote 0x7fffe15217d0>, args=<optimized out>, nargsf=<optimized out>, kwnames=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Include/internal/pycore_call.h:168
#30 PyObject_Vectorcall (callable=<_cython_3_0_11.cython_function_or_method at remote 0x7fffe15217d0>, args=<optimized out>, nargsf=<optimized out>, kwnames=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/call.c:327
#31 0x00007ffff7b58e2f in _PyEval_EvalFrameDefault (tstate=<optimized out>, frame=<optimized out>, throwflag=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Python/generated_cases.c.h:813
#32 0x00007ffff7b8745f in _PyObject_VectorcallTstate (tstate=0x7ffff7f41860 <_PyRuntime+282976>, callable=<function at remote 0x7fffdc8daa20>, args=0x7fffffffbcf8, nargsf=9223372036854775809, kwnames=0x0) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Include/internal/pycore_call.h:168
#33 PyObject_CallOneArg (func=<function at remote 0x7fffdc8daa20>, arg=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/call.c:395
#34 0x00007ffff7c7a606 in slot_tp_finalize (self=<CachingFileManager(_opener=<type at remote 0x7fffe1468ac0>, _args=('/tmp/pytest-of-mockbuild/pytest-8/test_reload_separate_variables_time_split1/temp_boutdata_1_T.nc',), _mode='r', _kwargs={'clobber': True, 'diskless': False, 'persist': False, 'format': 'NETCDF4'}, _use_default_lock=True, _lock=<_thread.lock at remote 0x7fffd6b20780>, _cache=<LRUCache at remote 0x7fffdc8e03c0>, _manager_id='e7b86aeb-52e5-45ad-a514-9f0dcf4bb559', _key=<_HashedSequence(hashvalue=-7063547784399903334) at remote 0x7fffd6127fc0>, _ref_counter=<_RefCounter(_counts={<_HashedSequence(hashvalue=443758223283057862) at remote 0x7fffd6c4d400>: 1, <_HashedSequence(hashvalue=8835520193079304715) at remote 0x7fffd7d97bb0>: 1, <_HashedSequence(hashvalue=3675166950999576538) at remote 0x7fffd7a619a0>: 1, <_HashedSequence(hashvalue=-7339155120130062816) at remote 0x7fffd6f747d0>: 1, <_HashedSequence(hashvalue=7609371609376905818) at remote 0x7fffd6d55b30>: 1, <_HashedSequence(hashvalue=-7674168586845967691) at remote 0x7fffd6d56ee0>: 1, <_Has...(truncated)) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/typeobject.c:9830
#35 0x00007ffff7b64581 in finalize_garbage (tstate=0x7ffff7f41860 <_PyRuntime+282976>, collectable=0x7fffffffbe00) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Python/gc.c:980
#36 gc_collect_main (tstate=0x7ffff7f41860 <_PyRuntime+282976>, generation=2, reason=_Py_GC_REASON_HEAP) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Python/gc.c:1408
#37 0x00007ffff7c25354 in _Py_HandlePending (tstate=0x7ffff7f41860 <_PyRuntime+282976>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Python/ceval_gil.c:1296
#38 0x00007ffff7b619ba in _PyEval_EvalFrameDefault (tstate=<optimized out>, frame=<optimized out>, throwflag=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Python/generated_cases.c.h:3606
#39 0x00007ffff7baf29d in _PyEval_EvalFrame (tstate=0x7ffff7f41860 <_PyRuntime+282976>, frame=0x7ffff7562760, throwflag=0) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Include/internal/pycore_ceval.h:119
#40 _PyEval_Vector (tstate=0x7ffff7f41860 <_PyRuntime+282976>, func=0x7fffdc93cae0, locals=0x0, args=0x7fffd6305230, argcount=<optimized out>, kwnames=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Python/ceval.c:1806
#41 _PyFunction_Vectorcall (func=<function at remote 0x7fffdc93cae0>, stack=0x7fffd6305230, nargsf=<optimized out>, kwnames=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/call.c:413
#42 _PyObject_VectorcallTstate (tstate=0x7ffff7f41860 <_PyRuntime+282976>, callable=<function at remote 0x7fffdc93cae0>, args=0x7fffd6305230, nargsf=<optimized out>, kwnames=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Include/internal/pycore_call.h:168
#43 method_vectorcall (method=<optimized out>, args=<optimized out>, nargsf=<optimized out>, kwnames=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/classobject.c:92
