User accounts are assigned to users from the labs of NRSP-8 members for
the purposes of:
- Developing and maintaining of lab database and web sites
- Performing computational genomics/genetics analysis
In principal, the following norms are observed on granting and the use
of the user accounts:
- Accounts: In principal one user account will be granted per lab or
research group. Multiple accounts may be granted per group on case-by-case basis.
The first/last name and an email address (or phone number) is required for each
- The PI of the lab/group assumes responsibility to inform the actual
users the user policies, make sure their proper use of the account, and ultimately
responsible as the "owner" of the account.
- The Users of the account assume the responsibility to the proper use
and managing of the account. Users are assumed to have already known the basics
of computer operations on the given platform (Windows or Linux), known the
Iowa State University
computer use policies and policies articulated in this document.
- Multiple users from a lab/group may share the use of a lab account, however,
the names and contact information (email/phone) of each user must be filed
with the system administrator. This is to insure that all users will receive
system alerts in a timely manner.
- Shared Resources: The server is designed to be used on shared basis.
The shared resources include hardware (disk space), computing power (CPU and RAM),
software programs and common data.
- Disk space: A soft limit of about 10 GB of disk quota is set
on each account. If an account is expected to use more than 10 GB, please
contact the system administrator for temporary resource allocations. Users should
remove their files from the server when analysis is done.
In principal, users should not install own blast data set and other large data
sets that are subject to share, such as the genome/chromosome build of a
species, or a SNP Chip data set. Redundent large data sets will deprive shared
disk space, create problems for backup and recovery such that they may suffer
from delays or fail due to unexpected huge volume.
- Software: All software installed on the system are on shared basis
in general. Regular users are discouraged from installing new software.
Should there be special needs for a new software, the owner of the account must
contact the system administrator for assistance.
In principal, users should not install software that are already on the
system. If you need a software that's not on the system, or you need an
upgrated version of shared program, please let us know - we will be happy to
add it because other users may also benefit from sharing. Exceptions are only
those occassional and small scripts (under 10 MB in size; do not need to
introduce large library to run).
- Shared Computing Power: The shared computing power includes CPU and
RAM. If you need to run intensive computing jobs (any process that takes a
significant portion of a CPU for extended time (10-20 minutes to hours),
is considered as intensive job), please check the availability of free
CPU to use before you submit any job.
Usually, blast, megablast, bowtie, bwa, blat, exonarate, or scripts that
handle huge amount of data, are considered to create large intensive jobs.
Contact the system administrator if you are in doubt. Specific server types,
limitations and capabilities of our servers are described below.
- The NewTech dual processor RHEL Linux server: Designated as a
students sand-box server to test concepts and small trials. No large jobs
should be attempted. Users are cautioned to watch for the CPU/disk usage.
- The Atipa 8-node CentOS Linux cluster: Our heavy-duty computing
server. It can run intensive parallel or serial jobs. (1) Parallel
jobs must be submitted through Torque/MPI to queue and run; (2)
Serial jobs must be allocated to run on a designated node where a maximum
2 intensive jobs may be run simultaneously; (3) User must check for
node/CPU availability before submitting a large job. (4) Avoid using
head-node to run any job other than light operations.
- The Dell quad core Windows server: To run Windows based applications
and VMware based systems. Check with the system administrator for details.
- The Dell dual quad core RHEL Linux server: The web/database
"production line" server. All user accounts on this server is designated to develop
and run jobs related to serve the web/database functions.
- Data Backup and recovery: In general, the user accounts on the shared
computer servers are NOT included in the backup plan due
to limited capacity on our backup device. Only those user accounts used for
collaborative database/web portal developments are included for weekly backup.
We have raid-5 disk configurations on all servers which may help to survive minor
disk failure (e.g. 1 out of 4 disks fail) but not considered as a "backup" measure.
If you have critical data under 1 GB that need us to backup, please make a request
to the Bioinfo-team by an email.
- The NewTech Sandbox: User accounts are NOT included for
backup. Users are adviced to download to own devices for backup.
- The Dell Server: Collaborative user account are included in the
weekly backup. Users are encouraged to keep own copies of data.
- The Atipa Cluster: User accounts are NOT included in the
backup due to large data volume. Users are encouraged to download periodically
to own devices for backup.
- The system administrator is responsible to maintain the systems, to make
sure it's in healthy status and properly shared for use by all users. The system
administrator will help to solve problems, allocate resources, and maintain the
system operations. In case of emergency, the system administrator reserves the
right to suspend or lock an account if there are repeated violations of the user
Contact the system administrator if you are in doubt.
The NAGRP Bioinformatics Team
– Draft: Nov. 18, 2008
– Modified: Feb. 21, 2009
– Modified: Jul. 10, 2010
– Modified: May 21, 2011
When you need helps, please include following necessary information to your
email to the system administrator:
(1) Where the problem occurred? (The local/remote computer name? Your
terminal (ssh/ftp/http[web])? The user account name? Working directory? Web URL?)
(2) What happened? (Operation you did? commands used? Software
name involved? etc.)
(3) What are the expectated and unexpected results?
(4) Copy of the entire error message.
Please be aware that just say "it didn't work!" won't help to get your
problems solved sooner because it will make us guess what have happened thus may
cause delay tracking down the problem (oftern we need to be able to reproduce the