snakemake: *** Error in `python3.9': free(): corrupted unsorted chunks: 0x0000558b6ab3dfb0 ***

Posting this here tentatively as I am not sure it is a snakemake bug

Snakemake version 6.3.0

Describe the bug Following on from this issue (https://github.com/snakemake/snakemake/issues/983) which I think I have largely now solved with better exception handling (pull request hopefully coming soon)

I now regularly (i.e. every time I run it) encounter this issue when using Snakemake with google life sciences executor. It’s a core dump so I have no idea how to even debug it.

Logs

*** Error in `/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9': free(): corrupted unsorted chunks: 0x0000558b6ab3dfb0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777f5)[0x7f1351e0f7f5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8038a)[0x7f1351e1838a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f1351e1c58c]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x5c65a)[0x558b6860565a]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1d9576)[0x558b68782576]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x19d407)[0x558b68746407]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xedccd)[0x558b68696ccd]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x373)[0x558b68759fd3]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xedccd)[0x558b68696ccd]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x373)[0x558b68759fd3]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xedccd)[0x558b68696ccd]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x373)[0x558b68759fd3]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xedccd)[0x558b68696ccd]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x373)[0x558b68759fd3]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xedccd)[0x558b68696ccd]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x373)[0x558b68759fd3]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xedccd)[0x558b68696ccd]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1b0456)[0x558b68759456]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x117)[0x558b68759d77]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xedccd)[0x558b68696ccd]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1bb352)[0x558b68764352]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xee7b4)[0x558b686977b4]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1b02fa)[0x558b687592fa]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x117)[0x558b68759d77]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xed06e)[0x558b6869606e]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1b0456)[0x558b68759456]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x117)[0x558b68759d77]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(PyObject_Call+0xbe)[0x558b686ed39e]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyEval_EvalFrameDefault+0x24b9)[0x558b68774ec9]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1b02fa)[0x558b687592fa]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x117)[0x558b68759d77]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xee7b4)[0x558b686977b4]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1b02fa)[0x558b687592fa]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x117)[0x558b68759d77]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(PyObject_Call+0x1df)[0x558b686ed4bf]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyEval_EvalFrameDefault+0x24b9)[0x558b68774ec9]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1b0456)[0x558b68759456]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x117)[0x558b68759d77]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xedccd)[0x558b68696ccd]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1b02fa)[0x558b687592fa]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x117)[0x558b68759d77]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xedccd)[0x558b68696ccd]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1bbf13)[0x558b68764f13]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xee7b4)[0x558b686977b4]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1bb352)[0x558b68764352]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xee7b4)[0x558b686977b4]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1b02fa)[0x558b687592fa]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x117)[0x558b68759d77]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xedccd)[0x558b68696ccd]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x373)[0x558b68759fd3]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xedccd)[0x558b68696ccd]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1bbf13)[0x558b68764f13]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xee7b4)[0x558b686977b4]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1b02fa)[0x558b687592fa]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x117)[0x558b68759d77]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xee7b4)[0x558b686977b4]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1b0456)[0x558b68759456]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyFunction_Vectorcall+0x117)[0x558b68759d77]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0xed06e)[0x558b6869606e]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x1b02fa)[0x558b687592fa]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(_PyEval_EvalCodeWithName+0x4b)[0x558b68803ebb]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(PyEval_EvalCode+0x23)[0x558b68759c53]
/home/mwatson9/miniconda3/envs/snakemake/bin/python3.9(+0x25af5d)[0x558b68803f5d]
======= Memory map: ========
