Hi Wissam,
I think that killing the longer request will unlock the situation ("kill
171175" in mysql command line).
It looks like a loop in a stored procedure that occured in early
robinhood 2.5's.
I suggest you upgrade to the latest release (2.5.5).
Regards,
Thomas
12/07/2015 08:04, Wissam Ali wrote:
Hi Thomas,
Here are the outputs requested. The first output is when rbh-find is
running and the second one when it gets stuck or to be more precise it
is not generating any output any more.
Command executed: nohup rbh-find -f /etc/robinhood.d/tmpfs/lustre.conf
-type f -atime +90d -ls > purge_list.txt &
A)
[root@hpc1 ~]# gstack 441
#0 0x0000003df340e4ed in read () from /lib64/libpthread.so.0
#1 0x00007f007e3208d9 in vio_read_buff () from
/opt/rocks/lib/mysql/libmysqlclient_r.so.16
#2 0x00007f007e3219ef in my_real_read () from
/opt/rocks/lib/mysql/libmysqlclient_r.so.16
#3 0x00007f007e321de5 in my_net_read () from
/opt/rocks/lib/mysql/libmysqlclient_r.so.16
#4 0x00007f007e31c2da in cli_safe_read () from
/opt/rocks/lib/mysql/libmysqlclient_r.so.16
#5 0x00007f007e31caa9 in cli_read_query_result () from
/opt/rocks/lib/mysql/libmysqlclient_r.so.16
#6 0x00007f007e31aefc in mysql_real_query () from
/opt/rocks/lib/mysql/libmysqlclient_r.so.16
#7 0x000000000044844d in _db_exec_sql ()
#8 0x000000000043c864 in listmgr_get_by_pk ()
#9 0x000000000044246f in ListMgr_GetNext ()
#10 0x000000000040aa19 in list_bulk ()
#11 0x000000000040c1fa in main ()
mysql> show processlist;
+------+-----------+------------------+------------------+---------+--------+--------------+------------------------------------------------------------------------------------------------------+
| Id | User | Host | db | Command |
Time | State | Info |
+------+-----------+------------------+------------------+---------+--------+--------------+------------------------------------------------------------------------------------------------------+
| 1116 | slurm | hpc1.local:59434 | slurm_acct_db | Sleep |
2006 | | NULL |
| 1119 | slurm | hpc1.local:33625 | slurm_acct_db | Sleep |
220 | | NULL |
| 1732 | robinhood | localhost | robinhood_lustre | Query |
171175 | NULL | SELECT CONCAT( n, '/', p) INTO p
|
| 1778 | robinhood | localhost | robinhood_lustre | Query |
87611 | NULL | SELECT parent_id, name INTO pid, n from NAMES
where id= NAME_CONST('pid',_latin1'DAB1E06F:2218003E' |
| 1781 | robinhood | localhost | robinhood_lustre | Query |
86300 | NULL | SELECT parent_id, name INTO pid, n from NAMES
where id= NAME_CONST('pid',_latin1'DAB1E06F:22180001' |
| 1799 | robinhood | localhost | robinhood_lustre | Query |
85521 | Sending data | SELECT parent_id, name INTO pid, n from NAMES
where id= NAME_CONST('pid',_latin1'DAB1E06F:22180001' |
| 1802 | robinhood | localhost | robinhood_lustre | Query |
85250 | NULL | SELECT CONCAT( n, '/', p) INTO p
|
| 1844 | robinhood | localhost | robinhood_lustre | Query |
0 | init | SELECT
owner,gr_name,size,last_access,last_mod,type,mode,nlink,link,this_path(parent_id,name)
FROM E |
| 1849 | root | localhost | NULL | Query |
0 | NULL | show processlist |
+------+-----------+------------------+------------------+---------+--------+--------------+------------------------------------------------------------------------------------------------------+
9 rows in set (0.01 sec)
B)
[root@hpc1 ~]# gstack 441
#0 0x0000003df340e4ed in read () from /lib64/libpthread.so.0
#1 0x00007f007e3208d9 in vio_read_buff () from
/opt/rocks/lib/mysql/libmysqlclient_r.so.16
#2 0x00007f007e3219ef in my_real_read () from
/opt/rocks/lib/mysql/libmysqlclient_r.so.16
#3 0x00007f007e321de5 in my_net_read () from
/opt/rocks/lib/mysql/libmysqlclient_r.so.16
#4 0x00007f007e31c2da in cli_safe_read () from
/opt/rocks/lib/mysql/libmysqlclient_r.so.16
#5 0x00007f007e31caa9 in cli_read_query_result () from
/opt/rocks/lib/mysql/libmysqlclient_r.so.16
#6 0x00007f007e31aefc in mysql_real_query () from
/opt/rocks/lib/mysql/libmysqlclient_r.so.16
#7 0x000000000044844d in _db_exec_sql ()
#8 0x000000000043c864 in listmgr_get_by_pk ()
#9 0x000000000044246f in ListMgr_GetNext ()
#10 0x000000000040aa19 in list_bulk ()
#11 0x000000000040c1fa in main ()
mysql> show processlist;
+------+-----------+------------------+------------------+---------+--------+--------------+------------------------------------------------------------------------------------------------------+
| Id | User | Host | db | Command |
Time | State | Info |
+------+-----------+------------------+------------------+---------+--------+--------------+------------------------------------------------------------------------------------------------------+
| 1116 | slurm | hpc1.local:59434 | slurm_acct_db | Sleep |
2169 | | NULL |
| 1119 | slurm | hpc1.local:33625 | slurm_acct_db | Sleep |
82 | | NULL |
| 1732 | robinhood | localhost | robinhood_lustre | Query |
171338 | statistics | SELECT parent_id, name INTO pid, n from NAMES
where id= NAME_CONST('pid',_latin1'DAB1E06F:22180001' |
| 1778 | robinhood | localhost | robinhood_lustre | Query |
87774 | statistics | SELECT parent_id, name INTO pid, n from NAMES
where id= NAME_CONST('pid',_latin1'DAB1E06F:2218003E' |
| 1781 | robinhood | localhost | robinhood_lustre | Query |
86463 | Sending data | SELECT parent_id, name INTO pid, n from NAMES
where id= NAME_CONST('pid',_latin1'DAB1E06F:2218003E' |
| 1799 | robinhood | localhost | robinhood_lustre | Query |
85684 | Sending data | SELECT parent_id, name INTO pid, n from NAMES
where id= NAME_CONST('pid',_latin1'DAB1E06F:2218003E' |
| 1802 | robinhood | localhost | robinhood_lustre | Query |
85413 | Sending data | SELECT parent_id, name INTO pid, n from NAMES
where id= NAME_CONST('pid',_latin1'DAB1E06F:22180001' |
| 1844 | robinhood | localhost | robinhood_lustre | Query |
140 | Sending data | SELECT parent_id, name INTO pid, n from NAMES
where id= NAME_CONST('pid',_latin1'DAB1E06F:2218003E' |
| 1851 | root | localhost | NULL | Query |
0 | NULL | show processlist |
+------+-----------+------------------+------------------+---------+--------+--------------+------------------------------------------------------------------------------------------------------+
9 rows in set (0.00 sec)
mysql> show processlist;
+------+-----------+------------------+------------------+---------+--------+------------+------------------------------------------------------------------------------------------------------+
| Id | User | Host | db | Command | Time |
State | Info |
+------+-----------+------------------+------------------+---------+--------+------------+------------------------------------------------------------------------------------------------------+
| 1116 | slurm | hpc1.local:59434 | slurm_acct_db | Sleep |
2537 | | NULL |
| 1119 | slurm | hpc1.local:33625 | slurm_acct_db | Sleep |
151 | | NULL |
| 1732 | robinhood | localhost | robinhood_lustre | Query |
171706 | NULL | SELECT CONCAT( n, '/', p) INTO p
|
| 1778 | robinhood | localhost | robinhood_lustre | Query |
88142 | init | SELECT parent_id, name INTO pid, n from NAMES
where id= NAME_CONST('pid',_latin1'DAB1E06F:2218003E' |
| 1781 | robinhood | localhost | robinhood_lustre | Query |
86831 | NULL | SELECT CONCAT( n, '/', p) INTO p
|
| 1799 | robinhood | localhost | robinhood_lustre | Query |
86052 | NULL | SELECT parent_id, name INTO pid, n from NAMES
where id= NAME_CONST('pid',_latin1'DAB1E06F:22180001' |
| 1802 | robinhood | localhost | robinhood_lustre | Query |
85781 | NULL | SELECT CONCAT( n, '/', p) INTO p
|
| 1844 | robinhood | localhost | robinhood_lustre | Query |
508 | statistics | SELECT parent_id, name INTO pid, n from NAMES
where id= NAME_CONST('pid',_latin1'DAB1E06F:22180001' |
| 1854 | root | localhost | NULL | Query | 0 |
NULL | show processlist |
+------+-----------+------------------+------------------+---------+--------+------------+------------------------------------------------------------------------------------------------------+
9 rows in set (0.00 sec)
Cheers,
Wissam
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