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PyJQ memory corruption #1059

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mfeit-internet2 opened this issue Aug 25, 2020 · 2 comments
Closed

PyJQ memory corruption #1059

mfeit-internet2 opened this issue Aug 25, 2020 · 2 comments
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The following test for jqfilter causes memory corruption in the Py2 and Py3 versions.

def test_args(self):
    f = JQFilter({"script": "."}, args={"value": 123})

python3 -m nose
.............*** Error in `python3': malloc(): memory corruption (fast): 0x000000000226048f ***
======= Backtrace: =========
/lib64/libc.so.6(+0x7f3e4)[0x7f51fd9a53e4]
/lib64/libc.so.6(+0x82b20)[0x7f51fd9a8b20]
/lib64/libc.so.6(__libc_calloc+0xb4)[0x7f51fd9ac184]
/lib64/libjq.so.1(jv_mem_calloc+0x9)[0x7f51ed62ac19]
/lib64/libjq.so.1(+0x157ae)[0x7f51ed6207ae]
/lib64/libjq.so.1(+0x1607b)[0x7f51ed62107b]
/lib64/libjq.so.1(jq_compile_args+0x30d)[0x7f51ed62412d]
/usr/lib64/python3.6/site-packages/_pyjq.cpython-36m-x86_64-linux-gnu.so(+0x71e5)[0x7f51ed85f1e5]
/lib64/libpython3.6m.so.1.0(+0xf71e2)[0x7f51fe7101e2]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x90)[0x7f51fe6c1160]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallKeywords+0x9c)[0x7f51fe6c17ec]
/lib64/libpython3.6m.so.1.0(+0x15098c)[0x7f51fe76998c]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x162b)[0x7f51fe75f37b]
/lib64/libpython3.6m.so.1.0(+0x14f987)[0x7f51fe768987]
/lib64/libpython3.6m.so.1.0(+0x15067a)[0x7f51fe76967a]
/lib64/libpython3.6m.so.1.0(+0x150903)[0x7f51fe769903]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x162b)[0x7f51fe75f37b]
/lib64/libpython3.6m.so.1.0(+0x14f987)[0x7f51fe768987]
/lib64/libpython3.6m.so.1.0(_PyFunction_FastCallDict+0x24f)[0x7f51fe76a9ff]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x10e)[0x7f51fe6c11de]
/lib64/libpython3.6m.so.1.0(_PyObject_Call_Prepend+0x61)[0x7f51fe6c12f1]
/lib64/libpython3.6m.so.1.0(PyObject_Call+0x43)[0x7f51fe6c0f63]
/lib64/libpython3.6m.so.1.0(+0xfa7e5)[0x7f51fe7137e5]
/lib64/libpython3.6m.so.1.0(+0xf71e2)[0x7f51fe7101e2]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x90)[0x7f51fe6c1160]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallKeywords+0x9c)[0x7f51fe6c17ec]
/lib64/libpython3.6m.so.1.0(+0x15098c)[0x7f51fe76998c]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x162b)[0x7f51fe75f37b]
/lib64/libpython3.6m.so.1.0(+0x1505ca)[0x7f51fe7695ca]
/lib64/libpython3.6m.so.1.0(+0x150903)[0x7f51fe769903]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x7f51fe75e0f7]
/lib64/libpython3.6m.so.1.0(+0x14f987)[0x7f51fe768987]
/lib64/libpython3.6m.so.1.0(_PyFunction_FastCallDict+0x24f)[0x7f51fe76a9ff]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x10e)[0x7f51fe6c11de]
/lib64/libpython3.6m.so.1.0(_PyObject_Call_Prepend+0x61)[0x7f51fe6c12f1]
/lib64/libpython3.6m.so.1.0(PyObject_Call+0x43)[0x7f51fe6c0f63]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x2067)[0x7f51fe75fdb7]
/lib64/libpython3.6m.so.1.0(+0x14f987)[0x7f51fe768987]
/lib64/libpython3.6m.so.1.0(_PyFunction_FastCallDict+0x24f)[0x7f51fe76a9ff]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x10e)[0x7f51fe6c11de]
/lib64/libpython3.6m.so.1.0(_PyObject_Call_Prepend+0x61)[0x7f51fe6c12f1]
