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# Production Container: `mechanical-rob` Failure
## Tags
* status: open
* priority: high
* type: bug
* assigned: fredm
* keywords: genenetwork, production, mechanical-rob
## Description
After deploying the latest commits to https://gn2-fred.genenetwork.org on 2025-02-19UTC-0600, with the following commits:
* genenetwork2: 2a3df8cfba6b29dddbe40910c69283a1afbc8e51
* genenetwork3: 99fd5070a84f37f91993f329f9cc8dd82a4b9339
* gn-auth: 073395ff331042a5c686a46fa124f9cc6e10dd2f
* gn-libs: 72a95f8ffa5401649f70978e863dd3f21900a611
I had the (not so) bright idea to run the `mechanical-rob` tests against it before pushing it to production, proper. Here's where I ran into problems: some of the `mechanical-rob` tests failed, specifically, the correlation tests.
Meanwhile, a run of the same tests against https://cd.genenetwork.org with the same commits was successful:
=> https://ci.genenetwork.org/jobs/genenetwork2-mechanical-rob/1531 See this.
This points to a possible problem with the setup of the production container, that leads to failures where none should be. This needs investigation and fixing.
### Update 2025-02-20
The MariaDB server is crashing. To reproduce:
* Go to https://gn2-fred.genenetwork.org/show_trait?trait_id=1435464_at&dataset=HC_M2_0606_P
* Click on "Calculate Correlations" to expand
* Click "Compute"
Observe that after a little while, the system fails with the following errors:
* `MySQLdb.OperationalError: (2013, 'Lost connection to MySQL server during query')`
* `MySQLdb.OperationalError: (2006, 'MySQL server has gone away')`
I attempted updating the configuration for MariaDB, setting the `max_allowed_packet` to 16M and then 64M, but that did not resolve the problem.
The log files indicate the following:
```
2025-02-20 7:46:07 0 [Note] Recovering after a crash using /var/lib/mysql/gn0-binary-log
2025-02-20 7:46:07 0 [Note] Starting crash recovery...
2025-02-20 7:46:07 0 [Note] Crash recovery finished.
2025-02-20 7:46:07 0 [Note] Server socket created on IP: '0.0.0.0'.
2025-02-20 7:46:07 0 [Warning] 'user' entry 'webqtlout@tux01' ignored in --skip-name-resolve mode.
2025-02-20 7:46:07 0 [Warning] 'db' entry 'db_webqtl webqtlout@tux01' ignored in --skip-name-resolve mode.
2025-02-20 7:46:07 0 [Note] Reading of all Master_info entries succeeded
2025-02-20 7:46:07 0 [Note] Added new Master_info '' to hash table
2025-02-20 7:46:07 0 [Note] /usr/sbin/mariadbd: ready for connections.
Version: '10.5.23-MariaDB-0+deb11u1-log' socket: '/run/mysqld/mysqld.sock' port: 3306 Debian 11
2025-02-20 7:46:07 4 [Warning] Access denied for user 'root'@'localhost' (using password: NO)
2025-02-20 7:46:07 5 [Warning] Access denied for user 'root'@'localhost' (using password: NO)
2025-02-20 7:46:07 0 [Note] InnoDB: Buffer pool(s) load completed at 250220 7:46:07
250220 7:50:12 [ERROR] mysqld got signal 11 ;
Sorry, we probably made a mistake, and this is a bug.
Your assistance in bug reporting will enable us to fix this for the next release.
To report this bug, see https://mariadb.com/kb/en/reporting-bugs
We will try our best to scrape up some info that will hopefully help
diagnose the problem, but since we have already crashed,
something is definitely wrong and this may fail.
Server version: 10.5.23-MariaDB-0+deb11u1-log source revision: 6cfd2ba397b0ca689d8ff1bdb9fc4a4dc516a5eb
key_buffer_size=10485760
read_buffer_size=131072
max_used_connections=1
max_threads=2050
thread_count=1
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 4523497 K bytes of memory
Hope that's ok; if not, decrease some variables in the equation.
