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Stack trace of bug where jemalloc hangs during large memory reallocation initiated by Arrow
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| Thread 1 "python3" received signal SIGINT, Interrupt. | |
| je_spin_adaptive (spin=<synthetic pointer>) at include/jemalloc/internal/spin.h:40 | |
| 40 include/jemalloc/internal/spin.h: No such file or directory. | |
| (gdb) where | |
| #0 je_spin_adaptive (spin=<synthetic pointer>) at include/jemalloc/internal/spin.h:40 | |
| #1 chunk_dss_max_update (new_addr=<optimized out>) at src/chunk_dss.c:83 | |
| #2 je_chunk_alloc_dss (tsdn=tsdn@entry=0x7ffff7fe8620, arena=arena@entry=0x7fffc0200140, new_addr=new_addr@entry=0x7fff37e00000, size=size@entry=2097152, alignment=alignment@entry=2097152, | |
| zero=zero@entry=0x7fffffffbac0, commit=commit@entry=0x7fffffffba10) at src/chunk_dss.c:122 | |
| #3 0x00007fffd346369f in chunk_alloc_core (dss_prec=dss_prec_secondary, commit=0x7fffffffba10, zero=0x7fffffffbac0, alignment=2097152, size=2097152, new_addr=0x7fff37e00000, arena=0x7fffc0200140, | |
| tsdn=0x7ffff7fe8620) at src/chunk.c:357 | |
| #4 chunk_alloc_default_impl (commit=0x7fffffffba10, zero=0x7fffffffbac0, alignment=2097152, size=2097152, new_addr=0x7fff37e00000, arena=0x7fffc0200140, tsdn=0x7ffff7fe8620) at src/chunk.c:430 | |
| #5 je_chunk_alloc_wrapper (tsdn=tsdn@entry=0x7ffff7fe8620, arena=arena@entry=0x7fffc0200140, chunk_hooks=chunk_hooks@entry=0x7fffffffba30, new_addr=new_addr@entry=0x7fff37e00000, size=size@entry=2097152, | |
| alignment=2097152, sn=sn@entry=0x7fffffffba20, zero=zero@entry=0x7fffffffbac0, commit=commit@entry=0x7fffffffba10) at src/chunk.c:490 | |
| #6 0x00007fffd3457097 in arena_chunk_ralloc_huge_expand_hard (cdiff=2097152, udiff=2097152, nchunk=0x7fff37e00000, zero=0x7fffffffbac0, sn=0x7fffffffba20, usize=4194304, oldsize=2097152, | |
| chunk=0x7fff37c00000, chunk_hooks=0x7fffffffba30, arena=0x7fffc0200140, tsdn=0x7ffff7fe8620) at src/arena.c:1040 | |
| #7 je_arena_chunk_ralloc_huge_expand (tsdn=tsdn@entry=0x7ffff7fe8620, arena=arena@entry=0x7fffc0200140, chunk=chunk@entry=0x7fff37c00000, oldsize=oldsize@entry=2097152, usize=usize@entry=4194304, | |
| zero=zero@entry=0x7fffffffbac0) at src/arena.c:1086 | |
| #8 0x00007fffd3471032 in huge_ralloc_no_move_expand (tsdn=0x7ffff7fe8620, ptr=ptr@entry=0x7fff37c00000, oldsize=oldsize@entry=2097152, usize=usize@entry=4194304, zero=zero@entry=false) at src/huge.c:274 | |
| #9 0x00007fffd3473317 in je_huge_ralloc_no_move (zero=false, usize_max=4194304, usize_min=4194304, oldsize=2097152, ptr=0x7fff37c00000, tsdn=0x7ffff7fe8620, tsdn@entry=0x0) at src/huge.c:319 | |
| #10 je_huge_ralloc (tsd=tsd@entry=0x7ffff7fe8620, arena=arena@entry=0x0, ptr=ptr@entry=0x7fff37c00000, oldsize=oldsize@entry=2097152, usize=usize@entry=4194304, alignment=alignment@entry=64, zero=false, | |
| tcache=tcache@entry=0x7fff3ac0d000) at src/huge.c:377 | |
| #11 0x00007fffd345c3bd in je_arena_ralloc (tsd=0x7ffff7fe8620, arena=arena@entry=0x0, ptr=ptr@entry=0x7fff37c00000, oldsize=oldsize@entry=2097152, size=size@entry=4194304, alignment=alignment@entry=64, | |
| zero=zero@entry=false, tcache=tcache@entry=0x7fff3ac0d000) at src/arena.c:3351 | |
