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Installation of SCE on small slusters

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Introduction

Whether you have installed previous versions of the Sun Grid Engine software or this is your first time, you must do some planning before you extract and install the software. This section describes the decisions that you must make, and, wherever possible, gives you criteria on which you can base your decisions.

We also assume that NFS is used for sharing files with master host.

Degree of sharing is not that important but generally $SGE_ROOT/$SGE_CELL should be shared.  Efficiency consideration that are sited by many are overblown and without careful measurements and determining real bottleneck you might fall into classical trap called "premature optimization". And as Donald Knuth used to say "Premature optimization is the source of all evil". and long before him Talleyrand gave the following advice to young diplomats: "First and foremost, not too too much zeal".  Just substitute "young diplomats" for novice SGE administrators.

The same issue applies to a choice between classic spooling vs. Berkeley DB. Without measurements the selection of Berkeley DB is fools gold.

Key Decisions

You must make several decisions before you can plan the installation:

Gather the Necessary Information

Write down and print key data for you installation so that you can refer to them easily and have lesser chances to mix things up when installing execution hosts. You can also try to use the following bullet point as as a simple checklist: 

Disk Space Requirements

The Grid Engine has extremely minimal space requirements (for modern size of disk drives disk ). And it is even somewhat strange to discuss it, But many years ago 1GBdrive was huge and 200MB big.  Generally it will be OK to use 1G partitions which is nothing in modern time. Here are minimal requirements as listed by Sun in 2010:

$SGE_ROOT Directory

You must create a directory into which to load the contents of the distribution media or install RPMs. This directory is called the root directory, or $SGE_ROOT. When the Grid Engine system is running, this directory also will store the current SGE configuration and all other data that must be spooled to disk.

Note  the $SGE_ROOT environment variable is used to refer to the directory into which the Sun Grid Engine software is installed. The $SGE_ROOT directory is the top level of the Grid Engine software directory tree. On startup, each Grid Engine execution host needs read access to the $SGE_ROOT/$SGE_CELL/common directory.

For ease of installation and administration, this directory should be readable on all hosts on which you intend to run the Grid Engine software installation procedure. For example, you can select a directory that is available across a network file system, such as NFS. If you choose to select file systems that are local to the hosts, you must copy the installation directory to each host before you start the installation procedure for the particular machine. See File Access Permissions for a description of required permissions.

NFS export

Generally the less you share the faster SGE operates and less overhead it provides for computational jobs But you should avoid too much zeal.

See Optimizing usage of NFS in Grid Engine for details.

Note

  • Because changing the installation directory or the spool directories requires a new installation of the system, use extra care to select a suitable installation directory. Note that all important information from a previous installation can be preserved. By default, the installation procedure installs the Grid Engine software, man pages, spool areas, and the configuration files in a directory hierarchy under the installation directory.

    File Access Permissions

    If you install the software logged in as root, you might have a problem configuring root read/write access for all hosts on a shared file system. Therefore, you might have problems putting the $SGE_ROOT files onto a network-wide file system.

    You can force Grid Engine software to run all Grid Engine system components through a non-root administrative user account, for example sgeadmin. With this setup, this particular user needs only read/write access to the shared $SGE_ROOT file system.

    The installation procedure asks whether files should be created and owned by an administrative user account. If you answer "Yes" and provide a valid user name, files are created by this user. Otherwise, the user name under which you run the installation procedure is used. Create an administrative user, and answer "Yes" to this question.

    Make sure in all cases that the account used for file handling on all hosts has read/write access to the $SGE_ROOT directory. Also, the installation procedure assumes that the host from which you access the Grid Engine software distribution media can write to the $SGE_ROOT directory.

    Network Services

    If you use tar file based installation you need to define SGE network services in /etc/services.

    If those lines are missing (RPMs add those lines) then add lines manually

    sge_qmaster     6444/tcp                # Grid Engine Qmaster Service
    sge_qmaster     6444/udp                # Grid Engine Qmaster Service
    sge_execd       6445/tcp                # Grid Engine Execution Service
    sge_execd       6445/udp                # Grid Engine Execution Service
     

    Master Host

    The master host controls the Grid Engine system. This host runs the master daemon sge_qmaster.

    The master host has pretty minimalistic requremnts for hardware and can run on modern desktops quite well:

  • Choosing Between Classic Spooling and Database Spooling

    During the installation, you are given the option to choose between classic spooling and Berkeley DB spooling. Use classic spooling.  Berkeley DB make sense only  for more then 32 nodes and even this is depends on speed of your netwrok and how many small tasks SGE will be running simultaneously.  At the beginning you will always be better off with classic spooling. When you learn the ropes you can always switch. 

    Group IDs

    You need to provide a range of IDs that will be assigned dynamically for jobs. The range must be big enough to provide enough numbers for the maximum number of Grid Engine jobs running at a single moment on a single host.

    A group ID is assigned to each Grid Engine job to monitor the resource utilization of the job. Each job will be assigned a unique ID while it is running. For example, a range of 20000-20100 allows 100 jobs to run concurrently on a single host. You can change the group ID range for your cluster configuration at any time, but the values in the UNIX group ID range must be unused on your system.

    Administration Hosts

    Operators and managers of the Grid Engine system use administration hosts to perform administrative tasks such as reconfiguring queues or adding Grid Engine users.

    The master host installation script automatically makes the master host an administration host. During the master host installation process, you can add other administration hosts. You can also manually add administration hosts on the master host at any time after installation.

    Submit Hosts Jobs can be submitted and controlled from submit hosts. The master host installation script automatically makes the master host a submit host.

    Cluster Queues The installation procedure creates a default cluster queue structure, which is suitable for getting acquainted with the system. The default queue can be removed after installation.

    Note No matter what directory is used for the installation of the software, the administrator can change most settings that were created by the installation procedure. This change can be made while the system is running. Consider the following when determining a queue structure:

    Scheduler Profiles

    You can choose from three scheduler profiles during the installation process: normal, high, and max. You can use these predefined profiles as a starting point for Grid Engine tuning.

    Using these profiles, you can optimize the scheduler for one or more of the following:



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