How to Upgrade Oracle Enterprise Manager Cloud Control 12c to EM13c

You have probably heard that Oracle released Enterprise Manager Cloud Control 13c on Friday. It’s the first product from Oracle with the number 13 in its release label. It seems Oracle doesn’t care about the bad luck of 13 🙂 The new version comes with great features and maybe the most significant one is the unification of hardware and software management. In Oracle Enterprise Manager 13c, some of the important hardware management features of “Ops Center” have been included into the Cloud Control product. My company is not a beta tester of Enterprise Manager, so I wanted to upgrade our EM12c system as soon as possible to test the new features by myself. I upgraded our EM12c system yesterday. Well, as I expected, the upgrade process was easy but you should be careful about prerequisites. Carefully check the certification matrix (in My Oracle Support website) before you decide to upgrade your system! EM13c OMS requires Oracle as repository database, and EM13c agents don’t support Enterprise Linux earlier than version 6. We have redhat Enterprise Linux 5.x targets and our repository database was so I have upgraded our repository database and decided to use the “old agents” with EM13c until we upgrade our servers to Enterprise Linux 6.x.

Please take a look at Enterprise Manager Cloud Control Upgrade Guide, before you start upgrading and make sure that you have backed up the repository database and OMS! I’ll try to provide a step by step guide on upgrading EM12c to EM13c running on Linux system, but this is just to give you an idea about overall process, you should always read and follow the official guide.

Important addition from Sumesh: If you have the below obsolete plug-ins in your EM12.1.0.3/4/5 system, then undeploy them from OMS and Agent before proceeding with upgrade to EM13.1:

  • EMC Symmetrix Array (oracle.em.sesy)
  • EMC Celerra Storage (oracle.em.secs)
  • EMC CLARiiON Array (oracle.em.secl)
  • Microsoft Biz Talk Server (oracle.em.smbs)
  • Exalogic Elastic Cloud Infrastructure (oracle.em.soee)

Make sure the Repopsitory Database and OMS machine are in the same time zone. Eg. UTC or PDT. If the timezone is not same then, Upgrade will fail at ‘Plug-ins Prequisites check’ step.

When upgrading, EM13c will need to access EMKey (the secret key to encrypt password etc), so we copy the EMKey to the Management Repository:

We also need to disable the optimizer adaptive feature. So we connect to our repository database and run the following SQL command:

If you have upgraded your database like, you also need to make sure that database compatibility parameter equal to the database version:

Then restart the repository database, to make the new changes have taken effect.

Download the installation files from Oracle web site, and run cksum to verify checksums and sizes of the files. EM13c installation doesn’t need you to unzip the files. All you need is to put all files into the same directory, mark em13100_linux64.bin as executable and run it with “oracle” user (the user you installed your current Enterprise Manager):


You’ll see a familiar screen which asks you to enter your email. Enter your email (or just leave it blank), and then click next button.


Because it’s just released there’s no available patches for EM13c right now, but I still wanted to be sure. Click next to continue.


Examine the list, and if there are important failures, fix them before you continue to upgrade. In the prerequisites check, “ip local port range” gives warning on my system because it’s set to wider range, so I have just decided to ignore the warning.


As you can see, there’s only “one system” upgrade option, so we pick it and continue.


We enter the new middleware location of EM13c.


Enter the SYS and SYSMAN passwords of the repository database. Deferred Data Migration (DDMP) is a post-upgrade activity to migrate the historical data of your old Enterprise Manager. Depending on how much data stored, it may take same time. So you may prefer to run the DDMP jobs later from the Post Upgrade Console.


You may get some warnings about the database, some of them can be fixed automatically by the installer (when you click YES), some of them need manual fixes. Fix them and continue.


Read the repost about the plugin upgrade, click next to continue.


Select additional plugins if you’re planning to use them. If you haven’t stopped the OMS, it’s time to stop it now. Run the following command in the terminal windows and then click next on your installer:

You also need to stop the agents running on the repository server and management servers! Go to the agent installation directory and run the following:

Although you stop the agents, you may still get a warning about them. Ignore it and continue to upgrade.

Enter the weblogic password, and enter the new location for OMS instance. If you forgot the password, you can recover it. EM13c wants you to choose a directory outside the middleware home.