Thread pointer: 0x7f599c000c58
Attempting backtrace. You can use the following information to find out
where mysqld died. If you see no messages after this, something went
terribly wrong...
stack_bottom = 0x7f6150282d78 thread_stack 0x49000
/usr/sbin/mariadbd(my_print_stacktrace+0x2e)[0x55f43330c14e]
/usr/sbin/mariadbd(handle_fatal_signal+0x475)[0x55f432e013b5]
sigaction.c:0(__restore_rt)[0x7f615a1cb140]
/usr/sbin/mariadbd(+0xcbffbe)[0x55f43314efbe]
/usr/sbin/mariadbd(+0xd730ec)[0x55f4332020ec]
/usr/sbin/mariadbd(+0xd1b36b)[0x55f4331aa36b]
/usr/sbin/mariadbd(+0xd1cd8e)[0x55f4331abd8e]
/usr/sbin/mariadbd(+0xc596f3)[0x55f4330e86f3]
/usr/sbin/mariadbd(_ZN7handler18ha_index_next_sameEPhPKhj+0x2a5)[0x55f432e092b5]
/usr/sbin/mariadbd(+0x7b54d1)[0x55f432c444d1]
/usr/sbin/mariadbd(_Z10sub_selectP4JOINP13st_join_tableb+0x1f8)[0x55f432c37da8]
/usr/sbin/mariadbd(_ZN10JOIN_CACHE24generate_full_extensionsEPh+0x134)[0x55f432d24224]
/usr/sbin/mariadbd(_ZN10JOIN_CACHE21join_matching_recordsEb+0x206)[0x55f432d245d6]
/usr/sbin/mariadbd(_ZN10JOIN_CACHE12join_recordsEb+0x1cf)[0x55f432d23eff]
/usr/sbin/mariadbd(_Z16sub_select_cacheP4JOINP13st_join_tableb+0x8a)[0x55f432c382fa]
/usr/sbin/mariadbd(_ZN4JOIN10exec_innerEv+0xd16)[0x55f432c63826]
/usr/sbin/mariadbd(_ZN4JOIN4execEv+0x35)[0x55f432c63cc5]
/usr/sbin/mariadbd(_Z12mysql_selectP3THDP10TABLE_LISTR4ListI4ItemEPS4_jP8st_orderS9_S7_S9_yP13select_resultP18st_select_lex_unitP13st_select_lex+0x106)[0x55f432c61c26]
/usr/sbin/mariadbd(_Z13handle_selectP3THDP3LEXP13select_resultm+0x138)[0x55f432c62698]
/usr/sbin/mariadbd(+0x762121)[0x55f432bf1121]
/usr/sbin/mariadbd(_Z21mysql_execute_commandP3THD+0x3d6c)[0x55f432bfdd1c]
/usr/sbin/mariadbd(_Z11mysql_parseP3THDPcjP12Parser_statebb+0x20b)[0x55f432bff17b]
/usr/sbin/mariadbd(_Z16dispatch_command19enum_server_commandP3THDPcjbb+0xdb5)[0x55f432c00f55]
/usr/sbin/mariadbd(_Z10do_commandP3THD+0x120)[0x55f432c02da0]
/usr/sbin/mariadbd(_Z24do_handle_one_connectionP7CONNECTb+0x2f2)[0x55f432cf8b32]
/usr/sbin/mariadbd(handle_one_connection+0x5d)[0x55f432cf8dad]
/usr/sbin/mariadbd(+0xbb4ceb)[0x55f433043ceb]
nptl/pthread_create.c:478(start_thread)[0x7f615a1bfea7]
x86_64/clone.S:97(__GI___clone)[0x7f6159dc6acf]
Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (0x7f599c012c50): SELECT ProbeSet.Name,ProbeSet.Chr,ProbeSet.Mb,
ProbeSet.Symbol,ProbeSetXRef.mean,
CONCAT_WS('; ', ProbeSet.description, ProbeSet.Probe_Target_Description) AS description,
ProbeSetXRef.additive,ProbeSetXRef.LRS,Geno.Chr, Geno.Mb
FROM ProbeSet INNER JOIN ProbeSetXRef
ON ProbeSet.Id=ProbeSetXRef.ProbeSetId
INNER JOIN Geno
ON ProbeSetXRef.Locus = Geno.Name
INNER JOIN Species
ON Geno.SpeciesId = Species.Id
