When loading big files using LOAD DATA INFILE Percona Server becomes unresponsive for some time during "Query end" stage. During this flushing new connections got stuck in Login status until LOAD DATA INFILE finsihes, this can take several minutes depending on the file size. 
This is processlist output after we changed permissions to several users to avoid them getting access during the process so Killed status might be connection being rejected: 
performance_schema> show processlist;
+--------+-----------------+---------------------+---------------------------+-------------+------+---------------------------------------------------------------+------------------------------------------------------------------------------------------------------+-----------+---------------+
| Id     | User            | Host                | db                        | Command     | Time | State                                                         | Info                                                                                                 | Rows_sent | Rows_examined |
+--------+-----------------+---------------------+---------------------------+-------------+------+---------------------------------------------------------------+------------------------------------------------------------------------------------------------------+-----------+---------------+
| 763513 | sysconfig       | 10.96.123.30:42632  | system_configurations     | Sleep       |   83 |                                                               | NULL                                                                                                 |         1 |             0 |
| 770141 | engin12         | 10.96.122.234:41073 | conf                      | Killed      |  180 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 776030 | testing         | localhost           | dsp_manager               | Query       |  103 | starting                                                      | show binary logs                                                                                     |         0 |             0 |
| 779746 | engin12         | 10.96.122.234:59783 | conf                      | Sleep       |    5 |                                                               | NULL                                                                                                 |         1 |             0 |
| 780089 | ppp             | 10.96.123.38:39834  | ppp                       | Query       |  484 | starting                                                      | commit                                                                                               |         0 |             0 |
| 785960 | ppp             | 10.96.123.38:37732  | ppp                       | Query       |  482 | starting                                                      | commit                                                                                               |         0 |             0 |
| 786387 | creat_123_serv  | 10.96.122.227:41110 | creative_approval_service | Query       |  482 | starting                                                      | commit                                                                                               |         0 |             0 |
| 786423 | testing         | localhost           | performance_schema        | Query       |    0 | starting                                                      | show processlist                                                                                     |         0 |             0 |
| 786519 | testing         | localhost           | ai                        | Query       |  840 | query end                                                     | load data local infile '/mnt/backups/db/utd/archive/20161124/ai/rrr_price_floor_10.txt' into table r |         0 |             0 |
| 788242 | slave           | 10.96.122.201:51043 | NULL                      | Binlog Dump | 1435 | Master has sent all binlog to slave; waiting for more updates | NULL                                                                                                 |         0 |             0 |
| 788358 | testing_user123 | 10.96.122.223:34029 | inventory_restriction     | Query       |  485 | starting                                                      | commit                                                                                               |         0 |             0 |
| 790646 | dspmgr          | 10.96.120.78:44732  | dsp_manager               | Killed      |  449 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 790796 | fastl123        | 10.96.122.153:56137 | fastl123_installer        | Killed      |  446 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 790797 | fastl123        | 10.96.122.153:56138 | fastl123_installer        | Killed      |  446 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 790798 | fastl123        | 10.96.122.153:56139 | fastl123_installer        | Killed      |  446 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 790799 | fastl123        | 10.96.122.153:56141 | fastl123_installer        | Killed      |  446 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 790801 | fastl123        | 10.96.122.152:52671 | fastl123_installer        | Query       |  496 | starting                                                      | commit                                                                                               |         0 |             0 |
| 790803 | fastl123        | 10.96.122.152:52673 | fastl123_installer        | Query       |  495 | starting                                                      | commit                                                                                               |         0 |             0 |
| 790901 | testingMatcher  | 10.83.125.21:53663  | testingMatcher            | Query       |  491 | starting                                                      | commit                                                                                               |         0 |             0 |
