HCL cluster

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Revision as of 16:06, 11 May 2010 by Rhiggins (talk | contribs) (Some networking issues on HCL cluster (unsolved))

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General Information

Layout of the Cluster

The hcl cluster is heterogeneous in computing hardware & network ability.

Nodes are from Dell, IBM, and HP, with Celeron, Pentium 4, Xeon, and AMD processors ranging in speeds from 1.8 to 3.6Ghz. Accordingly architectures and parameters such as Front Side Bus, Cache, and Main Memory all vary.

Operating System used is Debian “squeeze” with Linux kernel 2.6.32.

The network hardware consists of two Cisco 24+4 port Gigabit switches. Each node has two Gigabit ethernet ports - each eth0 is connected to the first switch, and each eth1 is connected to the second switch. The switches are also connected to each other. The bandwidth of each port can be configured to meet any value between 8Kb/s and 1Gb/s. This allows testing on a very large number of network topologies, As the bandwidth on the link connecting the two switches can also be configured, the cluster can actually act as two separate clusters connected via one link.

The diagram below shows a schematic of the cluster.

Detailed Cluster Specification

A table of hardware configuration is available here: Cluster Specification

Cluster Administration

Useful Tools

root on heterogeneous.ucd.ie has a number of Expect scripts to automate administration on the cluster (in /root/scripts). root_ssh will automatically log into a host, provide the root password and either return a shell to the user or execute a command that is passed as a second argument. Command syntax is as follows:

# root_ssh
usage: root_ssh [user@]<host> [command]

Example usage, to login and execute a command on each node in the cluster (note the file /etc/dsh/machines.list contains the hostnames of all compute nodes of the cluster):

# for i in `cat /etc/dsh/machines.list`; do root_ssh $i ps ax \| grep pbs; done

The above is sequential. To run parallel jobs, for example: apt-get update && apt-get -y upgrade, try the following trick with screen:

# for i in `cat /etc/dsh/machines.list`; do screen -L -d -m root_ssh $i apt-get update \&\& apt-get -y upgrade'; done

You can check the screenlog.* files for errors and delete them when you are happy. Sometimes all logs are sent to screenlog.0, not sure why.

Software packages available on HCL Cluster 2.0

Wit a fresh installation of operating systems on HCL Cluster the follow list of packages are avalible:

  • autoconf
  • automake
  • fftw2
  • git
  • gfortran
  • gnuplot
  • libtool
  • netperf
  • octave3.2
  • qhull
  • subversion
  • valgrind
  • gsl-dev
  • vim
  • python
  • mc
  • openmpi-bin
  • openmpi-dev
  • evince
  • libboost-graph-dev
  • libboost-serialization-dev
  • r-cran-strucchange
  • graphviz
  • doxygen

new hcl node install & configuration log

new heterogeneous.ucd.ie install log

Access and Security

All access and security for the cluster is handled by the gateway machine (heterogeneous.ucd.ie). This machine is not considered a compute node and should not be used as such. The only new incoming connections allowed are ssh, other incoming packets such as http that are responding to requests from inside the cluster (established or related) are also allowed. Incoming ssh packets are only accepted if they are originating from designated IP addresses. These IP's must be registered ucd IP's. csserver.ucd.ie is allowed, as is hclgate.ucd.ie, on which all users have accounts. Thus to gain access to the cluster you can ssh from csserver, hclgate or other allowed machines to heterogeneous. From there you can ssh to any of the nodes (hcl01-hcl16).

Access from outside the UCD network is only allowed once you have gained entry to a server that allows outside connections (such as csserver.ucd.ie)

Some networking issues on HCL cluster (unsolved)

"/sbin/route" should give:

Kernel IP routing table
Destination     Gateway         Genmask         Flags Metric Ref    Use Iface     *      UH    0      0        0 eth0
heterogeneous.u *      UH    0      0        0 eth0    *        U     0      0        0 eth1    *        U     0      0        0 eth0    *        U     0      0        0 eth0    *        U     0      0        0 eth1
default         heterogeneous.u         UG    0      0        0 eth0

For reasons unclear, sometimes many machines miss the entry:    *        U     0      0        0 eth1

For Open MPI, this leads to inability to do a system sockets "connect" call to any 192.*.21.* address (hangup). For this case, you can

  • switch off eth1:
mpirun --mca btl_tcp_if_exclude lo,eth1  ...


  • you can restore the above table on all nodes by running "sh /etc/network/if-up.d/00routes" as root

It is not yet clear why without this entry the connection to the "21" addresses can't be connected. We expect that in this case following rule should be matched (because of the mask):    *        U     0      0        0 eth0

The packets leave over the eth0 network interface then and should go over switch1 to switch2 and eth1 interface of the corresponding node

  • If one attempts a ping from one node A, via its eth0 interface, to the address of another node's (B) eth1 interface, the following is observed:
    • outgoing ping packets appear only on the eth0 interface of the first node A.
    • incoming ping packets appear only on eth1 interface of the second node B.
    • outgoing ping response packets appear on the eth0 interface of the second node B, never on the eth1 interface despite pinging the eth1 address specifically.

What explains this? With the routing tables as they are above, or in the damaged case, the ping may arrive to the correct interface, but the response from B is routed to A-eth0 via B-eth0.