[Rocks-Discuss] problem with yum on head node

Antonia Mey

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Oct 26, 2010, 6:40:33 AM10/26/10

to npaci-rocks...@sdsc.edu

Hi,
I am very inexperienced when it comes to clusters. I have a 10 node
rocks cluster and I want to install some programs to the headnode like
svn,xmgrace etc. I guess yum is the way to do so. However when i try and
even get an update like yum update, i get the following error:
" http://10.1.1.1/install/rocks-dist/i386/repodata/repomd.xml: [Errno
14] HTTP Error 502: Bad Gateway (Server unreachable)"
The cluster is behind a proxy which seems to be set correctly, as wget
works without a problem. In which config file do I set the repositories
I want to access and use with yum. I am normally used to apt, where i
set everything in /etc/apt/sources.list
this does not seem to exist for yum. My yum.conf file looks like this:
/
[main]
cachedir=/var/cache/yum
debuglevel=2
logfile=/var/log/yum.log
pkgpolicy=newest
distroverpkg=redhat-release
tolerant=1
exactarch=1
assumeyes=1

[Rocks-5.3]
name=Rocks 5.3
baseurl=http://10.1.1.1/install/rocks-dist/i386/

Any help would be greatly appreciated.
Regards,
Toni

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Alain Péan

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Oct 26, 2010, 8:28:17 AM10/26/10

to Discussion of Rocks Clusters

Hi Toni,

No repositories are setup by Rocks, and it seems to be so to avoid that
people do a 'yum update', that could break Rocks configuration (but some
people seem to have succeeded to update their cluster successfully,
configuring updates to avoid certain packages, search this list).

So, if you want, as it is my case, to install some addional packages via
yum, you have to configure the repositories yourself. I do so by copying
the files used by CentOS (and other related RedHat distros) from another
working workstation using CentOS 5.

This file is :
/etc/yum.repos.d/CentOS-Base.repo

Here is the content of mine :
# CentOS-Base.repo
#
# The mirror system uses the connecting IP address of the client and the
# update status of each mirror to pick mirrors that are updated to and
# geographically close to the client. You should use this for CentOS
updates
# unless you are manually picking other mirrors.
#
# If the mirrorlist= does not work for you, as a fall back you can try the
# remarked out baseurl= line instead.
#
#

[base]
name=CentOS-$releasever - Base
mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=os
#baseurl=http://mirror.centos.org/centos/$releasever/os/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5

#released updates
[updates]
name=CentOS-$releasever - Updates
mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=updates
#baseurl=http://mirror.centos.org/centos/$releasever/updates/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5

#packages used/produced in the build but not released
[addons]
name=CentOS-$releasever - Addons
mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=addons
#baseurl=http://mirror.centos.org/centos/$releasever/addons/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5

#additional packages that may be useful
[extras]
name=CentOS-$releasever - Extras
mirrorlist=http://mirrorlist.centos.org/?release=$releasever&arch=$basearch&repo=extras
#baseurl=http://mirror.centos.org/centos/$releasever/extras/$basearch/
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-CentOS-5
---------------------------------------------------------------------------------

Note that I added the 'Extra' CentOS repository, as it was on the
workstation, but it is perhaps not necessary.

You have also to import the authentication keys for CentOS repositories :
# rpm --import http://mirror.centos.org/centos/RPM-GPG-KEY-CentOS-5

Use it if you want to add a package on your frontend, but avoid to
update it. It was how I break my first Rocks installation !

If you want to add packages to all your compute nodes, it is best to do
it the 'Rocks way'.
That is download the rpm packages, put them in :
/export/rocks/install/contrib/5.3/x86_64/RPMs

and add them to extend-compute.xml, and rebuild the distribution. It is
explained in the documentation :
http://www.rocksclusters.org/roll-documentation/base/5.3/customization-adding-packages.html

Good luck !
Alain

Le 26/10/2010 12:40, Antonia Mey a �crit :

--
==========================================================
Alain P�an - LPP/CNRS
Administrateur Syst�me/R�seau
Laboratoire de Physique des Plasmas - UMR 7648
Observatoire de Saint-Maur
4, av de Neptune, Bat. A
94100 Saint-Maur des Foss�s
Tel : 01-45-11-42-39 - Fax : 01-48-89-44-33
==========================================================

Antonia Mey

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Oct 26, 2010, 9:01:09 AM10/26/10

to Discussion of Rocks Clusters

Dear Alain,
thank you very much, yum works now and I could install everything I
wanted. I'll steer clear of any 'yum update' attempts!
Thanks again,
Toni

