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DB

Upgrading an Ubuntu server on UpCloud to add more CPU, Memory and Disk Space

June 25, 2018 by Simon

Upgrading an Ubuntu server on UpCloud to add more CPU, Memory and Disk Space

If you have not read my previous posts I have now moved my blog from Vultr to the awesome UpCloud host (signup using this link to get $25 free credit).

Recently I compared Digital Ocean, Vultr and UpCloud Disk IO here and UpCloud came out on top by a long way (read the blog post here). Here is my blog post on moving from Vultr to UpCloud.

Spoiler: UpCloud performance is great.

Upcloud Site Speed in GTMetrix

Why Upgrade

I have 1 CPU, 1 GB memory and 50GB storage and it is running well?  I have PHP child workers set up and have set up the preferred use of memory over swap file usage.

View of htop querying processes on Ubuntu

Before UpCloud, when I had 512MB ram on Vultr I had multiple NGINX crashed a day so I used a bash script and scheduled a cron job to clear memory cache when memory fell below 100MB (view the script here).  To further increase the speed of the WordPress I have configured the OS to use memory over the disk.  About once a day free memory falls below 100MB (this is not a problem as my script clears cached items automatically).

Graph of memory falling below 100MB every day

I’d like to add more memory as I am working on some things (watch this space) and I will use the extra memory. I’d prefer the server is set up now for the expected workload.

How to Upgrade

This is how I upgraded from 1xCPU/2GB Memory/50GB Storage/2TB Transferred Data to a 2 CPU/4GB Mmeory/80GB Storage/4TB Transferred Data server.

UpCloud Pricing: https://www.upcloud.com/pricing/

Pricing table form https://www.upcloud.com/pricing/

Upgrade an UpCloud VM

I shut down my existing VM. Read this guide to setup a VM.

shutdown -P

Login to the UpCloud dashboard, select your server (confirm the server has shut down) and click General Settings, choose the upgrade and click Update.

Upgrade the Server, shut it down the server and choose upgrade

I confirmed the upgrade options (2x CPU, 4096 MB Memory).

Confirm Upgrade Options

Click Update

Upgrade Applied

After 10 seconds you can start your server from the UpCloud server.

I confirmed the CPU upgrade was visible in the VM

cat /proc/cpuinfo
processor       : 0
vendor_id       : GenuineIntel
cpu family      : 6
model           : 63
model name      : Intel(R) Xeon(R) CPU E5-2687W v3 @ 3.10GHz
stepping        : 2
microcode       : 0x1
cpu MHz         : 3099.978
cache size      : 16384 KB
physical id     : 0
siblings        : 2
core id         : 0
cpu cores       : 2
apicid          : 0
initial apicid  : 0
fpu             : yes
fpu_exception   : yes
cpuid level     : 13
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon rep_good nopl xtopology cpuid pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm invpcid_single pti fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid xsaveopt arat
bugs            : cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass
bogomips        : 6199.95
clflush size    : 64
cache_alignment : 64
address sizes   : 40 bits physical, 48 bits virtual
power management:

processor       : 1
vendor_id       : GenuineIntel
cpu family      : 6
model           : 63
model name      : Intel(R) Xeon(R) CPU E5-2687W v3 @ 3.10GHz
stepping        : 2
microcode       : 0x1
cpu MHz         : 3099.978
cache size      : 16384 KB
physical id     : 0
siblings        : 2
core id         : 1
cpu cores       : 2
apicid          : 1
initial apicid  : 1
fpu             : yes
fpu_exception   : yes
cpuid level     : 13
wp              : yes
flags           : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ss ht syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon rep_good nopl xtopology cpuid pni pclmulqdq ssse3 fma cx16 pcid sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand hypervisor lahf_lm abm invpcid_single pti fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid xsaveopt arat
bugs            : cpu_meltdown spectre_v1 spectre_v2 spec_store_bypass
bogomips        : 6199.95
clflush size    : 64
cache_alignment : 64
address sizes   : 40 bits physical, 48 bits virtual
power management:

Software Tweaks Post Upgrade.

I added these settings to the top of /etc/nginx/nginx.conf to ensure the extra CPU was used.

worker_processes auto;
worker_cpu_affinity auto;

I increased PHP FPM ( /etc/php/7.2/fpm/php.ini ) to increase memory usage and child workers. I doubled child workers and max memory limit.

memory_limit = 3072M
pm.max_children = 80
pm.start_servers = 30
pm.min_spare_servers = 10
pm.max_spare_servers = 30

I restarted NGINX and PHP

nginx -t
nginx -s reload
/etc/init.d/nginx restart
service php7.2-fpm restart

I tweaked WordPress max memory limits

define( 'WP_MEMORY_LIMIT','3072M');
define( 'WP_MAX_MEMORY_LIMIT','3072M');