WHERE ProbeSet.Name in ('1447591_x_at', '1422809_at', '1428917_at', '1438096_a_at', '1416474_at', '1453271_at', '1441725_at', '1452952_at', '1456774_at', '1438413_at', '1431110_at', '1453723_x_at', '1424124_at', '1448706_at', '1448762_at', '1428332_at', '1438389_x_at', '1455508_at', '1455805_x_at', '1433276_at', '1454989_at', '1427467_a_at', '1447448_s_at', '1438695_at', '1456795_at', '1454874_at', '1455189_at', '1448631_a_at', '1422697_s_at', '1423717_at', '1439484_at', '1419123_a_at', '1435286_at', '1439886_at', '1436348_at', '1437475_at', '1447667_x_at', '1421046_a_at', '1448296_x_at', '1460577_at', 'AFFX-GapdhMur/M32599_M_at', '1424393_s_at', '1426190_at', '1434749_at', '1455706_at', '1448584_at', '1434093_at', '1434461_at', '1419401_at', '1433957_at', '1419453_at', '1416500_at', '1439436_x_at', '1451413_at', '1455696_a_at', '1457190_at', '1455521_at', '1434842_s_at', '1442525_at', '1452331_s_at', '1428862_at', '1436463_at', '1438535_at', 'AFFX-GapdhMur/M32599_3_at', '1424012_at', '1440027_at', '1435846_x_at', '1443282_at', '1435567_at', '1450112_a_at', '1428251_at', '1429063_s_at', '1433781_a_at', '1436698_x_at', '1436175_at', '1435668_at', '1424683_at', '1442743_at', '1416944_a_at', '1437511_x_at', '1451254_at', '1423083_at', '1440158_x_at', '1424324_at', '1426382_at', '1420142_s_at', '1434553_at', '1428772_at', '1424094_at', '1435900_at', '1455322_at', '1453283_at', '1428551_at', '1453078_at', '1444602_at', '1443836_x_at', '1435590_at', '1434283_at', '1435240_at', '1434659_at', '1427032_at', '1455278_at', '1448104_at', '1421247_at', 'AFFX-MURINE_b1_at', '1460216_at', '1433969_at', '1419171_at', '1456699_s_at', '1456901_at', '1442139_at', '1421849_at', '1419824_a_at', '1460588_at', '1420131_s_at', '1446138_at', '1435829_at', '1434462_at', '1435059_at', '1415949_at', '1460624_at', '1426707_at', '1417250_at', '1434956_at', '1438018_at', '1454846_at', '1435298_at', '1442077_at', '1424074_at', '1428883_at', '1454149_a_at', '1423925_at', '1457060_at', '1433821_at', '1447923_at', '1460670_at', '1434468_at', '1454980_at', '1426913_at', '1456741_s_at', '1449278_at', '1443534_at', '1417941_at', '1433167_at', '1434401_at', '1456516_x_at', '1451360_at', 'AFFX-GapdhMur/M32599_5_at', '1417827_at', '1434161_at', '1448979_at', '1435797_at', '1419807_at', '1418330_at', '1426304_x_at', '1425492_at', '1437873_at', '1435734_x_at', '1420622_a_at', '1456019_at', '1449200_at', '1455314_at', '1428419_at', '1426349_s_at', '1426743_at', '1436073_at', '1452306_at', '1436735_at', '1439529_at', '1459347_at', '1429642_at', '1438930_s_at', '1437380_x_at', '1459861_s_at', '1424243_at', '1430503_at', '1434474_at', '1417962_s_at', '1440187_at', '1446809_at', '1436234_at', '1415906_at', 'AFFX-MURINE_B2_at', '1434836_at', '1426002_a_at', '1448111_at', '1452882_at', '1436597_at', '1455915_at', '1421846_at', '1428693_at', '1422624_at', '1423755_at', '1460367_at', '1433746_at', '1454872_at', '1429194_at', '1424652_at', '1440795_x_at', '1458690_at', '1434355_at', '1456324_at', '1457867_at', '1429698_at', '1423104_at', '1437585_x_at', '1437739_a_at', '1445605_s_at', '1436313_at', '1449738_s_at', '1437525_a_at', '1454937_at', '1429043_at', '1440091_at', '1422820_at', '1437456_x_at', '1427322_at', '1446649_at', '1433568_at', '1441114_at', '1456541_x_at', '1426985_s_at', '1454764_s_at', '1424071_s_at', '1429251_at', '1429155_at', '1433946_at', '1448771_a_at', '1458664_at', '1438320_s_at', '1449616_s_at', '1435445_at', '1433872_at', '1429273_at', '1420880_a_at', '1448645_at', '1449646_s_at