EM13c comes with BI Publisher. In our existing Enterprise Manager system, we haven’t configured BI Publisher, so I entered directory names to configure it. If you are upgrading an OMS that already has Oracle BI Publisher installed, then these fields should be prefilled and grayed out.


I accept the default ports and click next to continue.


Review the information you entered, and then click the upgrade button to start upgrading.


It took more than one hour on my system but I’m aware that our disks are a little bit slow so it may take less time on a better hardware.


As usual, you see a message box asking you to run “a root script”. It’s in middleware home. After you run the script (with root user), click OK and you’ll see the above screen saying the upgrade is completed.


Now EM13c is ready and waiting you to login 🙂 After you login, go to the “upgrade agents” page under the “setup menu” to upgrade your agents. If you have disabled DDMP jobs, you should also go to “post upgrade tasks” under the “setup menu” and start deferred data migration tasks.

Please share

AWS Big Data Specialist. Oracle Certified Professional (OCP) for EBS R12, Oracle 10g and 11g. Co-author of "Expert Oracle Enterprise Manager 12c" book published by Apress. Awarded as Oracle ACE (in 2011) and Oracle ACE Director (in 2016) for the continuous contributions to the Oracle users community. Founding member, and vice president of Turkish Oracle User Group (TROUG). Presented at various international conferences including Oracle Open World.


  1. Pingback: A Tip for Upgrading to Enterprise Manager 13c - Oracle - Oracle - Toad World

  2. Nice article Gokhan. I’ve put up a note of caution about the setting of COMPATIBLE in case the upgrade goes wrong. It might be worth adding a note here as well.

    By the way the stage you describe as taking over an hour took a similar length of time on my lab VM, but again that might not be indicative of general upgrade/install performance.

    • Gokhan Atil

      Hi Niall,

      Thanks for your feedback. As you said, people need to be careful about setting compatible parameter but Installer doesn’t continue unless you set the compatible parameter to same value with the version.

  3. Fayas

    Hi Gokhan,

    Thanks for your perfect document. I had installed the Oracle 13c Enterprise Manager as a fresh installation. Can u post how to install the agents on the target nodes. Appreciate your usual support.

    • Gokhan Atil

      Hi Fayas,

      Sure I’ll write a blog post about adding a new host and DB targets.

  4. Mamus

    Nice write up Gokhan,

    Cannot wait to upgrade, but will like to know if I can upgrade using my 11g database??

    Thanks, waiting for your reply.

    • Gokhan Atil

      Hi Mamus,

      I assume that you mention about your repository database. In this case, you must upgrade your database to, because EM13c supports only as repository database.

    • Mamus

      Hello Gokhan,

      Thank you for the reply. looking forward to this upgrade.

  5. Mikheil


    Helpful article Gokhan, Thanks.
    we also decided to upgrade but i have doubt about how 13c agent works on target host OS version Enterprise linux 5. what do you think, upgrade agent will be better choice or keep it as 12c version?
    As you mentioned in article “old Agents”, would you so kind to share your experience how do they work.

    Thanks in advance.

    • Mikheil

      as i checked we can’t upgrade agents on OS enterprise Linux 5 based on oracle licensing so you can skip this question.

    • Gokhan Atil

      Mikheil, although OEL 5 is not supported, if you can still install the EM13c agent to OEL 5, and as I see it works OK. Of course it’s better to use “supported” EM12c agent.

    • ricoflashfire


      i install agent 13c on OEL5 and i have this bug: Bug 22592461 : Database target status shows “Dynamic Category property error” in 13c Console.
      So i want to install agent 12c on my Cloud Control 13c.
      I want to push this install with Cloud control 13c, i have dowloaded and applied agent 12c but when i push an agent install i can choose Linux-64 but i can’t choose the agent version…
      Obviously with emcli it’s possible manually.
      Have you un solution in cloud control 13c with agent 12 and agent 13 applied to choose and push agent 12 and not only 13?

  6. Mauro Azevedo

    Nice article Gokhan, thanks.

    We decided to install a fresh Enterprise Manager 13c on VM RHEL6. we have two diferent vm one for OMS and another for repository. unfortunately the installation hangs on BI Publisher configuration, based on your experiency do you know any way to by pass BI Publisher configuration or how to solve the problem?

