"SocketTimeoutException: connect timed out" error

Modified on Fri, 16 Sep 2022 at 08:25 AM

This problem is often observed while trying to launch workflows from a self-hosted Git server, for e.g. Bitbucket, Gitlab etc.

This error signals that the backend/cron container cannot connect to the Git remote host. This can be caused by a missing proxy configuration.

ERROR i.s.t.c.GlobalErrorController - Oops... Unable to process request - Error ID: 6h3HBUkaPe03vgzoDPc5HO
java.net.SocketTimeoutException: connect timed out
        at java.base/java.net.PlainSocketImpl.socketConnect(Native Method)
        at java.base/java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:399)
        at java.base/java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:242)
        at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:224)
        at java.base/java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
        at java.base/java.net.Socket.connect(Socket.java:609)
        at java.base/sun.security.ssl.SSLSocketImpl.connect(SSLSocketImpl.java:289)
        at java.base/sun.net.NetworkClient.doConnect(NetworkClient.java:177)
        at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:474)
        at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:569)
        at java.base/sun.net.www.protocol.https.HttpsClient.<init>(HttpsClient.java:265)
        at java.base/sun.net.www.protocol.https.HttpsClient.New(HttpsClient.java:372)
        at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.getNewHttpClient(AbstractDelegateHttpsURLConnection.java:203)
        at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1187)
        at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1081)
        at java.base/sun.net.www.protocol.https.AbstractDelegateHttpsURLConnection.connect(AbstractDelegateHttpsURLConnection.java:189)
        at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1592)
        at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1520)
        at java.base/java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:527)
        at java.base/sun.net.www.protocol.https.HttpsURLConnectionImpl.getResponseCode(HttpsURLConnectionImpl.java:334)
        at nextflow.scm.RepositoryProvider.checkResponse(RepositoryProvider.groovy:167)
        at nextflow.scm.RepositoryProvider.invoke(RepositoryProvider.groovy:136)
        at nextflow.scm.RepositoryProvider.memoizedMethodPriv$invokeAndParseResponseString(RepositoryProvider.groovy:218)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1259)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1026)
        at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1029)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1012)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:101)
        at nextflow.scm.RepositoryProvider$_closure2.doCall(RepositoryProvider.groovy)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1026)
        at groovy.lang.Closure.call(Closure.java:412)
        at org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction.lambda$call$0(Memoize.java:137)
        at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:137)
        at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:113)
        at org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction.call(Memoize.java:136)
        at groovy.lang.Closure.call(Closure.java:428)
        at nextflow.scm.RepositoryProvider.invokeAndParseResponse(RepositoryProvider.groovy)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.runtime.callsite.PlainObjectMetaMethodSite.doInvoke(PlainObjectMetaMethodSite.java:43)
        at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite$PogoCachedMethodSiteNoUnwrapNoCoerce.invoke(PogoMetaMethodSite.java:193)
        at org.codehaus.groovy.runtime.callsite.PogoMetaMethodSite.callCurrent(PogoMetaMethodSite.java:61)
        at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callCurrent(AbstractCallSite.java:185)
        at nextflow.scm.BitbucketRepositoryProvider.getCloneUrl(BitbucketRepositoryProvider.groovy:114)
        at nextflow.scm.AssetManager.memoizedMethodPriv$getGitRepositoryUrl(AssetManager.groovy:394)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1259)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1026)
        at org.codehaus.groovy.runtime.InvokerHelper.invokePogoMethod(InvokerHelper.java:1029)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethod(InvokerHelper.java:1012)
        at org.codehaus.groovy.runtime.InvokerHelper.invokeMethodSafe(InvokerHelper.java:101)
        at nextflow.scm.AssetManager$_closure1.doCall(AssetManager.groovy)
        at nextflow.scm.AssetManager$_closure1.doCall(AssetManager.groovy)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.base/java.lang.reflect.Method.invoke(Method.java:566)
        at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107)
        at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323)
        at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:263)
        at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1026)
        at groovy.lang.Closure.call(Closure.java:412)
        at org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction.lambda$call$0(Memoize.java:137)
        at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:137)
        at org.codehaus.groovy.runtime.memoize.ConcurrentCommonCache.getAndPut(ConcurrentCommonCache.java:113)
        at org.codehaus.groovy.runtime.memoize.Memoize$MemoizeFunction.call(Memoize.java:136)
        at groovy.lang.Closure.call(Closure.java:406)
        at nextflow.scm.AssetManager.getGitRepositoryUrl(AssetManager.groovy)

SOLUTION

Update the HTTP proxy configuration in the backend and cron environment, for example:

export http_proxy="http://PROXY_SERVER:PORT"
export https_proxy="https://PROXY_SERVER:PORT"