Ok, the race condition seems not to be the real problem, since the patches didn't help. Don't want to do any assumptions anymore, but it seems like the python objects memory is deallocated before the sqlite connection was closed. The thing is, that this problem appears only on very heavy load with 40 parallel python processes and overall memory consumption of more than 240GiB. This high number is due to deactivated GC on our side, due to performance problems, we call it once the complete work is done. Unfortunately, I can't reproduce this error in "small", but here is the crash report (the crash comes from different parts of free(), sometimes with double free, sometimes invalid pointer or similar):

*** glibc detected *** /share/nds-buildtools/python/python-3.4.2-64_5/bin/python: free(): invalid next size (normal): 0x00000000058b72b0 ***
======= Backtrace: =========
/lib64/libc.so.6[0x36e6275f4e]
/lib64/libc.so.6[0x36e6278cf0]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(+0x23918)[0x7f785100a918]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(sqlite3_free+0x63)[0x7f785100b6b6]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(+0x3193d)[0x7f785101893d]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(+0x31a93)[0x7f7851018a93]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(+0x31e6d)[0x7f7851018e6d]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(+0x32735)[0x7f7851019735]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(+0x3115d)[0x7f785101815d]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(+0x3119e)[0x7f785101819e]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(+0x33df2)[0x7f785101adf2]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(+0x36441)[0x7f785101d441]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(+0x40e21)[0x7f7851027e21]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(+0xbbddf)[0x7f78510a2ddf]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(+0xbbcff)[0x7f78510a2cff]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(sqlite3_close+0x1d)[0x7f78510a2d23]
/share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so(pysqlite_connection_close+0x79)[0x7f7851002af9]
/share/nds-buildtools/python/python-3.4.2-64_5/bin/python(PyEval_EvalFrameEx+0x64e3)[0x4c52e3]
/share/nds-buildtools/python/python-3.4.2-64_5/bin/python(PyEval_EvalFrameEx+0x6e38)[0x4c5c38]
/share/nds-buildtools/python/python-3.4.2-64_5/bin/python(PyEval_EvalFrameEx+0x6e38)[0x4c5c38]
/share/nds-buildtools/python/python-3.4.2-64_5/bin/python(PyEval_EvalFrameEx+0x6e38)[0x4c5c38]
/share/nds-buildtools/python/python-3.4.2-64_5/bin/python(PyEval_EvalFrameEx+0x6e38)[0x4c5c38]
/share/nds-buildtools/python/python-3.4.2-64_5/bin/python(PyEval_EvalFrameEx+0x6e38)[0x4c5c38]
/share/nds-buildtools/python/python-3.4.2-64_5/bin/python(PyEval_EvalCodeEx+0x8a7)[0x4c72a7]
/share/nds-buildtools/python/python-3.4.2-64_5/bin/python(PyEval_EvalCode+0x3b)[0x4c736b]
/share/nds-buildtools/python/python-3.4.2-64_5/bin/python[0x4e7c61]
/share/nds-buildtools/python/python-3.4.2-64_5/bin/python(PyRun_FileExFlags+0x115)[0x4e9a85]
/share/nds-buildtools/python/python-3.4.2-64_5/bin/python(PyRun_SimpleFileExFlags+0xfa)[0x4eb2ea]
/share/nds-buildtools/python/python-3.4.2-64_5/bin/python(Py_Main+0xa74)[0x41d8e4]
/share/nds-buildtools/python/python-3.4.2-64_5/bin/python(main+0x155)[0x41a465]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x36e621ed5d]
/share/nds-buildtools/python/python-3.4.2-64_5/bin/python[0x41a249]
======= Memory map: ========
00400000-005fe000 r-xp 00000000 00:1a 491451                             /share/nds-buildtools/python/python-3.4.2-64_5/bin/python3.4
007fd000-00857000 rw-p 001fd000 00:1a 491451                             /share/nds-buildtools/python/python-3.4.2-64_5/bin/python3.4
00857000-00872000 rw-p 00000000 00:00 0 
00c84000-0dd92000 rw-p 00000000 00:00 0                                  [heap]
36e5e00000-36e5e20000 r-xp 00000000 fd:00 2964                           /lib64/ld-2.12.so