    • Gokhan Atil

      Hi Mauro,

      You may skip installing BI publisher if you uncheck the “enable BI publisher” option on the “shared location details” step.

  7. Mauro Azevedo

    Hi Gokhan,

    Thanks for your reply,

    we tried also installing with BI Publisher unchecked, it gives the same error. looking my logs we can see that OMS is not able to start Webtier as you can see.


    2016-01-08 15:03:18,388 [main] ERROR commands.BaseCommand logAndPrint.651 – WebTier Could Not Be Started.
    2016-01-08 15:03:18,388 [main] ERROR wls.OMSController main.253 – OMSController failed for start oms
    2016-01-08 15:03:18,390 [main] ERROR wls.OMSController main.254 – OMSController Error: WebTier Could Not Be Started.

    • Gokhan Atil

      Hi Mauro, if you send me the log file I can examine it. I have sent you an email (so you can reply).

  8. Mauro Azevedo

    Hi Gokhan, thanks for your time. I replied to you with all installation logs.


  9. Sahaj Jhingan

    Hi Gokhan.

    Thanks for sharing this.

    I’m in mid of OEM13c upgrade and I’m not sure if you came across this issue . In the mid of upgrade when it asks for weblogic password it doesn’t allow me to type in and upgrade crashes in a while after that.

    Any idea ?



    • Sahaj Jhingan

      Thanks Gokhan

      Someone was testing java application on the same server which coincided with the OEM13c upgrade.


  10. Sumesh

    Thanks Gokhan for the post.

    Can you pls add ‘Things to know before upgrading EM12c to 13.1’  This is will save time in performing upgrade.

    If you have the below obsolete plug-ins in your EM12.1.0.3 /4/5 system, then undeploy them from OMS and Agent before proceeding with upgrade to EM13.1

    (i) EMC Symmetrix Array (oracle.em.sesy)

    (ii) EMC Celerra Storage (oracle.em.secs)

    (iii) EMC CLARiiON Array (oracle.em.secl)

    (iv) Microsoft Biz Talk Server (oracle.em.smbs)

    (v) Exalogic Elastic Cloud Infrastructure (oracle.em.soee)

    Make sure the Repopsitory Database and OMS machine are in the same time zone. Eg. UTC or PDT

    2) If the timezone is not same then, Upgrade will fail at ‘Plug-ins Prequisites check’ step

  11. nnarimanov

    Hi Gokhan,

    Is there any easy way to detect whether environment is multi-OMS or single-OMS?

    • Gokhan Atil

      Login to EM web console, and click “setup > manage cloud control > management services”. In that page, you’ll see the existing OMS servers in the servers tab.

  12. Thanks Gokhan,
    I upgraded my environment yesterday.
    I realized that my unix admins want to install RHEL 7.0, which isn’t supported on, so that was my main incentive.

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  14. Wil

    Thanks Gokhan!  Very informative.

    I’d like to take a different approach from upgrading though.  I’d like to install a brand new EM 13c environment and then migrate targets from my current EM 12c in a phased approach.  Is there a way to do this and still retain all of the history for the targets I am migrating?  I’m about to open an SR with Oracle but figured I’d check here as well.


    • Gokhan Atil

      Hi Wil,

      I don’t know an officially supported way to do it. Let me know if Oracle Support tells you how to do it.

  15. Ash Sharif

    Thanks for the useful post. As mentioned that 13c OEM is certified against 12c database and we have to upgrade Database before upgrading the OEM. Did you upgrade it using PDB/CDB model or traditional way?



    • Gokhan Atil

      I upgraded the repository database to non-CDB architecture using DBUA.

  16. Do you have any advice on rolling back if something goes wrong? I know to keep backups of my repository DB and my OMS operating system files…

    I might be able to make it easier on myself if I drop a Flashback restore point on the DB before the backup… I guess if I am installing the app server binaries in a new home directory that might get me back to a baseline faster… Just trying to cover all the bases in case there was something I didn’t think of…

    • Gokhan Atil

      Hi David, I had daily backups of everything (except software library because of disk space problem) before I started the update and as I know, Oracle recommends to have backups of all components. So I can’t recommend you to rely on only flashbackup restore point although you install the EM13c binaries to a new folder. A guaranteed flashback restore point will surely help you to rewind the repository upgrade back quickly, but you may still need to restore OMS related stuff. Personally, I didn’t encounter any unrecoverable problem during my upgrades (and I did a lot including Grid Control 11g->12c, 12cRx-12cRx, 12c to 13c), but I still recommend you to have all backups in case you may need.

