diff options
Diffstat (limited to 'issues')
| -rw-r--r-- | issues/gn-guile/rendering-images-within-markdown-documents.gmi | 22 | ||||
| -rw-r--r-- | issues/gn-guile/rework-hard-dependence-on-github.gmi | 21 | ||||
| -rw-r--r-- | issues/production-container-mechanical-rob-failure.gmi | 224 | ||||
| -rw-r--r-- | issues/systems/penguin2-raid5.gmi | 61 | ||||
| -rw-r--r-- | issues/systems/tux04-production.gmi | 275 |
5 files changed, 603 insertions, 0 deletions
diff --git a/issues/gn-guile/rendering-images-within-markdown-documents.gmi b/issues/gn-guile/rendering-images-within-markdown-documents.gmi new file mode 100644 index 0000000..fe3ed39 --- /dev/null +++ b/issues/gn-guile/rendering-images-within-markdown-documents.gmi @@ -0,0 +1,22 @@ +# Rendering Images Linked in Markdown Documents + +## Tags + +* status: open +* priority: high +* type: bug +* assigned: alexm, bonfacem, fredm +* keywords: gn-guile, images, markdown + +## Description + +Rendering images linked within markdown documents does not work as expected — we cannot render images if they have a relative path. +As an example see the commit below: +=> https://github.com/genenetwork/gn-docs/commit/783e7d20368e370fb497974f843f985b51606d00 + +In that commit, we are forced to use the full github uri to get the images to load correctly when rendered via gn-guile. This, has two unfortunate consequences: + +* It makes editing more difficult, since the user has to remember to find and use the full github URL for their images. +* It ties the data and code to github + +This needs to be fixed, such that any and all paths relative to the markdown file are resolved at render time automatically. diff --git a/issues/gn-guile/rework-hard-dependence-on-github.gmi b/issues/gn-guile/rework-hard-dependence-on-github.gmi new file mode 100644 index 0000000..751e9fe --- /dev/null +++ b/issues/gn-guile/rework-hard-dependence-on-github.gmi @@ -0,0 +1,21 @@ +# Rework Hard Dependence on Github + +## Tags + +* status: open +* priority: medium +* type: bug +* assigned: alexm +* assigned: bonfacem +* assigned: fredm +* keywords: gn-guile, github + +## Description + +Currently, we have a hard-dependence on Github for our source repository — you can see this in lines 31, 41, 55 and 59 of the code linked below: + +=> https://git.genenetwork.org/gn-guile/tree/web/view/markdown.scm?id=0ebf6926db0c69e4c444a6f95907e0971ae9bf40 + +The most likely reason is that the "edit online" functionality might not exist in a lot of other popular source forges. + +This is rendered moot, however, since we do provide a means to edit the data on Genenetwork itself. We might as well get rid of this option, and only allow the "edit online" feature on Genenetwork and stop relying on its presence in the forges we use. diff --git a/issues/production-container-mechanical-rob-failure.gmi b/issues/production-container-mechanical-rob-failure.gmi new file mode 100644 index 0000000..a32194e --- /dev/null +++ b/issues/production-container-mechanical-rob-failure.gmi @@ -0,0 +1,224 @@ +# 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. + +Note Pjotr: this is likely a mariadb bug with 10.5.23, the most recent mariadbd we use (both tux01 and tux02 are older). The dump shows it balks on creating a new thread: pthread_create.c:478. Looks similar to https://jira.mariadb.org/browse/MDEV-32262 + +10.5, 10.6, 10.11 are affected. so running correlations on production crashes mysqld? I am not trying for obvious reasons ;) the threading issues of mariadb look scary - I wonder how deep it goes. + +We'll test for a different version of mariadb combining a Debian update because Debian on tux04 is broken. diff --git a/issues/systems/penguin2-raid5.gmi b/issues/systems/penguin2-raid5.gmi new file mode 100644 index 0000000..f03075d --- /dev/null +++ b/issues/systems/penguin2-raid5.gmi @@ -0,0 +1,61 @@ +# Penguin2 RAID 5 + +# Tags + +* assigned: @fredm, @pjotrp +* status: in progress + +# Description + +The current RAID contains 3 disks: + +``` +root@penguin2:~# cat /proc/mdstat +md0 : active raid5 sdb1[1] sda1[0] sdg1[4] +/dev/md0 33T 27T 4.2T 87% /export +``` + +using /dev/sda,sdb,sdg + +The current root and swap is on + +``` +# root +/dev/sdd1 393G 121G 252G 33% / +# swap +/dev/sdd5 partition 976M 76.5M -2 +``` + +We can therefore add four new disks in slots /dev/sdc,sde,sdf,sdh + +penguin2 has no out-of-band and no serial connector right now. That means any work needs to be done on the terminal. + +Boot loader menu: + +``` +menuentry 'Debian GNU/Linux' --class debian --class gnu-linux --class gnu --class os $menuentry_id_option 'gnulinux-simple-7ff268df-cb90-4cbc-9d76-7fd6677b4964' { + load_video + insmod gzio + if [ x$grub_platform = xxen ]; then insmod xzio; insmod lzopio; fi + insmod part_msdos + insmod ext2 + set root='hd2,msdos1' + if [ x$feature_platform_search_hint = xy ]; then + search --no-floppy --fs-uuid --set=root --hint-bios=hd2,msdos1 --hint-efi=hd2,msdos1 --hint-baremetal=ahci2,msdos1 7ff268df-cb90-4cbc-9d76-7fd6677b4964 + else + search --no-floppy --fs-uuid --set=root 7ff268df-cb90-4cbc-9d76-7fd6677b4964 + fi + echo 'Loading Linux 5.10.0-18-amd64 ...' + linux /boot/vmlinuz-5.10.0-18-amd64 root=UUID=7ff268df-cb90-4cbc-9d76-7fd6677b4964 ro quiet + echo 'Loading initial ramdisk ...' + initrd /boot/initrd.img-5.10.0-18-amd64 +} +``` + +Added to sdd MBR + +``` +root@penguin2:~# grub-install /dev/sdd +Installing for i386-pc platform. +Installation finished. No error reported. +``` diff --git a/issues/systems/tux04-production.gmi b/issues/systems/tux04-production.gmi new file mode 100644 index 0000000..01e1638 --- /dev/null +++ b/issues/systems/tux04-production.gmi @@ -0,0 +1,275 @@ +# Production on tux04 + +Lately we have been running production on tux04. Unfortunately Debian got broken and I don't see a way to fix it (something with python versions that break apt!). Also mariadb is giving problems: + +=> issues/production-container-mechanical-rob-failure.gmi + +and that is alarming. We might as well try an upgrade. I created a new partition on /dev/sda4 using debootstrap. + +Luckily not too much is running on this machine and if we mount things again, most should work. + +# Tasks + +* [X] cleanly shut down mariadb +* [X] reboot into new partition /dev/sda4 +* [X] git in /etc +* [X] make sure serial boot works (/etc/default/grub) +* [X] fix groups and users +* [X] get guix going +* [X] get mariadb going +* [X] fire up GN2 service +* [X] fire up SPARQL service +* [X] sheepdog +* [ ] fix CRON jobs and backups +* [ ] test full reboots + + +# Boot in new partition + +``` +blkid /dev/sda4 +/dev/sda4: UUID="4aca24fe-3ece-485c-b04b-e2451e226bf7" BLOCK_SIZE="4096" TYPE="ext4" PARTUUID="2e3d569f-6024-46ea-8ef6-15b26725f811" +``` + +After debootstrap there are two things to take care of: the /dev directory and grub. For good measure +I also capture some state + +``` +cd ~ +ps xau > cron.log +systemctl > systemctl.txt +cp /etc/network/interfaces . +cp /boot/grub/grub.cfg . +``` + +we should still have access to the old root partition, so I don't need to capture everything. + +## /dev + +I ran MAKEDEV and that may not be needed with udev. + +## grub + +We need to tell grub to boot into the new partition. The old root is on +UUID=8e874576-a167-4fa1-948f-2031e8c3809f /dev/sda2. + +Next I ran + +``` +tux04:~$ update-grub2 /dev/sda +Generating grub configuration file ... +Found linux image: /boot/vmlinuz-5.10.0-32-amd64 +Found initrd image: /boot/initrd.img-5.10.0-32-amd64 +Found linux image: /boot/vmlinuz-5.10.0-22-amd64 +Found initrd image: /boot/initrd.img-5.10.0-22-amd64 +Warning: os-prober will be executed to detect other bootable partitions. +Its output will be used to detect bootable binaries on them and create new boot entries. +Found Debian GNU/Linux 12 (bookworm) on /dev/sda4 +Found Windows