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Installation of Oracle SGE Engine Master Host on Red Hat

News Enterprise Unix System Administration Recommended Links Installation Planning Usage of NFS Network File System (NFS) Installation of the Execution Hosts
Private and Public key managemen Passwordless SSH login SSH Configuration RHEL NTP configuration Troubleshooting NTP on Red Hat Linux Mounting NFS directory owned by root Adding NFS partitions to /etc/fstab
SGE Queues Grid Engine Config Tips SGE Parallel Environment Configuring Hosts From the Command Line Perl Admin Tools and Scripts Humor Etc

Introduction

Oracle grid engine installation consists of two parts:

The master host installation procedure creates the appropriate directory hierarchy that the master daemon requires and starts the Grid Engine master daemon sge_qmaster on the master host (aka head node).  The master host is also registered as a host with administrative and submit permission. The installation procedure creates a default configuration for the system on which it is run. The installation script queries the system for the type of operating system. The script then makes meaningful settings based on this information.

If you do not plan to run jobs on master hosts (and for sizable cluster you should not do it) you do not need to install execution host on the head node.

If, at any time during the installation, you think something went wrong, you can quit the installation procedure and restart it.

RHEL checklist

Installation Planning Checklist

There are three types of installation mentioned in Oracle Beginner's Guide to Oracle Grid Engine 6.2. We will discuss small cluster

Tips

Content of the distribution tar file and the supported platforms

The Sun Grid Engine 6.2 software is distributed via through electronic download. Contrary to Oracle documentation there is just one tar file that contain all files in a single directory. The name of the file for OGE 6-2 release 7 is V24228-01.zip. Here is the content of the distribution tar file

# unzip  ../V24228-01.zip
Archive:  ../V24228-01.zip
  inflating: COPYRIGHT
  inflating: THIRDPARTYLICENSEREADME.txt
  inflating: oge-6_2u7-arco.tar.gz
  inflating: oge-6_2u7-arco.zip
  inflating: oge-6_2u7-bin-aix51.tar.gz
  inflating: oge-6_2u7-bin-darwin-ppc.tar.gz
  inflating: oge-6_2u7-bin-darwin-x86.tar.gz
  inflating: oge-6_2u7-bin-hp11-64.tar.gz
  inflating: oge-6_2u7-bin-hp11.tar.gz
  inflating: oge-6_2u7-bin-linux24-i586.tar.gz
  inflating: oge-6_2u7-bin-linux24-ia64.tar.gz
  inflating: oge-6_2u7-bin-linux24-x64.tar.gz
  inflating: oge-6_2u7-bin-solaris-i586.tar.gz
  inflating: oge-6_2u7-bin-solaris-i586.zip
  inflating: oge-6_2u7-bin-solaris-sparcv9.tar.gz
  inflating: oge-6_2u7-bin-solaris-sparcv9.zip
  inflating: oge-6_2u7-bin-solaris-x64.tar.gz
  inflating: oge-6_2u7-bin-solaris-x64.zip
  inflating: oge-6_2u7-bin-windows-x86.tar.gz
  inflating: oge-6_2u7-common.tar.gz
  inflating: oge-6_2u7-common.zip
  inflating: oge-6_2u7-inspect.tar.gz
  inflating: oge-6_2u7-inspect.zip
  inflating: oge-6_2u7-sources+gpl-code.tar.gz
  inflating: sdm-1_0u7-core.tar.gz
  inflating: sdm-1_0u7-core.zip
  inflating: sun-oge-arco-6.2-7.noarch.rpm
  inflating: sun-oge-bin-linux24-i586-6.2-7.i386.rpm
  inflating: sun-oge-bin-linux24-ia64-6.2-7.ia64.rpm
  inflating: sun-oge-bin-linux24-x64-6.2-7.x86_64.rpm
  inflating: sun-oge-common-6.2-7.noarch.rpm
  inflating: sun-oge-inspect-6.2-7.noarch.rpm
  inflating: sun-sdm-core-1.0-7.noarch.rpm
  inflating: webconsole3.0.2-linux.tar.gz
  inflating: webconsole3.0.2-solsparc.tar.gz   bad CRC c1bb0bee  (should be 6cd29ff0)
  inflating: webconsole3.0.2-solx86.tar.gz

As we can see the tar files contain platform-specific binaries and use the naming convention of sge-6_2-bin-architecture.tar.gz. 

There are also some RPM files

sun-oge-arco-6.2-7.noarch.rpm
sun-oge-bin-linux24-x64-6.2-7.x86_64.rpm
sun-oge-common-6.2-7.noarch.rpm
sun-oge-inspect-6.2-7.noarch.rpm
sun-sdm-core-1.0-7.noarch.rpm

As far as I can understand RPM listed are identical in content to corresponding tar files.

The Sun Grid Engine 6.2 software supports the following operating systems and platforms for execution hosts. Only Unixes can be used for master host:

Content of RPM and installation from RPM

RPMs shipped with SGE are not real RPMs. Additional installation is still required. They are proxy for tar files. And after you install them you can move the directory to necessary location and proceed with installation.  In addition RPM serve as a took to check presence of necessary libraries. Attempt to install binaries compiled for RHEL might fail on SLES because of libraries problems.

