Steps to Apply PSU patch on Oracle WebLogic 12c

Below are the steps to apply Oracle WebLogic Server PSU Patch: WLS PATCH SET UPDATE 12.2.1.3.190522 on Linux.

STEP 1: Download patch from Oracle Support portal.

Download patch in /scratch/u01/stage . You can prefer your own location to download the patch.

Weblogic PSU patch steps

STEP 2: Shut down WebLogic, Nodemanager and Managed Server.

[oracle@orahow stage]$ export ORACLE_HOME=/scratch/u01/Oracle/Middleware/Oracle_Home
[oracle@orahow stage]$ export PATH=$ORACLE_HOME/OPatch:$PATH
[oracle@orahow stage]$ cd /scratch/u01/Oracle/Middleware/Oracle_Home/user_projects/domains/<domain_name>/bin
./stopWebLogic.sh
./stopNodeManager.sh


Check everyting is down using:
ps -ef|grep -i NODE
ps -ef|grep -i ADMIN

If any other middleware tools like Oracle HTTP Server (OHS) is configured with weblogic you can stop it.
To stop OHS instance:
cd $ORACLE_HOME/OHS/user_projects/domains/<domain_name>/bin
sh stopComponent.sh ohs1
sh stopComponent.sh ohs2

STEP 3: Backup Weblogic Home.

[oracle@orahow bin]$ cd /scratch/u01/Oracle
[oracle@orahow u01]$ nohup cp -R Oracle Oracle_bkp_070919 &
You can also use tar command to backup weblogic home.

To stop managed server, login to em console and expand Environment in left pannel and click on server : https://hostname:port/console/. Click on control, select managed server and shutdown.

STEP 4: Unzip Patch

My patch location:  /scratch/u01/stag 
[oracle@orahow stage]$ unzip p29814665_122130_Generic.zip
[oracle@orahow stage]$ cd 29814665
[oracle@orahow 29814665]$ ls -lrt
total 32
-rwxr-x--- 1 oracle dba 27 May 30 06:22 README.html
drwxr-x--- 34 oracle dba 4096 May 30 06:22 files
drwxr-x--- 3 oracle dba 4096 May 30 06:22 etc
-rw-rw-r-- 1 oracle dba 19536 Jul 19 08:34 README.txt
[oracle@orahow 29814665]$

STEP 5 : Check opatch version.

 [oracle@orahow stage]$ export ORACLE_HOME=/scratch/u01/Oracle/Middleware/Oracle_Home
[oracle@orahow stage]$ export PATH=$ORACLE_HOME/OPatch:$PATH

Properly go through readme.txt file and check the recommended opatch version.
[oracle@orahow stage]$ $ORACLE_HOME/OPatch/opatch version
OPatch Version: 13.9.4.2.0
OPatch succeeded.

STEP 6: Goto patch directory and apply the patch using opatch utility.