Boot Manager on /dev/sdd1@/efi/Microsoft/Boot/bootmgfw.efi +Found Debian GNU/Linux 11 (bullseye) on /dev/sdf2 +``` + +Very good. Do a diff on grub.cfg and you see it even picked up the serial configuration. It only shows it added menu entries for the new boot. Very nice. + +At this point I feel safe to boot as we should be able to get back into the old partition. + +# /etc/fstab + +The old fstab looked like + +``` +UUID=8e874576-a167-4fa1-948f-2031e8c3809f / ext4 errors=remount-ro 0 1 +# /boot/efi was on /dev/sdc1 during installation +UUID=998E-68AF /boot/efi vfat umask=0077 0 1 +# swap was on /dev/sdc3 during installation +UUID=cbfcd84e-73f8-4cec-98ee-40cad404735f none swap sw 0 0 +UUID="783e3bd6-5610-47be-be82-ac92fdd8c8b8" /export2 ext4 auto 0 2 +UUID="9e6a9d88-66e7-4a2e-a12c-f80705c16f4f" /export ext4 auto 0 2 +UUID="f006dd4a-2365-454d-a3a2-9a42518d6286" /export3 auto auto 0 2 +/export2/gnu /gnu none defaults,bind 0 0 +# /dev/sdd1: PARTLABEL="bulk" PARTUUID="b1a820fe-cb1f-425e-b984-914ee648097e" +# /dev/sdb4 /export ext4 auto 0 2 +# /dev/sdd1 /export2 ext4 auto 0 2 +``` + +# reboot + +Next we are going to reboot, and we need a serial connector to the Dell out-of-band using racadm: + +``` +ssh IP +console com2 +racadm getsel +racadm serveraction powercycle +racadm serveraction powerstatus + +``` + +Main trick it so hit ESC, wait 2 sec and 2 when you want the bios boot menu. Ctrl-\ to escape console. Otherwise ESC (wait) ! to get to the boot menu. + +# First boot + +It still boots by default into the old root. That gave an error: + +[FAILED] Failed to start File Syste…a-2365-454d-a3a2-9a42518d6286 + +This is /export3. We can fix that later. + +When I booted into the proper partition the console clapped out. Also the racadm password did not work on tmux -- I had to switch to a standard console to log in again. Not sure why that is, but next I got: + +``` +Give root password for maintenance +(or press Control-D to continue): +``` + +and giving the root password I was in maintenance mode on the correct partition! + +To rerun grup I had to add `GRUB_DISABLE_OS_PROBER=false`. + +Once booting up it is a matter of mounting partitions and tick the check boxes above. + +The following contained errors: + +``` +/dev/sdd1 3.6T 1.8T 1.7T 52% /export2 +``` + +# Guix + +Getting guix going is a bit tricky because we want to keep the store! + +``` +cp -vau /mnt/old-root/var/guix/ /var/ +cp -vau /mnt/old-root/usr/local/guix-profiles /usr/local/ +cp -vau /mnt/old-root/usr/local/bin/* /usr/local/bin/ +cp -vau /mnt/old-root/etc/systemd/system/guix-daemon.service* /etc/systemd/system/ +cp -vau /mnt/old-root/etc/systemd/system/gnu-store.mount* /etc/systemd/system/ +``` + +Also had to add guixbuild users and group by hand. + +# nginx + +We use the streaming facility. Check that + +``` +nginx -V +``` + +lists --with-stream=static, see + +=> https://serverfault.com/questions/858067/unknown-directive-stream-in-etc-nginx-nginx-conf86/858074#858074 + +and load at the start of nginx.conf: + +``` +load_module /usr/lib/nginx/modules/ngx_stream_module.so; +``` + +and + +``` +nginx -t +``` + +passes + +Now the container responds to the browser with `Internal Server Error`. + +# container web server + +Visit the container with something like + +``` +nsenter -at 2838 /run/current-system/profile/bin/bash --login +``` + +The nginx log in the container has many + +``` +2025/02/22 17:23:48 [error] 136#0: *166916 connect() failed (111: Connection refused) while connecting to upstream, client: 127.0.0.1, server: genenetwork.org, request: "GET /gn3/gene/aliases/st%2029:1;o;s HTTP/1.1", upstream: "http://127.0.0.1:9800/gene/aliases/st%2029:1;o;s", host: "genenetwork.org" +``` + +that is interesting. Acme/https is working because GN2 is working: + +``` +curl https://genenetwork.org/api3/version +"1.0" +``` + +Looking at the logs it appears it is a redis problem first for GN2. + +Fred