Content  of RPM can be views by using rpm -qlp file command

After you install those RPMs the directory /opt/SGE can be relocated to its "proper place' using RPM option --prefix, for example

rpm -iv --prefix=/apps/sge gridengine-8.1.7-1.el6.x86_64.rpm

After that "real" installation should be performed as described below.

 

Creating SGE_ROOT directory and untarring files

For all supported operating systems, the software is distributed in tar.gz and zip formats. For Linux the tar method is the only one that is described in documentation but RPMs are actually a proxy for tar files and installation of RPMs is equivalent to unpacking tar files. As simple as that. 

Steps

  1. Create the installation directory. Should probably be a separte partition to simplify NFS export. For example:
    mkdir /sge
  2. Export SGE-ROOT env. variable: 
    export SGE_ROOT=/sge
  3. Untar the components for all architectures that are to be used by any of your master, execution, and submit hosts. In the simplest case when all you hosts are Linux 64 bit you need to untar just one tar file  gzip -dc oge-6_2u7-bin-linux24-x64.tar.gz
  4. Ensure that the file systems and directories that are to contain the Grid Engine software distribution and the spool and configuration files are set up properly by setting the access permissions as defined in File Access Permissions.  This is done by running
    ./util/setfileperm.sh $SGE_ROOT

Here is a simple script that can be used (you need to set env. variable SGE_BASE to the directory where you unzipped the installation files or specify this path explicitly):

export SGE_BASE=/tmp/oge # directory to in which you unziped the distributionexport SGE_ROOT=/sge
cd $SGE_ROOT
gzip -dc $SGE_BASE/oge-6_2u7-common.tar.gz | tar xvpf -
gzip -dc $SGE_BASE/oge-6_2u7-bin-linux24-x64.tar.gz | tar xvpf -
./util/setfileperm.sh $SGE_ROOT
The last step sets the files permissions and ownership equal to the current user. For example, if you are logged as root: 
# ./util/setfileperm.sh $SGE_ROOT

                    WARNING WARNING WARNING
                    -----------------------
We will set the the file ownership and permission to

   UserID:         0
   GroupID:        0
   In directory:   /opt/sge

We will also install the following binaries as SUID-root:

   $SGE_ROOT/utilbin//rlogin
   $SGE_ROOT/utilbin//rsh
   $SGE_ROOT/utilbin//testsuidroot
   $SGE_ROOT/bin//sgepasswd
   $SGE_ROOT/bin//authuser

Do you want to set the file permissions (yes/no) [NO] >> yes
Verifying and setting file permissions and owner in >3rd_party<
Verifying and setting file permissions and owner in >bin<
Verifying and setting file permissions and owner in >ckpt<
Verifying and setting file permissions and owner in >dtrace<
Verifying and setting file permissions and owner in >examples<
Verifying and setting file permissions and owner in >inst_sge<
Verifying and setting file permissions and owner in >install_execd<
Verifying and setting file permissions and owner in >install_qmaster<
Verifying and setting file permissions and owner in >lib<
Verifying and setting file permissions and owner in >mpi<
Verifying and setting file permissions and owner in >pvm<
Verifying and setting file permissions and owner in >qmon<
Verifying and setting file permissions and owner in >util<
Verifying and setting file permissions and owner in >utilbin<
Verifying and setting file permissions and owner in >start_gui_installer<
Verifying and setting file permissions and owner in >catman<
Verifying and setting file permissions and owner in >doc<
Verifying and setting file permissions and owner in >include<
Verifying and setting file permissions and owner in >man<
Verifying and setting file permissions and owner in >hadoop<

Your file permissions were set

Installing the Sun Grid Engine Master Host Interactively

Full installation includes the following tasks:

If you are novice, you should generally use GUI installer. It is simpler.

Update or install java

Usually java is already installed. For RHEL 5 sometimes Java need update. So you need to verify that. In case it is not, you need to install it:

yum install java
Loaded plugins: rhnplugin, security
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package java-1.6.0-openjdk.x86_64 1:1.6.0.0-1.27.1.10.8.el5_8 set to be updated
--> Processing Dependency: tzdata-java for package: java-1.6.0-openjdk
--> Processing Dependency: libgif.so.4()(64bit) for package: java-1.6.0-openjdk
--> Running transaction check
---> Package giflib.x86_64 0:4.1.3-7.3.3.el5 set to be updated
---> Package tzdata-java.x86_64 0:2012c-1.el5 set to be updated
--> Finished Dependency Resolution

Dependencies Resolved

========================================================================================================================
 Package                     Arch            Version                                Repository                     Size
========================================================================================================================
Installing:
 java-1.6.0-openjdk          x86_64          1:1.6.0.0-1.27.1.10.8.el5_8            rhel-x86_64-server-5           36 M
Installing for dependencies:
 giflib                      x86_64          4.1.3-7.3.3.el5                        rhel-x86_64-server-5           39 k
 tzdata-java                 x86_64          2012c-1.el5                            rhel-x86_64-server-5          181 k

