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|Contents||Bulletin||Scripting in shell and Perl||Network troubleshooting||History||Humor|
|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|
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.
There are three types of installation mentioned in Oracle Beginner's Guide to Oracle Grid Engine 6.2. We will discuss small cluster
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:
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.
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.
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_ROOTThe 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
Full installation includes the following tasks:
If you are novice, you should generally use GUI installer. It is simpler.
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 1:220.127.116.11-18.104.22.168.8.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 1:22.214.171.124-126.96.36.199.8.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-188.8.131.52-184.108.40.206.8.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 1:220.127.116.11-18.104.22.168.8.el5_8 Dependency Installed: giflib.x86_64 0:4.1.3-7.3.3.el5 tzdata-java.x86_64 0:2012c-1.el5
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.
# cat /etc/fstab | grep "/Apps" m17:/Apps /Apps nfs rw,hard,intr,tcp,rsize=32768,wsize=32768 1 2
/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 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):
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
Update /etc/services . You need to add two ports that are used by SGE
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
# echo $SGE_ROOT
export DISPLAY=10.14.17.7:0; echo $DISPLAY
That should start installer in X session on your workstation/PC.
Click Next. You will see select host screen
"1 out of 1 reachable hosts have configuration errors... ... ... ... Do you want to continue the installation"
Register sgemaster daemon and start it. That ensure proper environment after reboot:
NOTE: You can automate steps listed below by creating a small script:
#!/bin/bash # # Post install operations for SGE execution host # . /$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
# chkconfig sgemaster.$SGE_CLUSTER_NAME on sgeexecd.p6444 0:off 1:off 2:on 3:on 4:on 5:on 6:off
# service sgemaster.$SGE_CLUSTER_NAME startNOTE: The first start takes two-three minutes of more. It's really slow even on a very fast server.
Reboot master host and verify that the daemon correctly started
- Run the following command.% ps -ef | grep sge
- You should see that the sge_master daemon is running.
- 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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