| #12 0x00007fffd344f27b in je_iralloct (arena=0x0, tcache=0x7fff3ac0d000, zero=false, alignment=64, size=4194304, oldsize=2097152, ptr=0x7fff37c00000, tsd=<optimized out>) | |
| at include/jemalloc/internal/jemalloc_internal.h:1253 | |
| #13 rallocx (ptr=0x7fff37c00000, size=4194304, flags=<optimized out>) at src/jemalloc.c:2408 | |
| #14 0x00007fffd331fb30 in arrow::DefaultMemoryPool::Reallocate(long, long, unsigned char**) () from /usr/local/lib/python3.6/site-packages/pyarrow/libarrow.so.0 | |
| #15 0x00007fffd32f3764 in arrow::PoolBuffer::Reserve(long) () from /usr/local/lib/python3.6/site-packages/pyarrow/libarrow.so.0 | |
| #16 0x00007fffd32f3811 in arrow::PoolBuffer::Resize(long, bool) () from /usr/local/lib/python3.6/site-packages/pyarrow/libarrow.so.0 | |
| #17 0x00007fffd3345a10 in arrow::io::BufferOutputStream::Reserve(long) () from /usr/local/lib/python3.6/site-packages/pyarrow/libarrow.so.0 | |
| #18 0x00007fffd3345a76 in arrow::io::BufferOutputStream::Write(unsigned char const*, long) () from /usr/local/lib/python3.6/site-packages/pyarrow/libarrow.so.0 | |
| #19 0x00007fffd0d74620 in parquet::ArrowOutputStream::Write(unsigned char const*, long) () from /usr/local/lib/python3.6/site-packages/pyarrow/libparquet.so.1 | |
| #20 0x00007fffd0d4727a in parquet::SerializedPageWriter::WriteDictionaryPage(parquet::DictionaryPage const&) () from /usr/local/lib/python3.6/site-packages/pyarrow/libparquet.so.1 | |
| #21 0x00007fffd0d19499 in parquet::TypedColumnWriter<parquet::DataType<(parquet::Type::type)5> >::WriteDictionaryPage() () from /usr/local/lib/python3.6/site-packages/pyarrow/libparquet.so.1 | |
| #22 0x00007fffd0d148c6 in parquet::ColumnWriter::Close() () from /usr/local/lib/python3.6/site-packages/pyarrow/libparquet.so.1 | |
| #23 0x00007fffd0ce8600 in arrow::Status parquet::arrow::FileWriter::Impl::TypedWriteBatch<parquet::DataType<(parquet::Type::type)5>, arrow::DoubleType>(parquet::ColumnWriter*, std::shared_ptr<arrow::Array> const&, long, short const*, short const*) () from /usr/local/lib/python3.6/site-packages/pyarrow/libparquet.so.1 | |
| #24 0x00007fffd0ce5d95 in parquet::arrow::FileWriter::Impl::WriteColumnChunk(arrow::Array const&) () from /usr/local/lib/python3.6/site-packages/pyarrow/libparquet.so.1 | |
| #25 0x00007fffd0ce660d in parquet::arrow::FileWriter::WriteColumnChunk(arrow::Array const&) () from /usr/local/lib/python3.6/site-packages/pyarrow/libparquet.so.1 | |
| #26 0x00007fffd0ce68b1 in parquet::arrow::FileWriter::WriteTable(arrow::Table const&, long) () from /usr/local/lib/python3.6/site-packages/pyarrow/libparquet.so.1 | |
| #27 0x00007fffbffe9053 in __pyx_pw_7pyarrow_8_parquet_13ParquetWriter_5write_table(_object*, _object*, _object*) () | |
| from /usr/local/lib/python3.6/site-packages/pyarrow/_parquet.cpython-36m-x86_64-linux-gnu.so | |
| #28 0x00000000004f47bb in _PyCFunction_FastCallDict (kwargs=<optimized out>, nargs=<optimized out>, args=<optimized out>, func_obj=0x7fff5895bb88) at Objects/methodobject.c:231 | |
| #29 _PyCFunction_FastCallKeywords () at Objects/methodobject.c:294 | |
| #30 0x000000000054d5e9 in call_function () at Python/ceval.c:4842 | |
