Services or capabilities described in Amazon Web Services documentation might vary by Region. To see the differences applicable to the China Regions, see Getting Started with Amazon Web Services in China (PDF).

Troubleshooting Patch Manager

Use the following information to help you troubleshoot problems with Patch Manager, a tool in Amazon Systems Manager.

Issue: "Invoke-PatchBaselineOperation : Access Denied" error or "Unable to download file from S3" error for baseline_overrides.json

Problem: When the patching operations specified by your patch policy run, you receive an error similar to the following example.

Example error on Windows Server

----------ERROR-------
Invoke-PatchBaselineOperation : Access Denied
At C:\ProgramData\Amazon\SSM\InstanceData\i-02573cafcfEXAMPLE\document\orchestr
ation\792dd5bd-2ad3-4f1e-931d-abEXAMPLE\PatchWindows\_script.ps1:219 char:13
+ $response = Invoke-PatchBaselineOperation -Operation Install -Snapsho ...
+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ CategoryInfo : OperationStopped: (Amazon.Patch.Ba...UpdateOpera
tion:InstallWindowsUpdateOperation) [Invoke-PatchBaselineOperation], Amazo
nS3Exception
+ FullyQualifiedErrorId : PatchBaselineOperations,Amazon.Patch.Baseline.Op
erations.PowerShellCmdlets.InvokePatchBaselineOperation
failed to run commands: exit status 0xffffffff

Example error on Linux

[INFO]: Downloading Baseline Override from s3://aws-quicksetup-patchpolicy-123456789012-abcde/baseline_overrides.json
[ERROR]: Unable to download file from S3: s3://aws-quicksetup-patchpolicy-123456789012-abcde/baseline_overrides.json.
[ERROR]: Error loading entrance module.

Cause: You created a patch policy in Quick Setup, and some of your managed nodes already had an instance profile attached (for EC2 instances) or a service role attached (for non-EC2 machines).

However, as shown in the following image, you didn't select the Add required IAM policies to existing instance profiles attached to your instances check box.

When you create a patch policy, an Amazon S3 bucket is also created to store the policy's configuration baseline_overrides.json file. If you don't select the Add required IAM policies to existing instance profiles attached to your instances check box when creating the policy, the IAM policies and resource tags that are needed to access baseline_overrides.json in the S3 bucket are not automatically added to your existing IAM instance profiles and service roles.

Solution 1: Delete the existing patch policy configuration, then create a replacement, making sure to select the Add required IAM policies to existing instance profiles attached to your instances check box. This selection applies the IAM policies created by this Quick Setup configuration to nodes that already have an instance profile or service role attached. (By default, Quick Setup adds the required policies to instances and nodes that do not already have instance profiles or service roles.) For more information, see Automate organization-wide patching using a Quick Setup patch policy.

Solution 2: Manually add the required permissions and tags to each IAM instance profile and IAM service role that you use with Quick Setup. For instructions, see Permissions for the patch policy S3 bucket.

Issue: Patching fails without an apparent cause or error message

Problem: A patching operation fails without returning an error message.

Possible cause: If more than one invocation of AWS-RunPatchBaseline occurs at a time, they can conflict with one another, causing patching tasks to fail. This might not be indicated in patching logs.

To check whether concurrent patching operations might have interrupted each other, review the command history in Run Command, a tool in Amazon Systems Manager. For a managed node with a patching failure, check to see if multiple operations attempted to patch the machine within 2 minutes of one another. This scenario can sometimes cause a failure.

You can also use the Amazon Command Line Interface (Amazon CLI) to check for concurrent patching attempts by using the following command. Replace the value for node-id with the ID for your managed node.

aws ssm list-commands \
    --filter "key=DocumentName,value=AWS-RunPatchBaseline" \
    --query 'Commands[*].{CommandId:CommandId,RequestedDateTime:RequestedDateTime,Status:Status}' \
    --instance-id node-id \
    --output table

Solution: If you determine that patching failed because of competing patching operations on the same managed node, adjust your patching configurations to avoid this occurring again. For example, if two maintenance windows specify overlapping patching times, remove or revise one of them. If a maintenance windows specifies one patching operation, but a patch policy specifies a different one for the same time, consider removing the task from the maintenance window.

