Mako's homepage

Mako is our SGI Origin 2400 server. It was installed in November of 2001 and currently resides in the MIS NOC in the Hill Student Center.

Mako System Stats:

  • 64 300MHz MIPS R12000 CPUs
  • 32 GB of system RAM
  • 300 GB of Fast Wide SCSI storage

Getting an account

 To get an account on mako, you'll first need to obtain a structural biology UNIX account. Then log in to structural biology support and create a new request to ask for access to mako. When making this request, please tell us what type of jobs you plan to run so that the appropriate software can be added to the system if necessary.

Your account on mako will share the same username as your structural biology UNIX account. Initially, it will share the same password as well. However, your mako login account is independent of your structural biology account. Therefore if you change your structural biology password, your mako password will not be updated (and vice-versa).

Filesystem layout on Mako

For optimum reliability and performance, your structural biology home directory is not network-mounted on mako. Your home directory on mako is a seperate directory on a local mako filesystem. Also, files on mako are not backed up. Your local home directory is treated as scratch space. Move your scripts and results off the machine quickly to make space for others and to minimize your exposure to lost work as a result of potential disk failure.

The internal disks are divided into two filesystems:

  • / is the root filesystem which contains the operating system and all software.
  • /jaws is a 200 Gigabyte filesystem striped across six 36G disks. It is the primary home/scratch partition.

The /jaws filesystem can be accessed via NFS from any structural biology UNIX system at the path /sb/jaws. This will make it easier to copy files to/from mako before and after your runs.

Submitting compute jobs to Mako

Do not run compute jobs interactively on mako. Mako runs version 2.3 of PBS (Portable Batch System). All calculations must be submitted through the queue system. Please visit the using pbs page for info, including example PBS scripts.

Software

 Currently mako has Gaussian 98, Gaussian 03, cyana, nab, xplor, and several sander and pmemd binaries installed under /usr/local. If there is other software needed that's currently missing, please open a trouble ticket to request it.