36e601f000-36e6020000 r--p 0001f000 fd:00 2964                           /lib64/ld-2.12.so
36e6020000-36e6021000 rw-p 00020000 fd:00 2964                           /lib64/ld-2.12.so
36e6021000-36e6022000 rw-p 00000000 00:00 0 
36e6200000-36e638a000 r-xp 00000000 fd:00 3884                           /lib64/libc-2.12.so
36e638a000-36e658a000 ---p 0018a000 fd:00 3884                           /lib64/libc-2.12.so
36e658a000-36e658e000 r--p 0018a000 fd:00 3884                           /lib64/libc-2.12.so
36e658e000-36e658f000 rw-p 0018e000 fd:00 3884                           /lib64/libc-2.12.so
36e658f000-36e6594000 rw-p 00000000 00:00 0 
36e6600000-36e6602000 r-xp 00000000 fd:00 4585                           /lib64/libdl-2.12.so
36e6602000-36e6802000 ---p 00002000 fd:00 4585                           /lib64/libdl-2.12.so
36e6802000-36e6803000 r--p 00002000 fd:00 4585                           /lib64/libdl-2.12.so
36e6803000-36e6804000 rw-p 00003000 fd:00 4585                           /lib64/libdl-2.12.so
36e6a00000-36e6a17000 r-xp 00000000 fd:00 3891                           /lib64/libpthread-2.12.so
36e6a17000-36e6c17000 ---p 00017000 fd:00 3891                           /lib64/libpthread-2.12.so
36e6c17000-36e6c18000 r--p 00017000 fd:00 3891                           /lib64/libpthread-2.12.so
36e6c18000-36e6c19000 rw-p 00018000 fd:00 3891                           /lib64/libpthread-2.12.so
36e6c19000-36e6c1d000 rw-p 00000000 00:00 0 
36e6e00000-36e6e15000 r-xp 00000000 fd:00 8884                           /lib64/libz.so.1.2.3
36e6e15000-36e7014000 ---p 00015000 fd:00 8884                           /lib64/libz.so.1.2.3
36e7014000-36e7015000 r--p 00014000 fd:00 8884                           /lib64/libz.so.1.2.3
36e7015000-36e7016000 rw-p 00015000 fd:00 8884                           /lib64/libz.so.1.2.3
36e7200000-36e7207000 r-xp 00000000 fd:00 7022                           /lib64/librt-2.12.so
36e7207000-36e7406000 ---p 00007000 fd:00 7022                           /lib64/librt-2.12.so
36e7406000-36e7407000 r--p 00006000 fd:00 7022                           /lib64/librt-2.12.so
36e7407000-36e7408000 rw-p 00007000 fd:00 7022                           /lib64/librt-2.12.so
36e7600000-36e7683000 r-xp 00000000 fd:00 10439                          /lib64/libm-2.12.so
36e7683000-36e7882000 ---p 00083000 fd:00 10439                          /lib64/libm-2.12.so
36e7882000-36e7883000 r--p 00082000 fd:00 10439                          /lib64/libm-2.12.so
36e7883000-36e7884000 rw-p 00083000 fd:00 10439                          /lib64/libm-2.12.so
36e7a00000-36e7a1d000 r-xp 00000000 fd:00 5374                           /lib64/libselinux.so.1
36e7a1d000-36e7c1c000 ---p 0001d000 fd:00 5374                           /lib64/libselinux.so.1
36e7c1c000-36e7c1d000 r--p 0001c000 fd:00 5374                           /lib64/libselinux.so.1
36e7c1d000-36e7c1e000 rw-p 0001d000 fd:00 5374                           /lib64/libselinux.so.1
36e7c1e000-36e7c1f000 rw-p 00000000 00:00 0 
36e8200000-36e8216000 r-xp 00000000 fd:00 5071                           /lib64/libresolv-2.12.so
36e8216000-36e8416000 ---p 00016000 fd:00 5071                           /lib64/libresolv-2.12.so
36e8416000-36e8417000 r--p 00016000 fd:00 5071                           /lib64/libresolv-2.12.so
36e8417000-36e8418000 rw-p 00017000 fd:00 5071                           /lib64/libresolv-2.12.so
36e8418000-36e841a000 rw-p 00000000 00:00 0 
36e8600000-36e8616000 r-xp 00000000 fd:00 10440                          /lib64/libgcc_s-4.4.7-20120601.so.1
36e8616000-36e8815000 ---p 00016000 fd:00 10440                          /lib64/libgcc_s-4.4.7-20120601.so.1
36e8815000-36e8816000 rw-p 00015000 fd:00 10440                          /lib64/libgcc_s-4.4.7-20120601.so.1
36e8e00000-36e8e02000 r-xp 00000000 fd:00 18011                          /lib64/libutil-2.12.so
36e8e02000-36e9001000 ---p 00002000 fd:00 18011                          /lib64/libutil-2.12.so