If you determine that conflicting patching operations weren't the cause of the failure in this scenario, we recommend contacting Amazon Web Services Support.

Issue: Unexpected patch compliance results

Problem: When reviewing the patching compliance details generated after a Scan operation, the results include information that don't reflect the rules set up in your patch baseline. For example, an exception you added to the Rejected patches list in a patch baseline is listed as Missing. Or patches classified as Important are listed as missing even though your patch baseline specifies Critical patches only.

Cause: Patch Manager currently supports multiple methods of running Scan operations:

When a Scan operation runs, it overwrites the compliance details from the most recent scan. If you have more than one method set up to run a Scan operation, and they use different patch baselines with different rules, they will result in differing patch compliance results.

Solution: To avoid unexpected patch compliance results, we recommend using only one method at a time for running the Patch Manager Scan operation. For more information, see Avoiding unintentional patch compliance data overwrites.

Errors when running AWS-RunPatchBaseline on Linux

Issue: 'No such file or directory' error

Problem: When you run AWS-RunPatchBaseline, patching fails with one of the following errors.

IOError: [Errno 2] No such file or directory: 'patch-baseline-operations-X.XX.tar.gz'

Unable to extract tar file: /var/log/amazon/ssm/patch-baseline-operations/patch-baseline-operations-1.75.tar.gz.failed to run commands: exit status 155

Unable to load and extract the content of payload, abort.failed to run commands: exit status 152

Cause 1: Two commands to run AWS-RunPatchBaseline were running at the same time on the same managed node. This creates a race condition that results in the temporary file patch-baseline-operations* not being created or accessed properly.

Cause 2: Insufficient storage space remains under the /var directory.

Solution 1: Ensure that no maintenance window has two or more Run Command tasks that run AWS-RunPatchBaseline with the same Priority level and that run on the same target IDs. If this is the case, reorder the priority. Run Command is a tool in Amazon Systems Manager.

Solution 2: Ensure that only one maintenance window at a time is running Run Command tasks that use AWS-RunPatchBaseline on the same targets and on the same schedule. If this is the case, change the schedule.

Solution 3: Ensure that only one State Manager association is running AWS-RunPatchBaseline on the same schedule and targeting the same managed nodes. State Manager is a tool in Amazon Systems Manager.

Solution 4: Free up sufficient storage space under the /var directory for the update packages.

Issue: 'another process has acquired yum lock' error

Problem: When you run AWS-RunPatchBaseline, patching fails with the following error.

12/20/2019 21:41:48 root [INFO]: another process has acquired yum lock, waiting 2 s and retry.

Cause: The AWS-RunPatchBaseline document has started running on a managed node where it's already running in another operation and has acquired the package manager yum process.

Solution: Ensure that no State Manager association, maintenance window tasks, or other configurations that run AWS-RunPatchBaseline on a schedule are targeting the same managed node around the same time.

Issue: 'Permission denied / failed to run commands' error

Problem: When you run AWS-RunPatchBaseline, patching fails with the following error.

sh: 
/var/lib/amazon/ssm/instanceid/document/orchestration/commandid/PatchLinux/_script.sh: Permission denied
failed to run commands: exit status 126

Cause: /var/lib/amazon/ might be mounted with noexec permissions. This is an issue because SSM Agent downloads payload scripts to /var/lib/amazon/ssm and runs them from that location.

Solution: Ensure that you have configured exclusive partitions to /var/log/amazon and /var/lib/amazon, and that they're mounted with exec permissions.

Issue: 'Unable to download payload' error

Problem: When you run AWS-RunPatchBaseline, patching fails with the following error.

Unable to download payload: https://s3.amzn-s3-demo-bucket.region.amazonaws.com.cn/aws-ssm-region/patchbaselineoperations/linux/payloads/patch-baseline-operations-X.XX.tar.gz.failed to run commands: exit status 156

Cause: The managed node doesn't have the required permissions to access the specified Amazon Simple Storage Service (Amazon S3) bucket.

Solution: Update your network configuration so that S3 endpoints are reachable. For more details, see information about required access to S3 buckets for Patch Manager in SSM Agent communications with Amazon managed S3 buckets.

Issue: 'unsupported package manager and python version combination' error

Problem: When you run AWS-RunPatchBaseline, patching fails with the following error.

An unsupported package manager and python version combination was found. Apt requires Python3 to be installed.
failed to run commands: exit status 1

Cause: A supported version of python3 isn't installed on the Debian Server, Raspberry Pi OS, or Ubuntu Server instance.

Solution: Install a supported version of python3 (3.0 - 3.10) on the server, which is required for Debian Server, Raspberry Pi OS, and Ubuntu Server managed nodes.

Issue: Patch Manager isn't applying rules specified to exclude certain packages

Problem: You have attempted to exclude certain packages by specifying them in the /etc/yum.conf file, in the format exclude=package-name, but they aren't excluded during the Patch Manager Install operation.

Cause: Patch Manager doesn't incorporate exclusions specified in the /etc/yum.conf file.

Solution: To exclude specific packages, create a custom patch baseline and create a rule to exclude the packages you don't want installed.

Issue: Patching fails and Patch Manager reports that the Server Name Indication extension to TLS is not available

Problem: The patching operation issues the following message.

/var/log/amazon/ssm/patch-baseline-operations/urllib3/util/ssl_.py:369: 
SNIMissingWarning: An HTTPS request has been made, but the SNI (Server Name Indication) extension
to TLS is not available on this platform. This might cause the server to present an incorrect TLS 
certificate, which can cause validation failures. You can upgrade to a newer version of Python 
to solve this. 
For more information, see https://urllib3.readthedocs.io/en/latest/advanced-usage.html#ssl-warnings

Cause: This message doesn't indicate an error. Instead, it's a warning that the older version of Python distributed with the operating system doesn't support TLS Server Name Indication. The Systems Manager patch payload script issues this warning when connecting to Amazon APIs that support SNI.

Solution: To troubleshoot any patching failures when this message is reported, review the contents of the stdout and stderr files. If you haven't configured the patch baseline to store these files in an S3 bucket or in Amazon CloudWatch Logs, you can locate the files in the following location on your Linux managed node.

/var/lib/amazon/ssm/instance-id/document/orchestration/Run-Command-execution-id/awsrunShellScript/PatchLinux

Issue: Patch Manager reports 'No more mirrors to try'

Problem: The patching operation issues the following message.

[Errno 256] No more mirrors to try.

Cause: The repositories configured on the managed node are not working correctly. Possible causes for this include:

Solution: Patch Manager uses the managed node’s default package manager to perform patching operation. Double-check that repositories are configured and operating correctly.

Issue: Patching fails with 'Error code returned from curl is 23'

Problem: A patching operating that uses AWS-RunPatchBaseline fails with an error similar to the following:

05/01/2025 17:04:30 root [ERROR]: Error code returned from curl is 23

Cause: The curl tool in use on your systems lacks the permissions needed to write to the filesystem. This can occur when if the package manager's default curl tool was replaced by a different version, such as one installed with snap.

Solution: If the curl version provided by the package manager was uninstalled when a different version was installed, reinstall it.

If you need to keep multiple curl versions installed, ensure that the version associated with the package manager is in the first directory listed in the PATH variable. You can check this by running the command echo $PATH to see the current order of directories that are checked for executable files on your system.

Issue: Patching fails with ‘Error unpacking rpm package…’ message

Problem: A patching operation fails with an error similar to the following:

Error : Error unpacking rpm package python-urllib3-1.25.9-1.amzn2.0.2.noarch
python-urllib3-1.25.9-1.amzn2.0.1.noarch was supposed to be removed but is not!
failed to run commands: exit status 1

Cause 1: When a particular package is present in multiple package installers, such as both pip and yum or dnf, conflicts can occur when using the default package manager.

A common example occurs with the urllib3 package, which is found in pip, yum, and dnf.

Cause 2: The python-urllib3 package is corrupted. This can happen if the package files were installed or updated by pip after the rpm was package was previously installed by yum or dnf.

Solution: Remove the python-urllib3 package from pip by running the command sudo pip uninstall urllib3, keeping the package only in the default package manager (yum or dnf).

