########### OL6

[root@cluster-repo bugs]# wget http://dev.mysql.com/get/Downloads/MySQL-5.6/mysql-5.6.27.tar.gz

[root@cluster-repo bugs]# md5sum  mysql-5.7.8-rc.tar.gz
f6f1c39050f2428add2b0771c2766f82  mysql-5.7.8-rc.tar.gz

-- extract and build

cmake \
      -DBUILD_CONFIG=mysql_release \
      -DCMAKE_BUILD_TYPE=RelWithDebInfo \
      -DCMAKE_INSTALL_PREFIX:PATH=/data/ushastry/bugs/mysql-5.7.8-rc \
      -DWITH_SSL="bundled" \
      -DWITH_ZLIB="bundled" \
      -DMYSQL_DATADIR="/data/ushastry/bugs/mysql-5.7.8-rc/data" \
      -DMYSQL_UNIX_ADDR="/data/ushastry/bugs/mysql-5.7.8-rc/var/mysql.sock" \
      -DMYSQL_USER="mysql" \
      -DENABLED_LOCAL_INFILE=1 \
      -DMYSQL_MAINTAINER_MODE=1 \
      -DWITH_PERF_SCHEMA_STORAGE_ENGINE=1 \
      -DDOWNLOAD_BOOST=1 \
      -DWITH_BOOST=/tmp
      
make 
make install

-- conf used

[mysqld]
sql_mode=no_engine_substitution,no_unsigned_subtraction
default_tmp_storage_engine=MyISAM
sync_relay_log_info=100
relay_log_recovery=1
relay_log_info_repository=FILE
innodb_purge_threads=8
innodb_compression_pad_pct_max=37
innodb_compression_failure_threshold_pct=10
innodb_flush_neighbors=0
innodb_old_blocks_pct=50
innodb_max_dirty_pages_pct=75
innodb_max_dirty_pages_pct_lwm=0
innodb_adaptive_flushing=1
innodb_adaptive_flushing_lwm=10
innodb_adaptive_hash_index=0
innodb_flushing_avg_loops=30
innodb_max_purge_lag=0
innodb_max_purge_lag_delay=0
eq_range_index_dive_limit=1000
# block_create_myisam=1
gtid_mode=OFF
enforce_gtid_consistency=ON
lock_wait_timeout=60
# part_scan_max=1000
ssl=0
plugin_load=
skip_temp_pool=0
# block_ftwrl=1

long_query_time=10
#skip_partition=1
wait_timeout=10
interactive_timeout=120
max_allowed_packet=128M
slave_max_allowed_packet=256M
skip_name_resolve
back_log=4096
max_connections=5000
max_user_connections=4000
max_connect_errors=3000
key_buffer_size=16M
myisam_sort_buffer_size=256M
max_tmp_tables=64
read_buffer_size=1M
read_rnd_buffer_size=1M
sort_buffer_size=2M
table_open_cache=50000
table_definition_cache=60000
query_cache_limit=4M
query_cache_size=0
query_cache_type=0
thread_cache_size=500
thread_stack=196608
open_files_limit=32767
net_read_timeout=15
net_write_timeout=30
tmp_table_size=64M
max_heap_table_size=512M
# log_slow_extra=1
group_concat_max_len=1024
default_storage_engine=InnoDB
innodb_compression_level=1
# innodb_deadlock_detect=0
innodb_file_format=Barracuda
innodb_file_per_table=1
innodb_lock_wait_timeout=2
innodb_log_buffer_size=4M
innodb_log_compressed_pages=0
innodb_log_file_size=128M
innodb_old_blocks_time=1000
innodb_open_files=10240
innodb_read_io_threads=32
innodb_stats_on_metadata=0
innodb_thread_concurrency=256
innodb_write_io_threads=4
# innodb_zlib_wrap=0
# innodb_enable_slave_update_table_stats=1

innodb_io_capacity=1000
innodb_io_capacity_max=2000
innodb_lru_scan_depth=1024

innodb_flush_log_at_trx_commit=2
innodb_flush_method=O_DIRECT

innodb_doublewrite=0
# innodb_page_size=8K
innodb_buffer_pool_size=2G

datadir=/ /data/ushastry/bugs/mysql-5.7.8-rc/data
innodb_data_home_dir= /data/ushastry/bugs/mysql-5.7.8-rc/data
innodb_data_file_path=ibdata1:512M:autoextend

innodb_log_group_home_dir= /data/ushastry/bugs/mysql-5.7.8-rc/txlogs

#port=3307
# socket=/var/lib/mysql/mysql-3307.sock
# socket=/data/mysql/orig578/var/mysql.sock

# skip_log_bin
log_bin= /data/ushastry/bugs/mysql-5.7.8-rc/binlogs/bl
max_binlog_size=128M
binlog_cache_size=262144
max_binlog_cache_size=128M
sync_binlog=0
server_id=77

