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2003 Apr 24 09:25

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Re: [vox-tech] Need your help in recovering database.
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Re: [vox-tech] Need your help in recovering database.



Thank you All,

Thankyou very much for your cooperation. I doubt if I
am able to present you properly.

Replying to Tim:-
> > Didn't find any fields in table 'blast_genescan'

> Does "describe blast_genescan;" return the correct
> columns? If so, maybe the perl script needs a       
              
> closer look.

> >
> > This for all the tables.

> Do you mean that "describe table2;", "describe      
> table3;", and "describe table4;" all return no     >
columns?

This is after the command "use Entamoeba".

After searching the solution in
"http://www.innodb.com/ibman.html";
I could get I must have specified "max" size. I've
specified the max size along with some server
variables viz. 
set-variable = key_buffer=256M
set-variable = max_allowed_pack = 40M
...
set-variable = myisam_sort_buffer_size = 64M
set-variable = thread_cache = 8
set-variable = thread_concurrency = 4
...
innodb_data_file_path =
/ibdata/ibdata1:100M:autoextend:max:2000M

But then I could once get into the database
i.e. by command "use Entamoeba"
It flushed nothing only "database changed"
As I tried to select the rows from one of the four
tables it flushed
"Didn't find any fields in table 'blast_genescan'"
and was same for all other tables.

But after that I cant start server anymore its showing
error:
ERROR 2002: Can't connect to local MySQL server
through socket '/var/lib/mysql/mysql.sock' (2)

Replying to Jeff:-
> The fact that this exceeds 2GB is certainly         
   > suspicious.  There is a warning in the InnoDB    
 > documentation [1] to beware of OS filesize
> limitations. They don't seem to be specific about  >
the consequences, but I would not be surprised if  >
the file was corrupt by now.  I suspect that
> using multiple data files rather than the          >
autoextend option will be necessary if you are     >
dealing with large databases.

How would I do this if I have to rebuild the database.

> There are kernel patches (options by now?) that    >
support large file sizes, but they require          

But mine is 32 bit processor could I reconfigure the
kernel for 64-bit

> some cooperation on the part of the application    >
(mysql compile options) before they will take      >
effect.
How would I do this?

Is there any way I can recover or take back up of the
database "Entamoeba".

Replying to Tim again:-
> What is the output to "tail /var/log/myysqld.log"?

I am sending the content of mysqld.log file bellow
(after deleting the redundency):

Date in my system is wrong(Wed May  7 13:40:03 IST
2003)

030501 11:31:36  mysqld started
030501 11:31:38  Can't start server: Bind on TCP/IP
port: Address already in use
030501 11:31:38  Do you already have another mysqld
server running on port: 3306 ?
030501 11:31:38  Aborting

030501 11:31:38  /usr/local/mysql/bin/mysqld: Shutdown
Complete

030501 11:31:38  mysqld ended

030501 19:55:58  mysqld started
030501 19:56:03  InnoDB: Database was not shut down
normally.
InnoDB: Starting recovery from log files...
InnoDB: Starting log scan based on checkpoint at
InnoDB: log sequence number 0 3373779155
InnoDB: Doing recovery: scanned up to log sequence
number 0 3373779155
030501 19:56:04  InnoDB: Flushing modified pages from
the buffer pool...
030501 19:56:04  InnoDB: Started
/usr/local/mysql/bin/mysqld: ready for connections
030501 23:50:12  /usr/local/mysql/bin/mysqld: Normal
shutdown

030501 23:50:12  InnoDB: Starting shutdown...
030501 23:50:16  InnoDB: Shutdown completed
030501 23:50:16  /usr/local/mysql/bin/mysqld: Shutdown
Complete