Issue: Patching fails with 'Encounter service side error when uploading the inventory'

Problem: When running the AWS-RunPatchBaseline document, you receive the following error message:

Encounter service side error when uploading the inventory

Cause: Two commands to run AWS-RunPatchBaseline were running at the same time on the same managed node. This creates a race condition when initializing boto3 client during patching operations.

Solution: Ensure that no State Manager association, maintenance window tasks, or other configurations that run AWS-RunPatchBaseline on a schedule are targeting the same managed node around the same time.

Issue: Patching fails with ‘Errors were encountered while downloading packages’ message

Problem: During patching, you receive an error similar to the following:

YumDownloadError: [u'Errors were encountered while downloading 
packages.', u'libxml2-2.9.1-6.el7_9.6.x86_64: [Errno 5] [Errno 12] 
Cannot allocate memory', u'libxslt-1.1.28-6.el7.x86_64: [Errno 5] 
[Errno 12] Cannot allocate memory', u'libcroco-0.6.12-6.el7_9.x86_64: 
[Errno 5] [Errno 12] Cannot allocate memory', u'openldap-2.4.44-25.el7_9.x86_64: 
[Errno 5] [Errno 12] Cannot allocate memory',

Cause: This error can occur when insufficient memory is available on a managed node.

Solution: Configure the swap memory, or upgrade the instance to a different type to increase the memory support. Then start a new patching operation.

Issue: Patching fails with a message that 'The following signatures couldn't be verified because the public key is not available'

Problem: Patching fails on Ubuntu Server with an error similar to the following:

02/17/2022 21:08:43 root [ERROR]: W:GPG error: 
http://repo.mysql.com/apt/ubuntu  bionic InRelease: The following 
signatures couldn't be verified because the public key is not available: 
NO_PUBKEY 467B942D3A79BD29, E:The repository ' http://repo.mysql.com/apt/ubuntu bionic

Cause: The GNU Privacy Guard (GPG) key has expired or is missing.

Solution: Refresh the GPG key, or add the key again.

For example, using the error shown previously, we see that the 467B942D3A79BD29 key is missing and must be added. To do so, run either of the following commands:

sudo apt-key adv --keyserver hkps://keyserver.ubuntu.com --recv-keys 467B942D3A79BD29

sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 467B942D3A79BD29

Or, to refresh all keys, run the following command:

sudo apt-key adv --keyserver hkps://keyserver.ubuntu.com --refresh-keys

If the error recurs after this, we recommend reporting the issue to the organization that maintains the repository. Until a fix is available, you can edit the /etc/apt/sources.list file to omit the repository during the patching process.

To do so, open the sources.list file for editing, locate the line for the repository, and insert a # character at the beginning of the line to comment it out. Then save and close the file.

Issue: Patching fails with a 'NoMoreMirrorsRepoError' message

Problem: You receive an error similar to the following:

NoMoreMirrorsRepoError: failure: repodata/repomd.xml from pgdg94: [Errno 256] No more mirrors to try.

Cause: There is an error in the source repository.

Solution: We recommend reporting the issue to the organization that maintains the repository. Until the error is fixed, you can disable the repository at the operating system level. To do so, run the following command, replacing the value for repo-name with your repository name:

yum-config-manager --disable repo-name

Following is an example.

yum-config-manager --disable pgdg94

After you run this command, run another patching operation.

Issue: Patching fails with an 'Unable to download payload' message

Problem: You receive an error similar to the following:

Unable to download payload: 
https://s3.dualstack.eu-west-1.amazonaws.com/aws-ssm-eu-west-1/patchbaselineoperations/linux/payloads/patch-baseline-operations-1.83.tar.gz.
failed  to run commands: exit status 156

Cause: The managed node configuration contains errors or is incomplete.

Solution: Make sure that the managed node is configured with the following:

Issue: Patching fails with a message 'install errors: dpkg: error: dpkg frontend is locked by another process'

Problem: Patching fails with an error similar to the following:

install errors: dpkg: error: dpkg frontend is locked by another process
failed to run commands: exit status 2
Failed to install package; install status Failed

Cause: The package manager is already running another process on a managed node at the operating system level. If that other process takes a long time to complete, the Patch Manager patching operation can time out and fail.

Solution: After the other process that’s using the package manager completes, run a new patching operation.