MySQL Tweaks: I logged into MySQL

mysql -u root -p

I ran “SHOW GLOBAL STATUS” to view stats

mysql> SHOW GLOBAL STATUS;
+-----------------------------------------------+--------------------------------------------------+
| Variable_name                                 | Value                                            |
+-----------------------------------------------+--------------------------------------------------+
| Aborted_clients                               | 0                                                |
| Aborted_connects                              | 0                                                |
| Binlog_cache_disk_use                         | 0                                                |
| Binlog_cache_use                              | 0                                                |
| Binlog_stmt_cache_disk_use                    | 0                                                |
| Binlog_stmt_cache_use                         | 0                                                |
| Bytes_received                                | 3179986                                          |
| Bytes_sent                                    | 223872114                                        |
| Com_admin_commands                            | 0                                                |
| Com_assign_to_keycache                        | 0                                                |
| Com_alter_db                                  | 0                                                |
| Com_alter_db_upgrade                          | 0                                                |
| Com_alter_event                               | 0                                                |
| Com_alter_function                            | 0                                                |
| Com_alter_instance                            | 0                                                |
| Com_alter_procedure                           | 0                                                |
| Com_alter_server                              | 0                                                |
| Com_alter_table                               | 0                                                |
| Com_alter_tablespace                          | 0                                                |
| Com_alter_user                                | 0                                                |
| Com_analyze                                   | 0                                                |
| Com_begin                                     | 0                                                |
| Com_binlog                                    | 0                                                |
| Com_call_procedure                            | 0                                                |
| Com_change_db                                 | 284                                              |
| Com_change_master                             | 0                                                |
| Com_change_repl_filter                        | 0                                                |
| Com_check                                     | 0                                                |
| Com_checksum                                  | 0                                                |
| Com_commit                                    | 0                                                |
| Com_create_db                                 | 0                                                |
| Com_create_event                              | 0                                                |
| Com_create_function                           | 0                                                |
| Com_create_index                              | 0                                                |
| Com_create_procedure                          | 0                                                |
| Com_create_server                             | 0                                                |
| Com_create_table                              | 0                                                |
| Com_create_trigger                            | 0                                                |
| Com_create_udf                                | 0                                                |
| Com_create_user                               | 0                                                |
| Com_create_view                               | 0                                                |
| Com_dealloc_sql                               | 0                                                |
| Com_delete                                    | 18                                               |
| Com_delete_multi                              | 0                                                |
| Com_do                                        | 0                                                |
| Com_drop_db                                   | 0                                                |
| Com_drop_event                                | 0                                                |
| Com_drop_function                             | 0                                                |
| Com_drop_index                                | 0                                                |
| Com_drop_procedure                            | 0                                                |
| Com_drop_server                               | 0                                                |
| Com_drop_table                                | 0                                                |
| Com_drop_trigger                              | 0                                                |
| Com_drop_user                                 | 0                                                |
| Com_drop_view                                 | 0                                                |
| Com_empty_query                               | 0                                                |
| Com_execute_sql                               | 0                                                |
| Com_explain_other                             | 0                                                |
| Com_flush                                     | 0                                                |
| Com_get_diagnostics                           | 0                                                |
| Com_grant                                     | 0                                                |
| Com_ha_close                                  | 0                                                |
| Com_ha_open                                   | 0                                                |
| Com_ha_read                                   | 0                                                |
| Com_help                                      | 0                                                |
| Com_insert                                    | 342                                              |
| Com_insert_select                             | 0                                                |
| Com_install_plugin                            | 0                                                |
| Com_kill                                      | 0                                                |
| Com_load                                      | 0                                                |
| Com_lock_tables                               | 0                                                |
| Com_optimize                                  | 0                                                |
| Com_preload_keys                              | 0                                                |
| Com_prepare_sql                               | 0                                                |
| Com_purge                                     | 0                                                |
| Com_purge_before_date                         | 0                                                |
| Com_release_savepoint                         | 0                                                |
| Com_rename_table                              | 0                                                |
| Com_rename_user                               | 0                                                |
| Com_repair                                    | 0                                                |
| Com_replace                                   | 0                                                |
| Com_replace_select                            | 0                                                |
| Com_reset                                     | 0                                                |
| Com_resignal                                  | 0                                                |
| Com_revoke                                    | 0                                                |
| Com_revoke_all                                | 0                                                |
| Com_rollback                                  | 0                                                |
| Com_rollback_to_savepoint                     | 0                                                |
| Com_savepoint                                 | 0                                                |
| Com_select                                    | 16358                                            |
| Com_set_option                                | 849                                              |
| Com_signal                                    | 0                                                |
| Com_show_binlog_events                        | 0                                                |
| Com_show_binlogs                              | 0                                                |
| Com_show_charsets                             | 0                                                |
| Com_show_collations                           | 0                                                |
| Com_show_create_db                            | 0                                                |
| Com_show_create_event                         | 0                                                |
| Com_show_create_func                          | 0                                                |
| Com_show_create_proc                          | 0                                                |
| Com_show_create_table                         | 0                                                |
| Com_show_create_trigger                       | 0                                                |
| Com_show_databases                            | 3                                                |
| Com_show_engine_logs                          | 0                                                |
| Com_show_engine_mutex                         | 0                                                |
| Com_show_engine_status                        | 0                                                |
| Com_show_events                               | 0                                                |
| Com_show_errors                               | 0                                                |
| Com_show_fields                               | 921                                              |
| Com_show_function_code                        | 0                                                |
| Com_show_function_status                      | 0                                                |
| Com_show_grants                               | 0                                                |
| Com_show_keys                                 | 1                                                |
| Com_show_master_status                        | 0                                                |
| Com_show_open_tables                          | 0                                                |
| Com_show_plugins                              | 0                                                |
| Com_show_privileges                           | 0                                                |
| Com_show_procedure_code                       | 0                                                |
| Com_show_procedure_status                     | 0                                                |
| Com_show_processlist                          | 0                                                |
| Com_show_profile                              | 0                                                |
| Com_show_profiles                             | 0                                                |
| Com_show_relaylog_events                      | 0                                                |
| Com_show_slave_hosts                          | 0                                                |
| Com_show_slave_status                         | 0                                                |
| Com_show_status                               | 6                                                |
| Com_show_storage_engines                      | 0                                                |
| Com_show_table_status                         | 0                                                |
| Com_show_tables                               | 2                                                |
| Com_show_triggers                             | 0                                                |
| Com_show_variables                            | 6                                                |
| Com_show_warnings                             | 1                                                |
| Com_show_create_user                          | 0                                                |
| Com_shutdown                                  | 0                                                |
| Com_slave_start                               | 0                                                |
| Com_slave_stop                                | 0                                                |
| Com_group_replication_start                   | 0                                                |
| Com_group_replication_stop                    | 0                                                |
| Com_stmt_execute                              | 4                                                |
| Com_stmt_close                                | 4                                                |
| Com_stmt_fetch                                | 0                                                |
| Com_stmt_prepare                              | 4                                                |
| Com_stmt_reset                                | 0                                                |
| Com_stmt_send_long_data                       | 4                                                |
| Com_truncate                                  | 2                                                |
| Com_uninstall_plugin                          | 0                                                |
| Com_unlock_tables                             | 0                                                |
| Com_update                                    | 70                                               |
| Com_update_multi                              | 0                                                |
| Com_xa_commit                                 | 0                                                |
| Com_xa_end                                    | 0                                                |
| Com_xa_prepare                                | 0                                                |
| Com_xa_recover                                | 0                                                |
| Com_xa_rollback                               | 0                                                |
| Com_xa_start                                  | 0                                                |
| Com_stmt_reprepare                            | 0                                                |
| Connection_errors_accept                      | 0                                                |
| Connection_errors_internal                    | 0                                                |
| Connection_errors_max_connections             | 0                                                |
| Connection_errors_peer_address                | 0                                                |
| Connection_errors_select                      | 0                                                |
| Connection_errors_tcpwrap                     | 0                                                |
| Connections                                   | 292                                              |
| Created_tmp_disk_tables                       | 1124                                             |
| Created_tmp_files                             | 30                                               |
| Created_tmp_tables                            | 1369                                             |
| Delayed_errors                                | 0                                                |
| Delayed_insert_threads                        | 0                                                |
| Delayed_writes                                | 0                                                |
| Flush_commands                                | 1                                                |
| Handler_commit                                | 6094                                             |
| Handler_delete                                | 33                                               |
| Handler_discover                              | 0                                                |
| Handler_external_lock                         | 38571                                            |
| Handler_mrr_init                              | 0                                                |
| Handler_prepare                               | 0                                                |
| Handler_read_first                            | 2299                                             |
| Handler_read_key                              | 134761                                           |
| Handler_read_last                             | 237                                              |
| Handler_read_next                             | 310119                                           |
| Handler_read_prev                             | 2733                                             |
| Handler_read_rnd                              | 222350                                           |
| Handler_read_rnd_next                         | 472820                                           |
| Handler_rollback                              | 0                                                |
| Handler_savepoint                             | 0                                                |
| Handler_savepoint_rollback                    | 0                                                |
| Handler_update                                | 15605                                            |
| Handler_write                                 | 17310                                            |
| Innodb_buffer_pool_dump_status                | Dumping of buffer pool not started               |
| Innodb_buffer_pool_load_status                | Buffer pool(s) load completed at 180624 23:38:01 |
| Innodb_buffer_pool_resize_status              |                                                  |
| Innodb_buffer_pool_pages_data                 | 1035                                             |
| Innodb_buffer_pool_bytes_data                 | 16957440                                         |
| Innodb_buffer_pool_pages_dirty                | 0                                                |
| Innodb_buffer_pool_bytes_dirty                | 0                                                |
| Innodb_buffer_pool_pages_flushed              | 1936                                             |
| Innodb_buffer_pool_pages_free                 | 7144                                             |
| Innodb_buffer_pool_pages_misc                 | 13                                               |
| Innodb_buffer_pool_pages_total                | 8192                                             |
| Innodb_buffer_pool_read_ahead_rnd             | 0                                                |
| Innodb_buffer_pool_read_ahead                 | 0                                                |
| Innodb_buffer_pool_read_ahead_evicted         | 0                                                |
| Innodb_buffer_pool_read_requests              | 306665                                           |
| Innodb_buffer_pool_reads                      | 950                                              |
| Innodb_buffer_pool_wait_free                  | 0                                                |
| Innodb_buffer_pool_write_requests             | 26509                                            |
| Innodb_data_fsyncs                            | 1229                                             |
| Innodb_data_pending_fsyncs                    | 0                                                |
| Innodb_data_pending_reads                     | 0                                                |
| Innodb_data_pending_writes                    | 0                                                |
| Innodb_data_read                              | 16273920                                         |
| Innodb_data_reads                             | 1078                                             |
| Innodb_data_writes                            | 2857                                             |
| Innodb_data_written                           | 53379584                                         |
| Innodb_dblwr_pages_written                    | 1275                                             |
| Innodb_dblwr_writes                           | 109                                              |
| Innodb_log_waits                              | 0                                                |
| Innodb_log_write_requests                     | 450                                              |
| Innodb_log_writes                             | 585                                              |
| Innodb_os_log_fsyncs                          | 793                                              |
| Innodb_os_log_pending_fsyncs                  | 0                                                |
| Innodb_os_log_pending_writes                  | 0                                                |
| Innodb_os_log_written                         | 664064                                           |
| Innodb_page_size                              | 16384                                            |
| Innodb_pages_created                          | 56                                               |
| Innodb_pages_read                             | 988                                              |
| Innodb_pages_written                          | 1936                                             |
| Innodb_row_lock_current_waits                 | 0                                                |
| Innodb_row_lock_time                          | 0                                                |
| Innodb_row_lock_time_avg                      | 0                                                |
| Innodb_row_lock_time_max                      | 0                                                |
| Innodb_row_lock_waits                         | 0                                                |
| Innodb_rows_deleted                           | 2                                                |
| Innodb_rows_inserted                          | 19219                                            |
| Innodb_rows_read                              | 249102                                           |
| Innodb_rows_updated                           | 77                                               |
| Innodb_num_open_files                         | 81                                               |
| Innodb_truncated_status_writes                | 0                                                |
| Innodb_available_undo_logs                    | 128                                              |
| Key_blocks_not_flushed                        | 0                                                |
| Key_blocks_unused                             | 12751                                            |
| Key_blocks_used                               | 645                                              |
| Key_read_requests                             | 321877                                           |
| Key_reads                                     | 648                                              |
| Key_write_requests                            | 196                                              |
| Key_writes                                    | 150                                              |
| Locked_connects                               | 0                                                |
| Max_execution_time_exceeded                   | 0                                                |
| Max_execution_time_set                        | 0                                                |
| Max_execution_time_set_failed                 | 0                                                |
| Max_used_connections                          | 3                                                |
| Max_used_connections_time                     | 2018-06-24 23:43:48                              |
| Not_flushed_delayed_rows                      | 0                                                |
| Ongoing_anonymous_transaction_count           | 0                                                |
| Open_files                                    | 229                                              |
| Open_streams                                  | 0                                                |
| Open_table_definitions                        | 206                                              |
| Open_tables                                   | 786                                              |
| Opened_files                                  | 502                                              |
| Opened_table_definitions                      | 208                                              |
| Opened_tables                                 | 817                                              |
| Performance_schema_accounts_lost              | 0                                                |
| Performance_schema_cond_classes_lost          | 0                                                |
| Performance_schema_cond_instances_lost        | 0                                                |
| Performance_schema_digest_lost                | 0                                                |
| Performance_schema_file_classes_lost          | 0                                                |
| Performance_schema_file_handles_lost          | 0                                                |
| Performance_schema_file_instances_lost        | 0                                                |
| Performance_schema_hosts_lost                 | 0                                                |
| Performance_schema_index_stat_lost            | 0                                                |
| Performance_schema_locker_lost                | 0                                                |
| Performance_schema_memory_classes_lost        | 0                                                |
| Performance_schema_metadata_lock_lost         | 0                                                |
| Performance_schema_mutex_classes_lost         | 0                                                |
| Performance_schema_mutex_instances_lost       | 0                                                |
| Performance_schema_nested_statement_lost      | 0                                                |
| Performance_schema_prepared_statements_lost   | 0                                                |
| Performance_schema_program_lost               | 0                                                |
| Performance_schema_rwlock_classes_lost        | 0                                                |
| Performance_schema_rwlock_instances_lost      | 0                                                |
| Performance_schema_session_connect_attrs_lost | 0                                                |
| Performance_schema_socket_classes_lost        | 0                                                |
| Performance_schema_socket_instances_lost      | 0                                                |
| Performance_schema_stage_classes_lost         | 0                                                |
| Performance_schema_statement_classes_lost     | 0                                                |
| Performance_schema_table_handles_lost         | 0                                                |
| Performance_schema_table_instances_lost       | 0                                                |
| Performance_schema_table_lock_stat_lost       | 0                                                |
| Performance_schema_thread_classes_lost        | 0                                                |
| Performance_schema_thread_instances_lost      | 0                                                |
| Performance_schema_users_lost                 | 0                                                |
| Prepared_stmt_count                           | 0                                                |
| Qcache_free_blocks                            | 1                                                |
| Qcache_free_memory                            | 16760152                                         |
| Qcache_hits                                   | 0                                                |
| Qcache_inserts                                | 0                                                |
| Qcache_lowmem_prunes                          | 0                                                |
| Qcache_not_cached                             | 16355                                            |
| Qcache_queries_in_cache                       | 0                                                |
| Qcache_total_blocks                           | 1                                                |
| Queries                                       | 19164                                            |
| Questions                                     | 19155                                            |
| Select_full_join                              | 0                                                |
| Select_full_range_join                        | 0                                                |
| Select_range                                  | 2677                                             |
| Select_range_check                            | 0                                                |
| Select_scan                                   | 2098                                             |
| Slave_open_temp_tables                        | 0                                                |
| Slow_launch_threads                           | 0                                                |
| Slow_queries                                  | 0                                                |
| Sort_merge_passes                             | 12                                               |
| Sort_range                                    | 4859                                             |
| Sort_rows                                     | 244452                                           |
| Sort_scan                                     | 854                                              |
| Ssl_accept_renegotiates                       | 0                                                |
| Ssl_accepts                                   | 0                                                |
| Ssl_callback_cache_hits                       | 0                                                |
| Ssl_cipher                                    |                                                  |
| Ssl_cipher_list                               |                                                  |
| Ssl_client_connects                           | 0                                                |
| Ssl_connect_renegotiates                      | 0                                                |
| Ssl_ctx_verify_depth                          | 0                                                |
| Ssl_ctx_verify_mode                           | 0                                                |
| Ssl_default_timeout                           | 0                                                |
| Ssl_finished_accepts                          | 0                                                |
| Ssl_finished_connects                         | 0                                                |
| Ssl_server_not_after                          |                                                  |
| Ssl_server_not_before                         |                                                  |
| Ssl_session_cache_hits                        | 0                                                |
| Ssl_session_cache_misses                      | 0                                                |
| Ssl_session_cache_mode                        | NONE                                             |
| Ssl_session_cache_overflows                   | 0                                                |
| Ssl_session_cache_size                        | 0                                                |
| Ssl_session_cache_timeouts                    | 0                                                |
| Ssl_sessions_reused                           | 0                                                |
| Ssl_used_session_cache_entries                | 0                                                |
| Ssl_verify_depth                              | 0                                                |
| Ssl_verify_mode                               | 0                                                |
| Ssl_version                                   |                                                  |
| Table_locks_immediate                         | 11962                                            |
| Table_locks_waited                            | 0                                                |
| Table_open_cache_hits                         | 19395                                            |
| Table_open_cache_misses                       | 817                                              |
| Table_open_cache_overflows                    | 12                                               |
| Tc_log_max_pages_used                         | 0                                                |
| Tc_log_page_size                              | 0                                                |
| Tc_log_page_waits                             | 0                                                |
| Threads_cached                                | 2                                                |
| Threads_connected                             | 1                                                |
| Threads_created                               | 3                                                |
| Threads_running                               | 1                                                |
| Uptime                                        | 2944                                             |
| Uptime_since_flush_status                     | 2944                                             |
+-----------------------------------------------+--------------------------------------------------+
353 rows in set (0.00 sec)