  17. George Fitzpatrick

    I recently upgraded my dev OMS from 12cr5 to 13cr1 – the OMS/repository upgrade was uneventful.

    As part of the prep work for the upgrade, I “moved’ the central agent (the agent running on the OMS server ) outside the OMS home directory strucure. The relocated agent was running successfully as 12cr5.

    After the upgrade of the OMS to 13cr1, I used the Agent Upgrade wizard to upgrade the 12cr5 central agent to 13cr1, and althouhg the submitted job indicated a successful upgrade, the 13cr1 agent could not upload to the OMS. In an emctl status agent, the OMS version showed as unknown, the OMS status was unreachable. A re-secure of the agent succeeded, but no change in status of OMS , nor did attempts to upload succeed.

    After several exchanges with Oracle support, they offered patch 22568679 as a solution. In the readme of the patch , which I could not find using the patch search in Patches and Updates , it instructs the customer to create a patch plan to apply the patch. At this point the OMS thinks the agent is still 12cr5, since there has been no communication with the (broken) 13cr1 agent, and the patch plan create process will not allow a 13cr1 patch to be applied to what it thinks is a 12cr5 agent.

    Connecting to My Oracle Support directly, searching for and downloading the patch from there, then connect to the server directly and apply the patch from the command line using opatch.
    Once the patch was applied, the 13cr1 agent agent connected and uploaded successfully.

    So far, any Linux x64 or Windows 64-bit agent that I have attempted to upgrade using the Agent Upgrade wizard results in a broken agent. I have an open SR with Oracle support, waiting for a more acceptable solution. Caveat emptor !

    • Gokhan Atil

      Hi George, thanks for sharing your experience and letting us know that patch!

  18. AlexVin

    Why didn’t you have this error?

    EM13c: 12c to 13c OMS Upgrade Fails At Repository Configuration With Error “ORA-20251: Cost Center already Exists” (Doc ID 2095025.1)

    • Gokhan Atil

      Hi Alexey, thank you very much for sharing this valuable information!

      In My Oracle Support document, it says a new record will be inserted into EM_COST_CENTERS table for all users whose department value is not blank, and it may cause duplicate values. We have only 4 EM users (excluding default ones), and as I see, the department value of them are blank. It should be the reason why I didn’t hit this bug.

    • AlexVin

      I looked, in my configuration from the user department is also empty, but an error occurs. how to select the users with non-empty department?

    • Gokhan Atil

      After you login with emcli, run the following command (one line):

      emcli list -resource="Administrators" -search="DEPARTMENT IS NOT NULL" -columns="USER_NAME"

    • AlexVin

      $ emcli list -resource=”Administrators” -search=”DEPARTMENT IS NOT NULL” -columns=”USER_NAME”


      INFO: error(s) happened in performing the action:
      ORA-20251: Cost Center already Exists : :
      ORA-06512: at “SYSMAN.EM_COST_CENTER”, line 147
      ORA-06512: at “SYSMAN.EM_COST_CENTER”, line 209
      ORA-06512: at “SYSMAN.EM_COST_CENTER”, line 266
      ORA-06512: at “SYSMAN.EM_COST_CENTER”, line 436
      ORA-06512: at line 64

    • Gokhan Atil

      It seems the bug document does not describe all required conditions to reproduce the problem. I’ll try to check the cost_center_data_upgrade.sql and try to understand the problem.

  19. I have the same issue, oracle says that is only for blanks but it will also fails if you have same value.
    to fix this I only updated the values manually and retry the operation and worked fine. (at least this part)

    check all users and add different cost center for each one.



    • Gokhan Atil

      Christian, it’s better to use EM CLI commands or web console to update user information. Please check my blog post about this error.

  20. Nancy

    We have existing 12c agents on OEL5. We would like to do a fresh install of 13c OMS. Support is telling us that 12c agents are supported with 13c OMS only if we do an upgrade; otherwise we need to install the 13c agent which we cannot. The certification page shows that 12c agents are supported, so what we are being told doesn’t seem correct. Is it true that 12c agents are supported only if the OMS is upgraded from 12c to 13c?