Issue: Patching on Ubuntu Server fails with a 'dpkg was interrupted' error

Problem: On Ubuntu Server, patching fails with an error similar to the following:

E: dpkg was interrupted, you must manually run
'dpkg --configure -a' to correct the problem.

Cause: One or more packages is misconfigured.

Solution: Perform the following steps:

Issue: The package manager utility can't resolve a package dependency

Problem: The native package manager on the managed node is unable to resolve a package dependency and patching fails. The following error message example indicates this type of failure on an operating system that uses yum as the package manager.

09/22/2020 08:56:09 root [ERROR]: yum update failed with result code: 1, 
message: [u'rpm-python-4.11.3-25.amzn2.0.3.x86_64 requires rpm = 4.11.3-25.amzn2.0.3', 
u'awscli-1.18.107-1.amzn2.0.1.noarch requires python2-botocore = 1.17.31']

Cause: On Linux operating systems, Patch Manager uses the native package manager on the machine to run patching operations. such as yum, dnf, apt, and zypper. The applications automatically detect, install, update, or remove dependent packages as required. However, some conditions can result in the package manager being unable to complete a dependency operation, such as:

Solution: Patching might fail because of a dependency issue for a wide variety of reasons. Therefore, we recommend that you contact Amazon Web Services Support to assist with troubleshooting.

Errors when running AWS-RunPatchBaseline on Windows Server

Issue: mismatched product family/product pairs

Problem: When you create a patch baseline in the Systems Manager console, you specify a product family and a product. For example, you might choose:

Cause: If you attempt to create a patch baseline with a mismatched product family/product pair, an error message is displayed. The following are reasons this can occur:

Solution: To avoid this issue in the console, always choose options from the Currently available options sublists.

You can also view the products that have available patches by using the describe-patch-properties command in the Amazon CLI or the DescribePatchProperties API command.

Issue: AWS-RunPatchBaseline output returns an HRESULT (Windows Server)

Problem: You received an error like the following.

----------ERROR-------
Invoke-PatchBaselineOperation : Exception Details: An error occurred when 
attempting to search Windows Update.
Exception Level 1:
 Error Message: Exception from HRESULT: 0x80240437
 Stack Trace: at WUApiLib.IUpdateSearcher.Search(String criteria)..
(Windows updates)
11/22/2020 09:17:30 UTC | Info | Searching for Windows Updates.
11/22/2020 09:18:59 UTC | Error | Searching for updates resulted in error: Exception from HRESULT: 0x80240437
----------ERROR-------
failed to run commands: exit status 4294967295

Cause: This output indicates that the native Windows Update APIs were unable to run the patching operations.

Solution: Check the HResult code in the following microsoft.com topics to identify troubleshooting steps for resolving the error:

Issue: managed node doesn't have access to Windows Update Catalog or WSUS

Problem: You received an error like the following.

Downloading PatchBaselineOperations PowerShell module from https://s3.aws-api-domain/path_to_module.zip to C:\Windows\TEMP\Amazon.PatchBaselineOperations-1.29.zip.

Extracting PatchBaselineOperations zip file contents to temporary folder.

Verifying SHA 256 of the PatchBaselineOperations PowerShell module files.

Successfully downloaded and installed the PatchBaselineOperations PowerShell module.

Patch Summary for

PatchGroup :

BaselineId :

Baseline : null

SnapshotId :

RebootOption : RebootIfNeeded

OwnerInformation :

OperationType : Scan

OperationStartTime : 1970-01-01T00:00:00.0000000Z

OperationEndTime : 1970-01-01T00:00:00.0000000Z

InstalledCount : -1

InstalledRejectedCount : -1

InstalledPendingRebootCount : -1

InstalledOtherCount : -1

FailedCount : -1

MissingCount : -1

NotApplicableCount : -1

UnreportedNotApplicableCount : -1

EC2AMAZ-VL3099P - PatchBaselineOperations Assessment Results - 2020-12-30T20:59:46.169

----------ERROR-------

Invoke-PatchBaselineOperation : Exception Details: An error occurred when attempting to search Windows Update.

