topic Re: Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site in ArcGIS Enterprise Questions

Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site

Sakib_Meharan_Siddiquei — Mon, 12 Aug 2024 14:21:04 GMT

Hi all,

Hope you are doing great.

I am trying to upgrade ArcGIS Enterprise from version 10.9.1 to 11.3, on a multi-machine environment on Linux, Ubuntu 20.4.

I have successfully performed the Portal upgrade, and the Portal Web Adaptor.

And I also ran the ArcGIS Server Setup, which was also successful, the problem I am experiencing is in the post-Upgrade phase of ArcGIS Server, with the command ./upgradeserver.sh -s, and this is the error: Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site.

I have checked the permissions on all the folders, and I cannot go and alter the security-config.json file, as it is federated with Portal.

I thought the ArcGIS Server keystore got corrupted, but on the catalina logs I find only this:

WARNING: The web application [arcgis#admin] appears to have started a thread named [GPJobExecutorSingletonExecutorThread] but has failed to stop it. This is very likely to create a memory leak. Stack trace of thread:

java.base@17.0.10/jdk.internal.misc.Unsafe.park(Native Method)

java.base@17.0.10/java.util.concurrent.locks.LockSupport.parkNanos(Unknown Source)

java.base@17.0.10/java.util.concurrent.locks.AbstractQueuedSynchronizer$ConditionObject.awaitNanos(Unknown Source)

java.base@17.0.10/java.util.concurrent.LinkedBlockingQueue.poll(Unknown Source)

com.esri.arcgis.discovery.admin.rediscovery.GPJobExecutorSingleton$ExecutorThread.run(GPJobExecutorSingleton.java:554)

And on the Server logs:

"SEVERE" code="7185" source="Admin" process="778379" thread="1" methodName="" machine="//" user="" elapsed="0.0" requestID="96f03588-26f1-4143-9a05-dae52748442e">Failed to synchronize machine '//' with the site. Cannot invoke "com.esri.arcgis.discovery.admin.services.Service.getProvider()" because "<local11>" is null. You can attempt the synchronization again by using the synchronize Administrative REST API on the server machine resource.

Has anyone by chance ever experienced this problem?

I would be very grateful if you can provide me with a hint to fix this issue.

Thanks & Regards,

Sakib

Re: Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site

ChiefKeefSosa300 — Tue, 19 Nov 2024 05:33:36 GMT

Hi Sakib, I also encountered the same problem with you. I try to upgrade arcgis server 11.2 to 11.3 and suddenly Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site in browser. I already send an email regarding this problem. Have you solved it yet?

Re: Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site

ChapalChoudhury — Mon, 03 Feb 2025 00:21:56 GMT

Hi all,

I have also encountered the exact same issue while trying to upgrade from version 10.9.1 to 11.4 by running both silently and with the upgrade wizard.

Looks like the first 3 stages of the server upgrade process was successful but failed at the 4th stage and did not proceed with the remaining 3 stages (see the attached screenshot).

Initialize upgrade and check licenses - Succeeded
Upgrade site configurations - Succeeded
Upgrade and start System Utility services - Succeeded
Synchronize local machine with site - Failed
Configure Extensions and data providers – Not started
Generate SSL Certificate and Enable SSL– Not started
Final checks and cleanup– Not started

Has anyone got a solution to the issue?

Re: Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site

FarrukhZahid — Mon, 17 Feb 2025 10:19:36 GMT

Hi Chief. Any update on your email? Did you find any solution for this? I am facing the same issue on windows platform 11.0 to 11.4 "Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site"

Re: Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site

Jay_Geisen — Mon, 07 Jul 2025 15:04:30 GMT

I'm curious how (any of) you sorted this issue out? We're running into similar errors, post 11.5 upgrade.

Re: Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site

MikaelJ — Fri, 03 Oct 2025 12:14:42 GMT

@Sakib_Meharan_Siddiquei @Jay_Geisen

any updates on this issue? I am facing this for couple of machines when upgrading to 11.5 from 11.3

Re: Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site

Jay_Geisen — Mon, 06 Oct 2025 15:45:31 GMT

We fixed the issue we were having by re-running the License Authorization file for all three of our GIS Server machines. Not sure why this worked, but it seemed to do the trick.

Re: Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site

MikaelJ — Tue, 07 Oct 2025 12:07:45 GMT

Oh, kinda interesting.

For me, solution was upgrade of Edge or Chrome.

Re: Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site

RyanAglietti — Fri, 31 Oct 2025 19:57:12 GMT

I also needed to update chrome to get the post install to finish. However, I was still not able to log into the Manager afterwards. I had to uninstall 11.4 web adaptor, install and configure 11.5 web adaptor and then I was finally able to get into Manager.

Re: Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site

Kristofer — Thu, 18 Dec 2025 17:25:04 GMT

Dear All, We had also faced the same issue when trying to upgrade ArcGIS server 11.3 to 11.5 and getting the error Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site.

Solution that workout for me:

1) STOP ArcGIS Server service completely - Wait 1 full minute
2) Clean Server temp & work directories -Delete contents (NOT the folders)
<ArcGIS Server install>\framework\runtime\tomcat\temp
<ArcGIS Server install>\framework\runtime\tomcat\work
3) Restart ArcGIS Server & start upgrade process

Thanks & Regards,

Kristofer

Re: Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site

MelissaK — Thu, 15 Jan 2026 19:29:14 GMT

I saw the same error "ArcGIS Server upgrade step 2 of 2 : Failed. Synchronize with site" when upgrading from 11.4 to 12.0. My solution was to repair ArcGIS Server and continue with upgrade.

Re: Upgrading ArcGIS Server step 2 of 2: Failed. Synchronize with site

LoganNoll — Sun, 01 Mar 2026 22:18:46 GMT

Kristofer,

Thanks for sharing!

We ran into this same issue going from 11.1 to 11.5. I ran the same process you mentioned and it cleared the error for us.

"Solution that workout for me: