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Running Workflows on Amazon EC2 using Pegasus

This tutorial takes you step-by-step through the process of setting up your environment to run workflows on Amazon EC2 using Pegasus. We assume you are already familiar with Pegasus and have a workflow that already runs on a local cluster or grid site. This tutorial will show you how to make that workflow run on Amazon.

1. Get an AWS account

     You need this before you can do anything
    
     Go to http://aws.amazon.com
    You will need a credit card. They bill monthly, and charge by the hour.

2. Once you have an account get your security credentials
    You need these for authentication.
    
    Go to aws.amazon.com and click on "Your Account" -> "Security Credentials"
    In various locations on that page are several account IDs. Write these ones down:
        Access Key ID
        Secret Access Key
        AWS Account ID
    We will refer to these as: ACCESS_KEY, SECRET_KEY, and ACCOUNT_ID
    
3. Create X.509 certificates
    These will be used to sign VM images later.
    
    On the same page click on X.509 certificates and "Create a new Certificate"
    You should get two files: a cert-.pem and a pk-.pem. They will have long names.
    Save those files somewhere on your machine.
    We will refer to these files as CERT.PEM and KEY.PEM

4. Install Condor on your submit host
    This is part 1 of 2 of setting up your submit host
    
    You need to have a host outside the cloud running a Condor central
    manager. We will refer to this host as your "submit host". We
    assume that you have a submit host already if you are running
    Pegasus.
    
    First you need to install Condor. That is a bit involved, so we
    will skip most of it. Go to: http://cs.wisc.edu/condor to get
    more information about how to install a basic condor manager.
    
    Once you have a basic manager working we need to modify the
    configuration a bit.
    
    Edit your condor_config file and append to HOSTALLOW_WRITE:
        HOSTALLOW_WRITE = <what it was before>, *.compute-1.amazonaws.com
        
    Now edit your condor_config.local and add:
        HIGHPORT = 41000
        LOWPORT = 40000
        UPDATE_COLLECTOR_WITH_TCP=True
        COLLECTOR_SOCKET_CACHE_SIZE=1000
        
    Finally, restart Condor
    
    VERY IMPORTANT: The firewall on the submit host should be configured
    so that anything from *.compute-1.amazonaws.com can connect to port
    9618, and ports 40000-41000. These ports are used by Condor.

5. Install Coord on your submit host
    This is part 2 of 2 of setting up your submit host
    
    Coord is a tool we use to configure virtual clusters on Amazon EC2.
    Right now it is really, really basic, but we plan on adding
    functionality later. It currently supports Condor workers and,
    optionally, GlusterFS, NFS, and PVFS file systems. See the README
    file in the Coord distribution for more information.
    
    On your submit host, check out Coord from subversion:
        $ svn co https://juve.isi.edu/svn/juve/coord
        
    Set COORD_HOME in your environment:
        $ export COORD_HOME=/path/to/coord
        
    Start the Coord server:
        $ python $COORD_HOME/coord.py
        
    It should say its running on port 40566
    You can put it in the background or restart it when you launch your VMs.
    
6. Log into the Amazon Management Console
    This is a web application that lets you manage cloud resources.

    We will refer to this webapp as the "console", and we will refer to
    the links on the left side of the console as "areas".
        
    Go to: http://console.aws.amazon.com
    Click "Sign in to the AWS console"
    Change the region on the upper-left side of the console to "US East".
    
    IMPORTANT: When you use this make sure you stick to one Region (US East
    or US West). Most things in Amazon don't work across regions.
    
    VERY IMPORTANT: For this tutorial please use region "US East". Or you
    won't be able to find our public VM image.

7. From the console create a keypair
    These are the credentials you use to log into worker nodes.
    
    Go to the "Key Pairs" area in the console
    Click "Create Key Pair"
    Call it "ec2-keypair" and click OK.
    It should popup a download box. Save the file.
    We will refer to this file as KEYPAIR.
    
8. From the console create a security group
    This is how you authorize machines outside the cloud to access your nodes.
    
    We will assume your submit host is "host.example.com", and that it has
    an IP of "192.168.1.1". The security group we create here will give
    "host.example.com" unrestricted access to your nodes.
    
    Go to the "Security Groups" area in the console
    Call your new group "host.example.com", add a description, and create the group
    Click on the group and add three entries:
    
        Method    Protocol    From Port    To Port        Source (IP or Group)
        All        tcp         1            65535        192.168.1.1/32
        All        udp            1            65535        192.168.1.1/32
        All        icmp        -1            -1             192.168.1.1/32
        
    Note that those are CIDR addresses, so don't forget the /32.

9. Launch the Pegasus public image
    This is how you launch a virtual machine (or virtual cluster).
    
    We are going to use a pre-configured image developed specifically for
    Pegasus. It contains Pegasus, Condor, Globus, and Coord.
    
    Go to the "AMIs" area in the console
    
    Filter by "Public Images" and "Fedora" using the drop-downs and type
    in "coord". It may take a few seconds to give you a list.
    
    Select the one called "fedora-8-x86_64-coord" and click "Launch".
    
    A launch wizard will pop up.
    
    Select the number of instances (1 for now), and instance type (m1.large),
    then "Continue".
    
    On the "Advanced Instance Options" page add the following to "User Data"
    and hit "Continue":
        ROLES=CONDOR;CONDOR_HOST=host.example.com
        
    Next, select the keypair you created earlier, and "Continue"

    Next, select the security group you created earlier and "Continue".

    On the last page click "Launch"
    
    VERY IMPORTANT: Select the security group and keypair you created
    earlier or else it won't work. Also, make sure you replace
    "host.example.com" in the User Data with your submit host.
    
    ALSO IMPORTANT: The "User Data" is how you tell the image what to
    do. See the README file from the Coord distribution for more options.
    
10. Log into your node
    This is how you SSH to a node you launched.
    
    Go to the "Instances" area in the console.
    
    You should see the instance you just launched go from "pending"
    to "running". You may need to hit "Refresh" a couple times.
    
    When it says "running" click on it and get the "Public DNS"
    (call it PUBLIC_DNS).
    
    From your submit host ssh to the worker:
        $ ssh -i KEYPAIR root@PUBLIC_DNS
    
    VERY IMPORTANT: Make sure you log in from your submit host otherwise
    this won't work because the security group does not match.

11. Check your submit host
    Make sure the workers showed up
    
    On your submit host run:
        $ condor_status
    
    You should see something that looks like this:
    
        Name               OpSys      Arch   State     Activity LoadAv Mem   ActvtyTime
        slot1@ec2-204-236- LINUX      X86_64 Unclaimed Idle     0.080  3843  0+00:00:04
        slot2@ec2-204-236- LINUX      X86_64 Unclaimed Idle     0.000  3843  0+00:00:05

                         Total Owner Claimed Unclaimed Matched Preempting Backfill

            X86_64/LINUX     2     0       0         2       0          0        0

                   Total     2     0       0         2       0          0        0

    If you don't see anything, then wait a few minutes. If you still don't
    see anything, then you need to debug Condor. Check the CollectorLog to
    see if the workers tried to connect. If it doesn't work contact:
    pegasus-support@isi.edu.
    
12. Run a test job
    Make sure the workers are usable
    
    Once the workers show up in condor_status you can test to make sure they
    will run jobs.
    
    Create a file called "vanilla.sub" on your submit host with this inside:
        universe = vanilla
        executable = /bin/hostname
        transfer_executable = false
        output = test_$(cluster).$(process).out
        error = test_$(cluster).$(process).err
        log = test_$(cluster).$(process).log
        requirements = (Arch == Arch) && (OpSys == OpSys) && (Disk != 0) && (Memory != 0)
        should_transfer_files = YES
        when_to_transfer_output = ON_EXIT
        copy_to_spool = false
        notification = NEVER
        queue 1
        
    Submit the test job:
        $ condor_submit vanilla.sub
        
    Check on the job:
        $ condor_q
        
    After a few minutes it should run. Then check the output:
        $ cat test_*.out
    You should see a hostname that looks like it came from Amazon.
    
13. Modify the image and register a copy
    This is how you create your own custom image.
    
    At this point you can install whatever you want on the running worker
    node. You might want to install programs, libraries, and tools used
    by your workflow. If you don't want to install anything that's OK, you
    can complete this step without modifying the image.
    
    VERY IMPORTANT: One thing you should do here is make sure that
    /etc/grid-security/certificates    contains all the CA certificates you
    need to run your workflow. There is already a pretty good collection
    of them there, but not everything. In particular you should make sure
    to check that all the CAs for the GridFTP servers you use are represented.
    
    In the "Instances" area of the console click on the running instance
    and select "Instance Actions" -> "Create Image (EBS AMI)".
    
    Give it a name and a description and click "Create Image".
    