Read more on SHOW GLOBAL STATUS here. Read more on the values here.

I can see NO major errors here (possibly due to UpClouds awesome disk IO) so I won’t be making memory tweaks in MySQL. Sign Up using this link and get $25 credit free on UpCloud and see for yourself how fast they are.

Configure Ubuntu System Memory Usage

Edit /etc/sysctl.conf

Add the following to allow things to sit in ram longer

vm.vfs_cache_pressure=50

Snip from: https://www.kernel.org/doc/Documentation/sysctl/vm.txt

This percentage value controls the tendency of the kernel to reclaim the memory which is used for caching of directory and inode objects.

At the default value of vfs_cache_pressure=100 the kernel will attempt to reclaim dentries and inodes at a "fair" rate with respect to pagecache and swapcache reclaim.  Decreasing vfs_cache_pressure causes the kernel to prefer to retain dentry and inode caches. When vfs_cache_pressure=0, the kernel will never reclaim dentries and inodes due to memory pressure and this can easily lead to out-of-memory conditions. Increasing vfs_cache_pressure beyond 100 causes the kernel to prefer to reclaim dentries and inodes.

Increasing vfs_cache_pressure significantly beyond 100 may have negative performance impact. Reclaim code needs to take various locks to find freeable directory and inode objects. With vfs_cache_pressure=1000, it will look for ten times more freeable objects than there are."

Read these pages here and here regarding setting MySQL memory.

Reboot

shutdown -r now

Resize the disk

The 2x CPU, 4GB memory plan comes with 80GB storage allowance.  My disk at present is 50GB and I will update the size soon following this guide soon.

Upgrade disk from 50gb to 80GB soon

Quick Benchmark

I used loader.io to load 500 users to access my site in 1 minute.

HTOP showing 2x busy CPU's running at 60%

The benchmark worked with no errors.

Loader.io Success with 500 concurrent users

This benchmark was performed with no Cloudflare caching. I should get Cloudflare caching working again to lower the average response time. I loaded my website manually in Google Chrome while loader.io threw 500 users at my site and it loaded very fast.

Conclusion

After a few days, I checked my memory logs and there were no low memory triggers (just normal internal memory management triggers). Ubuntu was happier.

No Low memory low triggers

This graph was taken before I set “vm.vfs_cache_pressure” so I will update this graph in a few days.

I hope this guide helps someone.