030501 23:50:19  mysqld ended

030504 01:11:08  mysqld started
InnoDB: The first specified data file ./ibdata1 did
not exist:
InnoDB: a new database to be created!
030504  1:11:15  InnoDB: Setting file ./ibdata1 size
to 10 MB
InnoDB: Database physically writes the file full:
wait...
030504  1:11:20  InnoDB: Log file ./ib_logfile0 did
not exist: new to be created
InnoDB: Setting log file ./ib_logfile0 size to 20 MB
InnoDB: Database physically writes the file full:
wait...
030504  1:11:29  InnoDB: Log file ./ib_logfile1 did
not exist: new to be created
InnoDB: Setting log file ./ib_logfile1 size to 20 MB
InnoDB: Database physically writes the file full:
wait...
InnoDB: Doublewrite buffer not found: creating new
InnoDB: Doublewrite buffer created
InnoDB: Creating foreign key constraint system tables
InnoDB: Foreign key constraint system tables created
030504  1:11:42  InnoDB: Started
/usr/local/mysql/bin/mysqld: ready for connections
030504  1:12:28  InnoDB error:
Cannot find table Entamoeba/blast_genescan from the
internal data dictionary
of InnoDB though the .frm file for the table exists.
Maybe you
have deleted and recreated InnoDB data files but have
forgotten
to delete the corresponding .frm files of InnoDB
tables, or you
have moved .frm files to another database?
Look from section 15.1 of
http://www.innodb.com/ibman.html
how you can resolve the problem.

030504  1:12:28  InnoDB error:
Cannot find table Entamoeba/contig_detail from the
internal data dictionary
of InnoDB though the .frm file for the table exists.
Maybe you
have deleted and recreated InnoDB data files but have
forgotten
to delete the corresponding .frm files of InnoDB
tables, or you
have moved .frm files to another database?
Look from section 15.1 of
http://www.innodb.com/ibman.html
how you can resolve the problem.

030504 02:52:05  mysqld started
/usr/local/mysql/bin/mysqld: unrecognized option
`--skip_locking'
/usr/local/mysql/bin/mysqld  Ver 3.23.53a-max for
pc-linux-gnu on i686
Copyright (C) 2000 MySQL AB, by Monty and others
This software comes with ABSOLUTELY NO WARRANTY. This
is free software,
and you are welcome to modify and redistribute it
under the GPL license
Starts the MySQL server

Usage: /usr/local/mysql/bin/mysqld [OPTIONS]

  --ansi		Use ANSI SQL syntax instead of MySQL syntax
  -b, --basedir=path	Path to installation directory.
All paths are
			usually resolved relative to this
  --big-tables		Allow big result sets by saving all
temporary sets
			on file (Solves most 'table full' errors)
  --bind-address=IP	Ip address to bind to
  --bootstrap		Used by mysql installation scripts
  --character-sets-dir=...
                        Directory where character sets
are
  --chroot=path		Chroot mysqld daemon during startup
  --core-file		Write core on errors
  -h, --datadir=path	Path to the database root
  --default-character-set=charset
			Set the default character set
  --default-table-type=type
			Set the default table type for tables
  --delay-key-write-for-all-tables
			Don't flush key buffers between writes for any
MyISAM
			table
  --enable-locking	Enable system locking
  -T, --exit-info	Used for debugging;  Use at your own
risk!
  --flush		Flush tables to disk between SQL commands
  -?, --help		Display this help and exit
  --init-file=file	Read SQL commands from this file at
startup
  -L, --language=...	Client error messages in given
language. May be
			given as a full path
  --local-infile=[1|0]  Enable/disable LOAD DATA LOCAL
INFILE
  -l, --log[=file]	Log connections and queries to file
  --log-bin[=file]      Log queries in new binary
format (for replication)
  --log-bin-index=file  File that holds the names for
last binary log files
  --log-update[=file]	Log updates to file.# where # is
a unique number
			if not given.
  --log-isam[=file]	Log all MyISAM changes to file
  --log-long-format	Log some extra information to
update log
  --low-priority-updates INSERT/DELETE/UPDATE has
lower priority than selects
  --log-slow-queries=[file]
			Log slow queries to this log file.  Defaults
logging
                        to hostname-slow.log
  --pid-file=path	Pid file used by safe_mysqld
  --myisam-recover[=option[,option...]] where options
is one of DEAULT,
			BACKUP or FORCE.
  --memlock		Lock mysqld in memory
  -n, --new		Use very new possible 'unsafe' functions
  -o, --old-protocol	Use the old (3.20) protocol
  -P, --port=...	Port number to use for connection

  -O, --set-variable var=option
			Give a variable an value. --help lists variables
  -Sg, --skip-grant-tables
			Start without grant tables. This gives all users
			FULL ACCESS to all tables!
  --safe-mode		Skip some optimize stages (for testing)
  --safe-show-database  Don't show databases for which
the user has no
                        privileges
  --safe-user-create	Don't new users cretaion without
privileges to the
		        mysql.user table
  --skip-concurrent-insert
		        Don't use concurrent insert with MyISAM
  --skip-delay-key-write
			Ignore the delay_key_write option for all tables
  --skip-host-cache	Don't cache host names
  --skip-locking	Don't use system locking. To use
isamchk one has
			to shut down the server.
  --skip-name-resolve	Don't resolve hostnames.
			All hostnames are IP's or 'localhost'
  --skip-networking	Don't allow connection with
TCP/IP.
  --skip-new		Don't use new, possible wrong routines.

  --skip-stack-trace    Don't print a stack trace on
failure
  --skip-show-database  Don't allow 'SHOW DATABASE'
commands
  --skip-thread-priority
			Don't give threads different priorities.
  --socket=...		Socket file to use for connection
  -t, --tmpdir=path	Path for temporary files
  --sql-mode=option[,option[,option...]] where option
can be one of:
                        REAL_AS_FLOAT,
PIPES_AS_CONCAT, ANSI_QUOTES,
                        IGNORE_SPACE, SERIALIZE,
ONLY_FULL_GROUP_BY.
  --transaction-isolation
		        Default transaction isolation level
  --temp-pool           Use a pool of temporary files
  -u, --user=user_name	Run mysqld daemon as user
  -V, --version		output version information and exit
  -W, --warnings        Log some not critical warnings
to the log file

  --innodb_data_home_dir=dir   The common part for
Innodb table spaces
  --innodb_data_file_path=dir  Path to individual
files and their sizes
  --innodb_flush_method=#  With which method to flush
data
  --innodb_flush_log_at_trx_commit[=#]
			  Value 0: write and flush once per second
                          Value 1: write and flush at
each commit
                          Value 2: write at commit,
flush once per second
  --innodb_log_arch_dir=dir    Where full logs should
be archived
  --innodb_log_archive[=#]     Set to 1 if you want to
have logs archived
  --innodb_log_group_home_dir=dir  Path to innodb log
files.
  --skip-innodb		       Don't use Innodb (will save
memory)


Default options are read from the following files in
the given order:
/etc/my.cnf /usr/local/mysql/var/my.cnf ~/.my.cnf
The following groups are read: mysqld server
The following options may be given as the first
argument:
--print-defaults	Print the program argument list and
exit
--no-defaults		Don't read default options from any
options file
--defaults-file=#	Only read default options from the
given file #
--defaults-extra-file=# Read this file after the
global files are read

To see what values a running MySQL server is using,
type
'mysqladmin variables' instead of 'mysqld --help'.
The default values (after parsing the command line
arguments) are:

basedir:    
/usr/local/mysql-max-3.23.53a-pc-linux-gnu-i686/
datadir:     /var/lib/mysql/
tmpdir:      /tmp/
language:   
/usr/local/mysql-max-3.23.53a-pc-linux-gnu-i686/share/mysql/english/
pid file:    /var/lib/mysql/localhost.pid
TCP port:    3306
Unix socket: /var/lib/mysql/mysql.sock

system locking is not in use

Possible variables for option --set-variable (-O) are:
back_log              current value: 50
binlog_cache_size     current value: 32768
connect_timeout       current value: 5
delayed_insert_timeout  current value: 300
delayed_insert_limit  current value: 100
delayed_queue_size    current value: 1000
flush_time            current value: 0
innodb_mirrored_log_groups  current value: 1
innodb_log_files_in_group  current value: 2
innodb_log_file_size  current value: 5242880
innodb_log_buffer_size  current value: 1048576
innodb_buffer_pool_size  current value: 8388608
innodb_additional_mem_pool_size  current value:
1048576
innodb_file_io_threads  current value: 4
innodb_lock_wait_timeout  current value: 50
innodb_thread_concurrency  current value: 8
innodb_force_recovery  current value: 0
interactive_timeout   current value: 28800
join_buffer_size      current value: 131072
key_buffer_size       current value: 8388600
long_query_time       current value: 10
lower_case_table_names  current value: 0
max_allowed_packet    current value: 1048576
max_binlog_cache_size  current value: 4294967295
max_binlog_size       current value: 1073741824
max_connections       current value: 100
max_connect_errors    current value: 10
max_delayed_threads   current value: 20
max_heap_table_size   current value: 16777216
max_join_size         current value: 4294967295
max_sort_length       current value: 1024
max_tmp_tables        current value: 32
max_user_connections  current value: 0
max_write_lock_count  current value: 4294967295
myisam_max_extra_sort_file_size  current value: 256
myisam_max_sort_file_size  current value: 2047
myisam_sort_buffer_size  current value: 8388608
net_buffer_length     current value: 16384
net_retry_count       current value: 10
net_read_timeout      current value: 30
net_write_timeout     current value: 60
open_files_limit      current value: 0
query_buffer_size     current value: 0
record_buffer         current value: 131072
record_rnd_buffer     current value: 0
slave_net_timeout     current value: 3600
slow_launch_time      current value: 2
sort_buffer           current value: 2097144
table_cache           current value: 64
thread_concurrency    current value: 10
thread_cache_size     current value: 0
tmp_table_size        current value: 33554432
thread_stack          current value: 65536
wait_timeout          current value: 28800
030504 02:52:05  mysqld ended

030504  5:08:42  /usr/local/mysql/bin/mysqld: Normal
shutdown

030504  5:08:43  InnoDB: Starting shutdown...
030504  5:08:44  InnoDB: Shutdown completed
030504  5:08:44  /usr/local/mysql/bin/mysqld: Shutdown
Complete

030504 05:08:44  mysqld ended


030506 13:00:39  mysqld started
/usr/local/mysql/bin/mysqld: unrecognized option
`--skip_locking'
/usr/local/mysql/bin/mysqld  Ver 3.23.53a-max for
pc-linux-gnu on i686
Copyright (C) 2000 MySQL AB, by Monty and others
This software comes with ABSOLUTELY NO WARRANTY. This
is free software,
and you are welcome to modify and redistribute it
under the GPL license
Starts the MySQL server

Usage: /usr/local/mysql/bin/mysqld [OPTIONS]

  --ansi		Use ANSI SQL syntax instead of MySQL syntax
  -b, --basedir=path	Path to installation directory.
All paths are
			usually resolved relative to this
  --big-tables		Allow big result sets by saving all
temporary sets
			on file (Solves most 'table full' errors)
  --bind-address=IP	Ip address to bind to
  --bootstrap		Used by mysql installation scripts
  --character-sets-dir=...
                        Directory where character sets
are
  --chroot=path		Chroot mysqld daemon during startup
  --core-file		Write core on errors
  -h, --datadir=path	Path to the database root
  --default-character-set=charset
			Set the default character set
  --default-table-type=type
			Set the default table type for tables
  --delay-key-write-for-all-tables
			Don't flush key buffers between writes for any
MyISAM
			table
  --enable-locking	Enable system locking
  -T, --exit-info	Used for debugging;  Use at your own
risk!
  --flush		Flush tables to disk between SQL commands
  -?, --help		Display this help and exit
  --init-file=file	Read SQL commands from this file at
startup
  -L, --language=...	Client error messages in given
language. May be
			given as a full path
  --local-infile=[1|0]  Enable/disable LOAD DATA LOCAL
INFILE
  -l, --log[=file]	Log connections and queries to file
  --log-bin[=file]      Log queries in new binary
format (for replication)
  --log-bin-index=file  File that holds the names for
last binary log files
  --log-update[=file]	Log updates to file.# where # is
a unique number
			if not given.
  --log-isam[=file]	Log all MyISAM changes to file
  --log-long-format	Log some extra information to
update log
  --low-priority-updates INSERT/DELETE/UPDATE has
lower priority than selects
  --log-slow-queries=[file]
			Log slow queries to this log file.  Defaults
logging
                        to hostname-slow.log
  --pid-file=path	Pid file used by safe_mysqld
  --myisam-recover[=option[,option...]] where options
is one of DEAULT,
			BACKUP or FORCE.
  --memlock		Lock mysqld in memory
  -n, --new		Use very new possible 'unsafe' functions
  -o, --old-protocol	Use the old (3.20) protocol
  -P, --port=...	Port number to use for connection

  -O, --set-variable var=option
			Give a variable an value. --help lists variables
  -Sg, --skip-grant-tables
			Start without grant tables. This gives all users
			FULL ACCESS to all tables!
  --safe-mode		Skip some optimize stages (for testing)
  --safe-show-database  Don't show databases for which
the user has no
                        privileges
  --safe-user-create	Don't new users cretaion without
privileges to the
		        mysql.user table
  --skip-concurrent-insert
		        Don't use concurrent insert with MyISAM
  --skip-delay-key-write
			Ignore the delay_key_write option for all tables
  --skip-host-cache	Don't cache host names
  --skip-locking	Don't use system locking. To use
isamchk one has
			to shut down the server.
  --skip-name-resolve	Don't resolve hostnames.
			All hostnames are IP's or 'localhost'
  --skip-networking	Don't allow connection with
TCP/IP.
  --skip-new		Don't use new, possible wrong routines.

  --skip-stack-trace    Don't print a stack trace on
failure
  --skip-show-database  Don't allow 'SHOW DATABASE'
commands
  --skip-thread-priority
			Don't give threads different priorities.
  --socket=...		Socket file to use for connection
  -t, --tmpdir=path	Path for temporary files
  --sql-mode=option[,option[,option...]] where option
can be one of:
                        REAL_AS_FLOAT,
PIPES_AS_CONCAT, ANSI_QUOTES,
                        IGNORE_SPACE, SERIALIZE,
ONLY_FULL_GROUP_BY.
  --transaction-isolation
		        Default transaction isolation level
  --temp-pool           Use a pool of temporary files
  -u, --user=user_name	Run mysqld daemon as user
  -V, --version		output version information and exit
  -W, --warnings        Log some not critical warnings
to the log file

  --innodb_data_home_dir=dir   The common part for
Innodb table spaces
  --innodb_data_file_path=dir  Path to individual
files and their sizes
  --innodb_flush_method=#  With which method to flush
data
  --innodb_flush_log_at_trx_commit[=#]
			  Value 0: write and flush once per second
                          Value 1: write and flush at
each commit
                          Value 2: write at commit,
flush once per second
  --innodb_log_arch_dir=dir    Where full logs should
be archived
  --innodb_log_archive[=#]     Set to 1 if you want to
have logs archived
  --innodb_log_group_home_dir=dir  Path to innodb log
files.
  --skip-innodb		       Don't use Innodb (will save
memory)


Default options are read from the following files in
the given order:
/etc/my.cnf /usr/local/mysql/var/my.cnf ~/.my.cnf
The following groups are read: mysqld server
The following options may be given as the first
argument:
--print-defaults	Print the program argument list and
exit
--no-defaults		Don't read default options from any
options file
--defaults-file=#	Only read default options from the
given file #
--defaults-extra-file=# Read this file after the
global files are read

To see what values a running MySQL server is using,
type
'mysqladmin variables' instead of 'mysqld --help'.
The default values (after parsing the command line
arguments) are:

basedir:    
/usr/local/mysql-max-3.23.53a-pc-linux-gnu-i686/
datadir:     /var/lib/mysql/
tmpdir:      /tmp/
language:   
/usr/local/mysql-max-3.23.53a-pc-linux-gnu-i686/share/mysql/english/
pid file:    /var/lib/mysql/localhost.pid
TCP port:    3306
Unix socket: /var/lib/mysql/mysql.sock

