In esxupdate.log log of vSAN Witness node ESXi host, you see entries similar to:
2018-09-07T03:00:41Z esxupdate: 69840: esxupdate: ERROR: An esxupdate error exception was caught: 2018-09-07T03:00:41Z esxupdate: 69840: esxupdate: ERROR: Traceback (most recent call last): 2018-09-07T03:00:41Z esxupdate: 69840: esxupdate: ERROR: File "/build/mts/release/bora-8935087/bora/build/esx/release/vmvisor/sys-boot/lib64/python3.5/site-packages/vmware/esximage/Metadata.py", line 75, in ReadMetadataZip 2018-09-07T03:00:41Z esxupdate: 69840: esxupdate: ERROR: File "/build/mts/release/bora-8935087/bora/build/esx/release/vmvisor/sys-boot/lib64/python3.5/zipfile.py", line 1235, in read 2018-09-07T03:00:41Z esxupdate: 69840: esxupdate: ERROR: File "/build/mts/release/bora-8935087/bora/build/esx/release/vmvisor/sys-boot/lib64/python3.5/zipfile.py", line 830, in read 2018-09-07T03:00:41Z esxupdate: 69840: esxupdate: ERROR: File "/build/mts/release/bora-8935087/bora/build/esx/release/vmvisor/sys-boot/lib64/python3.5/zipfile.py", line 920, in _read1 2018-09-07T03:00:41Z esxupdate: 69840: esxupdate: ERROR: MemoryError
In the VC GUI Host and Cluster view : Host > Monitor > Task & Events > Tasks shows the following error
Status: The host returns esxupdate error code:99. An unhandled exception was encountered.Check the Update Manager log files and esxupdate log files for more details
Environment
VMware vSAN 6.x
Cause
This issue occurs due to smaller hostd resource group in vSAN Witness node ESXi hosts compared to normal ESXi hosts to process large number of metadata files during host scan or remediation.
Resolution
Upgrade vCenter to 7.0U1 or higher
Workaround:
Additional Information
Using vSphere Update Manager to upgrade hosts in parallel might result in the witness host being upgraded in parallel with one of the data hosts in a stretched cluster / 2-Node configurations. To avoid upgrade problems, do not configure VMware Update Manager to upgrade a witness host in parallel with the data hosts in a stretched cluster. Upgrade the witness host after all data hosts have been successfully upgraded and have exited maintenance mode.