#init_file=/usr/facebook/scripts/db/generate_uuid.sql
tmpdir=/tmp
slave_load_tmpdir=/tmp

slow_query_log_file= /data/ushastry/bugs/mysql-5.7.8-rc/log/slow.log
slow_query_log=1
long_query_time=2
log_slow_slave_statements=1

secure_file_priv=""
log-error=/data/ushastry/bugs/mysql-5.7.8-rc/log/log.err



bin/mysql_install_db --defaults-file=./my.cnf --insecure --basedir=/data/ushastry/bugs/mysql-5.7.8-rc --datadir=/data/ushastry/bugs/mysql-5.7.8-rc/data -v
bin/mysqld --defaults-file=./my.cnf --core-file --user=root &


-- Linkbench - https://github.com/facebook/linkbench/blob/master/README.md

-- Note: replace 'linkbench'@'localhost' with 'linkbench'@'%' to allow remote connections
CREATE USER 'linkbench'@'localhost' IDENTIFIED BY 'mypassword';
CREATE USER 'linkbench'@'127.0.0.1' IDENTIFIED BY 'mypassword';
-- Grant all privileges on linkdb to this user
GRANT ALL ON linkdb.* TO 'linkbench'@'localhost';
GRANT ALL ON linkdb.* TO 'linkbench'@'127.0.0.1';
GRANT ALL ON *.* TO 'linkbench'@'127.0.0.1';
flush privileges;


I ran linkbench and reproduce with:
* 5.7.8 RC
* file system

[root@cluster-repo mysql-5.7.8-rc]# df -T
Filesystem           Type  1K-blocks     Used Available Use% Mounted on
/dev/mapper/vg_clusterrepo-lv_root
                     ext4   11083008  6521512   3998504  62% /
tmpfs                tmpfs   3061272        0   3061272   0% /dev/shm
/dev/xvda1           ext4     495844   177353    292891  38% /boot
/dev/xvdb1           ext4   51605436 31933164  17050868  66% /data
[root@cluster-repo mysql-5.7.8-rc]#


* kernel:

[root@cluster-repo mysql-5.7.8-rc]# rpm -qa|grep kernel
kernel-2.6.32-573.3.1.el6.x86_64
kernel-headers-2.6.32-573.3.1.el6.x86_64
dracut-kernel-004-388.0.1.el6.noarch
kernel-devel-2.6.32-573.3.1.el6.x86_64
kernel-2.6.32-573.1.1.el6.x86_64
kernel-uek-2.6.39-400.250.2.el6uek.x86_64
kernel-uek-2.6.39-400.250.10.el6uek.x86_64
kernel-uek-firmware-2.6.39-400.250.10.el6uek.noarch
kernel-firmware-2.6.32-573.3.1.el6.noarch
kernel-uek-2.6.39-400.264.1.el6uek.x86_64
kernel-devel-2.6.32-573.1.1.el6.x86_64
libreport-plugin-kerneloops-2.0.9-24.0.1.el6.x86_64
kernel-uek-firmware-2.6.39-400.264.1.el6uek.noarch
kernel-uek-firmware-2.6.39-400.250.2.el6uek.noarch
kernel-2.6.32-504.23.4.el6.x86_64
kernel-debug-devel-2.6.32-573.3.1.el6.x86_64
abrt-addon-kerneloops-2.0.8-34.0.2.el6.x86_64

* OS:

[root@cluster-repo mysql-5.7.8-rc]# cat /etc/*release
LSB_VERSION=base-4.0-amd64:base-4.0-noarch:core-4.0-amd64:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-noarch
Oracle Linux Server release 6.7
NAME="Oracle Linux Server"
VERSION="6.7"
ID="ol"
VERSION_ID="6.7"
PRETTY_NAME="Oracle Linux Server 6.7"
ANSI_COLOR="0;31"
CPE_NAME="cpe:/o:oracle:linux:6:7"
HOME_URL="https://linux.oracle.com/"
BUG_REPORT_URL="https://bugzilla.oracle.com/"

ORACLE_BUGZILLA_PRODUCT="Oracle Linux 6"
ORACLE_BUGZILLA_PRODUCT_VERSION=6.7
ORACLE_SUPPORT_PRODUCT="Oracle Linux"
ORACLE_SUPPORT_PRODUCT_VERSION=6.7
Red Hat Enterprise Linux Server release 6.7 (Santiago)
Oracle Linux Server release 6.7


[root@cluster-repo mysql-5.7.8-rc]# cat docs/INFO_SRC
commit: ae3b133e5f7b13d1edf7acf7eee6af2c2b4014e2
date: 2015-07-20 14:02:16 +0200
build-date: 2015-07-20 14:16:07 +0200
short: ae3b133
branch: mysql-5.7.8-rc-release

MySQL source 5.7.8


// Linkbench 

[root@cluster-repo linkbench-master]# mvn --version
Apache Maven 3.2.5 (12a6b3acb947671f09b81f49094c53f426d8cea1; 2014-12-14T22:59:23+05:30)
Maven home: /usr/share/apache-maven
Java version: 1.8.0_51, vendor: Oracle Corporation
Java home: /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.51-3.b16.el6_7.x86_64/jre
Default locale: en_US, platform encoding: UTF-8
OS name: "linux", version: "2.6.39-400.250.2.el6uek.x86_64", arch: "amd64", family: "unix"