| 790910 | testingMatcher  | 10.83.125.21:53664  | testingMatcher            | Killed      |  766 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 790911 | testingMatcher  | 10.83.125.21:53665  | testingMatcher            | Killed      |  766 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 790912 | testingMatcher  | 10.83.125.21:53666  | testingMatcher            | Killed      |  766 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 790913 | testingMatcher  | 10.83.125.21:53667  | testingMatcher            | Killed      |  766 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 790914 | testingMatcher  | 10.83.125.21:53668  | testingMatcher            | Killed      |  766 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 790915 | testingMatcher  | 10.83.125.21:53669  | testingMatcher            | Killed      |  766 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 790916 | testingMatcher  | 10.83.125.21:53670  | testingMatcher            | Killed      |  766 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 790917 | testingMatcher  | 10.83.125.21:53671  | testingMatcher            | Killed      |  766 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 790918 | testingMatcher  | 10.83.125.21:53672  | testingMatcher            | Killed      |  766 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 791191 | engin12         | 10.96.122.141:58556 | arw                       | Killed      |  316 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 791210 | dspmgr          | 10.96.122.199:46862 | dsp_manager               | Killed      |  312 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 791234 | fastl123        | 10.96.122.14:37170  | fastl123_stats            | Killed      |  303 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 791422 | ppp             | 10.96.123.38:34256  | ppp                       | Killed      |  364 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 791423 | ppp             | 10.96.123.38:34258  | ppp                       | Killed      |  364 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 791424 | ppp             | 10.96.123.38:34257  | ppp                       | Killed      |  364 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 791433 | dspmgr          | 10.96.120.78:47808  | dsp_manager               | Killed      |  257 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792019 | fastl123        | 10.96.122.152:57568 | fastl123_installer        | Killed      |  415 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792020 | fastl123        | 10.96.122.152:57569 | fastl123_installer        | Killed      |  414 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792021 | fastl123        | 10.96.122.152:57570 | fastl123_installer        | Killed      |  454 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792022 | fastl123        | 10.96.122.152:57571 | fastl123_installer        | Killed      |  424 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792023 | fastl123        | 10.96.122.152:57572 | fastl123_installer        | Killed      |  440 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792054 | ai              | 10.96.122.229:46898 | ai                        | Query       |  479 | starting                                                      | commit                                                                                               |         0 |             0 |
| 792066 | testing_user123 | 10.96.122.223:49000 | inventory_restriction     | Killed      |  429 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792068 | fastl123        | 10.96.122.152:57741 | fastl123_installer        | Killed      |  444 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792073 | readonly        | 10.83.40.170:54683  | NULL                      | Query       |  473 | Sending data                                                  | SHOW GLOBAL STATUS                                                                                   |         0 |             0 |
| 792074 | testingMatcher  | 10.83.125.21:53866  | testingMatcher            | Killed      |  469 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792075 | testingMatcher  | 10.83.125.21:53867  | testingMatcher            | Killed      |  473 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 792076 | testingMatcher  | 10.83.125.21:53868  | testingMatcher            | Killed      |  473 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 792077 | testingMatcher  | 10.83.125.21:53869  | testingMatcher            | Killed      |  473 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 792078 | testingMatcher  | 10.83.125.21:53870  | testingMatcher            | Killed      |  473 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 792079 | testing         | localhost           | dsp_manager               | Killed      |  473 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792080 | testingMatcher  | 10.83.125.21:53871  | testingMatcher            | Killed      |  472 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 792081 | testingMatcher  | 10.83.125.21:53872  | testingMatcher            | Killed      |  472 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 792082 | testingMatcher  | 10.83.125.21:53873  | testingMatcher            | Killed      |  472 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 792083 | testingMatcher  | 10.83.125.21:53874  | testingMatcher            | Killed      |  472 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 792084 | testingMatcher  | 10.83.125.21:53875  | testingMatcher            | Killed      |  472 | cleaning up                                                   | NULL                                                                                                 |         1 |             0 |
| 792085 | testing         | localhost           | dsp_manager               | Killed      |  471 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792086 | testing         | localhost           | dsp_manager               | Killed      |  470 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792087 | creat_123_serv  | 10.83.124.54:44097  | NULL                      | Killed      |  470 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792088 | creat_123_serv  | 10.83.124.54:44096  | NULL                      | Killed      |  470 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792089 | creat_123_serv  | 10.83.124.54:44098  | NULL                      | Killed      |  470 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792090 | testing         | localhost           | dsp_manager               | Killed      |  469 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792091 | creat_123_serv  | 10.83.124.54:44099  | NULL                      | Killed      |  469 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792092 | creat_123_serv  | 10.83.124.54:44100  | NULL                      | Killed      |  469 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792093 | creat_123_serv  | 10.83.124.54:44101  | NULL                      | Killed      |  469 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792094 | testing         | localhost           | dsp_manager               | Killed      |  468 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792095 | creat_123_serv  | 10.83.124.53:52018  | NULL                      | Killed      |  468 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792096 | creat_123_serv  | 10.83.124.53:52019  | NULL                      | Killed      |  468 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792097 | creat_123_serv  | 10.83.124.53:52020  | NULL                      | Killed      |  468 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792098 | creat_123_serv  | 10.83.124.54:44102  | NULL                      | Killed      |  468 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792099 | creat_123_serv  | 10.83.124.54:44103  | NULL                      | Killed      |  468 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792100 | creat_123_serv  | 10.83.124.54:44104  | NULL                      | Killed      |  467 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792101 | testing         | localhost           | dsp_manager               | Killed      |  467 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792102 | creat_123_serv  | 10.83.124.53:52021  | NULL                      | Killed      |  467 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792103 | creat_123_serv  | 10.83.124.53:52022  | NULL                      | Killed      |  467 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792104 | creat_123_serv  | 10.83.124.53:52024  | NULL                      | Killed      |  467 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792105 | creat_123_serv  | 10.83.124.54:44106  | NULL                      | Killed      |  466 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792106 | creat_123_serv  | 10.83.124.54:44105  | NULL                      | Killed      |  466 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792107 | creat_123_serv  | 10.83.124.54:44108  | NULL                      | Killed      |  466 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792108 | testing         | localhost           | dsp_manager               | Killed      |  466 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792109 | creat_123_serv  | 10.83.124.53:52025  | NULL                      | Killed      |  466 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792110 | creat_123_serv  | 10.83.124.53:52026  | NULL                      | Killed      |  466 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792111 | creat_123_serv  | 10.83.124.53:52028  | NULL                      | Killed      |  466 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792112 | creat_123_serv  | 10.83.124.54:44109  | NULL                      | Killed      |  465 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792113 | creat_123_serv  | 10.83.124.54:44110  | NULL                      | Killed      |  465 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792114 | creat_123_serv  | 10.83.124.54:44111  | NULL                      | Killed      |  465 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792115 | creat_123_serv  | 10.83.124.54:44112  | NULL                      | Killed      |  465 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792116 | testing         | localhost           | dsp_manager               | Killed      |  465 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792117 | creat_123_serv  | 10.83.124.53:52029  | NULL                      | Killed      |  465 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792118 | creat_123_serv  | 10.83.124.53:52030  | NULL                      | Killed      |  465 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792119 | creat_123_serv  | 10.83.124.53:52031  | NULL                      | Killed      |  465 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792120 | fastl123        | 10.96.122.152:57910 | fastl123_installer        | Killed      |  434 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792121 | creat_123_serv  | 10.83.124.54:44113  | NULL                      | Killed      |  464 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792122 | testing         | localhost           | dsp_manager               | Killed      |  464 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792123 | creat_123_serv  | 10.83.124.53:52032  | NULL                      | Killed      |  464 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792124 | creat_123_serv  | 10.83.124.53:52033  | NULL                      | Killed      |  464 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792125 | creat_123_serv  | 10.83.124.53:52034  | NULL                      | Killed      |  464 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792126 | creat_123_serv  | 10.83.124.53:52035  | NULL                      | Killed      |  464 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792127 | creat_123_serv  | 10.83.124.54:44114  | NULL                      | Killed      |  463 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792128 | testing         | localhost           | dsp_manager               | Killed      |  463 | cleaning up                                                   | NULL                                                                                                 |         0 |             0 |
| 792129 | creat_123_serv  | 10.83.124.53:52036  | NULL                      | Killed      |  463 | login                                                         | NULL                                                                                                 |         0 |             0 |
| 792130 | creat_123_serv  | 10.83.124.54:44117  | NULL                      | Killed      |  462 | login                                                         | NULL                                                                                                 |         0 |             0 |
+--------+-----------------+---------------------+---------------------------+-------------+------+---------------------------------------------------------------+------------------------------------------------------------------------------------------------------+-----------+---------------+
101 rows in set (0.01 sec)



pt-pmp suggests some locking related release_resources mutex in thread handling used in Percona Server: 
[<email address hidden> pmp]#  perl pt-pmp -p 23791 -i 3 -s 1
Mon Nov 28 11:09:39 PST 2016

warning: no loadable sections found in added symbol-file system-supplied DSO at 0x7fff993fd000

warning: no loadable sections found in added symbol-file system-supplied DSO at 0x7fff993fd000

warning: no loadable sections found in added symbol-file system-supplied DSO at 0x7fff993fd000
    192 __lll_lock_wait(libpthread.so.0),_L_lock_1233(libpthread.so.0),pthread_mutex_lock(libpthread.so.0),THD::release_resources,handle_connection,pfs_spawn_thread,start_thread(libpthread.so.0),clone(libc.so.6)
     84 poll(libc.so.6),vio_io_wait,vio_socket_io_wait,vio_read,net_read_raw_loop,net_read_packet,my_net_read,Protocol_classic::read_packet,Protocol_classic::get_command,do_command,handle_connection,pfs_spawn_thread,start_thread(libpthread.so.0),clone(libc.so.6)
     30 libaio::??(libaio.so.1),LinuxAIOHandler::collect,LinuxAIOHandler::poll,os_aio_handler,fil_aio_wait,io_handler_thread,start_thread(libpthread.so.0),clone(libc.so.6)
     24 nanosleep(libpthread.so.0),os_thread_sleep,buf_lru_manager,start_thread(libpthread.so.0),clone(libc.so.6)
     15 pthread_cond_wait,Stage_manager::enroll_for,MYSQL_BIN_LOG::change_stage,MYSQL_BIN_LOG::ordered_commit,MYSQL_BIN_LOG::commit,ha_commit_trans,trans_commit,mysql_execute_command,mysql_parse,dispatch_command,do_command,handle_connection,pfs_spawn_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      9 pthread_cond_wait,os_event::wait_low,srv_worker_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 pthread_cond_wait,os_event::wait_low,srv_purge_coordinator_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 pthread_cond_wait,os_event::wait_low,buf_resize_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 pthread_cond_wait,os_event::wait_low,buf_dump_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 pthread_cond_wait,compress_gtid_table,pfs_spawn_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 pthread_cond_timedwait,os_event::timed_wait,os_event::wait_time_low,srv_monitor_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 pthread_cond_timedwait,os_event::timed_wait,os_event::wait_time_low,srv_error_monitor_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 pthread_cond_timedwait,os_event::timed_wait,os_event::wait_time_low,lock_wait_timeout_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 pthread_cond_timedwait,os_event::timed_wait,os_event::wait_time_low,ib_wqueue_timedwait,fts_optimize_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 pthread_cond_timedwait,os_event::timed_wait,os_event::wait_time_low,dict_stats_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 pthread_cond_timedwait,MYSQL_BIN_LOG::wait_for_update_bin_log,Binlog_sender::send_binlog,Binlog_sender::run,mysql_binlog_send,com_binlog_dump,dispatch_command,do_command,handle_connection,pfs_spawn_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 poll(libc.so.6),Mysqld_socket_listener::listen_for_connection_event,mysqld_main,__libc_start_main(libc.so.6),_start
      3 nanosleep(libpthread.so.0),os_thread_sleep,srv_master_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 __lll_lock_wait(libpthread.so.0),_L_lock_1034(libpthread.so.0),pthread_mutex_lock(libpthread.so.0),MYSQL_BIN_LOG::set_status_variables,show_binlog_vars,PFS_status_variable_cache::manifest,PFS_status_variable_cache::do_materialize_global,table_global_status::rnd_init,ha_perfschema::rnd_init,handler::ha_rnd_init,init_read_record,join_init_read_record,sub_select,JOIN::exec,TABLE_LIST::materialize_derived,join_materialize_derived,QEP_TAB::prepare_scan,sub_select,JOIN::exec,handle_query,execute_sqlcom_select,mysql_execute_command,mysql_parse,dispatch_command,do_command,handle_connection,pfs_spawn_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 __lll_lock_wait(libpthread.so.0),_L_lock_1034(libpthread.so.0),pthread_mutex_lock(libpthread.so.0),MYSQL_BIN_LOG::change_stage,MYSQL_BIN_LOG::ordered_commit,MYSQL_BIN_LOG::commit,ha_commit_trans,trans_commit,mysql_execute_command,mysql_parse,dispatch_command,do_command,handle_connection,pfs_spawn_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 do_sigwait(libpthread.so.0),sigwait(libpthread.so.0),signal_hand,pfs_spawn_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      3 do_sigwaitinfo(libc.so.6),sigwaitinfo(libc.so.6),timer_notify_thread_func,pfs_spawn_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      2 read(libpthread.so.0),my_read,my_b_fill,MYSQL_BIN_LOG::do_write_cache,MYSQL_BIN_LOG::write_cache,binlog_cache_data::flush,MYSQL_BIN_LOG::flush_thread_caches,MYSQL_BIN_LOG::process_flush_stage_queue,MYSQL_BIN_LOG::ordered_commit,MYSQL_BIN_LOG::commit,ha_commit_trans,trans_commit_stmt,mysql_execute_command,mysql_parse,dispatch_command,do_command,handle_connection,pfs_spawn_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      1 write(libpthread.so.0),my_write,_my_b_write,MYSQL_BIN_LOG::do_write_cache,MYSQL_BIN_LOG::write_cache,binlog_cache_data::flush,MYSQL_BIN_LOG::flush_thread_caches,MYSQL_BIN_LOG::process_flush_stage_queue,MYSQL_BIN_LOG::ordered_commit,MYSQL_BIN_LOG::commit,ha_commit_trans,trans_commit_stmt,mysql_execute_command,mysql_parse,dispatch_command,do_command,handle_connection,pfs_spawn_thread,start_thread(libpthread.so.0),clone(libc.so.6)
      1 ut_time_ms,buf_flush_page_cleaner_coordinator,start_thread(libpthread.so.0),clone(libc.so.6)
      1 pthread_mutex_unlock(libpthread.so.0),os_event_reset,buf_flush_page_cleaner_coordinator,start_thread(libpthread.so.0),clone(libc.so.6)
      1 ::??,::??,buf_flush_page_cleaner_coordinator,start_thread(libpthread.so.0),clone(libc.so.6)