 [oracle@orahow stage]$ cd 29814665 
[oracle@orahow stage]$ export ORACLE_HOME=/scratch/u01/Oracle/Middleware/Oracle_Home
[oracle@orahow stage]$ export PATH=$ORACLE_HOME/OPatch:$PATH 
[oracle@orahow 29814665]$ opatch apply
Oracle Interim Patch Installer version 13.9.4.2.0
Copyright (c) 2019, Oracle Corporation. All rights reserved.
Oracle Home : /scratch/u01/Oracle/Middleware/Oracle_Home
Central Inventory : /scratch/u01/oraInventory
from : /scratch/u01/Oracle/Middleware/Oracle_Home/oraInst.loc
OPatch version : 13.9.4.2.0
OUI version : 13.9.4.0.0
Log file location : /scratch/u01/Oracle/Middleware/Oracle_Home/cfgtoollogs/opatch/opatch2019-09-04_03-16-08AM_1.log
OPatch detects the Middleware Home as "/scratch/u01/Oracle/Middleware/Oracle_Home"
Verifying environment and performing prerequisite checks…
OPatch continues with these patches: 29814665
Do you want to proceed? [y|n]
y
User Responded with: Y
All checks passed.
Please shutdown Oracle instances running out of this ORACLE_HOME on the local system.
(Oracle Home = '/scratch/u01/Oracle/Middleware/Oracle_Home')
Is the local system ready for patching? [y|n]
y
User Responded with: Y
Backing up files…
Applying interim patch '29814665' to OH '/scratch/u01/Oracle/Middleware/Oracle_Home'
ApplySession: Optional component(s) [ oracle.wls.cam.wlst, 12.2.1.3.0 ] , [ oracle.wls.cam.wlst, 12.2.1.3.0 ] , [ oracle.webservices.wls.jaxrpc, 12.2.1.3.0 ] , [ oracle.webservices.wls.jaxrpc, 12.2.1.3.0 ] , [ oracle.fmwconfig.common.wls.shared, 12.2.1.3.0 ] , [ oracle.wls.core.app.server.nativelib, 12.2.1.3.0 ] , [ oracle.wls.server.examples, 12.2.1.3.0 ] , [ oracle.wls.rdmu, 12.2.1.3.0 ] , [ oracle.wls.server.mt.examples, 12.2.1.3.0 ] not present in the Oracle Home or a higher version is found.
Patching component oracle.webservices.orawsdl, 12.2.1.3.0…
Patching component oracle.webservices.orawsdl, 12.2.1.3.0…
Patching component oracle.com.fasterxml.jackson.dataformat.jackson.dataformat.xml, 2.7.9.0.0…
Patching component oracle.com.fasterxml.jackson.dataformat.jackson.dataformat.xml, 2.7.9.0.0…
Patching component oracle.org.bouncycastle, 12.2.1.3.0…
Patching component oracle.org.bouncycastle, 12.2.1.3.0…
Patching component oracle.wls.jrf.tenancy.common.sharedlib, 12.2.1.3.0…
Patching component oracle.wls.jrf.tenancy.common.sharedlib, 12.2.1.3.0…
Patching component oracle.fmwconfig.common.wls.shared.internal, 12.2.1.3.0…
Patching component oracle.com.fasterxml.jackson.jaxrs.jackson.jaxrs.base, 2.7.9.0.0…
Patching component oracle.com.fasterxml.jackson.jaxrs.jackson.jaxrs.base, 2.7.9.0.0…
Patching component oracle.fmwconfig.common.config.shared, 12.2.1.3.0…
Patching component oracle.wls.shared.with.cam, 12.2.1.3.0…
Patching component oracle.wls.shared.with.cam, 12.2.1.3.0…
Patching component oracle.wls.jrf.tenancy.common, 12.2.1.3.0…
Patching component oracle.wls.jrf.tenancy.common, 12.2.1.3.0…
Patching component oracle.wls.evaluation.database, 12.2.1.3.0…
Patching component oracle.wls.evaluation.database, 12.2.1.3.0…
Patching component oracle.wls.core.app.server, 12.2.1.3.0…
Patching component oracle.wls.core.app.server, 12.2.1.3.0…
Patching component oracle.wls.core.app.server, 12.2.1.3.0…
Patching component oracle.webservices.base, 12.2.1.3.0…
Patching component oracle.webservices.base, 12.2.1.3.0…
Patching component oracle.fmw.upgrade.fmwconfig, 12.2.1.3.0…
Patching component oracle.webservices.jrf, 12.2.1.3.0…
Patching component oracle.webservices.jrf, 12.2.1.3.0…
Patching component oracle.wls.jrf.tenancy.ee.only.sharedlib, 12.2.1.3.0…
Patching component oracle.wls.jrf.tenancy.ee.only.sharedlib, 12.2.1.3.0…
Patching component oracle.wls.rcu, 12.2.1.3.0…
Patching component oracle.wls.rcu, 12.2.1.3.0…
Patching component oracle.wls.security.core.sharedlib, 12.2.1.3.0…
Patching component oracle.wls.security.core.sharedlib, 12.2.1.3.0…
Patching component oracle.wls.security.core.sharedlib, 12.2.1.3.0…