Alain P�an wrote:
> Hi Toni,
>
> No repositories are setup by Rocks, and it seems to be so to avoid
> that people do a 'yum update', that could break Rocks configuration
> (but some people seem to have succeeded to update their cluster
> successfully, configuring updates to avoid certain packages, search
> this list).
>
> So, if you want, as it is my case, to install some addional packages
> via yum, you have to configure the repositories yourself. I do so by
> copying the files used by CentOS (and other related RedHat distros)
> from another working workstation using CentOS 5.
>
>

> Note that I added the 'Extra' CentOS repository, as it was on the
> workstation, but it is perhaps not necessary.
>
> You have also to import the authentication keys for CentOS repositories :
> # rpm --import http://mirror.centos.org/centos/RPM-GPG-KEY-CentOS-5
>
> Use it if you want to add a package on your frontend, but avoid to
> update it. It was how I break my first Rocks installation !
>
> If you want to add packages to all your compute nodes, it is best to
> do it the 'Rocks way'.
> That is download the rpm packages, put them in :
> /export/rocks/install/contrib/5.3/x86_64/RPMs
>
> and add them to extend-compute.xml, and rebuild the distribution. It
> is explained in the documentation :
> http://www.rocksclusters.org/roll-documentation/base/5.3/customization-adding-packages.html
>
>
> Good luck !
> Alain
>

--
Antonia Mey, PhD candidate

School of Physics & Astronomy
University Park
Nottingham
NG7 2RD

ppxa...@nottingham.ac.uk
+441159515130

Richard Chang

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Oct 26, 2010, 9:19:38 AM10/26/10

to npaci-rocks...@sdsc.edu

On 10/26/2010 4:10 PM, Antonia Mey wrote:
> Hi,
> I am very inexperienced when it comes to clusters. I have a 10 node rocks cluster and I want to install some programs to the headnode like svn,xmgrace etc. I guess yum is the way to do so. However when i try and even get an update like yum update, i get the following error:
> " http://10.1.1.1/install/rocks-dist/i386/repodata/repomd.xml: [Errno 14] HTTP Error 502: Bad Gateway (Server unreachable)"
> The cluster is behind a proxy which seems to be set correctly, as wget works without a problem. In which config file do I set the repositories I want to access and use with yum. I am normally used to apt, where i set everything in /etc/apt/sources.list
> this does not seem to exist for yum. My yum.conf file looks like this:
> /
> [main]
> cachedir=/var/cache/yum
> debuglevel=2
> logfile=/var/log/yum.log
> pkgpolicy=newest
> distroverpkg=redhat-release
> tolerant=1
> exactarch=1
> assumeyes=1
>
> [Rocks-5.3]
> name=Rocks 5.3
> baseurl=http://10.1.1.1/install/rocks-dist/i386/
>
> Any help would be greatly appreciated.
> Regards,
> Toni
>

Toni,
Where have you put the proxy details ?. If you have put it in the environment variable http_proxy ,then yum will try to access the Rocks repository through the proxy.

It is always better to input it in the yum.conf file. This is the yum.conf that I use:

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

[main]
cachedir=/var/cache/yum
debuglevel=2
logfile=/var/log/yum.log
pkgpolicy=newest

proxy=http://xx.xx.xx.xx:port
proxy_username=user_name
proxy_password=password
distroverpkg=redhat-release
tolerant=1
exactarch=1
assumeyes=1

[Rocks-5.3]
name=Rocks 5.3
proxy=_none_
baseurl=http://10.10.1.1/install/rocks-dist/x86_64

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

This way, whatever packages are available in the local Rocks repo are installed and whatever are not in the local repo are fetched from the remote site.

You can try this and let us know how it goes through. Remember to unset the variable http_proxy before running yum again.

regards,
Richard.

Antonia Mey

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Nov 12, 2010, 10:12:06 AM11/12/10

to npaci-rocks...@sdsc.edu

Hi,
I was wondering how I can limit the number of jobs run per user. So as
an example if I have 30 nodes in total that a user at any given time can
only have jobs on 20 nodes running.
Also how can I change the priority on the q based on wall time submissions?
Thanks for the help,
Toni

--
Antonia Mey, PhD candidate

School of Physics & Astronomy
University Park
Nottingham
NG7 2RD

ppxa...@nottingham.ac.uk
+441159515130

Bart Brashers

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Nov 12, 2010, 12:49:17 PM11/12/10

to Discussion of Rocks Clusters

Using the Torque roll or the SGE roll?

Bart

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Broka, Andi

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Nov 12, 2010, 2:08:19 PM11/12/10

to Discussion of Rocks Clusters

Hi Antonia,

If you're using SGE you can limit maximum number of running jobs for all users by setting "maxujobs" parameter in "scheduler configuration"

$ qconf -msconf

If you want more fine grained limits based on different users, queues, hosts, etc you should use Resource Quotas System.

$ qconf -mrqs

Then add the following configuration

{
name ppxasjsm
description "specific limitations for user ppxasjsm"
enabled TRUE
limit users ppxasjsm to slots=20
}