Please consider using my referral code and get $25 credit for free.

https://www.upcloud.com/register/?promo=D84793

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Revision History

1.0 Initial Post

Filed Under: Backup, Cloud, DB, Domain, GUI, NGINX, Performance, PHP, Scalability, Server, Ubuntu, UpCloud, Upgrade VM Tagged With: add, an, and, cpu, Disk, memory, more, on, server, Space, to, ubuntu, UpCloud, Upgrading

Wordfence Security Plugin for WordPress

October 10, 2017 by Simon

WordFence is a great security plugin for WordPress that allows you to secure your WordPress installation and prevent brute force attacks, rate-limit visitors (or Bots), block banned IP’s that are accessing your site and more.

Fyi

20th Dec 2017: Wordfence report Backdoor in Captcha Plugin Affects 300K WordPress Sites

Backup

Before I started I performed a quick mysql backup from the command line to ensure my WordPress is backed up. Read my guide on installing WordPress from the command line (here) and securin Ubuntu (here).

/usr/bin/mysqldump --all-databases > /mysql-database-dump-prewordfence.sql -u 'user' -p'xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx'

Don’t forget to backup your WordPress files.

sudo cp -R /www-root/* /backup/www-backup/

Download and extract WordFence

I downloaded and installed the Wordfence plugin via command line. I visited https://wordpress.org/plugins/wordfence/ and got the plugin URL for the latest version (e.g https://downloads.wordpress.org/plugin/wordfence.6.3.19.zip).

I downloaded the plugin zip file from the command line to my WordPress plugins folder. Read my guide (here) on managing WordPress from the command line.

cd /www-root/wp-content/plugins/
sudo wget https://downloads.wordpress.org/plugin/wordfence.6.3.19.zip
sudo unzip /www-root/wp-content/plugins/wordfence.6.3.19.zip
rm -R /www-root/wp-content/plugins/*.zip

Now the Wordfence plugin can be activated in WordPress.

Activate Wordfence

Enter your email to receive Wordfence alerts.

WordFence EmmiL Alerts

Your Wordfence Dashboard will show local and global issues and statistics.

WordFence Dashboard

I set these default Wordfence options.

ON

More Wordfence Options

More Options

Set Permissions (for Firewall)

You may need to create a log folder (e.g /www/wp-content/wflogs/)  and set permissions to allow Wordfence to work.

cd /www-root/wp-content/
mkdir wflogs
sudo chmod -R 777 /www-root/wp-content/wflogs/

Now I can enable the Wordfence firewall via the WordFence plugin at /wp-admin/admin.php?page=WordfenceWAF

Wordfence Firewall

Don’t forget to configure the Wordfence firewall.

WordFence Firewall

Firewall Install Options

I do not have FTP setup so I’ll do a manual install based on these instructions.

WordPress Install Options

I manually added this to my ~/nxinx/sites-available/default config.

I added this to my nginx config.

location ~ ^/\.user\.ini {
    deny all;
}

This did not work as specified in the official Wordfence docs (https://docs.wordfence.com/en/Web_Application_Firewall_FAQ#NGINX) so I added the following.

location ~ (\.ini) {
    return 403;
}

Accessing a test /test.user.ini file in a web browser returns a 403  (always test access)

403 Forbidden

nginx

I added this to my active php.ini configuration file.

auto_prepend_file = '/www-root/wordfence-waf.php'

I restart PHP.

sudo systemctl restart php7.0-fpm

I added my IP to the Wordfence whitelist textbox to ensure I am not blocked: /wp-admin/admin.php?page=WordfenceSecOpt 

Tip: Grab your IPV4 address from https://ipv4.icanhazip.com/

Recent Wordfence Scan Summary (1st Scan)

Wordfence Dashboard allows you to see local and global stats.

Recent Scan

Wordfence (In Progress) Scan summary.

Scan Summary

My Issues

Wordfence alerted me that I needed to update WordPress and some plugins  (see my guide on installing and managing your WordPress via the Command Line here).

I updated my WordPress core files (via the command line).

sudo wp core update
> Success: WordPress is up to date.

I updated my  WordPress plugins (via the command line).

sudo wp plugin update --all

Output:

>Enabling Maintenance mode...
>Downloading update from https://downloads.wordpress.org/plugin/>add-to-any.1.7.19.zip...
>Unpacking the update...
>Installing the latest version...
>Removing the old version of the plugin...
>Plugin updated successfully.
>Downloading update from https://downloads.wordpress.org/plugin/>display-posts-shortcode.2.9.0.zip...
>Unpacking the update...
>Installing the latest version...
>Removing the old version of the plugin...
>Plugin updated successfully.
>Downloading update from https://downloads.wordpress.org/plugin/>wordpress-seo.5.5.1.zip...
>Unpacking the update...
>Installing the latest version...
>Removing the old version of the plugin...
>Plugin updated successfully.
>Disabling Maintenance mode...
>+-------------------------+-------------+-------------+---------+
>| name                    | old_version | new_version | status  |
>+-------------------------+-------------+-------------+---------+
>| add-to-any              | 1.7.17      | 1.7.19      | Updated |
>| display-posts-shortcode | 2.8.0       | 2.9.0       | Updated |
>| wordpress-seo           | 5.4.2       | 5.5.1       | Updated |
>+-------------------------+-------------+-------------+---------+
>Success: Updated 3 of 3 plugins.

I manually updated my WordPress theme (from my.studiopress.com website) and uploaded via SSH

 scp ~/Downloads/genesis.2.5.3.zip [email protected]:/www-root/wp-content/themes/genesis.2.5.3.zip

I could then SSH into my server and extract the theme.

cd /www-root/wp-content/themes/
unzip genesis.2.5.3.zip
rm -R genesis.2.5.3.zip

Wordfence Dashboard

Wordfence allows you to see worldwide Blocked IP’s by the Wordfence network.

IPs

You can also see local successful or failed login attempts. The Ukraine IP 91.200.12.49 tried to log in to my WordPress installation but was banned globally as it was seen unsuccessfully logging into 900 other global servers, good work Wordfence.

Failed Logins

Attacks blocked locally.

Stats

View global WordPress attacks by countries

Global Attack Stats

Wordfence Features I like

  • Finding abandoned plugins
  • See Globally banned IP’s
  • See local failed login attempts
  • Brute force protection.
  • Stats on local blocked events.
  • Identification of old files.
  • Simple reports.

Wordfence Features I don’t like

  • Your mouse must be active in the window for scans to complete/seen.
  • Setup firewall almost requires FTP.

Wordfence: 7.02 updated (listed here)

Revised Dashboard looks nice

Wordfence 702

More to come, I will update this guide over time.

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[contact-form-7 id=”30″ title=”Ask a Question”]Revision Historyv1.2 added info on Wordfence 7.0.2

v1.1 added info on Captcha plugin backdoor detected by Wordfence

v1.0 Initial Post

etc

Filed Under: Cloud, DB, Firewall, Malware, MySQL, Security, VM, Vultr, Wordpress Tagged With: plugin, security, Wordfence, wordpress

Installing Redis 3.x onto Ubuntu 16.04

September 7, 2017 by Simon

This post will show you how to install Redis 3.x onto Ubuntu 16.04

Redis is a server-side (Lua based) schema-free open source (in Memory) NoSQL Key/Value store database that supports replication between servers. Redis has an Eventual Consistency replication between servers (over Immediate Consistency) between servers. Eventual consistency is evil in some peoples minds, eventual consistency does require different coding considerations (to guaranteed valid data but does offer speed benefits).

Redis is the worlds 9th most popular database behind Oracle, MySQL, Microsoft SQL Server, PostgreSQL, MongoDB, DB2, Microsoft Access, Cassandra. Redis is the most popular key-value store database. View the database trend chart here.

When to use Redis over MySQL or MongoDB

Here is a great guide on when to use Redis over MongoDB. Read my previous guide on building a scalable and secure MySQL Cluster.

Redis has a place where a relational database or NoSQL document stores do not (but it is more work). Read more here.