builds the container with `/home/fredm/opt/guix-production/bin/guix`. Machines are defined in + +``` +fredm@tux04:/export3/local/home/fredm/gn-machines +``` + +The shared dir for redis is at + +--share=/export2/guix-containers/genenetwork/var/lib/redis=/var/lib/redis + +with + +``` +root@genenetwork-production /var# ls lib/redis/ -l +-rw-r--r-- 1 redis redis 629328484 Feb 22 17:25 dump.rdb +``` + +In production.scm it is defined as + +``` +(service redis-service-type + (redis-configuration + (bind "127.0.0.1") + (port 6379) + (working-directory "/var/lib/redis"))) +``` + +The defaults are the same as the definition of redis-service-type (in guix). Not sure why we are duplicating. + +After starting redis by hand I get another error `500 DatabaseError: The following exception was raised while attempting to access http://auth.genenetwork.org/auth/data/authorisation: database disk image is malformed`. The problem is it created +a DB in the wrong place. Alright, the logs in the container say: + +``` +Feb 23 14:04:31 genenetwork-production shepherd[1]: [redis-server] 3977:C 23 Feb 2025 14:04:31.040 # oO0OoO0OoO0Oo Redis is starting oO0OoO0OoO0Oo +Feb 23 14:04:31 genenetwork-production shepherd[1]: [redis-server] 3977:C 23 Feb 2025 14:04:31.040 # Redis version=7.0.12, bits=64, commit=00000000, modified=0, pid=3977, just started +Feb 23 14:04:31 genenetwork-production shepherd[1]: [redis-server] 3977:C 23 Feb 2025 14:04:31.040 # Configuration loaded +Feb 23 14:04:31 genenetwork-production shepherd[1]: [redis-server] 3977:M 23 Feb 2025 14:04:31.041 * Increased maximum number of open files to 10032 (it was originally set to 1024). +Feb 23 14:04:31 genenetwork-production shepherd[1]: [redis-server] 3977:M 23 Feb 2025 14:04:31.041 * monotonic clock: POSIX clock_gettime +Feb 23 14:04:31 genenetwork-production shepherd[1]: [redis-server] 3977:M 23 Feb 2025 14:04:31.041 * Running mode=standalone, port=6379. +Feb 23 14:04:31 genenetwork-production shepherd[1]: [redis-server] 3977:M 23 Feb 2025 14:04:31.042 # Server initialized +Feb 23 14:04:31 genenetwork-production shepherd[1]: [redis-server] 3977:M 23 Feb 2025 14:04:31.042 # WARNING Memory overcommit must be enabled! Without it, a background save or replication may fail under low memory condition. To fix this issue add 'vm.overcommit_memory = 1' to /etc/sysctl.conf and then reboot or run the command 'sysctl vm.overcommit_memory=1' for this to take effect. +Feb 23 14:04:31 genenetwork-production shepherd[1]: [redis-server] 3977:M 23 Feb 2025 14:04:31.042 # Wrong signature trying to load DB from file +Feb 23 14:04:31 genenetwork-production shepherd[1]: [redis-server] 3977:M 23 Feb 2025 14:04:31.042 # Fatal error loading the DB: Invalid argument. Exiting. +Feb 23 14:04:31 genenetwork-production shepherd[1]: Service redis (PID 3977) exited with 1. +``` + +This is caused by a newer version of redis. This is odd because we are using the same version from the container?! + +Actually it turned out the redis DB was corrupted on the SSD! Same for some other databases (ugh). + +Fred copied all data to an enterprise level storage, and we rolled back to some older DBs, so hopefully we'll be OK for now. + +# Reinstating backups + +In the next step we need to restore backups as described in + +=> /topics/systems/backups-with-borg + +I already created an ibackup user. Next we test the backup script for mariadb. + +One important step is to check the database: + +``` +/usr/bin/mariadb-check -c -u user -p* db_webqtl +``` + +A successful mariadb backup consists of multiple steps + +``` +2025-02-27 11:48:28 +0000 (ibackup@tux04) SUCCESS 0 <32m43s> mariabackup-dump +2025-02-27 11:48:29 +0000 (ibackup@tux04) SUCCESS 0 <00m00s> mariabackup-make-consistent +2025-02-27 12:16:37 +0000 (ibackup@tux04) SUCCESS 0 <28m08s> borg-tux04-sql-backup +2025-02-27 12:16:46 +0000 (ibackup@tux04) SUCCESS 0 <00m07s> drop-rsync-balg01 +``` |