Which is defined in sql/sql_class.cc as follows (PS 5.7.14-7): 
void THD::release_resources()
{
  DBUG_ASSERT(m_release_resources_done == false);

  Global_THD_manager::get_instance()->release_thread_id(m_thread_id);

  mysql_mutex_lock(&LOCK_status);
  add_to_status(&global_status_var, &status_var, false);
  /*
    Status queries after this point should not aggregate THD::status_var
    since the values has been added to global_status_var.
    The status values are not reset so that they can still be read
    by performance schema.
  */
  status_var_aggregated= true;
  mysql_mutex_unlock(&LOCK_status);

  /* Ensure that no one is using THD */
  mysql_mutex_lock(&LOCK_thd_data);
  mysql_mutex_lock(&LOCK_query_plan);

  /* Close connection */
#ifndef EMBEDDED_LIBRARY
  if (is_classic_protocol() && get_protocol_classic()->get_vio())
  {
    vio_delete(get_protocol_classic()->get_vio());
    get_protocol_classic()->end_net();
  }
#endif

  /* modification plan for UPDATE/DELETE should be freed. */
  DBUG_ASSERT(query_plan.get_modification_plan() == NULL);
  mysql_mutex_unlock(&LOCK_query_plan);
  mysql_mutex_unlock(&LOCK_thd_data);
  mysql_mutex_lock(&LOCK_thd_query);
  mysql_mutex_unlock(&LOCK_thd_query);

  stmt_map.reset();                     /* close all prepared statements */
  if (!cleanup_done)
    cleanup();

  mdl_context.destroy();
  ha_close_connection(this);
  /*
    Debug sync system must be closed after ha_close_connection, because
    DEBUG_SYNC is used in InnoDB connection handlerton close.
  */
#if defined(ENABLED_DEBUG_SYNC)
  /* End the Debug Sync Facility. See debug_sync.cc. */
  debug_sync_end_thread(this);
#endif /* defined(ENABLED_DEBUG_SYNC) */

  plugin_thdvar_cleanup(this, m_enable_plugins);

  DBUG_ASSERT(timer == NULL);

  if (timer_cache)
    thd_timer_destroy(timer_cache);

#ifndef EMBEDDED_LIBRARY
  if (rli_fake)
  {
    rli_fake->end_info();
    delete rli_fake;
    rli_fake= NULL;
  }
  mysql_audit_free_thd(this);
#endif

  if (current_thd == this)
    restore_globals();
  m_release_resources_done= true;
}


Seems these 3 might be related (Percona Server slow query log patch maybe?)
mysql_mutex_lock(&LOCK_thd_query);
mysql_mutex_lock(&LOCK_thd_data);
mysql_mutex_lock(&LOCK_query_plan);


Tested community version (5.7.16) with exactly the same dataset and load and problem is not present, also problem was not present in 5.6 series. 


How to repeat: 
Fire a VM with 2 cores and 2G of RAM, good IO capacity (maybe something around 10k IOPS), 1G of innodb_buffer_pool_size and load a file bigger than buffer pool capacity. We reproduced the error with files of 2G and 5G, sync_binlog=0 and innodb_flush_log_at_trx_commit=2 seems not related after few tests with different configurations. 
On a side note the table loaded is using unique keys and text fields which can increment the flushing during commit stage.