Increased timeout at LDAP side but of no use.
I' changed the timeout in web.xml to 0 but it did not fix the issue.

Mar 16, 2015 1:54:20 PM hudson.security.LDAPSecurityRealm$LDAPUserDetailsService loadUserByUsername
WARNING: Failed to search LDAP for username=<User.name>
org.acegisecurity.ldap.LdapDataAccessException: LdapCallback;LDAP response read timed out, timeout used:60000ms.; nested exception is javax.naming.NamingException: LDAP response read timed out, timeout used:60000ms.; remaining name ''
at org.acegisecurity.ldap.LdapTemplate$LdapExceptionTranslator.translate(LdapTemplate.java:295)
at org.acegisecurity.ldap.LdapTemplate.execute(LdapTemplate.java:128)
at org.acegisecurity.ldap.LdapTemplate.searchForSingleEntry(LdapTemplate.java:246)
at org.acegisecurity.ldap.search.FilterBasedLdapUserSearch.searchForUser(FilterBasedLdapUserSearch.java:119)
at hudson.security.LDAPSecurityRealm$LDAPUserDetailsService.loadUserByUsername(LDAPSecurityRealm.java:839)
at hudson.security.LDAPSecurityRealm$LDAPUserDetailsService.loadUserByUsername(LDAPSecurityRealm.java:790)
at hudson.security.LDAPSecurityRealm.loadUserByUsername(LDAPSecurityRealm.java:672)
at hudson.security.GlobalMatrixAuthorizationStrategy$DescriptorImpl.doCheckName_(GlobalMatrixAuthorizationStrategy.java:314)
at hudson.security.GlobalMatrixAuthorizationStrategy$DescriptorImpl.doCheckName(GlobalMatrixAuthorizationStrategy.java:298)
at sun.reflect.GeneratedMethodAccessor348.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:483)
at org.kohsuke.stapler.Function$InstanceFunction.invoke(Function.java:298)
at org.kohsuke.stapler.Function.bindAndInvoke(Function.java:161)
at org.kohsuke.stapler.Function.bindAndInvokeAndServeResponse(Function.java:96)
at org.kohsuke.stapler.MetaClass$1.doDispatch(MetaClass.java:121)
at org.kohsuke.stapler.NameBasedDispatcher.dispatch(NameBasedDispatcher.java:53)
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:745)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:875)
at org.kohsuke.stapler.MetaClass$12.dispatch(MetaClass.java:391)
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:745)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:875)
at org.kohsuke.stapler.MetaClass$4.doDispatch(MetaClass.java:211)
at org.kohsuke.stapler.NameBasedDispatcher.dispatch(NameBasedDispatcher.java:53)
at org.kohsuke.stapler.Stapler.tryInvoke(Stapler.java:745)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:875)
at org.kohsuke.stapler.Stapler.invoke(Stapler.java:648)
at org.kohsuke.stapler.Stapler.service(Stapler.java:237)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at hudson.util.PluginServletFilter$1.doFilter(PluginServletFilter.java:96)
at hudson.util.PluginServletFilter.doFilter(PluginServletFilter.java:88)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:84)
at hudson.security.UnwrapSecurityExceptionFilter.doFilter(UnwrapSecurityExceptionFilter.java:51)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at jenkins.security.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:117)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.providers.anonymous.AnonymousProcessingFilter.doFilter(AnonymousProcessingFilter.java:125)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.ui.rememberme.RememberMeProcessingFilter.doFilter(RememberMeProcessingFilter.java:142)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:271)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at jenkins.security.BasicHeaderProcessor.doFilter(BasicHeaderProcessor.java:86)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:249)
at hudson.security.HttpSessionContextIntegrationFilter2.doFilter(HttpSessionContextIntegrationFilter2.java:67)
at hudson.security.ChainedServletFilter$1.doFilter(ChainedServletFilter.java:87)
at hudson.security.ChainedServletFilter.doFilter(ChainedServletFilter.java:76)
at hudson.security.HudsonFilter.doFilter(HudsonFilter.java:164)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.kohsuke.stapler.compression.CompressionFilter.doFilter(CompressionFilter.java:46)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at hudson.util.CharacterEncodingFilter.doFilter(CharacterEncodingFilter.java:81)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:220)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:122)
at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:612)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:170)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:950)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:421)
at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1070)
at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:611)
at org.apache.tomcat.util.net.JIoEndpoint$SocketProcessor.run(JIoEndpoint.java:314)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
at java.lang.Thread.run(Thread.java:745)
Caused by: javax.naming.NamingException: LDAP response read timed out, timeout used:60000ms.; remaining name ''
at com.sun.jndi.ldap.Connection.readReply(Connection.java:478)
at com.sun.jndi.ldap.LdapClient.getSearchReply(LdapClient.java:640)
at com.sun.jndi.ldap.LdapClient.search(LdapClient.java:563)
at com.sun.jndi.ldap.LdapCtx.doSearch(LdapCtx.java:1985)
at com.sun.jndi.ldap.LdapCtx.searchAux(LdapCtx.java:1844)
at com.sun.jndi.ldap.LdapCtx.c_search(LdapCtx.java:1769)
at com.sun.jndi.ldap.LdapCtx.c_search(LdapCtx.java:1786)
at com.sun.jndi.toolkit.ctx.ComponentDirContext.p_search(ComponentDirContext.java:418)
at com.sun.jndi.toolkit.ctx.PartialCompositeDirContext.search(PartialCompositeDirContext.java:396)
at com.sun.jndi.toolkit.ctx.PartialCompositeDirContext.search(PartialCompositeDirContext.java:378)
at javax.naming.directory.InitialDirContext.search(InitialDirContext.java:286)
at org.acegisecurity.ldap.LdapTemplate$3.doInDirContext(LdapTemplate.java:249)
at org.acegisecurity.ldap.LdapTemplate.execute(LdapTemplate.java:126)
... 80 more