36e9001000-36e9002000 r--p 00001000 fd:00 18011                          /lib64/libutil-2.12.so
36e9002000-36e9003000 rw-p 00002000 fd:00 18011                          /lib64/libutil-2.12.so
36ea600000-36ea602000 r-xp 00000000 fd:00 5005                           /lib64/libkeyutils.so.1.3
36ea602000-36ea801000 ---p 00002000 fd:00 5005                           /lib64/libkeyutils.so.1.3
36ea801000-36ea802000 r--p 00001000 fd:00 5005                           /lib64/libkeyutils.so.1.3
36ea802000-36ea803000 rw-p 00002000 fd:00 5005                           /lib64/libkeyutils.so.1.3
36eaa00000-36eaa03000 r-xp 00000000 fd:00 6725                           /lib64/libcom_err.so.2.1
36eaa03000-36eac02000 ---p 00003000 fd:00 6725                           /lib64/libcom_err.so.2.1
36eac02000-36eac03000 r--p 00002000 fd:00 6725                           /lib64/libcom_err.so.2.1
36eac03000-36eac04000 rw-p 00003000 fd:00 6725                           /lib64/libcom_err.so.2.1
36eb200000-36eb3b9000 r-xp 00000000 fd:00 9400                           /usr/lib64/libcrypto.so.1.0.1e
36eb3b9000-36eb5b8000 ---p 001b9000 fd:00 9400                           /usr/lib64/libcrypto.so.1.0.1e
36eb5b8000-36eb5d3000 r--p 001b8000 fd:00 9400                           /usr/lib64/libcrypto.so.1.0.1e
36eb5d3000-36eb5df000 rw-p 001d3000 fd:00 9400                           /usr/lib64/libcrypto.so.1.0.1e
36eb5df000-36eb5e3000 rw-p 00000000 00:00 0 
36eb600000-36eb641000 r-xp 00000000 fd:00 6869                           /lib64/libgssapi_krb5.so.2.2
36eb641000-36eb841000 ---p 00041000 fd:00 6869                           /lib64/libgssapi_krb5.so.2.2
36eb841000-36eb842000 r--p 00041000 fd:00 6869                           /lib64/libgssapi_krb5.so.2.2
36eb842000-36eb844000 rw-p 00042000 fd:00 6869                           /lib64/libgssapi_krb5.so.2.2
36ec600000-36ec60a000 r-xp 00000000 fd:00 5394                           /lib64/libkrb5support.so.0.1
36ec60a000-36ec809000 ---p 0000a000 fd:00 5394                           /lib64/libkrb5support.so.0.1
36ec809000-36ec80a000 r--p 00009000 fd:00 5394                           /lib64/libkrb5support.so.0.1
36ec80a000-36ec80b000 rw-p 0000a000 fd:00 5394                           /lib64/libkrb5support.so.0.1
36eca00000-36eca29000 r-xp 00000000 fd:00 5413                           /lib64/libk5crypto.so.3.1
36eca29000-36ecc29000 ---p 00029000 fd:00 5413                           /lib64/libk5crypto.so.3.1
36ecc29000-36ecc2a000 r--p 00029000 fd:00 5413                           /lib64/libk5crypto.so.3.1
36ecc2a000-36ecc2b000 rw-p 0002a000 fd:00 5413                           /lib64/libk5crypto.so.3.1
36ecc2b000-36ecc2c000 rw-p 00000000 00:00 0 
36ece00000-36ecedb000 r-xp 00000000 fd:00 6862                           /lib64/libkrb5.so.3.3
36ecedb000-36ed0db000 ---p 000db000 fd:00 6862                           /lib64/libkrb5.so.3.3
36ed0db000-36ed0e5000 r--p 000db000 fd:00 6862                           /lib64/libkrb5.so.3.3
36ed0e5000-36ed0e7000 rw-p 000e5000 fd:00 6862                           /lib64/libkrb5.so.3.3
36ede00000-36ede62000 r-xp 00000000 fd:00 22840                          /usr/lib64/libssl.so.1.0.1e
36ede62000-36ee061000 ---p 00062000 fd:00 22840                          /usr/lib64/libssl.so.1.0.1e
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36ee065000-36ee06c000 rw-p 00065000 fd:00 22840                          /usr/lib64/libssl.so.1.0.1e
7f783c000000-7f783c021000 rw-p 00000000 00:00 0 
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7f7842d72000-7f7842db2000 rw-p 00000000 00:00 0 
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7f7847bb4000-7f7847bf4000 rw-p 00000000 00:00 0 
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7f784bcb6000-7f784bcf6000 rw-p 00000000 00:00 0 
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7f784c976000-7f784c9b6000 rw-p 00000000 00:00 0 
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7f784d9c5000-7f784da05000 rw-p 00000000 00:00 0 
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7f784ebc6000-7f784ec06000 rw-p 00000000 00:00 0 