| #31 0x00000000005469da in _PyEval_EvalFrameDefault () at Python/ceval.c:3344 | |
| #32 0x0000000000544d5f in PyEval_EvalFrameEx (throwflag=0, f=0x21ecb9f8) at Python/ceval.c:751 | |
| #33 _PyEval_EvalCodeWithName () at Python/ceval.c:4172 | |
| #34 0x000000000054e73b in fast_function () at Python/ceval.c:4983 | |
| #35 0x000000000054d6cc in call_function () at Python/ceval.c:4863 | |
| #36 0x0000000000545aea in _PyEval_EvalFrameDefault () at Python/ceval.c:3328 | |
| #37 0x0000000000544d5f in PyEval_EvalFrameEx (throwflag=0, f=0x7fffa67f1dd8) at Python/ceval.c:751 | |
| #38 _PyEval_EvalCodeWithName () at Python/ceval.c:4172 | |
| #39 0x000000000054e73b in fast_function () at Python/ceval.c:4983 | |
| #40 0x000000000054d6cc in call_function () at Python/ceval.c:4863 | |
| #41 0x0000000000545aea in _PyEval_EvalFrameDefault () at Python/ceval.c:3328 | |
| ---Type <return> to continue, or q <return> to quit--- | |
| #42 0x000000000054e67d in PyEval_EvalFrameEx (throwflag=0, f=0x1c800398) at Python/ceval.c:751 | |
| #43 _PyFunction_FastCall (globals=<optimized out>, nargs=<optimized out>, args=<optimized out>, co=<optimized out>) at Python/ceval.c:4924 | |
| #44 fast_function () at Python/ceval.c:4959 | |
| #45 0x000000000054d6cc in call_function () at Python/ceval.c:4863 | |
| #46 0x0000000000545aea in _PyEval_EvalFrameDefault () at Python/ceval.c:3328 | |
| #47 0x000000000054e67d in PyEval_EvalFrameEx (throwflag=0, f=0x7fff54991208) at Python/ceval.c:751 | |
| #48 _PyFunction_FastCall (globals=<optimized out>, nargs=<optimized out>, args=<optimized out>, co=<optimized out>) at Python/ceval.c:4924 | |
| #49 fast_function () at Python/ceval.c:4959 | |
| #50 0x000000000054d6cc in call_function () at Python/ceval.c:4863 | |
| #51 0x0000000000545aea in _PyEval_EvalFrameDefault () at Python/ceval.c:3328 | |
| #52 0x0000000000544d5f in PyEval_EvalFrameEx (throwflag=0, f=0x980d18) at Python/ceval.c:751 | |
| #53 _PyEval_EvalCodeWithName () at Python/ceval.c:4172 | |
| #54 0x0000000000544ad3 in PyEval_EvalCodeEx (closure=0x0, kwdefs=0x0, defcount=0, defs=0x0, kwcount=0, kws=0x0, argcount=0, args=0x0, locals=locals@entry=0x7ffff709a1f8, | |
| globals=globals@entry=0x7ffff709a1f8, _co=_co@entry=0x7ffff70145d0) at Python/ceval.c:4193 | |
| #55 PyEval_EvalCode (co=co@entry=0x7ffff70145d0, globals=globals@entry=0x7ffff709a1f8, locals=locals@entry=0x7ffff709a1f8) at Python/ceval.c:728 | |
| #56 0x0000000000594092 in run_mod () at Python/pythonrun.c:980 | |
| #57 0x00000000005944da in PyRun_FileExFlags () at Python/pythonrun.c:933 | |
| #58 0x00000000005942bc in PyRun_SimpleFileExFlags () at Python/pythonrun.c:396 | |
| #59 0x0000000000599b4f in run_file (p_cf=0x7fffffffd8f0, filename=0x92a2a0 L"scripts/parquet_export.py", fp=0x9bcbd0) at Modules/main.c:338 | |
| #60 Py_Main () at Modules/main.c:809 | |
| #61 0x00000000004a9039 in main () at ./Programs/python.c:69 | |
| #62 0x00007ffff7100830 in __libc_start_main (main=0x4a8f50 <main>, argc=2, argv=0x7fffffffdb08, init=<optimized out>, fini=<optimized out>, rtld_fini=<optimized out>, stack_end=0x7fffffffdaf8) | |
| at ../csu/libc-start.c:291 | |
| #63 0x0000000000591739 in _start () | |
| (gdb) |
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