Patching component oracle.webservices.wls, 12.2.1.3.0…
Patching component oracle.webservices.wls, 12.2.1.3.0…
Patching component oracle.webservices.wls, 12.2.1.3.0…
Patching component oracle.commons.fileupload.commons.fileupload, 1.3.2.0.0…
Patching component oracle.commons.fileupload.commons.fileupload, 1.3.2.0.0…
Patching component oracle.com.fasterxml.jackson.jaxrs.jackson.jaxrs.json.provider, 2.7.9.0.0…
Patching component oracle.com.fasterxml.jackson.jaxrs.jackson.jaxrs.json.provider, 2.7.9.0.0…
Patching component oracle.wls.admin.console.en, 12.2.1.3.0…
Patching component oracle.wls.admin.console.en, 12.2.1.3.0…
Patching component oracle.wls.libraries, 12.2.1.3.0…
Patching component oracle.wls.libraries, 12.2.1.3.0…
Patching component oracle.wls.libraries, 12.2.1.3.0…
Patching component oracle.com.fasterxml.jackson.core.jackson.annotations, 2.7.9.0.0…
Patching component oracle.com.fasterxml.jackson.core.jackson.annotations, 2.7.9.0.0…
Patching component oracle.wls.common.cam.wlst, 12.2.1.3.0…
Patching component oracle.wls.common.cam.wlst, 12.2.1.3.0…
Patching component oracle.com.fasterxml.jackson.module.jackson.module.jsonschema, 2.7.9.0.0…
Patching component oracle.com.fasterxml.jackson.module.jackson.module.jsonschema, 2.7.9.0.0…
Patching component oracle.com.fasterxml.jackson.module.jackson.module.jaxb.annotations, 2.7.9.0.0…
Patching component oracle.com.fasterxml.jackson.module.jackson.module.jaxb.annotations, 2.7.9.0.0…
Patching component oracle.com.fasterxml.jackson.core.jackson.databind, 2.7.9.1.0…
Patching component oracle.com.fasterxml.jackson.core.jackson.databind, 2.7.9.1.0…
Patching component oracle.com.fasterxml.jackson.core.jackson.core, 2.7.9.0.0…
Patching component oracle.com.fasterxml.jackson.core.jackson.core, 2.7.9.0.0…
Patching component oracle.wls.security.core, 12.2.1.3.0…
Patching component oracle.wls.wlsportable.mod, 12.2.1.3.0…
Patching component oracle.jrf.tenancy.se, 12.2.1.3.0…
Patching component oracle.wls.http.pubsub.server, 12.2.1.3.0…
Patching component oracle.apache.commons.collections.mod, 3.2.0.0.2…
Patching component oracle.wls.common.cam, 12.2.1.3.0…
Patching component oracle.wls.workshop.code.completion.support, 12.2.1.3.0…
Patching component oracle.java.activation, 12.2.1.3.0…
Patching component oracle.apache.commons.lang.mod, 2.6.0.0.2…
Patching component oracle.java.xml.bind, 2.3.0.0.0…
Patching component oracle.java.servlet, 12.2.1.3.0…
Patching component oracle.legacy_oc4j_xml_schemas, 12.2.1.3.0…
Patching component oracle.wls.common.nodemanager, 12.2.1.3.0…
Patching component oracle.wls.shared.with.inst, 12.2.1.3.0…
Patching component oracle.wls.shared.with.coh.standalone, 12.2.1.3.0…
Patching component oracle.jaxb.impl, 2.3.0.0.0…
Patching component oracle.wls.admin.console.nonen, 12.2.1.3.0…
Patching component oracle.wls.clients, 12.2.1.3.0…
Patching component oracle.wls.shared.with.inst.sharedlib, 12.2.1.3.0…
Patching component oracle.wls.thirdparty.javax.json, 12.2.1.3.0…
Patching component oracle.jrf.tenancy.ee, 12.2.1.3.0…
Patching component oracle.wls.inst.only, 12.2.1.3.0…
Patching component oracle.jaxb.tools, 2.3.0.0.0…
Patching component oracle.jaxb.core, 2.3.0.0.0…
Patching component oracle.diagnostics.common, 12.2.1.3.0…
Patching component oracle.wls.weblogic.sca, 12.2.1.3.0…
Patching component org.codehaus.woodstox, 4.2.0.0.0…
Patching component oracle.wls.core.app.server.tier1nativelib, 12.2.1.3.0…
Patching component oracle.jrf.tenancy, 12.2.1.3.0…
Patching component oracle.java.jaxws, 12.2.1.3.0…
Patch 29814665 successfully applied.
Sub-set patch [29016089] has become inactive due to the application of a super-set patch [29814665].
Please refer to Doc ID 2161861.1 for any possible further required actions.
Log file location: /scratch/u01/Oracle/Middleware/Oracle_Home/cfgtoollogs/opatch/opatch2019-09-04_03-16-08AM_1.log
OPatch succeeded.