Redis is great in situations where caching or where memory is available on the server.

grep MemTotal /proc/meminfo
MemTotal:        4046404 kB

grep MemFree /proc/meminfo
MemFree:         3559244 kB

Free Memory

free -m
              total        used        free      shared  buff/cache   available
Mem:           3951         241        3213           9         496        3474

Installing Redis on Ubuntu

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install redis-server

Backup the conf file

cp /etc/redis/redis.conf /etc/redis/redis.conf.bak

Open the redis cli (and test it).

redis-cli
127.0.0.1:6379> ping
PONG

Show Redis info (from the redis-cli)

redis-cli
127.0.0.1:6379> info
# Server
redis_version:3.0.6
redis_git_sha1:00000000
redis_git_dirty:0
redis_build_id:687a2a319020fa42
redis_mode:standalone
os:Linux 4.4.0-116-generic x86_64
arch_bits:64
multiplexing_api:epoll
gcc_version:5.3.1
process_id:17920
run_id:6b657bf624b1a91f7ba40c4c8a693024ca88d887
tcp_port:6379
uptime_in_seconds:34
uptime_in_days:0
hz:10
lru_clock:11819524
config_file:/etc/redis/redis.conf

# Clients
connected_clients:1
client_longest_output_list:0
client_biggest_input_buf:0
blocked_clients:0

# Memory
used_memory:508784
used_memory_human:496.86K
used_memory_rss:6905856
used_memory_peak:508784
used_memory_peak_human:496.86K
used_memory_lua:36864
mem_fragmentation_ratio:13.57
mem_allocator:jemalloc-3.6.0

# Persistence
loading:0
rdb_changes_since_last_save:0
rdb_bgsave_in_progress:0
rdb_last_save_time:1521768930
rdb_last_bgsave_status:ok
rdb_last_bgsave_time_sec:-1
rdb_current_bgsave_time_sec:-1
aof_enabled:0
aof_rewrite_in_progress:0
aof_rewrite_scheduled:0
aof_last_rewrite_time_sec:-1
aof_current_rewrite_time_sec:-1
aof_last_bgrewrite_status:ok
aof_last_write_status:ok

# Stats
total_connections_received:2
total_commands_processed:1
instantaneous_ops_per_sec:0
total_net_input_bytes:28
total_net_output_bytes:7
instantaneous_input_kbps:0.00
instantaneous_output_kbps:0.00
rejected_connections:0
sync_full:0
sync_partial_ok:0
sync_partial_err:0
expired_keys:0
evicted_keys:0
keyspace_hits:0
keyspace_misses:0
pubsub_channels:0
pubsub_patterns:0
latest_fork_usec:0
migrate_cached_sockets:0

# Replication
role:master
connected_slaves:0
master_repl_offset:0
repl_backlog_active:0
repl_backlog_size:1048576
repl_backlog_first_byte_offset:0
repl_backlog_histlen:0

# CPU
used_cpu_sys:0.04
used_cpu_user:0.02
used_cpu_sys_children:0.00
used_cpu_user_children:0.00

# Cluster
cluster_enabled:0

# Keyspace

Benchmarking your Redis (quick)

redis-benchmark -h 127.0.0.1 -p 6379 -t set,lpush -n 100000 -q
SET: 90252.70 requests per second
LPUSH: 130548.30 requests per second

Benchmarking your Redis (slow)

redis-benchmark -n 100000
====== PING_INLINE ======
  100000 requests completed in 1.34 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

97.65% <= 1 milliseconds
99.96% <= 4 milliseconds
100.00% <= 4 milliseconds
74794.31 requests per second

====== PING_BULK ======
  100000 requests completed in 1.02 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

99.74% <= 1 milliseconds
100.00% <= 1 milliseconds
98231.83 requests per second

====== SET ======
  100000 requests completed in 0.93 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

99.99% <= 1 milliseconds
100.00% <= 1 milliseconds
107066.38 requests per second

====== GET ======
  100000 requests completed in 1.03 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

99.76% <= 1 milliseconds
99.95% <= 3 milliseconds
100.00% <= 4 milliseconds
96618.36 requests per second

====== INCR ======
  100000 requests completed in 0.87 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

99.85% <= 1 milliseconds
100.00% <= 1 milliseconds
115340.26 requests per second

====== LPUSH ======
  100000 requests completed in 0.78 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

99.89% <= 1 milliseconds
100.00% <= 1 milliseconds
128205.13 requests per second

====== LPOP ======
  100000 requests completed in 0.81 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

99.61% <= 1 milliseconds
100.00% <= 1 milliseconds
124069.48 requests per second

====== SADD ======
  100000 requests completed in 1.38 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

97.02% <= 1 milliseconds
99.97% <= 2 milliseconds
99.97% <= 3 milliseconds
100.00% <= 3 milliseconds
72516.32 requests per second

====== SPOP ======
  100000 requests completed in 1.40 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

98.36% <= 1 milliseconds
99.85% <= 4 milliseconds
99.85% <= 5 milliseconds
99.92% <= 6 milliseconds
99.95% <= 10 milliseconds
100.00% <= 10 milliseconds
71326.68 requests per second

====== LPUSH (needed to benchmark LRANGE) ======
  100000 requests completed in 1.27 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

95.40% <= 1 milliseconds
99.84% <= 2 milliseconds
99.85% <= 4 milliseconds
99.92% <= 5 milliseconds
99.98% <= 6 milliseconds
100.00% <= 6 milliseconds
78492.93 requests per second

====== LRANGE_100 (first 100 elements) ======
  100000 requests completed in 2.16 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

95.95% <= 1 milliseconds
99.81% <= 2 milliseconds
99.82% <= 3 milliseconds
99.84% <= 4 milliseconds
99.90% <= 5 milliseconds
99.93% <= 7 milliseconds
99.94% <= 8 milliseconds
99.98% <= 10 milliseconds
100.00% <= 10 milliseconds
46382.19 requests per second

====== LRANGE_300 (first 300 elements) ======
  100000 requests completed in 5.49 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

1.99% <= 1 milliseconds
91.78% <= 2 milliseconds
98.61% <= 3 milliseconds
99.65% <= 4 milliseconds
99.81% <= 5 milliseconds
99.90% <= 6 milliseconds
99.96% <= 9 milliseconds
99.96% <= 10 milliseconds
99.98% <= 11 milliseconds
100.00% <= 11 milliseconds
18221.57 requests per second

====== LRANGE_500 (first 450 elements) ======
  100000 requests completed in 8.79 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

0.04% <= 1 milliseconds
60.33% <= 2 milliseconds
86.38% <= 3 milliseconds
97.11% <= 4 milliseconds
99.24% <= 5 milliseconds
99.54% <= 6 milliseconds
99.69% <= 7 milliseconds
99.80% <= 8 milliseconds
99.87% <= 9 milliseconds
99.90% <= 10 milliseconds
99.91% <= 11 milliseconds
99.92% <= 12 milliseconds
99.93% <= 13 milliseconds
99.98% <= 14 milliseconds
99.99% <= 15 milliseconds
100.00% <= 16 milliseconds
100.00% <= 16 milliseconds
11381.74 requests per second

====== LRANGE_600 (first 600 elements) ======
  100000 requests completed in 9.66 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

0.01% <= 1 milliseconds
3.03% <= 2 milliseconds
94.78% <= 3 milliseconds
98.32% <= 4 milliseconds
98.90% <= 5 milliseconds
99.32% <= 6 milliseconds
99.60% <= 7 milliseconds
99.82% <= 8 milliseconds
99.92% <= 9 milliseconds
99.93% <= 10 milliseconds
99.94% <= 11 milliseconds
99.94% <= 12 milliseconds
99.95% <= 15 milliseconds
99.95% <= 16 milliseconds
99.95% <= 18 milliseconds
99.98% <= 19 milliseconds
99.99% <= 20 milliseconds
100.00% <= 20 milliseconds
10350.90 requests per second

====== MSET (10 keys) ======
  100000 requests completed in 1.22 seconds
  50 parallel clients
  3 bytes payload
  keep alive: 1

97.69% <= 1 milliseconds
99.95% <= 5 milliseconds
100.00% <= 6 milliseconds
82101.80 requests per second

How to save and query a simple key/value integer

127.0.0.1:6379> set testvalue 123
OK
127.0.0.1:6379> get testvalue
"123"

How to save and query a simple key/value string

127.0.0.1:6379> set testvalue "Hello World"
OK
127.0.0.1:6379> get testvalue
"Hello World"

Saving and querying multiple values

127.0.0.1:6379> mset testvalue1 "a" testvalue2 "b"
OK
127.0.0.1:6379> mget testvalue1 testvalue2
1) "a"
2) "b"

Clear all

127.0.0.1:6379> flushall
OK

Add to list (new items at the top)

127.0.0.1:6379> lpush testlist "a"
(integer) 1
127.0.0.1:6379> lpush testlist "b"
(integer) 2
127.0.0.1:6379> lpush testlist "c"
(integer) 3
127.0.0.1:6379> lrange testlist 0 -1
1) "c"
2) "b"
3) "a"

Add to list (new items at the bottom)

127.0.0.1:6379> rpush testlist "a"
(integer) 1
127.0.0.1:6379> rpush testlist "b"
(integer) 2
127.0.0.1:6379> rpush testlist "c"
(integer) 3
127.0.0.1:6379> lrange testlist 0 -1
1) "a"
2) "b"
3) "c"

Redis Documentation

redis.io

redis.io/­documentation

https://redis.io/commands/

Redis Crash Course Tutorial

More

5 uses of redis as a database.

