The MPI version of phyml is now installed on the AIX power7 cluster. This is alpha code - check your results carefully! The manual is here and here is an example loadleveler script to run phytime:
#!/bin/sh # @ output = $(Executable).$(Cluster).out # @ error = $(Executable).$(Cluster).err # @ notification = never # @ job_type = parallel # @ class = p7aix_dev # @ group = UC # @ blocking = unlimited # @ wall_clock_limit = 00:33:00 # @ total_tasks = 8 # @ rset = rset_mcm_affinity # @ mcm_affinity_options = mcm_accumulate,mcm_mem_pref # @ queue # This is a quick test: /usr/local/bin/phytime -i seq1.txt
The MPI version of RAxML is now installed on the AIX power7 cluster. This is alpha code - check your results carefully! The manual is here and here is an example loadleveler script to run RAxML:
#!/bin/sh # @ output = $(Executable).$(Cluster).out # @ error = $(Executable).$(Cluster).err # @ notification = never # @ job_type = parallel # @ class = p7aix_dev # @ group = UC # @ blocking = unlimited # @ wall_clock_limit = 0:30:00 # @ total_tasks = 8 # @ rset = rset_mcm_affinity # @ mcm_affinity_options = mcm_accumulate,mcm_mem_pref # @ queue /usr/local/pkg/raxml/version/bin/raxmlHPC-MPI -m GTRGAMMA -n result -x 12345 -p 12345 -s raxml_inputphy.txt -N 8
The NAMD molecular dynamics package is now upgraded to version 2.9 on the AIX system. Compilation issues required us to remove large file (> 2GB) support. Please let us know if this is an issue for you. To run NAMD, use a loadleveler script like this:
#!/bin/sh
# @ output = $(Executable).$(Cluster).out
# @ error = $(Executable).$(Cluster).err
# @ notification = complete
# @ job_type = parallel
# @ class = p7aix
# @ group = UC
# @ blocking = unlimited
# @ wall_clock_limit = 24:00:00
# @ total_tasks = 32
# @ rset = rset_mcm_affinity
# @ task_affinity = core(1)
# @ mcm_affinity_options = mcm_accumulate,mcm_mem_pref
# @ queue
/usr/local/pkg/namd/version/namd2 /tmp/apoa1/apoa1.namd
Please visit https://wiki.canterbury.ac.nz/display/BlueFern/LoadLeveler+Group+Definitions for important information about loadleveler groups.
Because of a hardware failure, backups of our /hpc/* filesystems did not run last night, and so files newer than a couple of days old will not be recoverable until the problem is fixed. Let's be careful out there!
Update 11 May 2012
Backups are now operating normally.