STEP 7: Check the latest applied patch.

 [oracle@orahow stage]$ export ORACLE_HOME=/scratch/u01/Oracle/Middleware/Oracle_Home
[oracle@orahow stage]$ export PATH=$ORACLE_HOME/OPatch:$PATH
[oracle@orahow stage]$ opatch lsinventory
Oracle Interim Patch Installer version 13.9.4.2.0
Copyright (c) 2019, Oracle Corporation. All rights reserved.
Oracle Home : /scratch/u01/Oracle/Middleware/Oracle_Home
Central Inventory : /scratch/u01/oraInventory
from : /scratch/u01/Oracle/Middleware/Oracle_Home/oraInst.loc
OPatch version : 13.9.4.2.0
OUI version : 13.9.4.0.0
Log file location : /scratch/u01/Oracle/Middleware/Oracle_Home/cfgtoollogs/opatch/opatch2019-09-07_04-55-07AM_1.log
OPatch detects the Middleware Home as "/scratch/u01/Oracle/Middleware/Oracle_Home"
Lsinventory Output file location : /scratch/u01/Oracle/Middleware/Oracle_Home/cfgtoollogs/opatch/lsinv/lsinventory2019-09-07_04-55-07AM.txt

Local Machine Information::
Hostname: den01dxj.us.oracle.com
ARU platform id: 226
ARU platform description:: Linux x86-64
Interim patches (5) :
Patch 29814665 : applied on Wed Sep 04 03:18:49 PDT 2019
Unique Patch ID: 22937216
Patch description: "WLS PATCH SET UPDATE 12.2.1.3.0(ID:20190522.070630)"
Created on 30 May 2019, 06:22:48 hrs PST8PDT
Bugs fixed:
25369207, 29338121, 29448643, 29312272, 26987594, 27010571, 26075541
27823500, 27248932, 25294832, 26131085, 27659077, 26403575, 29667975
28278427, 29726561, 29701537, 29411629, 29789769, 28748179, 28984617
28774974, 28891448, 28874066, 26943614, 28651365, 29140555, 27086845
29140516, 28895280, 26791760, 29140540, 29140549, 29140508, 29140551
28550962, 27397287, 28958819, 27033250, 28149607, 28110087, 26267487
28632521, 26624375, 27213775, 28503638, 28138954, 28103938, 28559579
28594324, 26353793, 28626991, 28166483, 28313163, 28142116, 28319690
27912485, 27561226, 27927071, 27469756, 27486993, 28140800, 27928833
25580220, 28311332, 27988175, 28172380, 28360225, 28171852, 28375173
28071913, 28409586, 28375702, 27411153, 26502060, 27603087, 27234961
27187631, 27516977, 27819370, 27617877, 26145911, 26268190, 27693510
27417245, 27284496, 27947832, 26026959, 26499391, 23076695, 25488428
26626528, 27445260, 26098043, 27948303, 27934864, 27803728, 26473149
27272911, 26731253, 27118731, 27131483, 25993295, 25800186, 25987400
26439373, 26080417, 26929163, 26806438, 25665727, 26608537, 26936500
27055227, 26144830, 25750303, 26248394, 26589850, 27111664, 26547016
26828499, 26835012, 27117282, 26985581, 23103220, 25387569
Patch 26355633 : applied on Thu May 10 00:31:37 PDT 2018
Unique Patch ID: 21447583
Patch description: "One-off"
Created on 1 Aug 2017, 21:40:20 hrs UTC
Bugs fixed:
26355633
Patch 26287183 : applied on Thu May 10 00:31:21 PDT 2018
Unique Patch ID: 21447582
Patch description: "One-off"
Created on 1 Aug 2017, 21:41:27 hrs UTC
Bugs fixed:
26287183
Patch 26261906 : applied on Thu May 10 00:30:56 PDT 2018
Unique Patch ID: 21344506
Patch description: "One-off"
Created on 12 Jun 2017, 23:36:08 hrs UTC
Bugs fixed:
25559137, 25232931, 24811916
Patch 26051289 : applied on Thu May 10 00:30:47 PDT 2018
Unique Patch ID: 21455037
Patch description: "One-off"
Created on 31 Jul 2017, 22:11:57 hrs UTC
Bugs fixed:
26051289

OPatch succeeded.

Known Issues during patching:

You may face below error while applying the patch.

[oracle@orahow 29814665]$ opatch apply
Oracle Interim Patch Installer version 13.9.4.2.0
Copyright (c) 2019, Oracle Corporation. All rights reserved.
Oracle Home : /scratch/u01/Oracle/Middleware/Oracle_Home
Central Inventory : /scratch/u01/oraInventory
from : /scratch/u01/Oracle/Middleware/Oracle_Home/oraInst.loc
OPatch version : 13.9.4.2.0
OUI version : 13.9.4.0.0
Log file location : /scratch/u01/Oracle/Middleware/Oracle_Home/cfgtoollogs/opatch/opatch2019-09-04_02-46-33AM_1.log
OPatch detects the Middleware Home as "/scratch/u01/Oracle/Middleware/Oracle_Home"
Verifying environment and performing prerequisite checks…
Conflicts/Supersets for each patch are:
Patch : 29814665
Conflict with 29921455 Conflict details: /scratch/u01/Oracle/Middleware/Oracle_Home/oracle_common/modules/com.oracle.webservices.wls.wls-soap-stack-impl.jar:weblogic/wsee/workarea/WorkContextFormatInfo.class /scratch/u01/Oracle/Middleware/Oracle_Home/oracle_common/modules/com.oracle.webservices.wls.wls-soap-stack-impl.jar:weblogic/wsee/workarea/WorkContextXmlInputAdapter.class /scratch/u01/Oracle/Middleware/Oracle_Home/oracle_common/modules/com.oracle.webservices.wls.wls-soap-stack-impl.jar:weblogic/wsee/workarea/WorkContextXmlInputAdapter$1.class /scratch/u01/Oracle/Middleware/Oracle_Home/oracle_common/modules/com.oracle.webservices.wls.wls-soap-stack-impl.jar:weblogic/wsee/workarea/WorkContextXmlInputAdapter$2.class Bug Superset of 29016089 Super set bugs are: 28360225, 28103938, 27927071, 27033250, 23076695, 27469756, 26806438, 27213775, 27603087, 26248394, 28311332, 28891448, 27272911, 26624375, 26929163, 28651365, 27693510, 28550962, 27617877, 27912485, 29140540, 26791760, 25987400, 28375702, 28319690, 27561226, 29140549, 27445260, 28984617, 26589850, 25800186, 25488428, 29140516, 28110087, 27988175, 26502060, 26943614, 27117282, 28503638, 28594324, 26608537, 27486993, 27934864, 26499391, 26985581, 28874066, 26439373, 27947832, 28409586, 27111664, 27187631, 28138954, 28313163, 28748179, 28774974, 28140800, 27284496, 27118731, 27803728, 26026959, 28149607, 28166483, 28632521, 25750303, 25580220, 26268190, 28559579, 27516977, 28958819, 26828499, 27397287, 26353793, 26145911, 27411153, 29140508, 26835012, 28895280, 27819370, 29140555, 29140551, 28071913, 28626991, 26473149, 26626528, 23103220, 25387569, 26547016, 26267487, 26731253, 26144830, 27086845, 28375173, 28171852, 28142116, 27417245, 26080417, 26936500, 27234961, 27928833, 27131483, 27055227, 27948303, 26098043, 28172380, 25665727, 25993295
Following patches have conflicts: [ 29814665 29921455 ]
Use the MOS Patch Conflict Checker "https://support.oracle.com/epmos/faces/PatchConflictCheck" to resolve.
See MOS documents 1941934.1 and 1299688.1 for additional information and resolution methods.
UtilSession failed: Please rebuild the superset patch [29814665] to make sure it supersedes all the relevant patch(es) [29016089,29921455].
The rebuild patch should contain bug fix [28360225, 27927071, 28103938, 27033250, 23076695, 26806438, 27469756, 28278427, 26248394, 27213775, 27603087, 28311332, 28891448, 27272911, 26624375, 26929163, 28651365, 27693510, 28550962, 27617877, 27912485, 29140540, 26791760, 25987400, 28375702, 28319690, 27561226, 29140549, 29701537, 27445260, 28984617, 26589850, 25800186, 25488428, 29140516, 28110087, 27248932, 27988175, 26502060, 26943614, 27117282, 27659077, 28503638, 28594324, 26608537, 29667975, 29338121, 29448643, 25369207, 27486993, 26075541, 27934864, 26499391, 26985581, 29789769, 26403575, 27010571, 28874066, 26439373, 27947832, 28409586, 29312272, 27111664, 27187631, 28138954, 28313163, 28748179, 27118731, 27284496, 28140800, 28774974, 27803728, 25294832, 26026959, 28149607, 26987594, 28166483, 25750303, 28632521, 25580220, 26268190, 27516977, 28559579, 28958819, 26828499, 27397287, 26353793, 26145911, 27411153, 27823500, 26835012, 29140508, 27819370, 28895280, 29140555, 29140551, 28071913, 28626991, 26473149, 26131085, 23103220, 26626528, 25387569, 26547016, 26267487, 26731253, 26144830, 27086845, 28375173, 28171852, 28142116, 27417245, 26080417, 26936500, 27234961, 27928833, 29726561, 27055227, 27131483, 27948303, 29411629, 26098043, 25665727, 28172380, 25993295, 29921455].
Log file location: /scratch/u01/Oracle/Middleware/Oracle_Home/cfgtoollogs/opatch/opatch2019-09-04_02-46-33AM_1.log
OPatch failed with error code 73

