memory

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

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).

Read the full article here: https://fearby.com/article/upgrading-an-ubuntu-server-on-upcloud-to-add-more-cpu-memory-and-disk-space/

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.

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.

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/

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.

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

Click Update

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 the memory usage and child workers. I doubled child workers and max memeory 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.

Quick Benchmark

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

The benchmark worked with no errors.

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.

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

Upgrading the RAM, CPU and Memory on a Vultr Ubuntu VM in the cloud

Upgrading the RAM, CPU and Memory on a Vultr Ubuntu VM in the cloud is quite simple.

I have a number of guides on moving hasting away form CPanel, Setting up VM’s on AWS, Vultr or Digital Ocean along with installing and managing WordPress from the command line. I prefer Vultr as they are located in the country (Australia) and are easy to use.

First, you need to shut down the server from within the VM (SSH), I used the command.

sudo shutdown now

Once the VM is shut down (wait a few minutes) you can turn off the VM in the Vultr GUI.

You can then go to Settings, Change Plan and review upgrade options.

Snapshot

Don’t forget to take a final snapshot.

Goto the Snapshots page (read this guide to restore a snapshot) and click Take Snapshot.

You can see snapshot progress on the main screen.

It may take a while for your snapshot to change from Pending to Processing.

Upgrade

When the snapshot is done it will auto boot and allow you to upgrade.

Choose the Upgrade specifications (Settings, Change Plan)

Click Upgrade

Confirm

The upgrade process will take a few minutes (I could see the CU and Ram was updated but the Storage was pending)

Testing

After the upgrade happened the VM will autoboot, login and check tour specifications (Useful Linux Commands).

I use the htop command to view specification information.

I did a quick benchmark pre-optimizing and I can see a speed bump of 0.2s. Time to optimize.

I threw 50 concurrent clients at my website (with loader.io) and the server handled it fine with no increase above memory capacity like before.

Optimize

Now I need to Optimize. Truth be told I did optimize and harden PHP and crashed PHP-FPM so I had o restore a VM snapshot.

Troubleshooting

If all else fails (post-upgrade configuration) you can restore the Vultr VM from a snapshot.

I hope this guide helps someone.

P.S If you don’t have a VM on Vultr click this link to set one up in minutes (setup guide here).

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Revision History

v1.0 Initial post

How to upgrade a Digital Ocean Ubuntu VM and increase the vCPU or memory

This blog post will show you how you can increase the memory and CPU allocation of an Ubuntu Server (Droplet) on Digital Ocean.

If you don’t have an Ubuntu server on Digital Ocean use this link ( https://m.do.co/c/99a5082b6de5 ) and get $10 free credit (2 months free). Read my guide here on setting it up.

Before you begin, ensure you have backed up your server. You can read here about setting up a new server on Digital Ocean from scratch, connecting to your server via SCP or automatically syncing files away from your server to another server with rsync .

In Jan 2018 Digital Ocean doubled the ram of $5/m servers from 512MB to 1GB so it’s time for me to get the free upgrade.

Connect to your server (via SSH or Web Console) and shut it down

shutdown -h now

After the server has shut down login to digital Ocean GUI and click (open) the server you want to upgrade.

Click Resize and choose the new upgraded server capacity

Click Resize (if the resize button is disabled you need to power off the server (via command line or via the power menu in Digital Ocean for the Droplet))

Click the Power On button under the Access tab when the resize is completed to restart the VM.

Congratulations, you will now have an upgraded server 🙂 Thank You Digital Ocean for the free RAM.

If you don’t have an Ubuntu server on Digital Ocean use this link ( https://m.do.co/c/99a5082b6de5 ) and get $10 free credit (2 months free). Read my guide here on setting it up.

Hope this helps someone.

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v1.0 Initial Post

Computer hardware, clock cycles and code ramblings

Modern computers have insane amounts of processing power compared to computers from 5 years ago. Computer memory and storage is cheap but that is no excuse to design and develop bloated webpages and apps. Consumers and customers are very impatient and there are loads of statistics on users abandoning an app or website because it takes more than three seconds to respond or load an app.

You can control the speed of software running on your home computer by upgrading it but you cannot guarantee the performance of apps that run on shared hosting platforms or web hosts. You can buy a CPanel based web-host or a dedicated server from $5 a month, how can they make money? They do this by virtually hosting your service (web server etc) alongside other hosts and running multiple services on a single processor core. Shared servers are very economical but you are sharing the resources with other users.

If you want maximum performance you can always buy a dedicated server from a cloud server provider but each provider may secretly share the resource’s of that server (more information here: http://blog.cloudharmony.com/2014/07/comparing-cloud-compute-services.html ) and performance may be impacted. Dedicated servers can be very expensive and can run into thousands of dollars per month.