/lib64/libpython3.6m.so.1.0(PyObject_Call+0x43)[0x7f51fe6c0f63]
/lib64/libpython3.6m.so.1.0(+0xfbb2d)[0x7f51fe714b2d]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x90)[0x7f51fe6c1160]
/lib64/libpython3.6m.so.1.0(+0x15098c)[0x7f51fe76998c]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x7f51fe75e0f7]
/lib64/libpython3.6m.so.1.0(+0x1505ca)[0x7f51fe7695ca]
/lib64/libpython3.6m.so.1.0(+0x150903)[0x7f51fe769903]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x7f51fe75e0f7]
/lib64/libpython3.6m.so.1.0(_PyFunction_FastCallDict+0x15a)[0x7f51fe76a90a]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x10e)[0x7f51fe6c11de]
/lib64/libpython3.6m.so.1.0(_PyObject_Call_Prepend+0x61)[0x7f51fe6c12f1]
/lib64/libpython3.6m.so.1.0(PyObject_Call+0x43)[0x7f51fe6c0f63]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x2067)[0x7f51fe75fdb7]
/lib64/libpython3.6m.so.1.0(+0x14f987)[0x7f51fe768987]
/lib64/libpython3.6m.so.1.0(_PyFunction_FastCallDict+0x24f)[0x7f51fe76a9ff]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x10e)[0x7f51fe6c11de]
/lib64/libpython3.6m.so.1.0(_PyObject_Call_Prepend+0x61)[0x7f51fe6c12f1]
/lib64/libpython3.6m.so.1.0(PyObject_Call+0x43)[0x7f51fe6c0f63]
/lib64/libpython3.6m.so.1.0(+0xfbb2d)[0x7f51fe714b2d]
/lib64/libpython3.6m.so.1.0(_PyObject_FastCallDict+0x90)[0x7f51fe6c1160]
/lib64/libpython3.6m.so.1.0(+0x15098c)[0x7f51fe76998c]
/lib64/libpython3.6m.so.1.0(_PyEval_EvalFrameDefault+0x3a7)[0x7f51fe75e0f7]
======= Memory map: ========
00400000-00401000 r-xp 00000000 fd:00 13544                              /usr/bin/python3.6
00601000-00602000 r--p 00001000 fd:00 13544                              /usr/bin/python3.6
00602000-00603000 rw-p 00002000 fd:00 13544                              /usr/bin/python3.6
01dd3000-02343000 rw-p 00000000 00:00 0                                  [heap]
7f51e0000000-7f51e0021000 rw-p 00000000 00:00 0
7f51e0021000-7f51e4000000 ---p 00000000 00:00 0
7f51e695a000-7f51e695b000 ---p 00000000 00:00 0
7f51e695b000-7f51e715b000 rw-p 00000000 00:00 0
7f51e715b000-7f51e7172000 r-xp 00000000 fd:00 34199861                   /usr/lib64/libelf-0.176.so
7f51e7172000-7f51e7371000 ---p 00017000 fd:00 34199861                   /usr/lib64/libelf-0.176.so
7f51e7371000-7f51e7372000 r--p 00016000 fd:00 34199861                   /usr/lib64/libelf-0.176.so
7f51e7372000-7f51e7373000 rw-p 00017000 fd:00 34199861                   /usr/lib64/libelf-0.176.so
7f51e7373000-7f51e7377000 r-xp 00000000 fd:00 33597599                   /usr/lib64/libattr.so.1.1.0
7f51e7377000-7f51e7576000 ---p 00004000 fd:00 33597599                   /usr/lib64/libattr.so.1.1.0
7f51e7576000-7f51e7577000 r--p 00003000 fd:00 33597599                   /usr/lib64/libattr.so.1.1.0
7f51e7577000-7f51e7578000 rw-p 00004000 fd:00 33597599                   /usr/lib64/libattr.so.1.1.0
7f51e7578000-7f51e758d000 r-xp 00000000 fd:00 33554508                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f51e758d000-7f51e778c000 ---p 00015000 fd:00 33554508                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f51e778c000-7f51e778d000 r--p 00014000 fd:00 33554508                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f51e778d000-7f51e778e000 rw-p 00015000 fd:00 33554508                   /usr/lib64/libgcc_s-4.8.5-20150702.so.1
