Auckland Cluster Testing
From BeSTGRID
Contents |
[edit] Application Status
| RPM | Software | Patches | Dependencies | Build Process | Install Process |
|---|---|---|---|---|---|
| beast-1.4.7-1 | BEAST | None | java 1.5 | none | Create symlinks for bin |
| mrbayes-3.1.2-1 | MrBayes | None | readline-devel and libtercap-devel | make | Create symlink for mb |
| cluslaw-1.8-1 | cluslaw | None | none | make | Create symlinks |
| cluslawmpi-0.13-1 | cluslaw (MPI version) | None | openmpi | make | Create symlinks |
| lamarc-2.1.2b-1 | Lamarc | None | gtk2-devel | configure --enable-buildwx --prefix=location; make | make install |
| modeltest-3.7-1 | ModelTest | None | None | make (need tarball) | create symlinks |
[edit] Development System
on VM in data center. I will use it for development before test cluster stabilizes. To ensure consistency with Rocks environment I am using rpms from standard rolls, if available. Currently they are under /home/yhal003/RPMS
OS: CentOS 4.4 IP: 130.216.189.66
[edit] Dependencies
packages not available in default rolls and needed for the distribution.
libtermcap-devel.i386
[edit] Issues
- when run without arguments, beast needs X for file chooser. probably not an issue, but...
[edit] Log
Just to keep track of environment.
- installed gcc
- installed subversion
- installed jdk 1.5. Created semilinks for java and javac in /usr/bin
- tested BEAST.
- installed readline-devel and libtercap-devel (needed by mrBayes)
- compiled and tested mrBayes (without mpi, without Cantebury fixes)
- installed gcc4-c++.i386 rpm with yum (not from roll repos since couldn't satisfy dependencies...)
- installed gtk2-devel.i386 (not from rolls)
- compiled and tested lamarc (with default wxWidgets)
- compiled and tested cluslaw.
- installed emacs
- installed openmpi (not from rolls, but all rpms were there)
- compiled and tested cluslaw mpi version.
- compiled and tested modelTest
- installed cvs
- installed rpm-build
- created RPM from beast
- created RPM from mrbayes
- created RPM from clustalw
- created RPM for clustalw MPI version
- created RPM for lamarc
- created RPM for modeltest
[edit] Test System
Rocks with one head node and 2 compute nodes
[edit] Configuration
- public NIC
- IP 130.216.77.36
- eth1
- netmask 255.255.254.0
- gateway 130.216.77.254
- MAC 00:11:43:22:74:00
- private NIC
- IP 10.1.1.1
- eth0
- netmask 255.0.0.0
- MAC 00:01:02:56:DD:89
[edit] TODO
[edit] Possible Problems with Rocks Installation
- disk roll shows as as Unidentified
- Had to restart installation
- insert-ethers gives error: int() argument must be string or number.
- Had to reinstall head node
- Compute node shows language selection menu
- it failed to obtain IP for some reason. Could be problem with switch, dhcpd not running etc.
