Please refer to our new location on the FAS IT website:
> Life Sciences Research Computing
Please refer to our new location on the FAS IT website:
We manage a number of systems and services to make researchers more productive. Some of our systems and ways we can help are outlined below:
The Life Sciences cluster consists of the following hardware:
14 nodes: Dual Intel® Xeon™ CPU 3.06GHz, 2GB RAM, RHEL3 U8 ×86
36 nodes: Dual Intel® Xeon™ CPU 2.80GHz, 4GB RAM, RHEL3 U8 ×86
14 nodes: Dual Intel® Xeon™ CPU 2.80GHz, 2GB RAM, RHEL3 U8 ×86
22 nodes: Dual Intel® Xeon™ CPU 2.80GHz, 2.5GB RAM, RHEL3 U8 ×86_64
12 nodes: Quad Intel® Xeon™ CPU 2.80GHz, 8GB RAM, RHEL4 U3 ×86_64
1 node: Quad Genuine Intel® CPU 3.00GHz, 8GB RAM, RHEL4 U4 ×86_64
1 node: Dual Core AMD Opteron™ Processor 275, 4GB RAM, x86_64
1 node: Intel® Xeon™ CPU 3.20GHz, 4GB RAM RHEL4 U4, x86_64
1 node: Dual Core Intel® Xeon™ CPU 2.40GHz, 1GB RAM, RHEL4 U4, x86
Total: 229 cpus
Cluster head node: portal.cgr.harvard.edu
Dual Intel® Xeon™ CPU 3.06GHz, 2GB RAM, RHEL3 U8 ×86
Cluster Network: 1Us with 1GB NIC, IBM Blades chassis with 4 trunked ports, DellBlades with 1GB pass-through all connected into a Foundry Networks FastIron 1500 switch. 10 DellBlades have Infiniband network as well as 1GB pass-through network.
Admin host: serving the cluster is a IBM Blade server running DHCP, LSF licenses, Mathematica licenses. It contains Dual Intel® Xeon™ CPU 3.00GHz, 4GB RAM, RHEL4 U4 ×86
Disk Storage: All Nodes mount a central EMC SAN (through NSXs) on the cluster network via NFS. Each node has local scratch space which varies from 13GB to 67GB.
Tape Backup Robot: ADIC Scalar i2000 - 600 tape unit.
Backup Infrastructure: EMC Networker v7.2.2 on Linux, NDMP clients are 6 EMC NSXs. All zoned into one Cisco Fiber switch. Sustained tape backup speeds of 110-140+ MB/s from one NSX to one LTO-3 tape drive.
Queuing System: LSF v6.0 from Platform Computing (www.platform.com)
Current queues defined:
QUEUE_NAME PRIO STATUS MAX JL/U JL/P JL/H NJOBS PEND RUN SUSP
interact 86 Open:Active - 1 - - 0 0 0 0
dellblades 85 Open:Active - - - - 460 416 44 0
delllong 84 Open:Active - - - - 4 0 4 0
rsoft 83 Open:Active - 2 - - 0 0 0 0
hunter 82 Open:Active - - - - 0 0 0 0
giribet 81 Open:Active - - - - 80 0 80 0
flybase 70 Open:Active - - - - 0 0 0 0
blades 65 Open:Active - - - - 0 0 0 0
CGRshort 60 Open:Active - 50 - - 0 0 0 0
CGRnormal 50 Open:Active 40 - - - 460 420 40 0
CGRlong 40 Open:Active - 60 - - 0 0 0 0
short 30 Open:Active - 20 - - 0 0 0 0
normal 20 Open:Active - - - - 5285 5161 123 1
long 15 Open:Active - 10 - - 24 0 24 0
interact - for interactive jobs with a MAX of 12hrs runtime, 1 job per
user dellblades - for jobs to run on Dellblades1-10, primary group that uses these is the karplus group.
rsoft - for jobs from the Lieber lab to run rsoft based jobs, only run on host cfa15 for 12hrs MAX runtime.
hunter - for jobs from the hunter lab group to run on hunter1, they have priority access to this machine.
giribet - for jobs from the Giribet lab to run on giribet1-2. They have
exclusive access to these machines.
flybase - for jobs from the Flybase group, to run in hosts fb1-22. They have priority access to fb1-22.
CGRshort - for jobs from CGR members that have a MAX runtime of 1hr.
CGRnormal - for jobs form CGR members that have a MAX runtime of 24hrs. maximum of 40 jobs total at any one time.
CGRlong - for jobs from CGR members, no time limit. Maximum of 60 jobs per users at any one time.
short - for all external or CGR members that run jobs for a MAX of 1hr runtime. Total of 20 jobs per user.
normal - for all external or CGR members that run jobs for a MAX of 24hrs runtime.
long - for all external or CGR members, no time limit, 10 jobs MAX per user.
:::Last Updated on 13NOV2006:::
Each new desktop assigned to a new Life Sciences individual will be an up-to-date desktop system with the following features:
The current desktops being issued are the Dell Optiplex GX620 and more information about them can be found here.
Additionally all Windows computers will come issued with the following software (in its most up-to-date version):
Lastly, the desktop will be part of the domain and be subject to both antiviurs and Windows updates at regular intervals.
