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I have two web front ends with search service provisioned on both for fail over, and workflow farm with two endpoints, however when I turn one server off I get the following error:

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I also get this event log when trying to run a workflow with one WFE turned off:

A failure was reported when trying to invoke a service application: EndpointFailure Process Name: OWSTIMER Process ID: 11616 AppDomain Name: DefaultDomain AppDomain ID: 1 Service Application Uri: urn:schemas-microsoft-com:sharepoint:service:a3aa213f446947cb846a42494338c0ce#authority=urn:uuid:5717a627251143b99e95dd553149073c&authority=https://server name of turned off server:32844/Topology/topology.svc Active Endpoints: 1 Failed Endpoints:1 Affected Endpoint: http://server name of turned off server:32843/a3aa213f446947cb846a42494338c0ce/SearchService.svc

I am assuming the reason I get that error is because the server it is trying to reach is off, but then how should a search application with two servers in the topology be set up for fail over? My main concern is that Designer 2013 stop working the moment one server is down

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What you describing is not fail over but High Availability design. The errors you are reporting are expected as full topoolgy of the serach service expects the other components.

In Failover scenario you would need to have another farm where you would restore your databases and attach them to the failover farm (there are other methods of failing over like VMWare SRM that work differently but to the same end effect)

Your workflow farm topology seems to be wrong. Unless something changed the supported topology for WF Mangaer farm should have 1, 3 or 5 servers. (Unless you are using WF2010 which is coupled with the Sharepoint)

I don' think the error you are mentioning is related to WF execution (unless you have some action that explicitly calls Search) The result of Designer stop working when one of the servers is down is quite strange as well, maybe you have some entry in host file on the machine you use with designer and it is calling the wrong server (is situation the same when you turn of the other server?)

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I deleted my search application and recreated using the following script:

$APP1 = "WFE1"
$App2 = "WFE2"

$SearchAppPoolName = "SharePoint_SearchApp"
$SearchAppPoolAccountName = "domain\farmaccount"
$SearchServiceName = "SharePoint_Search_Service"
$SearchServiceProxyName = "SharePoint_Search_Proxy"
$DatabaseName = "SharePoint_Search_AdminDB"

#Create a Search Service Application Pool
$spAppPool = New-SPServiceApplicationPool -Name $SearchAppPoolName -Account $SearchAppPoolAccountName -Verbose

#Start Search Service Instance on all Application Servers
Start-SPEnterpriseSearchServiceInstance $App1 -ErrorAction SilentlyContinue
Start-SPEnterpriseSearchServiceInstance $App2 -ErrorAction SilentlyContinue
Start-SPEnterpriseSearchQueryAndSiteSettingsServiceInstance $App1 -ErrorAction SilentlyContinue
Start-SPEnterpriseSearchQueryAndSiteSettingsServiceInstance $App2 -ErrorAction SilentlyContinue

#Create Search Service Application
$ServiceApplication = New-SPEnterpriseSearchServiceApplication -Partitioned -Name $SearchServiceName -ApplicationPool $spAppPool.Name -DatabaseName $DatabaseName

#Create Search Service Proxy
New-SPEnterpriseSearchServiceApplicationProxy -Partitioned -Name $SearchServiceProxyName -SearchApplication $ServiceApplication

$clone = $ServiceApplication.ActiveTopology.Clone()
$App1SSI = Get-SPEnterpriseSearchServiceInstance -Identity $app1
$App2SSI = Get-SPEnterpriseSearchServiceInstance -Identity $app2

#We need only one admin component
New-SPEnterpriseSearchAdminComponent –SearchTopology $clone -SearchServiceInstance $App1SSI

#We need two content processing components for HA
New-SPEnterpriseSearchContentProcessingComponent –SearchTopology $clone -SearchServiceInstance $App1SSI
New-SPEnterpriseSearchContentProcessingComponent –SearchTopology $clone -SearchServiceInstance $App2SSI

#We need two analytics processing components for HA
New-SPEnterpriseSearchAnalyticsProcessingComponent –SearchTopology $clone -SearchServiceInstance $App1SSI
New-SPEnterpriseSearchAnalyticsProcessingComponent –SearchTopology $clone -SearchServiceInstance $App2SSI

#We need two crawl components for HA
New-SPEnterpriseSearchCrawlComponent –SearchTopology $clone -SearchServiceInstance $App1SSI
New-SPEnterpriseSearchCrawlComponent –SearchTopology $clone -SearchServiceInstance $App2SSI

#We need two query processing components for HA
New-SPEnterpriseSearchQueryProcessingComponent –SearchTopology $clone -SearchServiceInstance $App1SSI
New-SPEnterpriseSearchQueryProcessingComponent –SearchTopology $clone -SearchServiceInstance $App2SSI

#Set the primary and replica index location; ensure these drives and folders exist on application servers
$PrimaryIndexLocation = "D:\Data"
$ReplicaIndexLocation = "D:\Data_2"

#We need two index partitions and replicas for each partition. Follow the sequence.
New-SPEnterpriseSearchIndexComponent –SearchTopology $clone -SearchServiceInstance $App1SSI -RootDirectory $PrimaryIndexLocation -IndexPartition 0
New-SPEnterpriseSearchIndexComponent –SearchTopology $clone -SearchServiceInstance $App2SSI -RootDirectory $ReplicaIndexLocation -IndexPartition 0
New-SPEnterpriseSearchIndexComponent –SearchTopology $clone -SearchServiceInstance $App2SSI -RootDirectory $PrimaryIndexLocation -IndexPartition 1
New-SPEnterpriseSearchIndexComponent –SearchTopology $clone -SearchServiceInstance $App1SSI -RootDirectory $ReplicaIndexLocation -IndexPartition 1

$clone.Activate()

$ssa = Get-SPEnterpriseSearchServiceApplication
Get-SPEnterpriseSearchTopology -Active -SearchApplication $ssa

Make sure the proxies are added back to the web application, stop timer, delete cache, start timer and run a full crawl

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