So what can I control?

Writing (or installing) good code is essential, try and optimize everything and know your server’s limitations and bottlenecks. To understand bottlenecks, you need to know about computer hardware. A few lines of code can trigger millions or billions of actions inside a processor.

A computer has the following major components:

Hard drive (HDD/SSD): This is where your operating system, software and files are stored when the computer is turned off. Hard drives store magnetic charges (0’s and 1’s) onto spinning round metal platters. A zero is a negative charge and a 1 is a positive charge. Hard drives spin at 5400~15,000 RPM. Data is written with a read/write needle that needs to be positioned over the data bit to read and write. Hard drives are very slow but reliable and each data bit can be read/written to tens of thousands of times. Faster solid state drives don’t use spinning metal platters and work a bit like memory (see below). Solid State drives have limited writes per sector though. Read More: https://en.wikipedia.org/wiki/Hard_disk_drive

Memory (RAM): Computer memory is basically a large array or very fast storage that the processor reads and writes data (0’s and 1’s). Memory is like a massive spreadsheet grid and accessing data from memory is 1000x faster than accessing data from a hard drive. Memory stores data as static charges in silicon microchips and each storage bit can be changed millions of times. When a computer is turned off the memory is wiped. Read More: https://en.wikipedia.org/wiki/Computer_memory

Processor (CPU): This is the chip that does the primary calculations and controls just about everything. A processor can perform various pre determined functions and read and write to memory/hard drives or send data over a USB cable or network connection. Processor’s are quite dumb and it has to keep queues (pipelines) of things to do in it’s internal cache (memory) between cycles. A clock cycle is single step where the processor (and all of it’s cores) do one thing and get ready for the next clock cycle, all clock cycles in a software routine are linked and if one instruction fails all following linked instructions have to be cleared and dealt with or errors and blue screens can happen. A processors speed is a total of how may clock cycles it can perform in a second and a modern computer can process 3,500,000,000 (3.5 Ghz) cycles a second. A processor can calculate one complex instruction or multiple simple instructions in one cycle. Most processor have multiple cores that can each perform calculations in a clock cycle. But don’t be fooled many clock cycles are spent waiting for data to be read/written from memory/hard drive or loaded from the processors cache. A processors instruction pipeline has 4 main states for each possible action in a cycles execution pipeline (“Fetch”, “Decode”, “Execute” and “Write back”). (e.g The processor may be asked to add (fetch) variable1+variable2, the (decode) gets the values from memory, (execute) performs the calculation and “write back” writes the result back to memory. ) See a complete list of Intel instruction here and here ). Read More: https://en.wikipedia.org/wiki/Central_processing_unit

Processors are mostly waiting for data to be fetched to be processed. There is no such thing as 100% efficient code.

If software needs to read a file from a spinning hard drive has a mandatory latency period (https://en.wikipedia.org/wiki/Hard_disk_drive_performance_characteristics ) where the hard drives read needle moves in or out and reads the data form the right sectors and returns the data. A 3.5 Ghz computer has to wait an approximate 19,460,000 clock cycles for a sector on a hard drive to be under the read head. The data still has to be moved from the hard drive through the processor and into memory. Luckily processors have fantastic calculation branch prediction abilities ( https://en.wikipedia.org/wiki/Branch_predictor) and even though the software has asked for a file to be read the processor can work on 19 million other cycles before checking to see if the data has returned from the hard drive.

Caching content

One solution is to have software or servers cache certain files in memory to speed up the delivery of files. The latest DDR4 computer memory runs as blistering speeds of 2,400Mhz (2,400,000,000 cycles a second) so it should keep up with a 2.4Ghz computer? Memory is cheap and fast but computer memory has a huge limitation. You can’t just ask memory to return the value of a memory cell and expect it in a few cycles. The processor has to essentially guide the memory module to activate the required electrical columns and rows to allow that that value to be read and return it to a processor. This is like a giving instruction to a driver over a phone, it takes time for the driver to listen, turn a corner, drive down a street and then turn another corner just to get to the destination. The processor has to manage millions of memory read and writes a second. Memory can’t direct itself to the memory value, the processor has to do that.

Memory timings are called RAM timings and it is explained better here ( http://www.hardwaresecrets.com/understanding-ram-timings/ ). It takes modern DDR4 memory module about 15 clock cycles to just enable the column circuit for a memory cell to be activated, then another 15 clock cycles to activate the row and a whole load of other cycles to read the data. Reading a 1 MB file from memory may take 100,000,000 clock cycles (and that is not factoring in the processor is working on other tasks. A computer process is a name given to software code that has been handed over to the processor, software code is loaded into the processor/memory as instructions and depending on the code and user interactions different parts of the software’s instructions are loaded into the processor. In any given second a computer program may enter and leave a processor over 1,000 times and processors internal memory is quite small.