    • Nancy

      Can you use a 12c agent on the server that houses the 13c repository?

  21. Mike O'Reilly


    Thanks very much for a great article. It has been very helpful, as have the various comments.

    We are currently on OEM, and are about to upgrade to OEM 13c. We have a lot of schedule jobs configured in OEM. Have you had any problems with scheduled jobs after the 13c upgrade? is there any reason to think that the 13c upgrade won’t bring the scheduled jobs over into the 13c environment?

    • Gokhan Atil

      Hi Mike,

      I haven’t had any problem with scheduled jobs after the 13c upgrade. In any case, you may export jobs before the upgrade using “emcli export_jobs”. More info can be found at Oracle Enterprise Manager blog.

  22. Hi Gokhan, Good article and thanks for sharing this.

    I have installed a fresh 13c and database repository on another machine. When I execute emctl start oms, I’m getting below error as
    Webtier is down

    Below is the full status
    $ emctl status oms -details
    Oracle Enterprise Manager Cloud Control 13c Release 1
    Copyright (c) 1996, 2015 Oracle Corporation. All rights reserved.
    Enter Enterprise Manager Root (SYSMAN) Password :
    Console Server Host : fqdn
    HTTP Console Port : 7788
    HTTPS Console Port : 7802
    HTTP Upload Port : 4889
    HTTPS Upload Port : 4903
    EM Instance Home : /opt/oem/home/gc_inst1/em/EMGC_OMS1
    OMS Log Directory Location : /opt/oem/home/gc_inst1/em/EMGC_OMS1/sysman/log
    OMS is not configured with SLB or virtual hostname
    Agent Upload is locked.
    OMS Console is locked.
    Active CA ID: 1
    Console URL: https://fqdn:7802/em
    Upload URL: https://fqdn:4903/empbs/upload

    WLS Domain Information
    Domain Name : GCDomain
    Admin Server Host : fqdn
    Admin Server HTTPS Port: 7202

    Oracle Management Server Information
    Managed Server Instance Name: EMGC_OMS1
    Oracle Management Server Instance Host: fqdn
    WebTier is Down
    Oracle Management Server is Up
    JVMD Engine is Up

    BI Publisher Server Information
    BI Publisher Managed Server Name: BIP
    BI Publisher Server is Down

    BI Publisher HTTP Managed Server Port : 9701
    BI Publisher HTTPS Managed Server Port : 9803
    BI Publisher HTTP OHS Port : 9788
    BI Publisher HTTPS OHS Port : 9851
    BI Publisher is locked.
    BI Publisher Server named ‘BIP’ is configured to run at URL: https://fqdn:9851/xmlpserver
    BI Publisher Server Logs: /opt/oem/home/gc_inst1/user_projects/domains/GCDomain/servers/BIP/logs/
    BI Publisher Log : /opt/oem/home/gc_inst1/user_projects/domains/GCDomain/servers/BIP/logs/bipublisher/bipublisher.log

  23. Christian

    Nice article.

    I’m faceing this problem:

    Oracle OEM 12105 is running on Oracle Linux 6.8.
    Now, we want to make 2 Upgrades:

    1) Upgrade Linux to 7.2
    2) Upgrade OEM to 13.1

    As far a know, inplace update of Linux is a very tricky one.
    Therefore, I would prefer to install a new machine from scratch, holding Linux 7.2.
    But what would be the next step?
    If I install OEM13 there is no migration refering to OEM services, etc. However, if I try connect to the Repository Database from 12 this could not work, I guess.
    Is there a way to do an database migration “only”?

    Any tips?
    Thx Christian

  24. Ricardo Andrade

    For when a post , How to Upgrade Oracle Enterprise Manager Cloud EM13c to EM13cR2

  25. Mahesh Atnoor

    Hi Gokhan

    Thanks for posting such a detailed and descriptive article.
    I need some help / pointers for one of our requirement. We have a requirement of migrating OEM12cR4 running on RHEL5 on Host A to a new machine Host B with RHEL 6.7. OEM repository DB is installed and running on another machine Host C.
    Kindly provide me with some pointers for migrating OEM from one machine to another keeping the database intact (use the same DB).

