Sun Grid Engine (SGE) for debian

[Ri ki]

Hi,

I tried to install SGE by running the following on my debian jessie.

sudo apt-get install gridengine-master gridengine-exec gridengine-common gridengine-qmon gridengine-client

but got errors that it could not find these packages.

This is the output:

============================
Reading package lists... Done
Building dependency tree      
Reading state information... Done
Package gridengine-client is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

Package gridengine-exec is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source

Package gridengine-master is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
=============================



Anyone know the correct names of the SGE packages for Debian?

TIA

[Daniel Povey]

those are correct:

 dpkg -l | grep gridengine

ii  gridengine-client                      8.1.9+dfsg-1~bpo8+1                  amd64        Utilities for Grid Engine queue management

ii  gridengine-common                      8.1.9+dfsg-1~bpo8+1                  all          Distributed resource management - common files

ii  gridengine-exec                        8.1.9+dfsg-1~bpo8+1                  amd64        Distributed resource management - Execution Server

root@a14:~# cat /etc/debian_version

8.6

Below is our sources.list, must be somewhere in there.

root@a14:~# cat /etc/apt/sources.list

# 

# deb cdrom:[Debian GNU/Linux 8.5.0 _Jessie_ - Official amd64 DVD Binary-1 20160604-15:35]/ jessie contrib main

# deb cdrom:[Debian GNU/Linux 8.5.0 _Jessie_ - Official amd64 DVD Binary-1 20160604-15:35]/ jessie contrib main

# deb http://security.debian.org/ jessie/updates main contrib

# deb-src http://security.debian.org/ jessie/updates main contrib

# jessie-updates, previously known as 'volatile'

# A network mirror was not selected during install.  The following entries

# are provided as examples, but you should amend them as appropriate

# for your mirror of choice.

#

# deb http://ftp.debian.org/debian/ jessie-updates main contrib

# deb-src http://ftp.debian.org/debian/ jessie-updates main contrib

# 

deb http://ftp.us.debian.org/debian/ jessie main non-free contrib

deb-src http://ftp.us.debian.org/debian/ jessie main non-free contrib

deb http://security.debian.org/ jessie/updates main contrib non-free

deb-src http://security.debian.org/ jessie/updates main contrib non-free

# jessie-updates, previously known as 'volatile'

deb http://ftp.us.debian.org/debian/ jessie-updates main contrib non-free

deb-src http://ftp.us.debian.org/debian/ jessie-updates main contrib non-free

deb http://cran.cnr.berkeley.edu/bin/linux/debian jessie-cran3/

deb-src http://cran.cnr.berkeley.edu/bin/linux/debian jessie-cran3/

deb http://ftp.debian.org/debian jessie-backports main

deb https://apt.dockerproject.org/repo/ debian-jessie main

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[entn-at]

It seems the gridengine packages are in jessie-backports:

https://packages.debian.org/jessie-backports/gridengine-master

https://packages.debian.org/jessie-backports/gridengine-exec

https://packages.debian.org/jessie-backports/gridengine-client

Here is more information on using backports in Debian: https://backports.debian.org/Instructions/

[Ri ki]

Thanks a lot Dan and entn-at. I was able to install the SGE. However I am not able to start the qmon

This is the error i am getting:
====================================================
Warning: Cannot convert string "intro" to type Pixmap
Can't load icon 21cal. Pixmaps should reside in $SGE_ROOT/qmon/PIXMAPS.
=======================================================

As per the following blog(http://asrman.blogspot.com/2015/07/installing-and-setting-up-sun-grid_24.html), the pixmap warning could be ignored. Unfortunately for me though, the admin dialog doesnt show up.

And I dont see a qmon dir in my install. I do see that the pixmaps is installed correctly.

these are the files/dirs in my /usr/share/gridengine dir

-rwxr-xr-x 1 root root  1151 Jul 17  2016 busy-nodes
-rwxr-xr-x 1 root root   723 Jul 17  2016 dead-nodes
-rw-r--r-- 1 root root   424 Jul 17  2016 default-bootstrap
-rw-r--r-- 1 root root  1621 Jul 17  2016 default-configuration
-rwxr-xr-x 1 root root  1401 Jul 10  2016 gridengine-wrapper
-rwxr-xr-x 1 root root  1374 Jul 17  2016 idle-nodes
-rwxr-xr-x 1 root root  1372 Jul 17  2016 install_execd
-rwxr-xr-x 1 root root  1350 Jul 17  2016 install_qmaster
-rwxr-xr-x 1 root root 60988 Jul 17  2016 inst_sge
-rwxr-xr-x 1 root root 25151 Jul 17  2016 jobstats
drwxr-xr-x 4 root root  4096 May 12 02:39 mpi
-rwxr-xr-x 1 root root  1391 Jul 17  2016 nodes-in-job
drwxr-xr-x 3 root root  4096 May 12 02:39 pixmaps
drwxr-xr-x 3 root root  4096 May 12 02:39 pvm
-rw-r--r-- 1 root root 16158 Jul 17  2016 Qmon
-rwxr-xr-x 1 root root   656 Jul 17  2016 qselect-node-list
drwxr-xr-x 2 root root  4096 May 12 02:39 scripts
drwxr-xr-x 2 root root  4096 May 12 02:39 templates
drwxr-xr-x 7 root root  4096 May 12 02:39 util


as one can see i have pixmaps dir but i dont have a qmon dir to place the Pixmaps as suggested by the error.

Any pointers?

Thanks

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[Daniel Povey]

I don't use qmon-- something graphics related must be going wrong for you, but anyway I use qstat from the terminal.

[Ri ki]

Thanks Dan. I gave up on the GUI (qmon) and started using qconf as u suggested.

I am following this guide. However, when i make changes, they are not getting saved.

For example, as per the guide,

===============================

Creating a queue

To create a queue we have to run the following:

sudo qconf -aq

An editor will be open edit the following lines:

• qname -> normal.q
• hostlist (space separated) -> hostname (use the same as the admin host)
• slots (e.g. machine cores - 1) -> 7 (I have 8)
• shell -> /bin/bash
• h_rt -> 48:00:00 (hh:mm:ss)

============================

when i run the sudo qconf -aq command, it opens a tmp file in an editor and i make my changes and save the file.

However when i run the next command:

=====================================

Now save the file and check that the queue has been created:

sudo qconf -sql
=====================================

i get the following:

no cqueue list defined

What am i doing wrong?

Thank you for ur help.

[Ri ki]

sorry forgot to post the link to the guide:

https://github.com/babelomics/stevia-server/wiki/Installing-Sun-Grid-Engine

[Daniel Povey]

I don't think that's a very normal error; I haven't encountered it.  It may mean there is some internal problem with the installation.  At least that's what I'd guess.  If I were you I'd remove the packages and start again from scratch.  

Dan

[Daniel Povey]

Wait, per

https://arc.liv.ac.uk/pipermail/gridengine-users/2008-January/017387.html

it might be a name resolution problem.

This relates to DNS and things like that.

GridEngine is very finicky about name lookup things like IP addresses matching (and maybe even reverse name lookup, IIRC).  If your qmaster name is 'admin', you have to ensure that name lookup of the host 'admin' actually resolves to 'admin' itself.  This may involve messing with /etc/hosts.

Dan

[Ri ki]

Dan,

Thanks for your help.

My issue has been resolved basically by setting up the parallel environment smp and mpi. Once i configured those, i did not have any issues(atleast in my preliminary testing).

I am still unable to use the GUI to configure though. But i do not want to waste anymore time on it.

Thanks again