If you are facing patch conflict error, please rollback the patch using conflict patch ID and apply the patch again using opatch utility.

[oracle@orahow 29814665]$ opatch rollback -id 29921455
Oracle Interim Patch Installer version 13.9.4.2.0
Copyright (c) 2019, Oracle Corporation. All rights reserved.
Oracle Home : /scratch/u01/Oracle/Middleware/Oracle_Home
Central Inventory : /scratch/u01/oraInventory
from : /scratch/u01/Oracle/Middleware/Oracle_Home/oraInst.loc
OPatch version : 13.9.4.2.0
OUI version : 13.9.4.0.0
Log file location : /scratch/u01/Oracle/Middleware/Oracle_Home/cfgtoollogs/opatch/opatch2019-09-04_03-14-52AM_1.log
OPatch detects the Middleware Home as "/scratch/u01/Oracle/Middleware/Oracle_Home"
Patches will be rolled back in the following order:
29921455
The following patch(es) will be rolled back: 29921455
Please shutdown Oracle instances running out of this ORACLE_HOME on the local system.
(Oracle Home = '/scratch/u01/Oracle/Middleware/Oracle_Home')
Is the local system ready for patching? [y|n]
y
User Responded with: Y
Rolling back patch 29921455…
RollbackSession rolling back interim patch '29921455' from OH '/scratch/u01/Oracle/Middleware/Oracle_Home'
Patching component oracle.webservices.wls, 12.2.1.3.0…
RollbackSession removing interim patch '29921455' from inventory
Log file location: /scratch/u01/Oracle/Middleware/Oracle_Home/cfgtoollogs/opatch/opatch2019-09-04_03-14-52AM_1.log
OPatch succeeded.