* linkbench config changed to use maxid1=5,000,001, loaders=4, requesters=4, maxtime=7200
* linkbench pattern is do load step, then repeat 1-hour query steps. I get the error in the first hour for ext4 and in less than 20 hours for xfs


[root@cluster-repo linkbench-master]# cat config/FBWorkload.properties |grep max
# increase maxid1.
maxid1 = 5000001

[root@cluster-repo linkbench-master]# cat config/LinkConfigMysql.properties |grep loader
loaders = 4
loader_chunk_size = 2048
[root@cluster-repo linkbench-master]# cat config/LinkConfigMysql.properties |grep requester
requesters = 4
# maximum number of failures per requester to tolerate before aborting
[root@cluster-repo linkbench-master]# cat config/LinkConfigMysql.properties |grep maxtime
maxtime = 7200


[root@cluster-repo linkbench-master]# bash bin/linkbench -l

[root@cluster-repo linkbench-master]# bash bin/linkbench -r
.
9 90% = 28367 95% = 71740 99% = 71740 max = 71740
INFO 2015-10-06 00:21:45,333 [Thread-0]: ThreadID = 0 total requests = 148 requests/second = 0 found = 0 not found = 0 history queries = 0/66
INFO 2015-10-06 00:21:45,334 [main]: ADD_NODE count = 4  p25 = [0.4,0.5]ms  p50 = [0.5,0.6]ms  p75 = [0.5,0.6]ms  p95 = [0.5,0.6]ms  p99 = [0.5,0.6]ms  max = 0.776ms  mean = 0.591ms
INFO 2015-10-06 00:21:45,334 [main]: UPDATE_NODE count = 18  p25 = [18,19]ms  p50 = [34,35]ms  p75 = [56,57]ms  p95 = [70,71]ms  p99 = [70,71]ms  max = 125.172ms  mean = 43.986ms
INFO 2015-10-06 00:21:45,334 [main]: DELETE_NODE count = 8  p25 = [18,19]ms  p50 = [27,28]ms  p75 = [33,34]ms  p95 = [54,55]ms  p99 = [54,55]ms  max = 84.329ms  mean = 36.532ms
INFO 2015-10-06 00:21:45,335 [main]: GET_NODE count = 25  p25 = [14,15]ms  p50 = [25,26]ms  p75 = [47,48]ms  p95 = [70,71]ms  p99 = [71,72]ms  max = 144.389ms  mean = 37.729ms
INFO 2015-10-06 00:21:45,335 [main]: ADD_LINK count = 11  p25 = [94,95]ms  p50 = [100,200]ms  p75 = [100,200]ms  p95 = [100,200]ms  p99 = [100,200]ms  max = 161.351ms  mean = 125.306ms
INFO 2015-10-06 00:21:45,335 [main]: DELETE_LINK count = 9  p25 = [36,37]ms  p50 = [45,46]ms  p75 = [62,63]ms  p95 = [100,200]ms  p99 = [100,200]ms  max = 192.05ms  mean = 83.844ms
INFO 2015-10-06 00:21:45,335 [main]: UPDATE_LINK count = 12  p25 = [93,94]ms  p50 = [100,200]ms  p75 = [100,200]ms  p95 = [200,300]ms  p99 = [200,300]ms  max = 265.036ms  mean = 158.455ms
INFO 2015-10-06 00:21:45,336 [main]: COUNT_LINK count = 4  p25 = [26,27]ms  p50 = [50,51]ms  p75 = [50,51]ms  p95 = [50,51]ms  p99 = [50,51]ms  max = 58.746ms  mean = 46.518ms
INFO 2015-10-06 00:21:45,336 [main]: MULTIGET_LINK count = 1  p25 = [0,0.1]ms  p50 = [0,0.1]ms  p75 = [0,0.1]ms  p95 = [0,0.1]ms  p99 = [0,0.1]ms  max = 28.678ms  mean = 28.678ms
INFO 2015-10-06 00:21:45,336 [main]: GET_LINKS_LIST count = 90  p25 = [26,27]ms  p50 = [39,40]ms  p75 = [55,56]ms  p95 = [100,200]ms  p99 = [100,200]ms  max = 195.305ms  mean = 48.076ms
INFO 2015-10-06 00:21:45,336 [main]: REQUEST PHASE COMPLETED. 582 requests done in 199 seconds. Requests/second = 2
ERROR 2015-10-06 00:21:45,336 [main]: Benchmark did not complete cleanly: 4/4 request threads aborted.  See error log entries for details.

## Extract from error log

-- firstly (within <5min or so)

2015-10-05T18:28:32.923241Z 0 [Warning] InnoDB: Using innodb_file_format is deprecated and the parameter may be removed in future releases. See http://dev.mysql.com/doc/refman/5.7/en/innodb-file-format.html
2015-10-05T18:28:32.923360Z 0 [Note] InnoDB: PUNCH HOLE support available
2015-10-05T18:28:32.923388Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2015-10-05T18:28:32.923398Z 0 [Note] InnoDB: Uses event mutexes
2015-10-05T18:28:32.923407Z 0 [Note] InnoDB: GCC builtin __sync_synchronize() is used for memory barrier
2015-10-05T18:28:32.923417Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2015-10-05T18:28:32.923427Z 0 [Note] InnoDB: Using Linux native AIO
2015-10-05T18:28:32.930943Z 0 [Note] InnoDB: Number of pools: 1
2015-10-05T18:28:32.931294Z 0 [Note] InnoDB: Not using CPU crc32 instructions
2015-10-05T18:28:33.038057Z 0 [Note] InnoDB: Initializing buffer pool, total size = 2G, instances = 8, chunk size = 128M
2015-10-05T18:28:33.405386Z 0 [Note] InnoDB: Completed initialization of buffer pool
2015-10-05T18:28:33.499397Z 0 [Note] InnoDB: page_cleaner coordinator priority: -20
2015-10-05T18:28:33.499509Z 0 [Note] InnoDB: page_cleaner worker priority: -20
2015-10-05T18:28:33.499746Z 0 [Note] InnoDB: page_cleaner worker priority: -20
2015-10-05T18:28:33.499936Z 0 [Note] InnoDB: page_cleaner worker priority: -20
2015-10-05T18:28:33.555083Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2015-10-05T18:28:33.783421Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2015-10-05T18:28:33.783625Z 0 [Note] InnoDB: Setting file '/data/ushastry/bugs/mysql-5.7.8-rc/data/ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2015-10-05T18:28:33.883368Z 0 [Note] InnoDB: File '/data/ushastry/bugs/mysql-5.7.8-rc/data/ibtmp1' size is now 12 MB.
2015-10-05T18:28:33.885332Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2015-10-05T18:28:33.885346Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2015-10-05T18:28:33.886442Z 0 [Note] InnoDB: Waiting for purge to start
2015-10-05T18:28:33.936990Z 0 [Note] InnoDB: 5.7.8 started; log sequence number 2419354
2015-10-05T18:28:33.937494Z 0 [Note] InnoDB: Loading buffer pool(s) from /data/ushastry/bugs/mysql-5.7.8-rc/data/ib_buffer_pool
2015-10-05T18:28:33.937758Z 0 [Note] Plugin 'FEDERATED' is disabled.
2015-10-05T18:28:34.024558Z 0 [Note] Server hostname (bind-address): '*'; port: 3306
2015-10-05T18:28:34.024683Z 0 [Note] IPv6 is available.
2015-10-05T18:28:34.024731Z 0 [Note]   - '::' resolves to '::';
2015-10-05T18:28:34.024743Z 0 [Note] Server socket created on IP: '::'.
2015-10-05T18:28:34.199681Z 0 [Note] InnoDB: Buffer pool(s) load completed at 151005 23:58:34
2015-10-05T18:28:34.215303Z 0 [Note] Event Scheduler: Loaded 0 events
2015-10-05T18:28:34.215589Z 0 [Note] bin/mysqld: ready for connections.
Version: '5.7.8-rc-log'  socket: '/data/ushastry/bugs/mysql-5.7.8-rc/var/mysql.sock'  port: 3306  MySQL Community Server (GPL)
2015-10-05T18:29:40.348738Z 7 [Note] Aborted connection 7 to db: 'linkdb' user: 'linkbench' host: '127.0.0.1' (Got timeout reading communication packets)
2015-10-05T18:29:40.605739Z 9 [Note] Aborted connection 9 to db: 'linkdb' user: 'linkbench' host: '127.0.0.1' (Got timeout reading communication packets)
2015-10-05T18:29:40.781741Z 10 [Note] Aborted connection 10 to db: 'linkdb' user: 'linkbench' host: '127.0.0.1' (Got timeout reading communication packets)
2015-10-05T18:29:40.863833Z 11 [Note] Aborted connection 11 to db: 'linkdb' user: 'linkbench' host: '127.0.0.1' (Got timeout reading communication packets)
2015-10-05T18:29:41.491750Z 12 [Note] Aborted connection 12 to db: 'linkdb' user: 'linkbench' host: '127.0.0.1' (Got timeout reading communication packets)
2015-10-05T18:31:13.621036Z 2 [Note] Aborted connection 2 to db: 'linkdb' user: 'root' host: 'localhost' (Got timeout reading communication packets)
18:46:08 UTC - mysqld got signal 11 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.
Attempting to collect some information that could help diagnose the problem.
As this is a crash and something is definitely wrong, the information
collection process might fail.

key_buffer_size=16777216
read_buffer_size=1048576
max_used_connections=11
max_threads=5000
thread_count=8
connection_count=8
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 15441266 K  bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x6a0fca0
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 = 7fd4bb682e28 thread_stack 0x30000
bin/mysqld(my_print_stacktrace+0x35)[0xe97635]
bin/mysqld(handle_fatal_signal+0x4a4)[0x78b2b4]
/lib64/libpthread.so.0(+0xf790)[0x7fd5a18a7790]
bin/mysqld(_Z26page_cur_search_with_matchPK11buf_block_tPK12dict_index_tPK8dtuple_t15page_cur_mode_tPmS9_P10page_cur_tP8rtr_info+0x148)[0xff5258]
bin/mysqld(_Z27btr_cur_search_to_nth_levelP12dict_index_tmPK8dtuple_t15page_cur_mode_tmP9btr_cur_tmPKcmP5mtr_t+0x1596)[0x10f9d26]
bin/mysqld[0x10fbc2f]
bin/mysqld(_ZN11ha_innobase16records_in_rangeEjP12st_key_rangeS1_+0x2b5)[0xf7e825]
bin/mysqld(_ZN7handler27multi_range_read_info_constEjP15st_range_seq_ifPvjPjS3_P13Cost_estimate+0xa2)[0x7cbb22]
bin/mysqld(_ZN10DsMrr_impl16dsmrr_info_constEjP15st_range_seq_ifPvjPjS3_P13Cost_estimate+0x53)[0x7d2a23]
bin/mysqld[0xdbbf12]
bin/mysqld[0xdbc8e9]
bin/mysqld(_Z17test_quick_selectP3THD6BitmapILj64EEyybN8st_order10enum_orderEPK16QEP_shared_ownerP4ItemPS2_PP14QUICK_SELECT_I+0xbdc)[0xdc928c]
bin/mysqld(_ZN4JOIN17estimate_rowcountEv+0x3ad)[0xc7543d]
bin/mysqld(_ZN4JOIN14make_join_planEv+0x721)[0xc792e1]
bin/mysqld(_ZN4JOIN8optimizeEv+0x607)[0xc7e937]
bin/mysqld(_ZN13st_select_lex8optimizeEP3THD+0x672)[0xcc26f2]
bin/mysqld(_Z12handle_queryP3THDP3LEXP12Query_resultyy+0x217)[0xcc2987]
bin/mysqld[0xc84b33]
bin/mysqld(_Z21mysql_execute_commandP3THD+0x1687)[0xc86487]
bin/mysqld(_Z11mysql_parseP3THDP12Parser_state+0x3a8)[0xc89f08]
bin/mysqld(_Z16dispatch_commandP3THDP8COM_DATA19enum_server_command+0x1215)[0xc8b195]
bin/mysqld(_Z10do_commandP3THD+0x194)[0xc8c354]
bin/mysqld(handle_connection+0x28c)[0xd54fcc]
bin/mysqld(pfs_spawn_thread+0x160)[0xeb00e0]
/lib64/libpthread.so.0(+0x7a51)[0x7fd5a189fa51]
/lib64/libc.so.6(clone+0x6d)[0x7fd5a08099ad]

Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (695be00): select id1, id2, link_type, visibility, data, time, version from linkdb.linktable FORCE INDEX(`id1_type`)  where id1 = 4904939 and link_type = 123456790 and time >= 0 and time <= 9223372036854775807 and visibility = 1 order by time desc  limit 0,10000
Connection ID (thread ID): 17
Status: NOT_KILLED

The manual page at http://dev.mysql.com/doc/mysql/en/crashing.html contains
information that should help you find out what is causing the crash.
Writing a core file


-- Secondly, (restarted mysqld, and ran again bash bin/linkbench -r)

2015-10-05T18:48:18.436813Z 0 [Warning] InnoDB: Using innodb_file_format is deprecated and the parameter may be removed in future releases. See http://dev.mysql.com/doc/refman/5.7/en/innodb-file-format.html
2015-10-05T18:48:18.436956Z 0 [Note] InnoDB: PUNCH HOLE support available
2015-10-05T18:48:18.436990Z 0 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2015-10-05T18:48:18.437001Z 0 [Note] InnoDB: Uses event mutexes
2015-10-05T18:48:18.437011Z 0 [Note] InnoDB: GCC builtin __sync_synchronize() is used for memory barrier
2015-10-05T18:48:18.437022Z 0 [Note] InnoDB: Compressed tables use zlib 1.2.3
2015-10-05T18:48:18.437032Z 0 [Note] InnoDB: Using Linux native AIO
2015-10-05T18:48:18.444771Z 0 [Note] InnoDB: Number of pools: 1
2015-10-05T18:48:18.445134Z 0 [Note] InnoDB: Not using CPU crc32 instructions
2015-10-05T18:48:18.553061Z 0 [Note] InnoDB: Initializing buffer pool, total size = 2G, instances = 8, chunk size = 128M
2015-10-05T18:48:18.924325Z 0 [Note] InnoDB: Completed initialization of buffer pool
2015-10-05T18:48:19.024389Z 0 [Note] InnoDB: page_cleaner coordinator priority: -20
2015-10-05T18:48:19.024451Z 0 [Note] InnoDB: page_cleaner worker priority: -20
2015-10-05T18:48:19.024949Z 0 [Note] InnoDB: page_cleaner worker priority: -20
2015-10-05T18:48:19.025019Z 0 [Note] InnoDB: page_cleaner worker priority: -20
2015-10-05T18:48:19.079021Z 0 [Note] InnoDB: Highest supported file format is Barracuda.
2015-10-05T18:48:19.154628Z 0 [Note] InnoDB: Log scan progressed past the checkpoint lsn 8761705731
2015-10-05T18:48:19.182579Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 8762250308
2015-10-05T18:48:19.311576Z 0 [Note] InnoDB: Doing recovery: scanned up to log sequence number 8762250308
2015-10-05T18:48:19.312058Z 0 [Note] InnoDB: Database was not shutdown normally!
2015-10-05T18:48:19.312071Z 0 [Note] InnoDB: Starting crash recovery.
2015-10-05T18:48:19.563212Z 0 [Note] InnoDB: Transaction 32635 was in the XA prepared state.
2015-10-05T18:48:19.565545Z 0 [Note] InnoDB: 1 transaction(s) which must be rolled back or cleaned up in total 0 row operations to undo
2015-10-05T18:48:19.565567Z 0 [Note] InnoDB: Trx id counter is 33024
2015-10-05T18:48:19.565853Z 0 [Note] InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percent: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
2015-10-05T18:48:21.475258Z 0 [Note] InnoDB: Apply batch completed
2015-10-05T18:48:21.475331Z 0 [Note] InnoDB: Last MySQL binlog file position 0 71983288, file name bl.000022
2015-10-05T18:48:21.831786Z 0 [Note] InnoDB: Starting in background the rollback of uncommitted transactions
2015-10-05T18:48:21.831827Z 0 [Note] InnoDB: Rollback of non-prepared transactions completed
2015-10-05T18:48:21.831971Z 0 [Note] InnoDB: Removed temporary tablespace data file: "ibtmp1"
2015-10-05T18:48:21.831984Z 0 [Note] InnoDB: Creating shared tablespace for temporary tables
2015-10-05T18:48:21.832036Z 0 [Note] InnoDB: Setting file '/data/ushastry/bugs/mysql-5.7.8-rc/data/ibtmp1' size to 12 MB. Physically writing the file full; Please wait ...
2015-10-05T18:48:21.971326Z 0 [Note] InnoDB: File '/data/ushastry/bugs/mysql-5.7.8-rc/data/ibtmp1' size is now 12 MB.
2015-10-05T18:48:21.973105Z 0 [Note] InnoDB: 96 redo rollback segment(s) found. 96 redo rollback segment(s) are active.
2015-10-05T18:48:21.973118Z 0 [Note] InnoDB: 32 non-redo rollback segment(s) are active.
2015-10-05T18:48:21.974244Z 0 [Note] InnoDB: Waiting for purge to start
2015-10-05T18:48:22.024436Z 0 [Note] InnoDB: 5.7.8 started; log sequence number 8762250308
2015-10-05T18:48:22.024720Z 0 [Note] InnoDB: Loading buffer pool(s) from /data/ushastry/bugs/mysql-5.7.8-rc/data/ib_buffer_pool
2015-10-05T18:48:22.025276Z 0 [Note] Plugin 'FEDERATED' is disabled.
2015-10-05T18:48:22.050028Z 0 [Note] Recovering after a crash using /data/ushastry/bugs/mysql-5.7.8-rc/binlogs/bl
2015-10-05T18:48:22.366584Z 0 [Note] Starting crash recovery...
2015-10-05T18:48:22.366714Z 0 [Note] InnoDB: Starting recovery for XA transactions...
2015-10-05T18:48:22.366728Z 0 [Note] InnoDB: Transaction 32635 in prepared state after recovery
2015-10-05T18:48:22.366739Z 0 [Note] InnoDB: Transaction contains changes to 1 rows
2015-10-05T18:48:22.366749Z 0 [Note] InnoDB: 1 transactions in prepared state after recovery
2015-10-05T18:48:22.366758Z 0 [Note] Found 1 prepared transaction(s) in InnoDB
2015-10-05T18:48:22.366937Z 0 [Note] Crash recovery finished.
2015-10-05T18:48:22.447475Z 0 [Note] InnoDB: Resetting invalid page [page id: space=23, page number=1] type 0 to 5 when flushing.
2015-10-05T18:48:23.055792Z 0 [Note] InnoDB: Buffer pool(s) load completed at 151006  0:18:23
2015-10-05T18:48:23.183660Z 0 [Note] Server hostname (bind-address): '*'; port: 3306
2015-10-05T18:48:23.183802Z 0 [Note] IPv6 is available.
2015-10-05T18:48:23.183830Z 0 [Note]   - '::' resolves to '::';
2015-10-05T18:48:23.183841Z 0 [Note] Server socket created on IP: '::'.
2015-10-05T18:48:23.267543Z 0 [Note] Event Scheduler: Loaded 0 events
2015-10-05T18:48:23.268044Z 0 [Note] bin/mysqld: ready for connections.
Version: '5.7.8-rc-log'  socket: '/data/ushastry/bugs/mysql-5.7.8-rc/var/mysql.sock'  port: 3306  MySQL Community Server (GPL)
2015-10-05T18:48:29.394964Z 3 [ERROR] InnoDB: Database page corruption on disk or a failed file read of page [page id: space=23, page number=5593]. You may have to recover from a backup.
2015-10-05T18:48:29.395013Z 3 [Note] InnoDB: Page dump in ascii and hex (16384 bytes):

.
.
2015-10-05T18:48:30.976504Z 3 [Note] InnoDB: Uncompressed page, stored checksum in field1 0, calculated checksums for field1: crc32 4167772399/913779717, innodb 1285208427, none 3735928559, stor
ed checksum in field2 0, calculated checksums for field2: crc32 4167772399/913779717, innodb 1371122432, none 3735928559,  page LSN 0 0, low 4 bytes of LSN at page end 0, page number (if stored
to page already) 0, space id (if created with >= MySQL-4.1.1 and stored already) 0
InnoDB: Page may be a freshly allocated page
2015-10-05T18:48:30.976524Z 3 [Note] InnoDB: It is also possible that your operating system has corrupted its own file cache and rebooting your computer removes the error. If the corrupt page is
 an index page. You can also try to fix the corruption by dumping, dropping, and reimporting the corrupt table. You can use CHECK TABLE to scan your table for corruption. Please refer to http://
dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html for information about forcing recovery.
2015-10-05T18:48:30.976540Z 3 [ERROR] [FATAL] InnoDB: Aborting because of a corrupt database page in the system tablespace. Or,  there was a failure in tagging the tablespace  as corrupt.
2015-10-06 00:18:30 0x7f74b6939700  InnoDB: Assertion failure in thread 140139256059648 in file ut0ut.cc line 916
InnoDB: We intentionally generate a memory trap.
InnoDB: Submit a detailed bug report to http://bugs.mysql.com.
InnoDB: If you get repeated assertion failures or crashes, even
InnoDB: immediately after the mysqld startup, there may be
InnoDB: corruption in the InnoDB tablespace. Please refer to
InnoDB: http://dev.mysql.com/doc/refman/5.7/en/forcing-innodb-recovery.html
InnoDB: about forcing recovery.
18:48:30 UTC - mysqld got signal 6 ;
This could be because you hit a bug. It is also possible that this binary
or one of the libraries it was linked against is corrupt, improperly built,
or misconfigured. This error can also be caused by malfunctioning hardware.
Attempting to collect some information that could help diagnose the problem.
As this is a crash and something is definitely wrong, the information
collection process might fail.

key_buffer_size=16777216
read_buffer_size=1048576
max_used_connections=8
max_threads=5000
thread_count=2
connection_count=2
It is possible that mysqld could use up to
key_buffer_size + (read_buffer_size + sort_buffer_size)*max_threads = 15441266 K  bytes of memory
Hope that's ok; if not, decrease some variables in the equation.

Thread pointer: 0x7f746c0014b0
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 = 7f74b6938e28 thread_stack 0x30000
bin/mysqld(my_print_stacktrace+0x35)[0xe97635]
bin/mysqld(handle_fatal_signal+0x4a4)[0x78b2b4]
/lib64/libpthread.so.0(+0xf790)[0x7f759c99a790]
/lib64/libc.so.6(gsignal+0x35)[0x7f759b846625]
/lib64/libc.so.6(abort+0x175)[0x7f759b847e05]
bin/mysqld(_Z18ut_print_timestampP8_IO_FILE+0x0)[0x77a0e7]
bin/mysqld(_ZN2ib5fatalD1Ev+0xb3)[0x10d7483]
bin/mysqld(_Z20buf_page_io_completeP10buf_page_tb+0x3ff)[0x1111e8f]
bin/mysqld[0x11345fc]
bin/mysqld(_Z13buf_read_pageRK9page_id_tRK11page_size_t+0x40)[0x1134d80]
bin/mysqld(_Z16buf_page_get_genRK9page_id_tRK11page_size_tmP11buf_block_tmPKcmP5mtr_tb+0xd33)[0x11162d3]
bin/mysqld(_Z27btr_cur_search_to_nth_levelP12dict_index_tmPK8dtuple_t15page_cur_mode_tmP9btr_cur_tmPKcmP5mtr_t+0x850)[0x10f8fe0]
bin/mysqld(_Z29row_ins_clust_index_entry_lowmmP12dict_index_tmP8dtuple_tmP9que_thr_tb+0x240)[0x102e290]
bin/mysqld(_Z25row_ins_clust_index_entryP12dict_index_tP8dtuple_tP9que_thr_tmb+0xb3)[0x1032553]
bin/mysqld(_Z12row_ins_stepP9que_thr_t+0x35b)[0x103479b]
bin/mysqld[0x104ed15]
bin/mysqld(_ZN11ha_innobase9write_rowEPh+0x328)[0xf894d8]
bin/mysqld(_ZN7handler12ha_write_rowEPh+0x6e)[0x7d1c3e]
bin/mysqld(_Z12write_recordP3THDP5TABLEP9COPY_INFOS4_+0x27c)[0xdeeb6c]
bin/mysqld(_ZN14Sql_cmd_insert12mysql_insertEP3THDP10TABLE_LIST+0x880)[0xdf1720]
bin/mysqld(_ZN14Sql_cmd_insert7executeEP3THD+0xce)[0xdf1ebe]
bin/mysqld(_Z21mysql_execute_commandP3THD+0x14e1)[0xc862e1]
bin/mysqld(_Z11mysql_parseP3THDP12Parser_state+0x3a8)[0xc89f08]
bin/mysqld(_Z16dispatch_commandP3THDP8COM_DATA19enum_server_command+0x1215)[0xc8b195]
bin/mysqld(_Z10do_commandP3THD+0x194)[0xc8c354]
bin/mysqld(handle_connection+0x28c)[0xd54fcc]
bin/mysqld(pfs_spawn_thread+0x160)[0xeb00e0]
/lib64/libpthread.so.0(+0x7a51)[0x7f759c992a51]
/lib64/libc.so.6(clone+0x6d)[0x7f759b8fc9ad]