Transaction Summary
========================================================================================================================
Install       3 Package(s)
Upgrade       0 Package(s)

Total download size: 36 M
Is this ok [y/N]: y
Downloading Packages:
(1/3): giflib-4.1.3-7.3.3.el5.x86_64.rpm                                                         |  39 kB     00:00
(2/3): tzdata-java-2012c-1.el5.x86_64.rpm                                                        | 181 kB     00:01
(3/3): java-1.6.0-openjdk-1.6.0.0-1.27.1.10.8.el5_8.x86_64.rpm                                   |  36 MB     01:31
------------------------------------------------------------------------------------------------------------------------
Total                                                                                   339 kB/s |  36 MB     01:50
Running rpm_check_debug
Running Transaction Test
Finished Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing     : giflib                                                                                           1/3
  Installing     : tzdata-java                                                                                      2/3
  Installing     : java-1.6.0-openjdk                                                                               3/3

Installed:
  java-1.6.0-openjdk.x86_64 1:1.6.0.0-1.27.1.10.8.el5_8

Dependency Installed:
  giflib.x86_64 0:4.1.3-7.3.3.el5                            tzdata-java.x86_64 0:2012c-1.el5 

Export a common directory from the qmaster host

Most SGE installation share the whole /Apps directory from the master host with Apps/sge as a subdirectory.  It should be mounted under the same name on the execution host. See Usage of NFS in Grid Engine.

If master host is nos NFS server mount this directory.

/Apps/sge 10.194.186.254(rw,no_root_squash) 10.194.181.26(rw,no_root_squash) 

If master host is simultaneously NFS server restart the NFS daemon on qmaster host to reread export file:

# service nfs restart
Shutting down NFS mountd:                                  [  OK  ]
Shutting down NFS daemon:                                  [  OK  ]
Shutting down NFS quotas:                                  [  OK  ]
Shutting down NFS services:                                [  OK  ]
Starting NFS services:                                     [  OK  ]
Starting NFS quotas:                                       [  OK  ]
Starting NFS daemon:                                       [  OK  ]
Starting NFS mountd:                                       [  OK  ]

Create ssh passwordless keys and distribute public keys to execution hosts

Create passwordless login environment.

Tip: If you already have configured it just copy file authorized_hosts from already configured execution host.

cd /root/.ssh
scp sge01:/root/.ssh/authorized_hosts  . 
Check ssh access from the master host  to the node on which you install the execution host (b5 in the example below):
[0]root@m17: # ssh b5
The authenticity of host 'b5 (10.194.181.46)' can't be established.
RSA key fingerprint is 18:35:6e:96:11:77:27:fc:ac:1c:8e:46:36:2b:ae:2b.
Are you sure you want to continue connecting (yes/no)? yes
Warning: Permanently added 'b5,10.194.181.46' (RSA) to the list of known hosts.
Last login: Thu Jul 26 08:29:41 2012 from sge_master.firma.net

Add SGE services to /etc/services

Update /etc/services . You need to add two ports that are used by SGE

vi /etc/services

add lines (typically people use the default ports 6444 and 6445, but your mileage may vary)

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

Installation of SGE Qmaster

  1. To confirm that you have set the $SGE_ROOT environment variable, type:
    # echo $SGE_ROOT
  2. hange directory (cd) to the installation directory, $SGE_ROOT
    cd $SGE_ROOT
  3. Add host IP to the /etc/hosts (RHEL puts long name as host name which is not very convenient for SGE purposes)
  4. export display to your workstation/PC. You need to start X11 on your workstation (for example Exceed, if you use Windows workstation) For example:
    export DISPLAY=10.14.17.7:0; echo $DISPLAY
  5. Launch the GUI installer by executing the command
    ./start_gui_installer

    That should start installer in X session on your workstation/PC.

    Click Next

    Click Next. You will see select host screen

  6. Register sgemaster daemon and start it. That ensure proper environment after reboot:

    NOTE: You can automate steps listed below by creating a small script:

    #!/bin/bash
    #
    # Post install operations for SGE execution host
    #
    . /$SGE_ROOT/default/common/settings.sh
    
    # Add sgeexecd.$SGE_CLUSTER_NAME (or whatever is your cluster name) to default services on level 3 and 5
    chkconfig sgemaster.$SGE_CLUSTER_NAME on
    
    # On the execution host: start the sge_execd service
    service sgemaster.$SGE_CLUSTER_NAME start
    
    # add nessesary commands to /etc/profile
    echo ". /$SGE_ROOT/default/common/settings.sh" >> /etc/profile

     

  7. Reboot master host and verify that the daemon correctly started

  1. Run the following command.
    % ps -ef | grep sge
  2. You should see that the sge_master daemon is running.
  3. If you do not see similar output, the daemon required on the execution host is not running. Restart the daemon by hand. For example for Linux you can use service command:
    /sbin/service sgemaster.p6444 start

 


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