Using Redis at scale at Twitter

Digital Ocean guide on Redis

Coming soon PHP access to Redis.

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v1.2 Removed reference to Redis 4 in the blurb.

v1.1 Oops, this was Redis 3 and not 4 (thanks, Patrik)

v1.0 Initial version

Filed Under: DB, MongoDB, NoSQL, Redis, Server, Ubuntu Tagged With: dv, nosql, redis, ubuntu

Securing Ubuntu in the cloud

August 9, 2017 by Simon

It is easy to deploy servers to the cloud within a few minutes, you can have a cloud-based server that you (or others can use). ubuntu has a great guide on setting up basic security issues but what do you need to do.

If you do not secure your server expects it to be hacked into. Below are tips on securing your cloud server.

First, read more on scanning your server with Lynis security scan.

Always use up to date software

Always use update software, malicious users can detect what software you use with sites like shodan.io (or use port scan tools) and then look for weaknesses from well-published lists (e.g WordPress, Windows, MySQL, node, LifeRay, Oracle etc). People can even use Google to search for login pages or sites with passwords in HTML (yes that simple).  Once a system is identified by a malicious user they can send automated bots to break into your site (trying millions of passwords a day) or use tools to bypass existing defences (Security researcher Troy Hunt found out it’s child’s play).

Portscan sites like https://mxtoolbox.com/SuperTool.aspx?action=scan are good for knowing what you have exposed.

You can also use local programs like nmap to view open ports

Instal nmap

sudo apt-get install nmap

Find open ports

nmap -v -sT localhost

Starting Nmap 7.01 ( https://nmap.org ) at 2017-08-08 23:57 AEST
Initiating Connect Scan at 23:57
Scanning localhost (127.0.0.1) [1000 ports]
Discovered open port 80/tcp on 127.0.0.1
Discovered open port 3306/tcp on 127.0.0.1
Discovered open port 22/tcp on 127.0.0.1
Discovered open port 9101/tcp on 127.0.0.1
Discovered open port 9102/tcp on 127.0.0.1
Discovered open port 9103/tcp on 127.0.0.1
Completed Connect Scan at 23:57, 0.05s elapsed (1000 total ports)
Nmap scan report for localhost (127.0.0.1)
Host is up (0.00020s latency).
Not shown: 994 closed ports
PORT     STATE SERVICE
22/tcp   open  ssh
80/tcp   open  http
3306/tcp open  mysql
9101/tcp open  jetdirect
9102/tcp open  jetdirect
9103/tcp open  jetdirect

Read data files from: /usr/bin/../share/nmap
Nmap done: 1 IP address (1 host up) scanned in 0.17 seconds
           Raw packets sent: 0 (0B) | Rcvd: 0 (0B)

Limit ssh connections

Read more here.

Use ufw to set limits on login attempts

sudo ufw limit ssh comment 'Rate limit hit for openssh server'

Only allow known IP’s access to your valuable ports

sudo ufw allow from 123.123.123.123/32 to any port 22

Delete unwanted firewall rules

sudo ufw status numbered
sudo ufw delete 8

Only allow known IP’s to certain ports

sudo ufw allow from 123.123.123.123 to any port 80/tcp

Also, set outgoing traffic to known active servers and ports

sudo ufw allow out from 123.123.123.123 to any port 22

Don’t use weak/common Diffie-Hellman key for SSL certificates, more information here.

openssl req -new -newkey rsa:4096 -nodes -keyout server.key -out server.csr
 
Generating a 4096 bit RSA private key
...

More info on generating SSL certs here and setting here and setting up Public Key Pinning here.

Intrusion Prevention Software

Do run fail2ban: Guide here https://www.linode.com/docs/security/using-fail2ban-for-security

I use iThemes Security to secure my WordPress and block repeat failed logins from certain IP addresses.

iThemes Security can even lock down your WordPress.

You can set iThemes to auto lock out users on x failed logins

Remember to use allowed whitelists though (it is so easy to lock yourself out of servers).

Passwords

Do have strong passwords and change the root password provided by the hosts. https://howsecureismypassword.net/ is a good site to see how strong your password is from brute force password attempts. https://www.grc.com/passwords.htm is a good site to obtain a strong password.  Do follow Troy Hunt’s blog and twitter account to keep up to date with security issues.

Configure a Firewall Basics

You should install a firewall on your Ubuntu and configure it and also configure a firewall with your hosts (e.g AWS, Vultr, Digital Ocean).

Configure a Firewall on AWS

My AWS server setup guide here. AWS allow you to configure the firewall here in the Amazon Console.

Type Protocol Port Range Source Comment
HTTP TCP 80 0.0.0.0/0 Opens a web server port for later
All ICMP ALL N/A 0.0.0.0/0 Allows you to ping
All traffic ALL All 0.0.0.0/0 Not advisable long term but OK for testing today.
SSH TCP 22 0.0.0.0/0 Not advisable, try and limit this to known IP’s only.
HTTPS TCP 443 0.0.0.0/0 Opens a secure web server port for later

Configure a Firewall on Digital Ocean

Configuring a firewall on Digital Ocean (create a $5/m server here).  You can configure your Digital Ocean droplet firewall by clicking Droplet, Networking then Manage Firewall after logging into Digital Ocean.

Configure a Firewall on Vultr

Configuring a firewall on Vultr (create a $2.5/m server here).

Don’t forget to set IP rules for IPV4 and IPV6, Only set the post you need to allow and ensure applications have strong passwords.

Ubuntu has a firewall built in (documentation).

sudo ufw status

Enable the firewall

sudo ufw enable

Adding common ports

sudo ufw allow ssh/tcp
sudo ufw logging on
sudo ufw allow 22
sudo ufw allow 80
sudo ufw allow 53
sudo ufw allow 443
sudo ufw allow 873
sudo ufw enable
sudo ufw status
sudo ufw allow http
sudo ufw allow https

Add a whitelist for your IP (use http://icanhazip.com/ to get your IP) to ensure you won’t get kicked out of your server.

sudo ufw allow from 123.123.123.123/24 to any port 22

More help here.  Here is a  good guide on ufw commands. Info on port numbers here.

https://en.wikipedia.org/wiki/List_of_TCP_and_UDP_port_numbers

If you don’t have a  Digital Ocean server for $5 a month click here and if a $2.5 a month Vultr server here.

Backups

rsync is a good way to copy files to another server or use Bacula

sudo apt install bacula

Basics

Initial server setup guide (Digital Ocean).

Sudo (admin user)

Read this guide on the Linux sudo command (the equivalent if run as administrator on Windows).

Users

List users on an Ubuntu OS (or compgen -u)

cut -d: -f1 /etc/passwd

Common output

cut -d: -f1 /etc/passwd
root
daemon
bin
sys
sync
games
man
lp
mail
news
uucp
proxy
www-data
backup
list
irc
gnats
nobody
systemd-timesync
systemd-network
systemd-resolve
systemd-bus-proxy
syslog
_apt
lxd
messagebus
uuidd
dnsmasq
sshd
pollinate
ntp
mysql
clamav

Add User

sudo adduser new_username

e.g

sudo adduser bob
Adding user `bob' ...
Adding new group `bob' (1000) ...
Adding new user `bob' (1000) with group `bob' ...
Creating home directory `/home/bob' ...
etc..

Add user to a group

sudo usermod -a -G MyGroup bob

Show users in a group

getent group MyGroup | awk -F: '{print $4}'

This will show users in a group

Remove a user

sudo userdel username
sudo rm -r /home/username

Rename user

usermod -l new_username old_username

Change user password

sudo passwd username

Groups

Show all groups

compgen -ug

Common output

compgen -g
root
daemon
bin
sys
adm
tty
disk
lp
mail
proxy
sudo
www-data
backup
irc
etc

You can create your own groups but first, you must be aware of group ids

cat /etc/group

Then you can see your systems groups and ids.

Create a group

groupadd -g 999 MyGroup

Permissions

Read this https://help.ubuntu.com/community/FilePermissions

How to list users on Ubuntu.

Read more on setting permissions here.

Chmod help can be found here.

Install Fail2Ban

I used this guide on installing Fail2Ban.

apt-get install fail2ban

Check Fail2Ban often and add blocks to the firewall of known bad IPs

fail2ban-client status

Best practices

Ubuntu has a guide on basic security setup here.

Startup Processes

It is a good idea to review startup processes from time to time.

sudo apt-get install rcconf
sudo rcconf

Accounts

  • Read up on the concept of least privilege access for apps and services here.
  • Read up on chmod permissions.