7f51e778e000-7f51e77dc000 r-xp 00000000 fd:00 33748781                   /usr/lib64/libdw-0.176.so
7f51e77dc000-7f51e79dc000 ---p 0004e000 fd:00 33748781                   /usr/lib64/libdw-0.176.so
7f51e79dc000-7f51e79de000 r--p 0004e000 fd:00 33748781                   /usr/lib64/libdw-0.176.so
7f51e79de000-7f51e79df000 rw-p 00050000 fd:00 33748781                   /usr/lib64/libdw-0.176.so
7f51e79df000-7f51e79e3000 r-xp 00000000 fd:00 33597601                   /usr/lib64/libcap.so.2.22
7f51e79e3000-7f51e7be2000 ---p 00004000 fd:00 33597601                   /usr/lib64/libcap.so.2.22
7f51e7be2000-7f51e7be3000 r--p 00003000 fd:00 33597601                   /usr/lib64/libcap.so.2.22
7f51e7be3000-7f51e7be4000 rw-p 00004000 fd:00 33597601                   /usr/lib64/libcap.so.2.22
7f51e7be4000-7f51e7bf6000 r-xp 00000000 fd:00 33603905                   /usr/lib64/libnss_myhostname.so.2
7f51e7bf6000-7f51e7df5000 ---p 00012000 fd:00 33603905                   /usr/lib64/libnss_myhostname.so.2
7f51e7df5000-7f51e7df8000 r--p 00011000 fd:00 33603905                   /usr/lib64/libnss_myhostname.so.2
7f51e7df8000-7f51e7df9000 rw-p 00014000 fd:00 33603905                   /usr/lib64/libnss_myhostname.so.2
7f51e7df9000-7f51e7dff000 r-xp 00000000 fd:00 33806572                   /usr/lib64/libnss_dns-2.17.so
7f51e7dff000-7f51e7ffe000 ---p 00006000 fd:00 33806572                   /usr/lib64/libnss_dns-2.17.so
7f51e7ffe000-7f51e7fff000 r--p 00005000 fd:00 33806572                   /usr/lib64/libnss_dns-2.17.so
7f51e7fff000-7f51e8000000 rw-p 00006000 fd:00 33806572                   /usr/lib64/libnss_dns-2.17.so
7f51e8000000-7f51e8021000 rw-p 00000000 00:00 0
7f51e8021000-7f51ec000000 ---p 00000000 00:00 0
7f51ec1a6000-7f51ec1b2000 r-xp 00000000 fd:00 33806574                   /usr/lib64/libnss_files-2.17.so
7f51ec1b2000-7f51ec3b1000 ---p 0000c000 fd:00 33806574                   /usr/lib64/libnss_files-2.17.so
7f51ec3b1000-7f51ec3b2000 r--p 0000b000 fd:00 33806574                   /usr/lib64/libnss_files-2.17.so
7f51ec3b2000-7f51ec3b3000 rw-p 0000c000 fd:00 33806574                   /usr/lib64/libnss_files-2.17.so
7f51ec3b3000-7f51ec3b9000 rw-p 00000000 00:00 0 make[1]: *** [test] Aborted
@mfeit-internet2 mfeit-internet2 self-assigned this Aug 25, 2020
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Worked around this in the batch processor by prepending script to set the variables:

def jq_filter(script, args={}):

    if isinstance(script, list):
        script = "\n".join(script)

    arg_lines = "".join([
        "%s as $%s | " % (pscheduler.json_dump(value), name)
        for name, value in args.items()
    ])

    return pscheduler.JQFilter(arg_lines + script)

mfeit-internet2 added a commit that referenced this issue Sep 1, 2020
@mfeit-internet2
Added workaround for PyJQ memory corruption problem. #1059
446f661
@mfeit-internet2 mfeit-internet2 mentioned this issue Sep 1, 2020
Closed
mfeit-internet2 added a commit that referenced this issue Sep 1, 2020
@mfeit-internet2
Merge pull request #1060 from perfsonar/issue-1059
412a92d 
Added workaround for PyJQ memory corruption problem.  #1059
@mfeit-internet2
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Closing, but will revisit once I get notification that PyJQ is fixed.

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