', '1428341_at', '1431299_a_at', '1433427_at', '1418530_at', '1436247_at', '1454350_at', '1455860_at', '1417145_at', '1454952_s_at', '1435977_at', '1434807_s_at', '1428715_at', '1418117_at', '1447947_at', '1431781_at', '1428915_at', '1427197_at', '1427208_at', '1455460_at', '1423899_at', '1441944_s_at', '1455429_at', '1452266_at', '1454409_at', '1426384_a_at', '1428725_at', '1419181_at', '1454862_at', '1452907_at', '1433794_at', '1435492_at', '1424839_a_at', '1416214_at', '1449312_at', '1436678_at', '1426253_at', '1438859_x_at', '1448189_a_at', '1442557_at', '1446174_at', '1459718_x_at', '1437613_s_at', '1456509_at', '1455267_at', '1440480_at', '1417296_at', '1460050_x_at', '1433585_at', '1436771_x_at', '1424294_at', '1448648_at', '1417753_at', '1436139_at', '1425642_at', '1418553_at', '1415747_s_at', '1445984_at', '1440024_at', '1448720_at', '1429459_at', '1451459_at', '1428853_at', '1433856_at', '1426248_at', '1417765_a_at', '1439459_x_at', '1447023_at', '1426088_at', '1440825_s_at', '1417390_at', '1444744_at', '1435618_at', '1424635_at', '1443727_x_at', '1421096_at', '1427410_at', '1416860_s_at', '1442773_at', '1442030_at', '1452281_at', '1434774_at', '1416891_at', '1447915_x_at', '1429129_at', '1418850_at', '1416308_at', '1422858_at', '1447679_s_at', '1440903_at', '1417321_at', '1452342_at', '1453510_s_at', '1454923_at', '1454611_a_at', '1457532_at', '1438440_at', '1434232_a_at', '1455878_at', '1455571_x_at', '1436401_at', '1453289_at', '1457365_at', '1436708_x_at', '1434494_at', '1419588_at', '1433679_at', '1455159_at', '1428982_at', '1446510_at', '1434131_at', '1418066_at', '1435346_at', '1449415_at', '1455384_x_at', '1418817_at', '1442073_at', '1457265_at', '1447361_at', '1418039_at', '1428467_at', '1452224_at', '1417538_at', '1434529_x_at', '1442149_at', '1437379_x_at', '1416473_a_at', '1432750_at', '1428389_s_at', '1433823_at', '1451889_at', '1438178_x_at', '1441807_s_at', '1416799_at', '1420623_x_at', '1453245_at', '1434037_s_at', '1443012_at', '1443172_at', '1455321_at', '1438396_at', '1440823_x_at', '1436278_at', '1457543_at', '1452908_at', '1417483_at', '1418397_at', '1446589_at', '1450966_at', '1447877_x_at', '1446524_at', '1438592_at', '1455589_at', '1428629_at', '1429585_s_at', '1440020_at', '1417365_a_at', '1426442_at', '1427151_at', '1437377_a_at', '1433995_s_at', '1435464_at', '1417007_a_at', '1429690_at', '1427999_at', '1426819_at', '1454905_at', '1439516_at', '1434509_at', '1428707_at', '1416793_at', '1440822_x_at', '1437327_x_at', '1428682_at', '1435004_at', '1434238_at', '1417581_at', '1434699_at', '1455597_at', '1458613_at', '1456485_at', '1435122_x_at', '1452864_at', '1453122_at', '1435254_at', '1451221_at', '1460168_at', '1455336_at', '1427965_at', '1432576_at', '1455425_at', '1428762_at', '1455459_at', '1419317_x_at', '1434691_at', '1437950_at', '1426401_at', '1457261_at', '1433824_x_at', '1435235_at', '1437343_x_at', '1439964_at', '1444280_at', '1455434_a_at', '1424431_at', '1421519_a_at', '1428412_at', '1434010_at', '1419976_s_at', '1418887_a_at', '1428498_at', '1446883_at', '1435675_at', '1422599_s_at', '1457410_