Updates

Do update your operating system often.

sudo apt-get update
sudo apt-get upgrade

Minimal software

Only install what software you need

Exploits and Keeping up to date

Do keep up to date with exploits and vulnerabilities

  • Follow 0xDUDE on twitter.
  • Read the GDI.Foundation page.
  • Visit the Exploit Database
  • Vulnerability & Exploit Database
  • Subscribe to the Security Now podcast.

Secure your applications

  • NodeJS: Enable logging in applications you install or develop.

Ban repeat Login attempts with FailBan

Fail2Ban config

sudo nano /etc/fail2ban/jail.conf
[sshd]

enabled  = true
port     = ssh
filter   = sshd
logpath  = /var/log/auth.log
maxretry = 3

Hosts File Hardening

sudo nano /etc/host.conf

Add

order bind,hosts
nospoof on

Add a whitelist with your ip on /etc/fail2ban/jail.conf (see this)

[DEFAULT]
# "ignoreip" can be an IP address, a CIDR mask or a DNS host. Fail2ban will not                          
# ban a host which matches an address in this list. Several addresses can be                             
# defined using space separator.
                                                                         
ignoreip = 127.0.0.1 192.168.1.0/24 8.8.8.8

Restart the service

sudo service fail2ban restart
sudo service fail2ban status

Intrusion detection (logging) systems

Tripwire will not block or prevent intrusions but it will log and give you a heads up with risks and things of concern

Install Tripwire.

sudo apt-get install tiger tripwire

Running Tripwire

sudo tiger

This will scan your system for issues of note

sudo tiger
Tiger UN*X security checking system
   Developed by Texas A&M University, 1994
   Updated by the Advanced Research Corporation, 1999-2002
   Further updated by Javier Fernandez-Sanguino, 2001-2015
   Contributions by Francisco Manuel Garcia Claramonte, 2009-2010
   Covered by the GNU General Public License (GPL)

Configuring...

Will try to check using config for 'x86_64' running Linux 4.4.0-89-generic...
--CONFIG-- [con005c] Using configuration files for Linux 4.4.0-89-generic. Using
           configuration files for generic Linux 4.
Tiger security scripts *** 3.2.3, 2008.09.10.09.30 ***
20:42> Beginning security report for simon.
20:42> Starting file systems scans in background...
20:42> Checking password files...
20:42> Checking group files...
20:42> Checking user accounts...
20:42> Checking .rhosts files...
20:42> Checking .netrc files...
20:42> Checking ttytab, securetty, and login configuration files...
20:42> Checking PATH settings...
20:42> Checking anonymous ftp setup...
20:42> Checking mail aliases...
20:42> Checking cron entries...
20:42> Checking 'services' configuration...
20:42> Checking NFS export entries...
20:42> Checking permissions and ownership of system files...
--CONFIG-- [con010c] Filesystem 'fuse.lxcfs' used by 'lxcfs' is not recognised as a valid filesystem
20:42> Checking for indications of break-in...
--CONFIG-- [con010c] Filesystem 'fuse.lxcfs' used by 'lxcfs' is not recognised as a valid filesystem
20:42> Performing rootkit checks...
20:42> Performing system specific checks...
20:46> Performing root directory checks...
20:46> Checking for secure backup devices...
20:46> Checking for the presence of log files...
20:46> Checking for the setting of user's umask...
20:46> Checking for listening processes...
20:46> Checking SSHD's configuration...
20:46> Checking the printers control file...
20:46> Checking ftpusers configuration...
20:46> Checking NTP configuration...
20:46> Waiting for filesystems scans to complete...
20:46> Filesystems scans completed...
20:46> Performing check of embedded pathnames...
20:47> Security report completed for simon.
Security report is in `/var/log/tiger/security.report.simon.170809-20:42'.

My Output.

sudo nano /var/log/tiger/security.report.username.170809-18:42

Security scripts *** 3.2.3, 2008.09.10.09.30 ***
Wed Aug  9 18:42:24 AEST 2017
20:42> Beginning security report for username (x86_64 Linux 4.4.0-89-generic).

# Performing check of passwd files...
# Checking entries from /etc/passwd.
--WARN-- [pass014w] Login (bob) is disabled, but has a valid shell.
--WARN-- [pass014w] Login (root) is disabled, but has a valid shell.
--WARN-- [pass015w] Login ID sync does not have a valid shell (/bin/sync).
--WARN-- [pass012w] Home directory /nonexistent exists multiple times (3) in
         /etc/passwd.
--WARN-- [pass012w] Home directory /run/systemd exists multiple times (2) in
         /etc/passwd.
--WARN-- [pass006w] Integrity of password files questionable (/usr/sbin/pwck
         -r).

# Performing check of group files...

# Performing check of user accounts...
# Checking accounts from /etc/passwd.
--WARN-- [acc021w] Login ID dnsmasq appears to be a dormant account.
--WARN-- [acc022w] Login ID nobody home directory (/nonexistent) is not
         accessible.

# Performing check of /etc/hosts.equiv and .rhosts files...

# Checking accounts from /etc/passwd...

# Performing check of .netrc files...

# Checking accounts from /etc/passwd...

# Performing common access checks for root (in /etc/default/login, /securetty, and /etc/ttytab...
--WARN-- [root001w] Remote root login allowed in /etc/ssh/sshd_config

# Performing check of PATH components...
--WARN-- [path009w] /etc/profile does not export an initial setting for PATH.
# Only checking user 'root'

# Performing check of anonymous FTP...

# Performing checks of mail aliases...
# Checking aliases from /etc/aliases.

# Performing check of `cron' entries...
--WARN-- [cron005w] Use of cron is not restricted

# Performing check of 'services' ...
# Checking services from /etc/services.
--WARN-- [inet003w] The port for service ssmtp is also assigned to service
         urd.
--WARN-- [inet003w] The port for service pipe-server is also assigned to
         service search.

# Performing NFS exports check...

# Performing check of system file permissions...
--ALERT-- [perm023a] /bin/su is setuid to `root'.
--ALERT-- [perm023a] /usr/bin/at is setuid to `daemon'.
--ALERT-- [perm024a] /usr/bin/at is setgid to `daemon'.
--WARN-- [perm001w] The owner of /usr/bin/at should be root (owned by daemon).
--WARN-- [perm002w] The group owner of /usr/bin/at should be root.
--ALERT-- [perm023a] /usr/bin/passwd is setuid to `root'.
--ALERT-- [perm024a] /usr/bin/wall is setgid to `tty'.

# Checking for known intrusion signs...
# Testing for promiscuous interfaces with /bin/ip
# Testing for backdoors in inetd.conf

# Performing check of files in system mail spool...

# Performing check for rookits...
# Running chkrootkit (/usr/sbin/chkrootkit) to perform further checks...
--WARN-- [rootkit004w] Chkrootkit has detected a possible rootkit installation
Possible Linux/Ebury - Operation Windigo installetd

# Performing system specific checks...
# Performing checks for Linux/4...

# Checking boot loader file permissions...
--WARN-- [boot02] The configuration file /boot/grub/menu.lst has group
         permissions. Should be 0600
--FAIL-- [boot02] The configuration file /boot/grub/menu.lst has world
         permissions. Should be 0600
--WARN-- [boot06] The Grub bootloader does not have a password configured.

# Checking for vulnerabilities in inittab configuration...

# Checking for correct umask settings for init scripts...
--WARN-- [misc021w] There are no umask entries in /etc/init.d/rcS

# Checking Logins not used on the system ...

# Checking network configuration
--FAIL-- [lin013f] The system is not protected against Syn flooding attacks
--WARN-- [lin017w] The system is not configured to log suspicious (martian)
         packets

# Verifying system specific password checks...

# Checking OS release...
--WARN-- [osv004w] Unreleased Debian GNU/Linux version `stretch/sid'

# Checking installed packages vs Debian Security Advisories...

# Checking md5sums of installed files

# Checking installed files against packages...
--WARN-- [lin001w] File `/lib/modules/4.4.0-87-generic/modules.dep' does not
         belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-87-generic/modules.alias.bin' does
         not belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-87-generic/modules.devname' does
         not belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-87-generic/modules.softdep' does
         not belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-87-generic/modules.alias' does not
         belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-87-generic/modules.symbols.bin'
         does not belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-87-generic/modules.builtin.bin'
         does not belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-87-generic/modules.symbols' does
         not belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-87-generic/modules.dep.bin' does
         not belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-89-generic/modules.dep' does not
         belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-89-generic/modules.alias.bin' does
         not belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-89-generic/modules.devname' does
         not belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-89-generic/modules.softdep' does
         not belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-89-generic/modules.alias' does not
         belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-89-generic/modules.symbols.bin'
         does not belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-89-generic/modules.builtin.bin'
         does not belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-89-generic/modules.symbols' does
         not belong to any package.
--WARN-- [lin001w] File `/lib/modules/4.4.0-89-generic/modules.dep.bin' does
         not belong to any package.
--WARN-- [lin001w] File `/lib/udev/hwdb.bin' does not belong to any package.