Exception Level 1:

Error Message: Exception from HRESULT: 0x80072EE2

Stack Trace: at WUApiLib.IUpdateSearcher.Search(String criteria)

at Amazon.Patch.Baseline.Operations.PatchNow.Implementations.WindowsUpdateAgent.SearchForUpdates(String

searchCriteria)

At C:\ProgramData\Amazon\SSM\InstanceData\i-02573cafcfEXAMPLE\document\orchestration\3d2d4864-04b7-4316-84fe-eafff1ea58

e3\PatchWindows\_script.ps1:230 char:13

+ $response = Invoke-PatchBaselineOperation -Operation Install -Snapsho ...

+ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

+ CategoryInfo : OperationStopped: (Amazon.Patch.Ba...UpdateOperation:InstallWindowsUpdateOperation) [Inv

oke-PatchBaselineOperation], Exception

+ FullyQualifiedErrorId : Exception Level 1:

Error Message: Exception Details: An error occurred when attempting to search Windows Update.

Exception Level 1:

Error Message: Exception from HRESULT: 0x80072EE2

Stack Trace: at WUApiLib.IUpdateSearcher.Search(String criteria)

at Amazon.Patch.Baseline.Operations.PatchNow.Implementations.WindowsUpdateAgent.SearchForUpdates(String searc

---Error truncated----

Cause: This error could be related to the Windows Update components, or to a lack of connectivity to the Windows Update Catalog or Windows Server Update Services (WSUS).

Solution: Confirm that the managed node has connectivity to the Microsoft Update Catalog through an internet gateway, NAT gateway, or NAT instance. If you're using WSUS, confirm that the managed node has connectivity to the WSUS server in your environment. If connectivity is available to the intended destination, check the Microsoft documentation for other potential causes of HResult 0x80072EE2. This might indicate an operating system level issue.

Issue: PatchBaselineOperations PowerShell module is not downloadable

Problem: You received an error like the following.

Preparing to download PatchBaselineOperations PowerShell module from S3.
                    
Downloading PatchBaselineOperations PowerShell module from https://s3.aws-api-domain/path_to_module.zip to C:\Windows\TEMP\Amazon.PatchBaselineOperations-1.29.zip.
----------ERROR-------

C:\ProgramData\Amazon\SSM\InstanceData\i-02573cafcfEXAMPLE\document\orchestration\aaaaaaaa-bbbb-cccc-dddd-4f6ed6bd5514\

PatchWindows\_script.ps1 : An error occurred when executing PatchBaselineOperations: Unable to connect to the remote server

+ CategoryInfo : NotSpecified: (:) [Write-Error], WriteErrorException

+ FullyQualifiedErrorId : Microsoft.PowerShell.Commands.WriteErrorException,_script.ps1

failed to run commands: exit status 4294967295

Solution: Check the managed node connectivity and permissions to Amazon Simple Storage Service (Amazon S3). The managed node's Amazon Identity and Access Management (IAM) role must use the minimum permissions cited in SSM Agent communications with Amazon managed S3 buckets. The node must communicate with the Amazon S3 endpoint through the Amazon S3 gateway endpoint, NAT gateway, or internet gateway. For more information about the VPC Endpoint requirements for Amazon Systems Manager SSM Agent (SSM Agent), see Improve the security of EC2 instances by using VPC endpoints for Systems Manager.

Issue: missing patches

Problem: AWS-RunPatchbaseline completed successfully, but there are some missing patches.

The following are some common causes and their solutions.

Cause 1: The baseline isn't effective.

Solution 1: To check if this is the cause, use the following procedure.

Cause 2: The patch was replaced.

Solution 2: To check if this is true, use the following procedure.

Cause 3: The same patch might have different KB numbers because the WSUS and Window online updates are handled as independent Release Channels by Microsoft.

Solution 3: Check the patch eligibility. If the package isn't available under WSUS, install OS Build 14393.3115. If the package is available for all operating system builds, install OS Builds 18362.1256 and 18363.1256.

Using Amazon Web Services Support Automation runbooks

Amazon Web Services Support provides two Automation runbooks you can use to troubleshoot certain issues related to patching.

Contacting Amazon Web Services Support

If you can't find troubleshooting solutions in this section, and you have a Developer, Business, or Enterprise Amazon Web Services Support plan, you can create a technical support case at Amazon Web Services Support.

Before you contact Amazon Web Services Support, collect the following items: