Hi,

"Here, I can see ibdata4 twice, was it intentionally set? you mean with this, you were able to start server?"

It was unintentionally set, but only way I could get it online.

We are using default page size for InnoDB.

my.cnf--

[mysqlclient]
socket=/tmp/mysql.sock

[mysql]
socket=/tmp/mysql.sock
secure-auth=0

[mysqladmin]
socket=/tmp/mysql.sock

[mysqld]
datadir=/mysql4/data/
socket=/tmp/mysql.sock
tmpdir=/dev/shm/tmp/mysql/
slave-load-tmpdir=/ssd/temp/
back_log=4096 
port=3306
skip-external-locking
max_allowed_packet = 128M
max_heap_table_size = 67108864
max_user_connections=0
max_connections = 20000
group_concat_max_len = 2500
table_open_cache = 524288
table_definition_cache = 524288
tmp_table_size = 67108864
sort_buffer_size = 262144
read_buffer_size = 1M
read_rnd_buffer_size = 16777216
join_buffer_size = 16777216
query_cache_type = 0
query_cache_size = 0
max_connect_errors = 1000000
wait_timeout = 1
connect_timeout = 2
interactive_timeout = 1
skip-external-locking
log-error
slow_query_log = 0
min_examined_row_limit = 1000
log_queries_not_using_indexes = 1
long_query_time = 2
log_slow_sp_statements = 0
skip-name-resolve
thread_cache_size = 16384
user=root
log-warnings
innodb_data_home_dir = 
innodb_data_file_path = /ssd/data/ibdata1:806578M;/mysql3/inno_db/data/ibdata2:390354M;/mysql4/inno_db/data/ibdata3:729522M;/mysql5/inno_db/data/ibdata4:370481M;/mysql5/inno_db/data/ibdata4:153M:autoextend
innodb_log_group_home_dir = /mysql4/inno_db/logs
innodb_buffer_pool_size=528G
innodb_log_file_size=3G
innodb_flush_log_at_trx_commit=2
innodb_log_buffer_size=8M
innodb_max_dirty_pages_pct=75 
innodb_log_files_in_group=2
innodb_old_blocks_pct=37
innodb_max_purge_lag=0
innodb_max_purge_lag_delay=0
innodb_table_locks=0
innodb_thread_concurrency=0
innodb_flush_method=O_DIRECT
innodb_adaptive_hash_index_partitions=1
innodb_io_capacity=2000
innodb_io_capacity_max=4000
innodb_write_io_threads=64
innodb_read_io_threads=64
innodb_log_block_size=512
innodb_buffer_pool_instances=64
binlog-format=ROW
transaction-isolation=READ-COMMITTED
innodb_autoinc_lock_mode=2
innodb_thread_sleep_delay = 10000
innodb_adaptive_max_sleep_delay = 150000
innodb_concurrency_tickets = 5000 
slave_exec_mode = IDEMPOTENT
slave-skip-errors=126,1062,1535,1146,1677
slave_transaction_retries=50
log-slave-updates
expire_logs_days=26
log-bin=/mysql1/binlogs/mysql-bin
max_relay_log_size = 1G
max_binlog_size = 1G
relay-log=/mysql1/relaybinlogs/coredb2-relay-bin
binlog_cache_size = 33554432
binlog_stmt_cache_size = 33554432
server-id = 1
auto_increment_increment=2
max_sp_recursion_depth=255
innodb_file_per_table=0 
table_open_cache_instances=16
metadata_locks_hash_instances=8
innodb_sync_array_size=16
innodb_purge_threads=32

innodb_buffer_pool_dump_at_shutdown=1
innodb_buffer_pool_load_at_startup=0
innodb_buffer_pool_filename="/mysql1/ib_buffer_pool"


binlog_checksum=CRC32
relay_log_info_repository=TABLE 
slave_sql_verify_checksum=1
master_verify_checksum=1
relay_log_recovery=1 
master_info_repository=TABLE
key_buffer_size=0
innodb_old_blocks_time=0
innodb_autoextend_increment=64
innodb_checksum_algorithm=crc32

log_warnings=1

innodb_adaptive_flushing_lwm=10
innodb_max_dirty_pages_pct_lwm=0
innodb_flush_neighbors=0
innodb_flushing_avg_loops=45
innodb_sched_priority_cleaner=38
innodb_empty_free_list_algorithm=backoff
innodb_foreground_preflush=exponential_backoff  
innodb_cleaner_lsn_age_factor=high_checkpoint 
innodb_change_buffering=all 
innodb_adaptive_hash_index=1   
sync_binlog=10000
binlog_max_flush_queue_time=100000
binlog_row_image=full
slave_net_timeout=3600
net_read_timeout=30
net_write_timeout=60
innodb_flush_log_at_timeout=1
innodb_stats_on_metadata=0
innodb_read_ahead_threshold=0
innodb_random_read_ahead=0
sync_relay_log=0
innodb_adaptive_flushing=1
innodb_lru_scan_depth=1024
innodb_change_buffer_max_size=50
innodb_stats_auto_recalc=0 
innodb_purge_batch_size=300
innodb_spin_wait_delay=128
innodb_sync_spin_loops=30
query_prealloc_size=8192
query_alloc_block_size=8192
preload_buffer_size=32768
innodb_buffer_pool_populate=1
slave_parallel_workers=10

[mysqldump]
quick
max_allowed_packet = 16M

[mysql.server]
user=root
basedir=/opt/mysql/mysql/

[mysqld_safe]
flush_caches=1
numa_interleave=1
log-error=/mysql1/logs/mysql.log
pid-file=/mysql1/logs/mysqld.pid
core-file-size=unlimited
open-files-limit=1000000
malloc-lib=/usr/local/lib/libjemalloc.so

[xtrabackup]
tmpdir=/backups/tmp