#44 0x00007ffff7b5a320 in PyObject_Call (callable=<method at remote 0x7fffd6cd0b00>, args=(<Array(shape=(6, 8, 12, 7), ndim=4, numblocks=(1, 4, 3, 1), size=4032) at remote 0x7fffd6d018b0>, <Array(shape=(6, 8, 12, 7), ndim=4, numblocks=(1, 4, 3, 1), size=4032) at remote 0x7fffd6d00770>, <Array(shape=(6, 8, 12), ndim=3, numblocks=(1, 4, 3), size=576) at remote 0x7fffd6d03f50>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d01cd0>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d01130>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d01550>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d03a10>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d019d0>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d02a50>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d03cb0>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d02510>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remo...(truncated), kwargs={}) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/call.c:373
#45 PyCFunction_Call (callable=<method at remote 0x7fffd6cd0b00>, args=(<Array(shape=(6, 8, 12, 7), ndim=4, numblocks=(1, 4, 3, 1), size=4032) at remote 0x7fffd6d018b0>, <Array(shape=(6, 8, 12, 7), ndim=4, numblocks=(1, 4, 3, 1), size=4032) at remote 0x7fffd6d00770>, <Array(shape=(6, 8, 12), ndim=3, numblocks=(1, 4, 3), size=576) at remote 0x7fffd6d03f50>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d01cd0>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d01130>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d01550>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d03a10>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d019d0>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d02a50>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d03cb0>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remote 0x7fffd6d02510>, <Array(shape=(8, 12), ndim=2, numblocks=(4, 3), size=96) at remo...(truncated), kwargs={}) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/call.c:381
#46 _PyEval_EvalFrameDefault (tstate=<optimized out>, frame=<optimized out>, throwflag=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Python/generated_cases.c.h:1355
#47 0x00007ffff7baf3e7 in _PyEval_EvalFrame (tstate=0x7ffff7f41860 <_PyRuntime+282976>, frame=<optimized out>, throwflag=0) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Include/internal/pycore_ceval.h:119
#48 _PyEval_Vector (tstate=0x7ffff7f41860 <_PyRuntime+282976>, func=0x7fffd5f64c20, locals=0x0, args=0x7fffd6e2ff60, argcount=1, kwnames=<unknown at remote 0x1>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Python/ceval.c:1806
#49 _PyFunction_Vectorcall (func=<function at remote 0x7fffd5f64c20>, stack=0x7fffd6e2ff60, nargsf=1, kwnames=<unknown at remote 0x1>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/call.c:413
#50 _PyObject_VectorcallTstate (tstate=0x7ffff7f41860 <_PyRuntime+282976>, callable=<function at remote 0x7fffd5f64c20>, args=0x7fffd6e2ff60, nargsf=1, kwnames=<unknown at remote 0x1>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Include/internal/pycore_call.h:168
#51 method_vectorcall (method=method@entry=<method at remote 0x7fffd60aa480>, args=args@entry=0x7fffd6e2ff68, nargsf=<optimized out>, kwnames=kwnames@entry=('tmp_path_factory', 'bout_xyt_example_files', 'bout_v5', 'metric_3D', 'lengths')) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/classobject.c:62
#52 0x00007ffff7c31c18 in _PyVectorcall_Call (tstate=0x7ffff7f41860 <_PyRuntime+282976>, func=0x7ffff7baf030 <method_vectorcall>, callable=<method at remote 0x7fffd60aa480>, tuple=<optimized out>, kwargs=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/call.c:285
#53 _PyObject_Call (tstate=0x7ffff7f41860 <_PyRuntime+282976>, callable=<method at remote 0x7fffd60aa480>, args=<optimized out>, kwargs=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/call.c:348
#54 0x00007ffff7b5a320 in PyObject_Call (callable=<method at remote 0x7fffd60aa480>, args=(), kwargs={'tmp_path_factory': <TempPathFactory(_given_basetemp=None, _trace=<TagTracerSub(root=<TagTracer(_tags2proc={}, _writer=None, indent=0) at remote 0x7ffff6a1a270>, tags=('config', 'tmpdir')) at remote 0x7fffd8b2d480>, _retention_count=3, _retention_policy='all', _basetemp=<PosixPath at remote 0x7fffd62374c0>) at remote 0x7fffdaeacad0>, 'bout_xyt_example_files': <function at remote 0x7fffd87c3920>, 'bout_v5': False, 'metric_3D': False, 'lengths': (6, 2, 4, 7)}) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/call.c:373
