Posts Tagged ‘Torque’


February 20, 2011

My recent task was deployment of HPC cluster. It doesn’t make any sense to install each node separately and manually install all cluster software. There is simpler solution. Several software suites exist which allow you to automatically deploy head node and all compute nodes via PXE.


My first shot was OSCAR. Since I was actually redeploying  I had some old version of OSCAR installed. First surprise is – OSCAR doesn’t support upgrade. It effectively means you need to reinstall your head node. I tried to upgrade OSCAR manually but with no luck. It has complicated installation process and not obvious dependencies. After I reinstalled operating system and installed latest OSCAR package I couldn’t install it via its GUI. When I clicked button for fourth step I saw following error:

Tk::Error: Can’t set -options to `ARRAY(0xd34c710)’ for Tk::Optionmenu=HASH(0xd360660): No -label at /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/Tk/ line 256

An you can do nothing with that. Period.

Luckily new version of OSCAR just came out and after another full OS reinstall I had GUI working just fine. But when I tried to select Torque PBS for installation I ran into another error with broken dependency:

opkg-torque-server-2.1.13-1.noarch from unstable_rhel-5-x86_64 has depsolving problems

–> Missing Dependency: torque-modulefile is needed by package opkg-torque-server-2.1.13-1.noarch (unstable_rhel-5-x86_64)

Then I tried to contact developers. They issued several patches but for some weired reason their patches changed nothing. I decided to unselect Torque and install it manually later.  But I ran into another dependency error with MAUI since MAUI depends on Torque. I unselected MAUI. Then I ran into another dependency resolution error with LAM. I unselected LAM and after that I was able at least to install OSCAR packages on head node.

Next step was compute nodes deployment. After setting up correct PXE boot environment and booting one testing compute node I got failed installation due to lack of compute node’s NIC support. Luckily OSCAR has so called “Use Your Own Kernel (YOUK)” option which substitutes original kernel with head node’s kernel. It made it possible to start installation.

Unfortunately another error showed up. For some reason rsync connection between head and compute node breaks at random point in time. Rsync is the only way to deploy OS onto compute nodes. It means that story ends at this point. I’ve spent 3 weeks on OSCAR and was not able to deploy high performance computing cluster with help of it.


ROCKS was a breath of fresh air. One day was enough to install everything. The only issue I had is compute nodes deployment delay. Some nodes hung for 10-15 mins before downloading disto via TFTP. But it is almost not an issue.

opkg-torque-server-2.1.13-1.noarch from unstable_rhel-5-x86_64 has depsolving problems

–> Missing Dependency: torque-modulefile is needed by package opkg-torque-server-2.1.13-1.noarch (unstable_rhel-5-x86_64)


ROCKS post install configuration

February 20, 2011

If you use ROCKS to deploy cluster you still need to do some manual configuration. What I personally did was:

1. Disable hyperthreading in BIOS. HT is not helpful for compute intensive tasks. It’s better suited for I/O intensive applications.

2. Add compute nodes to /opt/torque/server_priv/nodes in the following format:

compute-1-2 np=8

Where compute-1-2 is node’s domain name and np is the number of processors (cores).

3. Add master.local to /etc/hosts.equiv (for Torque).

4. Install InfiniBand stack. Most of IB RPMs are already installed but I also added:

libibumad, opensm-libs, opensm, ibutils, infiniband-diags, ibutils-libs, libibmad, libmlx4, swig

I just downloaded them by

# yumdownloader package-name

then put them into /share/apps and installed by

# rocks run host compute “rpm -Uvh /share/apps/*.rpm”

Then you will need to set openibd service to run upon startup on all compute nodes and opensmd service on any ONE of compute nodes.

5. Then you need to set up queues. There is a ‘default’ queue which is decent for simple setup. But I have nodes of two types and it’s handy to have separate queues. ‘qmgr’ is a binary which controls Torque queues. I made simple text file which contained:

create queue srail queue_type=execution
set queue srail started=true
set queue srail enabled=true
set queue srail resources_default.neednodes=srail

create queue mrail queue_type=execution
set queue mrail started=true
set queue mrail enabled=true
set queue mrail resources_default.neednodes=mrail

Then I fed this file to qmgr:

# qmgr <

To check qmgr configuration call:

# qmgr -c ‘p s’

At last change node records in /opt/torque/server_priv/nodes from

compute-1-2 np=8


compute-1-2 np=8 mrail

6. ROCKS don’t support LVM. It installs everything on first hard drive it finds. If you have two hard drives just mount second drive to /state/partition1/home and add home partition to /etc/exportfs.