at', '1444437_at', '1421050_at', '1437885_at', '1459754_x_at', '1423807_a_at', '1435490_at', '1426760_at', '1449459_s_at', '1432098_a_at', '1437067_at', '1435574_at', '1433999_at', '1431289_at', '1428919_at', '1425678_a_at', '1434924_at', '1421640_a_at', '1440191_s_at', '1460082_at', '1449913_at', '1439830_at', '1425020_at', '1443790_x_at', '1436931_at', '1454214_a_at', '1455854_a_at', '1437061_at', '1436125_at', '1426385_x_at', '1431893_a_at', '1417140_a_at', '1435333_at', '1427907_at', '1434446_at', '1417594_at', '1426518_at', '1437345_a_at', '1420091_s_at', '1450058_at', '1435161_at', '1430348_at', '1455778_at', '1422653_at', '1447942_x_at', '1434843_at', '1454956_at', '1454998_at', '1427384_at', '1439828_at') AND
Species.Name = 'mouse' AND
ProbeSetXRef.ProbeSetFreezeId IN (
SELECT ProbeSetFreeze.Id
FROM ProbeSetFreeze WHERE ProbeSetFreeze.Name = 'HC_M2_0606_P')
Connection ID (thread ID): 41
Status: NOT_KILLED
Optimizer switch: index_merge=on,index_merge_union=on,index_merge_sort_union=on,index_merge_intersection=on,index_merge_sort_intersection=off,engine_condition_pushdown=off,index_condition_pushdown=on,derived_merge=on,derived_with_keys=on,firstmatch=on,loosescan=on,materialization=on,in_to_exists=on,semijoin=on,partial_match_rowid_merge=on,partial_match_table_scan=on,subquery_cache=on,mrr=off,mrr_cost_based=off,mrr_sort_keys=off,outer_join_with_cache=on,semijoin_with_cache=on,join_cache_incremental=on,join_cache_hashed=on,join_cache_bka=on,optimize_join_buffer_size=on,table_elimination=on,extended_keys=on,exists_to_in=on,orderby_uses_equalities=on,condition_pushdown_for_derived=on,split_materialized=on,condition_pushdown_for_subquery=on,rowid_filter=on,condition_pushdown_from_having=on,not_null_range_scan=off
The manual page at https://mariadb.com/kb/en/how-to-produce-a-full-stack-trace-for-mariadbd/ contains
information that should help you find out what is causing the crash.
Writing a core file...
Working directory at /export/mysql/var/lib/mysql
Resource Limits:
Limit Soft Limit Hard Limit Units
Max cpu time unlimited unlimited seconds
Max file size unlimited unlimited bytes
Max data size unlimited unlimited bytes
Max stack size 8388608 unlimited bytes
Max core file size 0 unlimited bytes
Max resident set unlimited unlimited bytes
Max processes 3094157 3094157 processes
Max open files 64000 64000 files
Max locked memory 65536 65536 bytes
Max address space unlimited unlimited bytes
Max file locks unlimited unlimited locks
Max pending signals 3094157 3094157 signals
Max msgqueue size 819200 819200 bytes
Max nice priority 0 0
Max realtime priority 0 0
Max realtime timeout unlimited unlimited us
Core pattern: core
Kernel version: Linux version 5.10.0-22-amd64 (debian-kernel@lists.debian.org) (gcc-10 (Debian 10.2.1-6) 10.2.1 20210110, GNU ld (GNU Binutils for Debian) 2.35.2) #1 SMP Debian 5.10.178-3 (2023-04-22)
2025-02-20 7:50:17 0 [Note] Starting MariaDB 10.5.23-MariaDB-0+deb11u1-log source revision 6cfd2ba397b0ca689d8ff1bdb9fc4a4dc516a5eb as process 3086167
2025-02-20 7:50:17 0 [Note] InnoDB: !!! innodb_force_recovery is set to 1 !!!