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7f784f805000-7f7850906000 rw-p 00000000 00:00 0 
7f7850906000-7f785091d000 r-xp 00000000 00:1a 484827                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_pickle.cpython-34m.so
7f785091d000-7f7850b1c000 ---p 00017000 00:1a 484827                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_pickle.cpython-34m.so
7f7850b1c000-7f7850b20000 rw-p 00016000 00:1a 484827                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_pickle.cpython-34m.so
7f7850b20000-7f7850d61000 rw-p 00000000 00:00 0 
7f7850d61000-7f7850d66000 r-xp 00000000 00:1a 484828                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_hashlib.cpython-34m.so
7f7850d66000-7f7850f66000 ---p 00005000 00:1a 484828                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_hashlib.cpython-34m.so
7f7850f66000-7f7850f67000 rw-p 00005000 00:1a 484828                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_hashlib.cpython-34m.so
7f7850f67000-7f7850fe7000 rw-p 00000000 00:00 0 
7f7850fe7000-7f785113d000 r-xp 00000000 00:1a 484839                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so
7f785113d000-7f785133c000 ---p 00156000 00:1a 484839                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so
7f785133c000-7f7851345000 rw-p 00155000 00:1a 484839                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_sqlite3.cpython-34m.so
7f7851345000-7f7851346000 rw-p 00000000 00:00 0 
7f7851346000-7f785135f000 r-xp 00000000 00:1a 484811                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/zlib.cpython-34m.so
7f785135f000-7f785155f000 ---p 00019000 00:1a 484811                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/zlib.cpython-34m.so
7f785155f000-7f7851561000 rw-p 00019000 00:1a 484811                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/zlib.cpython-34m.so
7f7851561000-7f7851569000 r-xp 00000000 00:1a 484837                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/binascii.cpython-34m.so
7f7851569000-7f7851768000 ---p 00008000 00:1a 484837                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/binascii.cpython-34m.so
7f7851768000-7f7851769000 rw-p 00007000 00:1a 484837                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/binascii.cpython-34m.so
7f7851769000-7f78517a9000 rw-p 00000000 00:00 0 
7f78517a9000-7f78517ab000 r-xp 00000000 00:1a 484815                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/grp.cpython-34m.so
7f78517ab000-7f78519ab000 ---p 00002000 00:1a 484815                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/grp.cpython-34m.so
7f78519ab000-7f78519ac000 rw-p 00002000 00:1a 484815                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/grp.cpython-34m.so
7f78519ac000-7f78519ec000 rw-p 00000000 00:00 0 
7f78519ec000-7f7851a21000 r-xp 00000000 00:1a 484822                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/pyexpat.cpython-34m.so
7f7851a21000-7f7851c20000 ---p 00035000 00:1a 484822                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/pyexpat.cpython-34m.so
7f7851c20000-7f7851c24000 rw-p 00034000 00:1a 484822                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/pyexpat.cpython-34m.so
7f7851c24000-7f7851c31000 r-xp 00000000 00:1a 484847                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_elementtree.cpython-34m.so
7f7851c31000-7f7851e30000 ---p 0000d000 00:1a 484847                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_elementtree.cpython-34m.so
7f7851e30000-7f7851e32000 rw-p 0000c000 00:1a 484847                     /share/nds-buildtools/python/python-3.4.2-64_5/lib/python3.4/lib-dynload/_elementtree.cpython-34m.so
7f7851e32000-7f7852172000 rw-p 00000000 00:00 0 
7f78521a6000-7f78523e6000 rw-p 00000000 00:00 0 
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