#55 PyCFunction_Call (callable=<method at remote 0x7fffd60aa480>, args=(), kwargs={'tmp_path_factory': <TempPathFactory(_given_basetemp=None, _trace=<TagTracerSub(root=<TagTracer(_tags2proc={}, _writer=None, indent=0) at remote 0x7ffff6a1a270>, tags=('config', 'tmpdir')) at remote 0x7fffd8b2d480>, _retention_count=3, _retention_policy='all', _basetemp=<PosixPath at remote 0x7fffd62374c0>) at remote 0x7fffdaeacad0>, 'bout_xyt_example_files': <function at remote 0x7fffd87c3920>, 'bout_v5': False, 'metric_3D': False, 'lengths': (6, 2, 4, 7)}) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/call.c:381
#56 _PyEval_EvalFrameDefault (tstate=<optimized out>, frame=<optimized out>, throwflag=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Python/generated_cases.c.h:1355
#57 0x00007ffff7c22c6e in _PyObject_VectorcallDictTstate (tstate=0x7ffff7f41860 <_PyRuntime+282976>, callable=<function at remote 0x7ffff717b740>, args=<optimized out>, nargsf=<optimized out>, kwargs=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/call.c:146
#58 0x00007ffff7c78da7 in _PyObject_Call_Prepend (tstate=0x7ffff7f41860 <_PyRuntime+282976>, callable=<function at remote 0x7ffff717b740>, obj=<optimized out>, args=(), kwargs={'pyfuncitem': <Function(keywords=<NodeKeywords at remote 0x7fffd60aa440>, own_markers=[<Mark(name='parametrize', args=('lengths', [(6, 2, 4, 7), (6, 2, 4, 1)]), kwargs={}, _param_ids_from=None, _param_ids_generated=None) at remote 0x7fffd60420b0>, <Mark(name='parametrize', args=('bout_v5,metric_3D', [(False, False), (True, False), (True, True)]), kwargs={}, _param_ids_from=None, _param_ids_generated=None) at remote 0x7fffd6042040>], extra_keyword_matches=set(), stash=<Stash at remote 0x7fffd80a69e0>, _report_sections=[], user_properties=[], originalname='test_combine_along_xy', _instance=<TestOpen() at remote 0x7fffd81db5f0>, _obj=<method at remote 0x7fffd60aa480>, _fixtureinfo=<FuncFixtureInfo at remote 0x7fffd60aa900>, fixturenames=['tmp_path_factory', 'bout_xyt_example_files', 'bout_v5', 'metric_3D', 'lengths', 'request'], funcargs={'tmp_path_factory': <TempPathFactory(_given_basetemp=None, _trace=<TagTracerSub(root=<TagTracer(_tags2proc={}, _writer=None, indent=0) at remote 0x7ffff6a1a270>, tags=('config...(truncated)) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/call.c:504
#59 slot_tp_call (self=<optimized out>, args=(), kwds={'pyfuncitem': <Function(keywords=<NodeKeywords at remote 0x7fffd60aa440>, own_markers=[<Mark(name='parametrize', args=('lengths', [(6, 2, 4, 7), (6, 2, 4, 1)]), kwargs={}, _param_ids_from=None, _param_ids_generated=None) at remote 0x7fffd60420b0>, <Mark(name='parametrize', args=('bout_v5,metric_3D', [(False, False), (True, False), (True, True)]), kwargs={}, _param_ids_from=None, _param_ids_generated=None) at remote 0x7fffd6042040>], extra_keyword_matches=set(), stash=<Stash at remote 0x7fffd80a69e0>, _report_sections=[], user_properties=[], originalname='test_combine_along_xy', _instance=<TestOpen() at remote 0x7fffd81db5f0>, _obj=<method at remote 0x7fffd60aa480>, _fixtureinfo=<FuncFixtureInfo at remote 0x7fffd60aa900>, fixturenames=['tmp_path_factory', 'bout_xyt_example_files', 'bout_v5', 'metric_3D', 'lengths', 'request'], funcargs={'tmp_path_factory': <TempPathFactory(_given_basetemp=None, _trace=<TagTracerSub(root=<TagTracer(_tags2proc={}, _writer=None, indent=0) at remote 0x7ffff6a1a270>, tags=('config...(truncated)) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/typeobject.c:9537
#60 0x00007ffff7b3f62b in _PyObject_MakeTpCall (tstate=0x7ffff7f41860 <_PyRuntime+282976>, callable=<HookCaller at remote 0x7ffff6a3e5c0>, args=<optimized out>, nargs=0, keywords=('pyfuncitem',)) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/call.c:242
#61 0x00007ffff7b5f200 in _PyEval_EvalFrameDefault (tstate=<optimized out>, frame=<optimized out>, throwflag=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Python/generated_cases.c.h:1502
#62 0x00007ffff7c22c6e in _PyObject_VectorcallDictTstate (tstate=0x7ffff7f41860 <_PyRuntime+282976>, callable=<function at remote 0x7ffff717b740>, args=<optimized out>, nargsf=<optimized out>, kwargs=<optimized out>) at /usr/src/debug/python3.13-3.13.0-1.fc42.x86_64/Objects/call.c:146