Trying to get some variables.
Some pointers may be invalid and cause the dump to abort.
Query (7f746c005910): INSERT INTO linkdb.linktable(id1, id2, link_type, visibility, data, time, version) VALUES (4896505, 4896505, 123456790, 1, x'476230395c595364334c275a603c4c5062255961462b2b3
84422', 1444070909355, 0) ON DUPLICATE KEY UPDATE visibility = VALUES(visibility)
Connection ID (thread ID): 3
Status: NOT_KILLED

The manual page at http://dev.mysql.com/doc/mysql/en/crashing.html contains
information that should help you find out what is causing the crash.
[root@cluster-repo mysql-5.7.8-rc]#


// 

stack_bottom = 7f74b6938e28 thread_stack 0x30000
bin/mysqld(my_print_stacktrace+0x35)[0xe97635]
bin/mysqld(handle_fatal_signal+0x4a4)[0x78b2b4]
/lib64/libpthread.so.0(+0xf790)[0x7f759c99a790]
/lib64/libc.so.6(gsignal+0x35)[0x7f759b846625]
/lib64/libc.so.6(abort+0x175)[0x7f759b847e05]
bin/mysqld(ut_print_timestamp(_IO_FILE*)+0x0)[0x77a0e7]
bin/mysqld(ib::fatal::~fatal()+0xb3)[0x10d7483]
bin/mysqld(buf_page_io_complete(buf_page_t*, bool)+0x3ff)[0x1111e8f]
bin/mysqld[0x11345fc]
bin/mysqld(buf_read_page(page_id_t const&, page_size_t const&)+0x40)[0x1134d80]
bin/mysqld(buf_page_get_gen(page_id_t const&, page_size_t const&, unsigned long, buf_block_t*, unsigned long, char const*, unsigned long, mtr_t*, bool)+0xd33)[0x11162d3]
bin/mysqld(btr_cur_search_to_nth_level(dict_index_t*, unsigned long, dtuple_t const*, page_cur_mode_t, unsigned long, btr_cur_t*, unsigned long, char const*, unsigned long, mtr_t*)+0x850)[0x10f8fe0]
bin/mysqld(row_ins_clust_index_entry_low(unsigned long, unsigned long, dict_index_t*, unsigned long, dtuple_t*, unsigned long, que_thr_t*, bool)+0x240)[0x102e290]
bin/mysqld(row_ins_clust_index_entry(dict_index_t*, dtuple_t*, que_thr_t*, unsigned long, bool)+0xb3)[0x1032553]
bin/mysqld(row_ins_step(que_thr_t*)+0x35b)[0x103479b]
bin/mysqld[0x104ed15]
bin/mysqld(ha_innobase::write_row(unsigned char*)+0x328)[0xf894d8]
bin/mysqld(handler::ha_write_row(unsigned char*)+0x6e)[0x7d1c3e]
bin/mysqld(write_record(THD*, TABLE*, COPY_INFO*, COPY_INFO*)+0x27c)[0xdeeb6c]
bin/mysqld(Sql_cmd_insert::mysql_insert(THD*, TABLE_LIST*)+0x880)[0xdf1720]
bin/mysqld(Sql_cmd_insert::execute(THD*)+0xce)[0xdf1ebe]
bin/mysqld(mysql_execute_command(THD*)+0x14e1)[0xc862e1]
bin/mysqld(mysql_parse(THD*, Parser_state*)+0x3a8)[0xc89f08]
bin/mysqld(dispatch_command(THD*, COM_DATA*, enum_server_command)+0x1215)[0xc8b195]
bin/mysqld(do_command(THD*)+0x194)[0xc8c354]
bin/mysqld(handle_connection+0x28c)[0xd54fcc]
bin/mysqld(pfs_spawn_thread+0x160)[0xeb00e0]
/lib64/libpthread.so.0(+0x7a51)[0x7f759c992a51]
/lib64/libc.so.6(clone+0x6d)[0x7f759b8fc9ad]