# Performing check of root directory...

# Checking device permissions...
--WARN-- [dev003w] The directory /dev/block resides in a device directory.
--WARN-- [dev003w] The directory /dev/char resides in a device directory.
--WARN-- [dev003w] The directory /dev/cpu resides in a device directory.
--FAIL-- [dev002f] /dev/fuse has world permissions
--WARN-- [dev003w] The directory /dev/hugepages resides in a device directory.
--FAIL-- [dev002f] /dev/kmsg has world permissions
--WARN-- [dev003w] The directory /dev/lightnvm resides in a device directory.
--WARN-- [dev003w] The directory /dev/mqueue resides in a device directory.
--FAIL-- [dev002f] /dev/rfkill has world permissions
--WARN-- [dev003w] The directory /dev/vfio resides in a device directory.

# Checking for existence of log files...
--FAIL-- [logf005f] Log file /var/log/btmp permission should be 660
--FAIL-- [logf007f] Log file /var/log/messages does not exist

# Checking for correct umask settings for user login shells...
--WARN-- [misc021w] There is no umask definition for the dash shell
--WARN-- [misc021w] There is no umask definition for the bash shell

# Checking symbolic links...

# Performing check of embedded pathnames...
20:47> Security report completed for username.

More on Tripwire here.

Hardening PHP

Hardening PHP config (and backing the PHP config it up), first create an info.php file in your website root folder with this info

<?php
phpinfo()
?>

Now look for what PHP file is loadingPHP Config

Back that your PHP config file

TIP: Delete the file with phpinfo() in it as it is a security risk to leave it there.

TIP: Read the OWASP cheat sheet on using PHP securely here and securing php.ini here.

Some common security changes

file_uploads = On
expose_php = Off
error_reporting = E_ALL
display_errors          = Off
display_startup_errors  = Off
log_errors              = On
error_log = /php_errors.log
ignore_repeated_errors  = Off

Don’t forget to review logs, more config changes here.

Antivirus

Yes, it is a good idea to run antivirus in Ubuntu, here is a good list of antivirus software

I am installing ClamAV as it can be installed on the command line and is open source.

sudo apt-get install clamav

ClamAV help here.

Scan a folder

sudo clamscan --max-filesize=3999M --max-scansize=3999M --exclude-dir=/www/* -i -r /

Setup auto-update antivirus definitions

sudo dpkg-reconfigure clamav-freshclam

I set auto updates 24 times a day (every hour) via daemon updates.

tip: Download manual antivirus update definitions. If you only have a 512MB server your update may fail and you may want to stop fresh claim/php/nginx and mysql before you update to ensure the antivirus definitions update. You can move this to a con job and set this to update at set times over daemon to ensure updates happen.

sudo /etc/init.d/clamav-freshclam stop

sudo service php7.0-fpm stop
sudo /etc/init.d/nginx stop
sudo /etc/init.d/mysql stop

sudo freshclam -v
Current working dir is /var/lib/clamav
Max retries == 5
ClamAV update process started at Tue Aug  8 22:22:02 2017
Using IPv6 aware code
Querying current.cvd.clamav.net
TTL: 1152
Software version from DNS: 0.99.2
Retrieving http://db.au.clamav.net/main.cvd
Trying to download http://db.au.clamav.net/main.cvd (IP: 193.1.193.64)
Downloading main.cvd [100%]
Loading signatures from main.cvd
Properly loaded 4566249 signatures from new main.cvd
main.cvd updated (version: 58, sigs: 4566249, f-level: 60, builder: sigmgr)
Querying main.58.82.1.0.C101C140.ping.clamav.net
Retrieving http://db.au.clamav.net/daily.cvd
Trying to download http://db.au.clamav.net/daily.cvd (IP: 193.1.193.64)
Downloading daily.cvd [100%]
Loading signatures from daily.cvd
Properly loaded 1742284 signatures from new daily.cvd
daily.cvd updated (version: 23644, sigs: 1742284, f-level: 63, builder: neo)
Querying daily.23644.82.1.0.C101C140.ping.clamav.net
Retrieving http://db.au.clamav.net/bytecode.cvd
Trying to download http://db.au.clamav.net/bytecode.cvd (IP: 193.1.193.64)
Downloading bytecode.cvd [100%]
Loading signatures from bytecode.cvd
Properly loaded 66 signatures from new bytecode.cvd
bytecode.cvd updated (version: 308, sigs: 66, f-level: 63, builder: anvilleg)
Querying bytecode.308.82.1.0.C101C140.ping.clamav.net
Database updated (6308599 signatures) from db.au.clamav.net (IP: 193.1.193.64)

sudo service php7.0-fpm restart
sudo /etc/init.d/nginx restart
sudo /etc/init.d/mysql restart 

sudo /etc/init.d/clamav-freshclam start

Manual scan with a bash script

Create a bash script

mkdir /script
sudo nano /scripts/updateandscanav.sh

# Include contents below.
# Save and quit

chmod +X /scripts/updateandscanav.sh

Bash script contents to update antivirus definitions.

sudo /etc/init.d/clamav-freshclam stop

sudo service php7.0-fpm stop
sudo /etc/init.d/nginx stop
sudo /etc/init.d/mysql stop

sudo freshclam -v

sudo service php7.0-fpm restart
sudo /etc/init.d/nginx restart
sudo /etc/init.d/mysql restart

sudo /etc/init.d/clamav-freshclam start

sudo clamscan --max-filesize=3999M --max-scansize=3999M -v -r /

Edit the crontab to run the script every hour

crontab -e
1 * * * * /bin/bash /scripts/updateandscanav.sh > /dev/null 2>&1

Uninstalling Clam AV

You may need to uninstall Clamav if you don’t have a lot of memory or find updates are too big.

sudo apt-get remove --auto-remove clamav
sudo apt-get purge --auto-remove clamav

Setup Unattended Ubuntu Security updates

sudo apt-get install unattended-upgrades
sudo unattended-upgrades -d

At login, you should receive

0 updates are security updates.

Other

  • Read this awesome guide.
  • install Fail2Ban
  • Do check your log files if you suspect suspicious activity.

Check out the extensive Hardening a Linux Server guide at thecloud.org.uk: https://thecloud.org.uk/wiki/index.php?title=Hardening_a_Linux_Server

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  • Application scalability on a budget (my journey)
  • Monitor server performance with NixStats and receive alerts by SMS, Push, Email, Telegram etc
  • Why I will never buy a new Apple Laptop until they fix the hardware cooling issues.

Wordpress

  • Replacing Google Analytics with Piwik/Matomo for a locally hosted privacy focused open source analytics solution
  • Setting web push notifications in WordPress with OneSignal
  • Telstra promised Fibre to the house (FTTP) when I had FTTN and this is what happened..
  • Check the compatibility of your WordPress theme and plugin code with PHP Compatibility Checker
  • Add two factor auth login protection to WordPress with YubiCo hardware YubiKeys and or 2FA Authenticator App
  • Monitor server performance with NixStats and receive alerts by SMS, Push, Email, Telegram etc
  • Upgraded to Wordfence Premium to get real-time login defence, malware scanner and two-factor authentication for WordPress logins
  • Wordfence Security Plugin for WordPress
  • Speeding up WordPress with the ewww.io ExactDN CDN and Image Compression Plugin
  • Installing and managing WordPress with WP-CLI from the command line on Ubuntu
  • Moving WordPress to a new self managed server away from CPanel
  • Moving WordPress to a new self managed server away from CPanel

General

  • Backing up your computer automatically with BackBlaze software (no data limit)
  • How to back up an iPhone (including photos and videos) multiple ways
  • US v Huawei: The battle for 5G
  • Using the WinSCP Client on Windows to transfer files to and from a Linux server over SFTP
  • Connecting to a server via SSH with Putty
  • Setting web push notifications in WordPress with OneSignal
  • Infographic: So you have an idea for an app
  • Restoring lost files on a Windows FAT, FAT32, NTFS or Linux EXT, Linux XFS volume with iRecover from diydatarecovery.nl
  • Building faster web apps with google tools and exceed user expectations
  • Why I will never buy a new Apple Laptop until they fix the hardware cooling issues.
  • Telstra promised Fibre to the house (FTTP) when I had FTTN and this is what happened..

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