Expected behavior
No segfault, no error.

Platform (please complete the following information)

• HDF5 version: hdf5-1.14.5-1.fc42
• OS and version: Fedora rawhide (future 42)
• Compiler and version: gcc-14.2.1-4.fc42.x86_64.rpm
• Build system (e.g. CMake, Autotools) and version: autotools: autoconf-2.72-3.fc41.noarch.rpm
• Any configure options you specified: ../configure --build=x86_64-redhat-linux-gnu --host=x86_64-redhat-linux-gnu --program-prefix= --disable-dependency-tracking --prefix=/usr --exec-prefix=/usr --bindir=/usr/bin --sbindir=/usr/sbin --sysconfdir=/etc --datadir=/usr/share --includedir=/usr/include --libdir=/usr/lib64 --libexecdir=/usr/libexec --localstatedir=/var --runstatedir=/run --sharedstatedir=/var/lib --mandir=/usr/share/man --infodir=/usr/share/info --disable-silent-rules --enable-fortran --enable-hl --enable-shared --with-szlib --enable-cxx --enable-java --with-default-plugindir=/usr/lib64/hdf5/plugin
• MPI library and version (parallel HDF5): serial version

Additional context
This only happens seemingly randomly, and apparently only after running several tests. I was not able to come up with a MRE beyond

git clone https://github.com/boutproject/xBOUT
cd xBOUT
pip install -r requirements.txt
pip install gelidum
pytest xbout

[hyoklee]

@dschwoerer , thank you for your report!
I updated your MRE to add missing pip steps.

Using your MRE, I got the following error on Ubuntu GH Action:

xbout/tests/test_boutdataset.py FFFssFssFssFsFssFFFFFF.sssssssssssssssFs [ 18%]
Fatal Python error: Segmentation fault

Current thread 0x00007f06b64fc640 (most recent call first):
  Garbage-collecting
  File "/home/runner/.local/lib/python3.10/site-packages/xarray/backends/file_manager.py", line 234 in close
  File "/home/runner/.local/lib/python3.10/site-packages/xarray/backends/file_manager.py", line 250 in __del__

Do you know how I can get the same error (i.e., HDF5 trace output) as yours?

By the way, when I tested xBOUT on Mac-12 / Intel, I don't see any segmentation fault issue other than 2 test failures.

[bmribler]

@dschwoerer Would you please provide a small reproducer of one of the segfaults? Thanks!

[dschwoerer]

@bmribler: As I tried to say above: I did not manage to come up with a more minimal producer -just running the segfaulting tests does not seem to reproduce it, so the only reproducer is running the full test suite until it segfaults.

If you want a backtrace, I did provide some, see above under details.

[bmribler]

@bmribler: As I tried to say above: I did not manage to come up with a more minimal producer -just running the segfaulting tests does not seem to reproduce it, so the only reproducer is running the full test suite until it segfaults.

If you want a backtrace, I did provide some, see above under details.

I was hoping for some C reproducer. :) Thanks.