The wait operation timed out

I am relatively new to MVC code first application development and I was trying to host an MVC code first application in a VPS. when tried to browse the website after publishing the application I was getting a wait operation timed out error. I tried to do a bit of research and found out enabling TCP/IP on SQL Configuration manager helped some but I had no luck. Added below is the stack trace, anyone know whats the issue please ?

[Win32Exception (0x80004005): The wait operation timed out]

[SqlException (0x80131904): Connection Timeout Expired.  The timeout period elapsed while attempting to consume the pre-login handshake acknowledgement.  This could be because the pre-login handshake failed or the server was unable to respond back in time.  The duration spent while attempting to connect to this server was - [Pre-Login] initialization=4223; handshake=2965; ]
   System.Data.ProviderBase.DbConnectionPool.TryGetConnection(DbConnection owningObject, UInt32 waitForMultipleObjectsTimeout, Boolean allowCreate, Boolean onlyOneCheckConnection, DbConnectionOptions userOptions, DbConnectionInternal& connection) +356
   System.Data.ProviderBase.DbConnectionPool.TryGetConnection(DbConnection owningObject, TaskCompletionSource`1 retry, DbConnectionOptions userOptions, DbConnectionInternal& connection) +117
   System.Data.ProviderBase.DbConnectionFactory.TryGetConnection(DbConnection owningConnection, TaskCompletionSource`1 retry, DbConnectionOptions userOptions, DbConnectionInternal oldConnection, DbConnectionInternal& connection) +267
   System.Data.ProviderBase.DbConnectionInternal.TryOpenConnectionInternal(DbConnection outerConnection, DbConnectionFactory connectionFactory, TaskCompletionSource`1 retry, DbConnectionOptions userOptions) +318
   System.Data.SqlClient.SqlConnection.TryOpenInner(TaskCompletionSource`1 retry) +211
   System.Data.SqlClient.SqlConnection.TryOpen(TaskCompletionSource`1 retry) +393
   System.Data.SqlClient.SqlConnection.Open() +122
   System.Data.Entity.Infrastructure.Interception.InternalDispatcher`1.Dispatch(TTarget target, Action`2 operation, TInterceptionContext interceptionContext, Action`3 executing, Action`3 executed) +104
   System.Data.Entity.Infrastructure.Interception.DbConnectionDispatcher.Open(DbConnection connection, DbInterceptionContext interceptionContext) +509
   System.Data.Entity.Migrations.DbMigrator.ExecuteStatementsInternal(IEnumerable`1 migrationStatements, DbConnection connection) +335
   System.Data.Entity.SqlServer.<>c__DisplayClass1.<Execute>b__0() +15
   System.Data.Entity.SqlServer.DefaultSqlExecutionStrategy.Execute(Func`1 operation) +238
   System.Data.Entity.Migrations.DbMigrator.ExecuteStatements(IEnumerable`1 migrationStatements, DbTransaction existingTransaction) +271
   System.Data.Entity.Migrations.DbMigrator.ExecuteOperations(String migrationId, VersionedModel targetModel, IEnumerable`1 operations, IEnumerable`1 systemOperations, Boolean downgrading, Boolean auto) +1232
   System.Data.Entity.Migrations.DbMigrator.ApplyMigration(DbMigration migration, DbMigration lastMigration) +524
   System.Data.Entity.Migrations.DbMigrator.Upgrade(IEnumerable`1 pendingMigrations, String targetMigrationId, String lastMigrationId) +193
   System.Data.Entity.Migrations.DbMigrator.UpdateInternal(String targetMigration) +609
   System.Data.Entity.Migrations.DbMigrator.EnsureDatabaseExists(Action mustSucceedToKeepDatabase) +613
   System.Data.Entity.Migrations.DbMigrator.Update(String targetMigration) +116
   System.Data.Entity.MigrateDatabaseToLatestVersion`2.InitializeDatabase(TContext context) +156
   System.Data.Entity.Internal.InternalContext.PerformInitializationAction(Action action) +72
   System.Data.Entity.Internal.InternalContext.PerformDatabaseInitialization() +483
   System.Data.Entity.Internal.RetryAction`1.PerformAction(TInput input) +177
   System.Data.Entity.Internal.LazyInternalContext.InitializeDatabaseAction(Action`1 action) +274
   System.Data.Entity.Internal.InternalContext.ForceOSpaceLoadingForKnownEntityTypes() +63
   System.Data.Entity.DbContext.System.Data.Entity.Infrastructure.IObjectContextAdapter.get_ObjectContext() +31
   OfficeTrack.DAL.Context.MasterContext..ctor() +47
   OfficeTrack.Web.MvcApplication.Application_Start() +206

[HttpException (0x80004005): Connection Timeout Expired.  The timeout period elapsed while attempting to consume the pre-login handshake acknowledgement.  This could be because the pre-login handshake failed or the server was unable to respond back in time.  The duration spent while attempting to connect to this server was - [Pre-Login] initialization=4223; handshake=2965; ]
   System.Web.HttpApplicationFactory.EnsureAppStartCalledForIntegratedMode(HttpContext context, HttpApplication app) +544
   System.Web.HttpApplication.RegisterEventSubscriptionsWithIIS(IntPtr appContext, HttpContext context, MethodInfo[] handlers) +186
   System.Web.HttpApplication.InitSpecial(HttpApplicationState state, MethodInfo[] handlers, IntPtr appContext, HttpContext context) +172
   System.Web.HttpApplicationFactory.GetSpecialApplicationInstance(IntPtr appContext, HttpContext context) +402
   System.Web.Hosting.PipelineRuntime.InitializeApplication(IntPtr appContext) +343

[HttpException (0x80004005): Connection Timeout Expired.  The timeout period elapsed while attempting to consume the pre-login handshake acknowledgement.  This could be because the pre-login handshake failed or the server was unable to respond back in time.  The duration spent while attempting to connect to this server was - [Pre-Login] initialization=4223; handshake=2965; ]
   System.Web.HttpRuntime.FirstRequestInit(HttpContext context) +579
   System.Web.HttpRuntime.EnsureFirstRequestInit(HttpContext context) +112
   System.Web.HttpRuntime.ProcessRequestNotificationPrivate(IIS7WorkerRequest wr, HttpContext context) +712

I had the same problem. Some SQL upgrade command was very long running and caused the error because the default timeout is set to 30 seconds. I've found the following article on SO to overcome this issue: EF Code First - Timeout expired. The timeout period elapsed prior to completion

For me, it worked setting the CommandTimeout to 180 seconds in the Configuration.cs file.

Good luck