558b685a9000-558b68605000 r--p 00000000 08:01 540380                     /home/mwatson9/miniconda3/envs/snakemake/bin/python3.9
558b68605000-558b6882c000 r-xp 0005c000 08:01 540380                     /home/mwatson9/miniconda3/envs/snakemake/bin/python3.9
558b6882c000-558b68918000 r--p 00283000 08:01 540380                     /home/mwatson9/miniconda3/envs/snakemake/bin/python3.9
558b68919000-558b6891f000 r--p 0036f000 08:01 540380                     /home/mwatson9/miniconda3/envs/snakemake/bin/python3.9
558b6891f000-558b68956000 rw-p 00375000 08:01 540380                     /home/mwatson9/miniconda3/envs/snakemake/bin/python3.9
558b68956000-558b68978000 rw-p 00000000 00:00 0
558b6945e000-558b6acb6000 rw-p 00000000 00:00 0                          [heap]
7f1338000000-7f1338021000 rw-p 00000000 00:00 0
7f1338021000-7f133c000000 ---p 00000000 00:00 0
7f1340000000-7f134004e000 rw-p 00000000 00:00 0
7f134004e000-7f1344000000 ---p 00000000 00:00 0
7f1346d4f000-7f1346e8f000 rw-p 00000000 00:00 0
7f1346e8f000-7f1346e90000 ---p 00000000 00:00 0
7f1346e90000-7f1347690000 rw-p 00000000 00:00 0
7f1347690000-7f1347691000 ---p 00000000 00:00 0
7f1347691000-7f1347e91000 rw-p 00000000 00:00 0
7f1347e91000-7f1347e9c000 r-xp 00000000 08:01 12804                      /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f1347e9c000-7f134809b000 ---p 0000b000 08:01 12804                      /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f134809b000-7f134809c000 r--p 0000a000 08:01 12804                      /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f134809c000-7f134809d000 rw-p 0000b000 08:01 12804                      /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f134809d000-7f13480b3000 r-xp 00000000 08:01 12805                      /lib/x86_64-linux-gnu/libnsl-2.23.so
7f13480b3000-7f13482b2000 ---p 00016000 08:01 12805                      /lib/x86_64-linux-gnu/libnsl-2.23.so
7f13482b2000-7f13482b3000 r--p 00015000 08:01 12805                      /lib/x86_64-linux-gnu/libnsl-2.23.so
7f13482b3000-7f13482b4000 rw-p 00016000 08:01 12805                      /lib/x86_64-linux-gnu/libnsl-2.23.so
7f13482b4000-7f13484f6000 rw-p 00000000 00:00 0
7f1348535000-7f1348575000 rw-p 00000000 00:00 0
7f1348575000-7f134857d000 r-xp 00000000 08:01 12807                      /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f134857d000-7f134877c000 ---p 00008000 08:01 12807                      /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f134877c000-7f134877d000 r--p 00007000 08:01 12807                      /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f134877d000-7f134877e000 rw-p 00008000 08:01 12807                      /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f134877e000-7f134dcbe000 rw-p 00000000 00:00 0
7f134dcbe000-7f134dcd5000 r-xp 00000000 08:01 12802                      /lib/x86_64-linux-gnu/libresolv-2.23.so
7f134dcd5000-7f134ded5000 ---p 00017000 08:01 12802                      /lib/x86_64-linux-gnu/libresolv-2.23.so
7f134ded5000-7f134ded6000 r--p 00017000 08:01 12802                      /lib/x86_64-linux-gnu/libresolv-2.23.so
7f134ded6000-7f134ded7000 rw-p 00018000 08:01 12802                      /lib/x86_64-linux-gnu/libresolv-2.23.so
7f134ded7000-7f134ded9000 rw-p 00000000 00:00 0
7f134ded9000-7f134dede000 r-xp 00000000 08:01 7913                       /lib/x86_64-linux-gnu/libnss_dns-2.23.so
7f134dede000-7f134e0de000 ---p 00005000 08:01 7913                       /lib/x86_64-linux-gnu/libnss_dns-2.23.so
7f134e0de000-7f134e0df000 r--p 00005000 08:01 7913                       /lib/x86_64-linux-gnu/libnss_dns-2.23.so
7f134e0df000-7f134e0e0000 rw-p 00006000 08:01 7913                       /lib/x86_64-linux-gnu/libnss_dns-2.23.so
7f134e0e0000-7f134e0eb000 r-xp 00000000 08:01 12797                      /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f134e0eb000-7f134e2ea000 ---p 0000b000 08:01 12797                      /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f134e2ea000-7f134e2eb000 r--p 0000a000 08:01 12797                      /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f134e2eb000-7f134e2ec000 rw-p 0000b000 08:01 12797                      /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f134e2ec000-7f134e2f2000 rw-p 00000000 00:00 0
7f134e2f7000-7f134e378000 rw-p 00000000 00:00 0
7f134e378000-7f134e383000 r--p 00000000 08:01 534949                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/datrie.cpython-39-x86_64-linux-gnu.so
7f134e383000-7f134e3bc000 r-xp 0000b000 08:01 534949                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/datrie.cpython-39-x86_64-linux-gnu.so
7f134e3bc000-7f134e3c5000 r--p 00044000 08:01 534949                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/datrie.cpython-39-x86_64-linux-gnu.so
7f134e3c5000-7f134e3c6000 ---p 0004d000 08:01 534949                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/datrie.cpython-39-x86_64-linux-gnu.so
7f134e3c6000-7f134e3c7000 r--p 0004d000 08:01 534949                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/datrie.cpython-39-x86_64-linux-gnu.so
7f134e3c7000-7f134e3ce000 rw-p 0004e000 08:01 534949                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/datrie.cpython-39-x86_64-linux-gnu.so
7f134e3ce000-7f134e70f000 rw-p 00000000 00:00 0
7f134e70f000-7f134e712000 r--p 00000000 08:01 538802                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/lib-dynload/termios.cpython-39-x86_64-linux-gnu.so
7f134e712000-7f134e713000 r-xp 00003000 08:01 538802                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/lib-dynload/termios.cpython-39-x86_64-linux-gnu.so