2025-02-20 7:50:17 0 [Note] InnoDB: Uses event mutexes
2025-02-20 7:50:17 0 [Note] InnoDB: Compressed tables use zlib 1.2.11
2025-02-20 7:50:17 0 [Note] InnoDB: Number of pools: 1
2025-02-20 7:50:17 0 [Note] InnoDB: Using crc32 + pclmulqdq instructions
2025-02-20 7:50:17 0 [Note] InnoDB: Using Linux native AIO
2025-02-20 7:50:17 0 [Note] InnoDB: Initializing buffer pool, total size = 17179869184, chunk size = 134217728
2025-02-20 7:50:17 0 [Note] InnoDB: Completed initialization of buffer pool
2025-02-20 7:50:17 0 [Note] InnoDB: Starting crash recovery from checkpoint LSN=1537379110991,1537379110991
2025-02-20 7:50:17 0 [Note] InnoDB: Last binlog file '/var/lib/mysql/gn0-binary-log.000134', position 82843148
2025-02-20 7:50:17 0 [Note] InnoDB: 128 rollback segments are active.
2025-02-20 7:50:17 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2025-02-20 7:50:17 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2025-02-20 7:50:17 0 [Note] InnoDB: Setting file './ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2025-02-20 7:50:17 0 [Note] InnoDB: File './ibtmp1' size is now 12 MB.
2025-02-20 7:50:17 0 [Note] InnoDB: 10.5.23 started; log sequence number 1537379111003; transaction id 3459549902
2025-02-20 7:50:17 0 [Note] Plugin 'FEEDBACK' is disabled.
2025-02-20 7:50:17 0 [Note] InnoDB: Loading buffer pool(s) from /export/mysql/var/lib/mysql/ib_buffer_pool
2025-02-20 7:50:17 0 [Note] Loaded 'locales.so' with offset 0x7f9551bc0000
2025-02-20 7:50:17 0 [Note] Recovering after a crash using /var/lib/mysql/gn0-binary-log
2025-02-20 7:50:17 0 [Note] Starting crash recovery...
2025-02-20 7:50:17 0 [Note] Crash recovery finished.
2025-02-20 7:50:17 0 [Note] Server socket created on IP: '0.0.0.0'.
2025-02-20 7:50:17 0 [Warning] 'user' entry 'webqtlout@tux01' ignored in --skip-name-resolve mode.
2025-02-20 7:50:17 0 [Warning] 'db' entry 'db_webqtl webqtlout@tux01' ignored in --skip-name-resolve mode.
2025-02-20 7:50:17 0 [Note] Reading of all Master_info entries succeeded
2025-02-20 7:50:17 0 [Note] Added new Master_info '' to hash table
2025-02-20 7:50:17 0 [Note] /usr/sbin/mariadbd: ready for connections.
Version: '10.5.23-MariaDB-0+deb11u1-log' socket: '/run/mysqld/mysqld.sock' port: 3306 Debian 11
2025-02-20 7:50:17 4 [Warning] Access denied for user 'root'@'localhost' (using password: NO)
2025-02-20 7:50:17 5 [Warning] Access denied for user 'root'@'localhost' (using password: NO)
2025-02-20 7:50:17 0 [Note] InnoDB: Buffer pool(s) load completed at 250220 7:50:17
```
A possible issue is the use of the environment variable SQL_URI at this point:
=> https://github.com/genenetwork/genenetwork2/blob/testing/gn2/wqflask/correlation/rust_correlation.py#L34
which is requested
=> https://github.com/genenetwork/genenetwork2/blob/testing/gn2/wqflask/correlation/rust_correlation.py#L7 from here.
I tried setting an environment variable "SQL_URI" with the same value as the config and rebuilt the container. That did not fix the problem.
Running the query directly in the default mysql client also fails with:
```
ERROR 2013 (HY000): Lost connection to MySQL server during query
```
Huh, so this was not a code problem.
Configured database to allow upgrade of tables if necessary and restarted mariadbd.
The problem still persists.
|
