Description:
Hi,
I tried to refresh opened files under mysqld on our linux server and found mysqladmin does not return back to the shell. I found the following was running on the server:
bioadmin@bontebok$ mysqladmin -hjerboas processlist
+-------+-----------+----------------------+----------------------------------+---------+------+----------------------+------------------------------------------------------------------------------------------------------+
| Id | User | Host | db | Command | Time | State | Info |
+-------+-----------+----------------------+----------------------------------+---------+------+----------------------+------------------------------------------------------------------------------------------------------+
| 36284 | guelden | bongo.gsf.de:4001 | Fusarium_graminearum | Sleep | 96 | | |
| 36308 | wwwpedant | grysbok.gsf.de:4071 | Saccharomyces_servazzii_CBS_4311 | Query | 8560 | statistics | explain SELECT rep.code FROM SC_orf, Upd, blast, blastindex, blastn_GeneticElement, blastx, blastx_S |
| 36836 | wwwpedant | nyala.gsf.de:2477 | Saccharomyces_servazzii_CBS_4311 | Sleep | 3557 | | |
| 36954 | wwwpedant | grysbok.gsf.de:4404 | Magnaporthe_grisea | Query | 2912 | Copying to tmp table | SELECT rep.code FROM blast_Scerevisiae, cogs, ecnum, funcat, interpro, orf, pfam, pirkw, pros, prot_ |
| 37351 | pedant | bontebok.gsf.de:1880 | | Refresh | 322 | Flushing tables | |
| 37423 | pedant | bontebok.gsf.de:1911 | | Query | 0 | | show processlist |
+-------+-----------+----------------------+----------------------------------+---------+------+----------------------+------------------------------------------------------------------------------------------------------+
bioadmin@bontebok$ mysqladmin: refresh failed; error: 'Lost connection to MySQL server during query'
bioadmin@bontebok$
The connection was lost after cca. 80 seconds, if that matters.
The crash dump says:
0x80702cb handle_segfault + 447
0x8282488 pthread_sighandler + 184
0x8283a23 __pthread_unlock + 147
0x8280ca4 pthread_mutex_unlock + 164
0x827ed89 pthread_cond_wait + 345
0x808de79 wait_for_tables__FP3THD + 53
0x806ca29 mysql_lock_tables__FP3THDPP8st_tableUi + 329
0x808e53c open_ltable__FP3THDP13st_table_list13thr_lock_type + 184
0x80d7c44 mysqld_extend_show_tables__FP3THDPCcT1 + 2392
0x807c6f6 mysql_execute_command__Fv + 9282
0x807e166 mysql_parse__FP3THDPcUi + 146
0x80797ad dispatch_command__F19enum_server_commandP3THDPcUi + 1461
0x80791ed do_command__FP3THD + 149
0x8078a0f handle_one_connection + 631
0x827fc3c pthread_start_thread + 220
0x82b53fa thread_start + 4
thd->query at 0x112e9328 = show table status
thd->thread_id=36284
I see some other crashes in the error log file:
0x80702cb handle_segfault + 447
0x8282488 pthread_sighandler + 184
0x8283a23 __pthread_unlock + 147
0x8280ca4 pthread_mutex_unlock + 164
0x827ed89 pthread_cond_wait + 345
0x80d028f safe_remove_from_cache__FP3THDP8st_table + 79
0x80d1636 mysql_alter_table__FP3THDPcT1P24st_ha_create_informationP13st_table_listRt4List1Z12create_fieldRt4List1Z3KeyRt4List1Z10Alter_dr + 838
0x807b487 mysql_execute_command__Fv + 4563
0x807e166 mysql_parse__FP3THDPcUi + 146
0x80797ad dispatch_command__F19enum_server_commandP3THDPcUi + 1461
0x80791ed do_command__FP3THD + 149
0x8078a0f handle_one_connection + 631
0x827fc3c pthread_start_thread + 220
0x82b53fa thread_start + 4
thd->query at 0x15db6a58 = /*!40000 ALTER TABLE blast ENABLE KEYS */
thd->thread_id=85798
--------------------
0x80702cb handle_segfault + 447
0x8282488 pthread_sighandler + 184
0x8283a23 __pthread_unlock + 147
0x8280ca4 pthread_mutex_unlock + 164
0x827ed89 pthread_cond_wait + 345
0x808de79 wait_for_tables__FP3THD + 53
0x806ca29 mysql_lock_tables__FP3THDPP8st_tableUi + 329
0x808e60c lock_tables__FP3THDP13st_table_list + 108
0x808e589 open_and_lock_tables__FP3THDP13st_table_list + 41
0x807a62b mysql_execute_command__Fv + 887
0x807e166 mysql_parse__FP3THDPcUi + 146
0x80797ad dispatch_command__F19enum_server_commandP3THDPcUi + 1461
0x80791ed do_command__FP3THD + 149
0x8078a0f handle_one_connection + 631
0x827fc3c pthread_start_thread + 220
0x82b53fa thread_start + 4
thd->query at 0x14dcee30 = select manual from blast where prot_data_id=1789
thd->thread_id=55201
---------------------
0x80702cb handle_segfault + 447
0x8282488 pthread_sighandler + 184
0x8283a23 __pthread_unlock + 147
0x8280ca4 pthread_mutex_unlock + 164
0x827ed89 pthread_cond_wait + 345
0x80d028f safe_remove_from_cache__FP3THDP8st_table + 79
0x80d1636 mysql_alter_table__FP3THDPcT1P24st_ha_create_informationP13st_table_listRt4List1Z12create_fieldRt4List1Z3KeyRt4List1Z10Alter_dr + 838
0x807b487 mysql_execute_command__Fv + 4563
0x807e166 mysql_parse__FP3THDPcUi + 146
0x80797ad dispatch_command__F19enum_server_commandP3THDPcUi + 1461
0x80791ed do_command__FP3THD + 149
0x8078a0f handle_one_connection + 631
0x827fc3c pthread_start_thread + 220
0x82b53fa thread_start + 4
thd->query at 0x84f9f98 = /*!40000 ALTER TABLE known3d ENABLE KEYS */
thd->thread_id=8
--------------------
0x80702cb handle_segfault + 447
0x8282488 pthread_sighandler + 184
0x82493d4 decode_bytes + 148
0x8249277 uf_blob + 171
0x8248787 _mi_pack_rec_unpack + 91
0x8255ff8 chk_data_link + 2880
0x80c3e2d check__9ha_myisamP3THDP15st_ha_check_opt + 597
0x80d0e75 mysql_admin_table__FP3THDP13st_table_listP15st_ha_check_optPCc13thr_lock_typebUiPFP3THDP13st_table_listP15st_ha_check_opt_iPM7h + 1537
0x80d12e5 mysql_check_table__FP3THDP13st_table_listP15st_ha_check_opt + 69
0x807b7b2 mysql_execute_command__Fv + 5374
0x807e166 mysql_parse__FP3THDPcUi + 146
0x80797ad dispatch_command__F19enum_server_commandP3THDPcUi + 1461
0x80791ed do_command__FP3THD + 149
0x8078a0f handle_one_connection + 631
0x827fc3c pthread_start_thread + 220
0x82b53fa thread_start + 4
thd->query at 0x910b478 = check table contig_data
thd->thread_id=157589
How to repeat:
Hmm, maybe one can reproduce the first crash with "refresh", the others do reappear time to time, but not reproducibly. We use oficial binaries.