    In the AMIs area of the console clear all the filters (set to "Owned by
    Me", "All Platforms") and hit refresh. You should see a new image pop
    up. After some time the state should change from "pending" to
    "available". You may need to hit refresh a few times.
    
    IMPORTANT: The image could stay in "pending" status for a long time.
    However, if it is still pending after an hour something is wrong.
    
14. Shut down your instance

    In the "Instances" area of the console click on the running instance
    and select "Instance Actions" -> "Terminate".
    
    VERY IMPORTANT: Amazon keeps charging until the status is "terminated".

15. Configure pegasus

    Add an ec2 site to your sites.xml:
        <site handle="ec2" sysinfo="INTEL64::LINUX">
            <profile namespace="env" key="PEGASUS_HOME">/usr/local/pegasus/default</profile>
            <profile namespace="env" key="GLOBUS_LOCATION">/usr/local/globus/default</profile>
            <profile namespace="env" key="LD_LIBRARY_PATH">/usr/local/globus/default/lib</profile>
            <profile namespace="pegasus" key="bundle.stagein">1</profile>
            <profile namespace="pegasus" key="bundle.stageout">1</profile>
            <profile namespace="pegasus" key="transfer.proxy">true</profile>
            <profile namespace="pegasus" key="style">glidein</profile>
            <profile namespace="condor" key="universe">vanilla</profile>
            <profile namespace="condor" key="requirements">(Arch==Arch)&&(Disk!=0)&&(Memory!=0)&&(OpSys==OpSys)&&(FileSystemDomain!="")</profile>
            <lrc url="rls://example.com"/>
            <gridftp url="gsiftp://" storage="" major="2" minor="4" patch="0"/>
            <jobmanager universe="vanilla" url="example.com/jobmanager-pbs" major="2" minor="4" patch="3"/>
            <jobmanager universe="transfer" url="example.com/jobmanager-fork" major="2" minor="4" patch="3"/>
            <workdirectory>/shared</workdirectory>
        </site>
        
    Add the path to your proxy to the "local" site in sites.xml:
        <!- This is needed so Pegasus can transfer the proxy to EC2 for gridftp ->
        <profile namespace="env" key="X509_USER_PROXY">/tmp/x509up_u724</profile>
    
    In your pegasus.properties file, disable thirdparty transfer mode:
        # Comment-out the next line to run on site "ec2"
        #pegasus.transfer.*.thirdparty.sites=*
        
    If you installed your application code in the image, then modify your
    Transformation Catalog to include the new entries. (Tip: Make sure the
    sysinfo of your "ec2" site matches the new transformations you add to
    the TC)

16. Plan your workflow
    Prepare your workflow to run on EC2.
    
    We assume you know how to do this already. Use "ec2" as the target site.
    If you run into any problems debug them before moving on to the next step.
    If you have problems contact: pegasus-support@isi.edu
    
17. Launch a larger virtual cluster

    You will do basically the same thing you did to launch the first worker.
    This time you will start a virtual cluster with 2 nodes that has a shared
    GlusterFS file system mounted on "/shared". Instead of using the Pegasus
    image, use the new image you created earlier.
    
    In the "AMIs" area select your new image and click "Launch"
    
    Select 2 instances, m1.large.
    
    Set "User Data" to:
        ROLES=CONDOR,GFS;GUID=123456;COORD_HOST=host.example.com;COORD_PORT=40566;NODES=2;GFS_TYPE=nufa;CONDOR_HOST=host.example.com

    VERY IMPORTANT: Don't just copy-paste the above, you need to replace
    "host.example.com" with the actual DNS name of your submit host. Twice!

    IMPORTANT: See the Coord README for what the "User Data" means if you
    are interested in that sort of thing.
        
    Choose your keypair and security group as before and launch the cluster.
    
    Wait until you see the workers show up in condor_status before proceeding.
    You should see twice as many as you did last time. You may want to run
    your vanilla.sub test job again to make sure they work.
    
18. Submit your workflow
    
    At this point you should submit your workflow.
    If you have problems contact: pegasus-support@isi.edu
    
    VERY IMPORTANT: You are virtually guaranteed to have problems at this
    point. Please contact us and we will help.

19. Clean Up
    
    Hopefully your workflow will run to completion. When you are finished
    make sure you terminate any running instances in the "Instances" area
    of the console.

20. Next steps

    Pegasus also supports using Amazon S3 as a storage service instead of
    a shared file system like GlusterFS. If you are interested in using
    S3 please contact pegasus-support@isi.edu and we will help you set it up.

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