Benchmarking

Choosing a good host to place your website/mobile app or API’s is very important, sometimes the biggest provider is not the fastest. You should benchmark how long actions take on your site and what the theoretical maximum limit is. Do you need more memory or cores? Hosts will always sell you more resources for money.

http://www.webpagetest.org/ is a great site to benchmark how long your website takes to deliver each part of your website to customers around the world. You can minify (shrink) your code and images to reduce the processing time per page load.

If you are keen research PHP caching plugins like OpCache ( http://php.net/manual/en/book.opcache.php ), MemcahedD (https://www.digitalocean.com/community/tutorials/how-to-install-and-use-memcache-on-ubuntu-14-04) for PHP or MySQL or WordPress WP-Total-Cache (https://wordpress.org/plugins/w3-total-cache/ ) plugin.

Placing your website or application databases close to your customers. In Australia, it takes 1/5 of a second minimum for a server outside of Australia to respond. A website that loads 30 resources would also add the delays between your server and customers (30×1/5 of a second add’s up).

Consider merging and minifying website resources ( http://www.minifyweb.com/ ) to lower the number of files and file sizes that you deliver to users. Most importantly monitor your website 24/7 to see if it is slowing down. I use http://monitis.com to monitor server performance remotely.

Summary

I hope I have not confused you too much. Try some videos below to learn more.

Good Videos:

How a CPU Works:

How Processors are Made:

How a Hard Drive works in Slow Motion – The Slow Mo Guys

What’s Inside a CPU?

Zoom Into a Microchip (Narrated)

How computers work in less than 20 minutes

Read some of my other development related guides here https://fearby.com/

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Caching MySQL queries in memory for xx seconds

PHP Opcache is a good caching plugin for PHP but what if you wanted a quicker in code way of selectively caching MySQL results in memory. More information on the underlying memcached.

Official Description:

Description: A high-performance memory object caching system. Danga Interactive developed memcached to enhance the speed of LiveJournal.com, a site which was already doing 20 million+ dynamic page views per day for 1 million users with a bunch of webservers and a bunch of database servers. memcached dropped the database load to almost nothing, yielding faster page load times for users, better resource utilization, and faster access to the databases on a memcache miss.

Danga Interactive developed memcached to enhance the speed of LiveJournal.com, a site which was already doing 20 million+ dynamic page views per day for 1 million users with a bunch of webservers and a bunch of database servers. memcached dropped the database load to almost nothing, yielding faster page load times for users, better resource utilization, and faster access to the databases on a memcache miss.

Memcached optimizes specific high-load serving applications that are designed to take advantage of its versatile no-locking memory access system. Clients are available in several different programming languages, to suit the needs of the specific application. Traditionally this has been used in mod_perl apps to avoid storing large chunks of data in Apache memory, and to share this burden across several machines. Caching other content is a good idea too.

Homepage: http://www.danga.com/memcached/

Follow this guide to install memcached.

Here is a simple script to query and cache MySQL data for 10 seconds.

$start = microtime(true);

$mem = new Memcached();
$mem->addServer("127.0.0.1", 11211);

mysql_connect("localhost", "dbuser", "dbpass") or die(mysql_error());
mysql_select_db("databasename") or die(mysql_error());

$query = "SELECT COUNT(*) AS TotalUsers FROM databasename WHERE 1";
$querykey = "TotalUsers" . md5($query);

$result = $mem->get($querykey);

if ($result) {
    
    print "

Data was: " . $result[0] . "

";
    print "

Caching success!

Retrieved data from memcached!

";

} else {
    
    $result = mysql_fetch_array(mysql_query($query)) or die(mysql_error());
    $mem->set($querykey, $result, 10);
    print "

Data was: " . $result[0] . "

";
    print "

Data not found in memcached.

Data retrieved from MySQL and stored in memcached for next time.

";
}

$end = microtime(true);
$time = number_format(($end - $start), 6);
 
echo 'This page loaded in ', $time, ' seconds';

For me, the cached page loaded 0.022076 seconds faster than without Memcache per page. A small MySQL database is fast but a cached database is faster.
V1.2 added memcached link

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

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

How to upgrade a Digital Ocean Ubuntu VM and increase the vCPU or memory

Computer hardware, clock cycles and code ramblings

Caching MySQL queries in memory for xx seconds

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