7f134e713000-7f134e715000 r--p 00004000 08:01 538802                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/lib-dynload/termios.cpython-39-x86_64-linux-gnu.so
7f134e715000-7f134e716000 r--p 00005000 08:01 538802                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/lib-dynload/termios.cpython-39-x86_64-linux-gnu.so
7f134e716000-7f134e718000 rw-p 00006000 08:01 538802                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/lib-dynload/termios.cpython-39-x86_64-linux-gnu.so
7f134e718000-7f134e898000 rw-p 00000000 00:00 0
7f134e898000-7f134e899000 r--p 00000000 08:01 517332                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/cryptography/hazmat/bindings/_padding.abi3.so
7f134e899000-7f134e89a000 r-xp 00001000 08:01 517332                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/cryptography/hazmat/bindings/_padding.abi3.so
7f134e89a000-7f134e89b000 r--p 00002000 08:01 517332                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/cryptography/hazmat/bindings/_padding.abi3.so
7f134e89b000-7f134e89c000 r--p 00002000 08:01 517332                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/cryptography/hazmat/bindings/_padding.abi3.so
7f134e89c000-7f134e89d000 rw-p 00003000 08:01 517332                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/cryptography/hazmat/bindings/_padding.abi3.so
7f134e89d000-7f134e91d000 rw-p 00000000 00:00 0
7f134e91d000-7f134e921000 r--p 00000000 08:01 535698                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_frozenlist.cpython-39-x86_64-linux-gnu.so
7f134e921000-7f134e92a000 r-xp 00004000 08:01 535698                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_frozenlist.cpython-39-x86_64-linux-gnu.so
7f134e92a000-7f134e92c000 r--p 0000d000 08:01 535698                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_frozenlist.cpython-39-x86_64-linux-gnu.so
7f134e92c000-7f134e92d000 ---p 0000f000 08:01 535698                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_frozenlist.cpython-39-x86_64-linux-gnu.so
7f134e92d000-7f134e92e000 r--p 0000f000 08:01 535698                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_frozenlist.cpython-39-x86_64-linux-gnu.so
7f134e92e000-7f134e92f000 rw-p 00010000 08:01 535698                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_frozenlist.cpython-39-x86_64-linux-gnu.so
7f134e92f000-7f134e9b0000 rw-p 00000000 00:00 0
7f134e9b0000-7f134e9b3000 r--p 00000000 08:01 535695                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_websocket.cpython-39-x86_64-linux-gnu.so
7f134e9b3000-7f134e9b5000 r-xp 00003000 08:01 535695                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_websocket.cpython-39-x86_64-linux-gnu.so
7f134e9b5000-7f134e9b6000 r--p 00005000 08:01 535695                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_websocket.cpython-39-x86_64-linux-gnu.so
7f134e9b6000-7f134e9b7000 r--p 00005000 08:01 535695                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_websocket.cpython-39-x86_64-linux-gnu.so
7f134e9b7000-7f134e9b8000 rw-p 00006000 08:01 535695                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_websocket.cpython-39-x86_64-linux-gnu.so
7f134e9b8000-7f134e9c1000 r--p 00000000 08:01 535699                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_http_parser.cpython-39-x86_64-linux-gnu.so
7f134e9c1000-7f134ea15000 r-xp 00009000 08:01 535699                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_http_parser.cpython-39-x86_64-linux-gnu.so
7f134ea15000-7f134ea1d000 r--p 0005d000 08:01 535699                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_http_parser.cpython-39-x86_64-linux-gnu.so
7f134ea1d000-7f134ea1e000 ---p 00065000 08:01 535699                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_http_parser.cpython-39-x86_64-linux-gnu.so
7f134ea1e000-7f134ea1f000 r--p 00065000 08:01 535699                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_http_parser.cpython-39-x86_64-linux-gnu.so
7f134ea1f000-7f134ea23000 rw-p 00066000 08:01 535699                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_http_parser.cpython-39-x86_64-linux-gnu.so
7f134ea23000-7f134ea66000 rw-p 00000000 00:00 0
7f134ea66000-7f134ea69000 r--p 00000000 08:01 535696                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_http_writer.cpython-39-x86_64-linux-gnu.so
7f134ea69000-7f134ea6f000 r-xp 00003000 08:01 535696                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_http_writer.cpython-39-x86_64-linux-gnu.so
7f134ea6f000-7f134ea70000 r--p 00009000 08:01 535696                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/site-packages/aiohttp/_http_writer.cpython-39-x86_64-linux-gnu.so
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7f13525a3000-7f13525a4000 rw-p 00004000 08:01 538796                     /home/mwatson9/miniconda3/envs/snakemake/lib/python3.9/lib-dynload/grp.cpython-39-x86_64-linux-gnu.so
7f13525a4000-7f13525a5000 r--p 00025000 08:01 12798                      /lib/x86_64-linux-gnu/ld-2.23.so
7f13525a5000-7f13525a6000 rw-p 00026000 08:01 12798                      /lib/x86_64-linux-gnu/ld-2.23.so
7f13525a6000-7f13525a7000 rw-p 00000000 00:00 0
7fff5e83c000-7fff5e85d000 rw-p 00000000 00:00 0                          [stack]
7fff5e8ad000-7fff5e8b0000 r--p 00000000 00:00 0                          [vvar]
7fff5e8b0000-7fff5e8b2000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)

Minimal example I haven’t produced one yet