    Mahesh Atnoor

  26. Giovani


    I can install an bd 12c for oem 13c. install After the agent 11g, this is compatible with oem 13c?


  27. Shameem

    Hi Gokhan .. I’m new to oem.

    What is meant by “repository database” here ?

    OEM itself has a separate database for its’ own? Or is it talking about normal target database…?

    I’am asking this because there are separate ‘MGMT..’  tablespaces ,  sysman user etc. etc..  All these objects resides in target db or a ‘separete oem database’ ?

    Thanks .. and sorry for the very basic question..



    • Gokhan Atil

      The repository database is a separate database to store the data of Oracle Enterprise Manager system. EM agents send raw data to OEM, and OEM stores these data on the repository database.

  28. Fayyaz

    I have below setup on Sparc 5.10:
    Repository :
    I am planning to upgrade to 13c using below steps

    1). Upgrade repository database to with Oct PSU

    if this is successful and I can launch the OEM console then I would like to
    Install OMS 13c on Red hat Linux 7.2 pointing to repository on Solaris.
    If this OK then migrate the OMS from Solaris to Linux.

    Will above work or do you see any issues? I see issues with last step only, isn’t it? is the last step supported?

  29. KevHutch


    Great article.  I’m attempting to upgrade from version just like you, to Oracle Enterprise Manager Cloud Control 13c.

    I’ve been following the Upgrade Guide with no issues until I get to step 4.1.5 which states that I should see the option to “Upgrade an existing Enterprise Manager system “.  However I only see option to install new.  It does not give the option to “upgrade” like your screenshot above shows for the Installation Type.

    I read through the upgrade guide again to ensure I didn’t miss a step.  Would you have any idea why the install tool is not recognizing that I already have OMS installed?

    Thanks much!

    • Gokhan Atil

      Hi Kev,

      Please check your Oracle Inventory. The /etc/oraInst.loc file might point to wrong inventory location the inventory could be deleted (accidentally) or corrupted. The installer checks the inventory files to find the existing Enterprise Manager installations.

  30. Abinaya


    I upgraded my EM from 12c Release 4 to 13c Release 2. I had configured my OMS with third party certificates.

    After the upgrade was completed, the OMS came up successfully. I was performing post upgrade steps as per the below guide.

    Below is the NOTE in the guide:
    This section is applicable only for Oracle WebLogic Server custom certificates, and not applicable for Enterprise Manager Console certificates. The Enterprise Manager Console certificates are automatically copied over during upgrade.

    When i tried to resecure wls with my custom wallet with the below steps

    emctl secure wls -wallet <wallet_location>
    emctl stop oms -all
    emctl start oms

    I got the below error message

    $ emctl start oms
    Oracle Enterprise Manager Cloud Control 13c Release 2
    Copyright (c) 1996, 2016 Oracle Corporation. All rights reserved.
    Starting Oracle Management Server…
    WebTier Successfully Started
    Oracle Management Server is not functioning because of the following reason:
    Unexpected error occurred. Check error and log files.
    Check the following log files:
    EM log files: MW_HOM/gc_inst_13R2/em/EMGC_OMS1/sysman/log/emctl.log, emoms.trc, emoms_pbs.trc
    JVMD Engine is Down
    Starting BI Publisher Server …
    BI Publisher Server is Down

    So i reverted WLS with demo certificate back and tried to start OMS , it came up successfully.

    I see same error “ Certificates does not conform to algorithm constraints” in the below scenarios

    1. Reconfiguring Oracle WebLogic Server with Custom Certificates and starting OMS
    2. Starting Central Management Agent (the agent is not able to communicate to OMS)
    3. When trying to logging in with emcli

    Can you please help here

  31. michel fernandes

    Hello, I’m having trouble setting up email sending in the cloud control13c, I’ve already registered the smtp server, port, email, admin permissions, created the rules. but I still do not get the notifications generated, can you give me a help?

  32. Adrian Castillo

    Hello Gokhan,

    you know if el agent 13c could monitor a database version oracle

  33. Abdul

    Hello Gokhan – hope you are doing well!

    Though I am sending comment to very old post but hope you will see it.

    I have oem 13c running on solaris x86 and database is 12.2 running on same host and now due to some licensing issue I have to migrate both repository and app to RHEL 7.

    would you help me in any guidance on this?


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