system locking is not in use

Possible variables for option --set-variable (-O) are:
back_log              current value: 50
binlog_cache_size     current value: 32768
connect_timeout       current value: 5
delayed_insert_timeout  current value: 300
delayed_insert_limit  current value: 100
delayed_queue_size    current value: 1000
flush_time            current value: 0
innodb_mirrored_log_groups  current value: 1
innodb_log_files_in_group  current value: 2
innodb_log_file_size  current value: 5242880
innodb_log_buffer_size  current value: 1048576
innodb_buffer_pool_size  current value: 8388608
innodb_additional_mem_pool_size  current value:
1048576
innodb_file_io_threads  current value: 4
innodb_lock_wait_timeout  current value: 50
innodb_thread_concurrency  current value: 8
innodb_force_recovery  current value: 0
interactive_timeout   current value: 28800
join_buffer_size      current value: 131072
key_buffer_size       current value: 8388600
long_query_time       current value: 10
lower_case_table_names  current value: 0
max_allowed_packet    current value: 1048576
max_binlog_cache_size  current value: 4294967295
max_binlog_size       current value: 1073741824
max_connections       current value: 100
max_connect_errors    current value: 10
max_delayed_threads   current value: 20
max_heap_table_size   current value: 16777216
max_join_size         current value: 4294967295
max_sort_length       current value: 1024
max_tmp_tables        current value: 32
max_user_connections  current value: 0
max_write_lock_count  current value: 4294967295
myisam_max_extra_sort_file_size  current value: 256
myisam_max_sort_file_size  current value: 2047
myisam_sort_buffer_size  current value: 8388608
net_buffer_length     current value: 16384
net_retry_count       current value: 10
net_read_timeout      current value: 30
net_write_timeout     current value: 60
open_files_limit      current value: 0
query_buffer_size     current value: 0
record_buffer         current value: 131072
record_rnd_buffer     current value: 0
slave_net_timeout     current value: 3600
slow_launch_time      current value: 2
sort_buffer           current value: 2097144
table_cache           current value: 64
thread_concurrency    current value: 10
thread_cache_size     current value: 0
tmp_table_size        current value: 33554432
thread_stack          current value: 65536
wait_timeout          current value: 28800
030506 13:00:40  mysqld ended

--- Jeff Newmiller <jdnewmil@dcn.davis.ca.us> wrote:
> On Wed, 23 Apr 2003, Tim Riley wrote:
> 
> > 
> > 
> > Jeff Newmiller wrote:
> 
> [...]
> 
> > > You don't seem to be familiar with InnoDB
> tables, Tim... they offer some
> > > useful features, but they aren't structured like
> normal MySQL files on
> > > disk. OTOH, my only experience with them has
> been setting them up a couple
> > > of times... I haven't used them for large
> databases, and am just barely
> > > aware of their configuration options.
> > 
> > You're right--I dunno about InnoDB. I hope Mysql
> doesn't fall into the feature
> > trap.
> 
> They haven't lost their old data storage formats...
> just added some new
> ones.
> 
> > The robustness and speed of version 3.22 is due to
> it's simplicity. (I have
> > a client running a database with over 50 tables.
> The largest table has over 40
> > million records, and its datafile size is over 4G,
> and the index file is over 2G.)
> 
> You clearly have enabled large file support in your
> kernel and an
> appropriately compiled mysqld.  The filesize
> limitation I mentioned is
> from the OS... not InnoDB.
> 
> > Mysql's simplicity is due to having 3 files per
> table--definition, data, and index--
> > and letting the operating system do the operating
> system stuff.
> 
> I don't see why 3 files is magic... one per table
> could be "simpler" to
> administer, and one file per index could be simpler
> to program (and less
> likely to have bugs).
> 
> I do think I see where the KISS principle has merit,
> but there are also
> valid reasons for taking the "data lump" approach
> (OS independence being
> one).  I happen to like the "per database" file
> architecture, since you
> can allocate tables to files individually or in
> groups, which makes
> offline archiving easier.
> 
> > On the other hand, Oracle was written when
> operating system resources were
> > limited, and therefore Oracle does a lot of
> operating system stuff. Oracle can be very
> > stable if its memory and disk resources are
> monitored
> > and extended as needed. However, this feature-rich
> database engine is bloated,
> > slower, and accident prone.
> > 
> > (Just food for thought.)
> 
> Yep.  Some people need Corvettes, and other people
> need Cadillacs.  If
> MySQL wants to have something for everyone I won't
> complain.
> 
>
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> Jeff Newmiller                        The     ..... 
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> Dead: OO#..  Playing
> Research Engineer (Solar/Batteries            O.O#. 
>      #.O#.  with
> /Software/Embedded Controllers)               .OO#. 
>      .OO#.  rocks...2k
>
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> 
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