The following Email clients are supported by the Division of Life Sciences. Outlook XP/2003/2007 Entourage Thunderbird Outlook Web Access (Webmail)
This page has two sections: Desktop/Laptop Software and Cluster Software
The following products are licensed by FAS and are available to FAS affiliates on CDs from the FAS Desktop Support team. Fill out a copy of the FAS Software Agreement form for each computer on which the software will be installed. Click http://www.fas.harvard.edu/~fascs/SoftAgreeForm.doc to download the form.
| OSX | Windows |
| Microsoft Office 2004 | Microsoft Office 2003 |
| FileMaker Pro v. 8 | FileMaker Pro v. 8 |
| OS X v. 10.4 (Tiger) and 10.3 (Panther) | Windows XP |
FAS offers a variety of downloadable software; access is by Pin Authentication.
The following list is both abbreviated and likely to be out of date; the current complete list is here: http://www.fas.harvard.edu/cgi-bin/software/download.pl?platform=all
| OSX | Windows | |
| AntiVirus Software | Virex 7.7 | VirusScan 8 Enterprise |
| Acrobat Professional | v. 7.0.3 (keyed) | v. 7 (keyed) |
| Dreamweaver | v. 7.0.1 (keyed) | v. 2004 (keyed) |
| EndNote | v. 9.0 (keyed) | v. X (keyed) |
| Mathematica | v. 5.2.2 | v. 5.2 |
| MatLab (requires VPN connection) | v. 7.2 | R2006a |
| Photoshop CS2 | v. 9.0 (keyed) | v. CS2 (keyed) |
| Statistical analysis
| SPSS 13.0 (keyed) Stata 9.0 (keyed) | MiniTab 14.2 (keyed) SPSS 14.0 (keyed) SPSS Smart Viewer 13.0 (keyed) Stata Intercooled v. 9.0 (keyed) |
| VPN Client | v. 4.9 | v. 4.0.4 |
You’ll have to install the KeyServer Client to use FAS’s “keyed” software. Keyed software is free to users, but when all the keys are in use, additional users can’t run the software.
MCB lecture and conference room schedules (and a couple of lab calendars) are hosted on the Life Sciences Meeting Maker server (request a Meeting Maker account by emailing support [-at-] lsdiv [dot] harvard [dot] edu). Please contact the HelpDesk at 6-2727 or email support [-at-] lsdiv [dot] harvard [dot] edu for help downloading and configuring the client software and connecting to the server.
| OSX | Windows | |
| MeetingMaker Client | 7.5 | 7.5 |
WinZip | License # is in the ReadMe file |
UIS SITE (http://www.uis.harvard.edu/enterprise_licensing/catalog/?searchby=vendor) has other products (including Adobe Creative Suite, Acrobat Professional and Photoshop). To browse the catalog and order from it, you’ll have to enter your Harvard ID and PIN. Licenses are sold separately from media. You’ll need one license for each computer the software will be installed on.
VectorNTI – Invitrogen continues to support the PC version of VectorNTI, and now offers it to educational users for free. Unfortunately, they are no longer updating the Macintosh version, though the most recent Mac version, 7.1, is still downloadable – note: this requires a bootable Panther (10.3.9) partition - contact FASCS for assistance with this (6-2727).
To get a free license to use the software, click the “Join Today” button on the VectorNTI User Community page; download the software from this page
Lasergene – Lasergene has been suggested as a replacement for VectorNTI for Mac users with Tiger. DNAStar offers a 15-day free Lasergene trial here.
Keep your OS and applications software updated to minimize the risk of being hacked. Here’s where to find these updates.
http://internal.mcb.harvard.edu/Tech/CompServices/ObtainSoftware/index.html#Updates
Applications running on the cluster are available to Harvard research groups. A few of the popular applications are:
* BLAST (NCBI and WU)
* EMBOSS
* Primer3
* QRNA and SNOSCAN
* Bioperl
* GMEP
* Mathematica (Bauer Lab only)
Access to the Cluster requires a Bauer Core account. Research groups may subscribe to the cluster by paying a nominal fee of $100 per month. More information is available at http://www.sysbio.harvard.edu/csb/resources/computational/linux.html
More information on Databases, Microarray analysis, Programming tools, Sequence analysis, and Visualization and modeling is available on the following web page: http://www.sysbio.harvard.edu/csb/resources/computational/resource.html
Access to networked resources is granted through Domain User accounts. Life Sciences Division affiliates, once they have a Harvard PIN, can request a Domain User Account on this web page:
https://www.lsdiv.harvard.edu/hu_auth/account.php
This uses a web form to collect the information we need to create your account. Fill in the requested information and click "Submit Form".
Accounts are usually created within 2 hours. We will notify you as soon as the account has been created (please be sure to include your current email address).
We provide integrated web hosting solutions in Windows or Linux environments using IIS (Windows only) or Apache. Databases include MySQL (with phpMyAdmin), SQL and Oracle. Supported scripting languages are PHP, ASP, ASP.NET and PERL. Contact Brian Gottesman for assistance.
How do I get my computer on the network?
Fill out the Machine Registration Request form here.
Why do I need a Domain User Account?
You need a Domain User Account to use Life Sciences Division networked resources – this includes LSDiv Email, Network Attached Storage, DNA Sequencing Facility, Bauer Center instruments, and Imaging Center printers and microscopes. Apply online for a new Domain User Account here.
What are the requirements for Domain User passwords?
To be "valid" a password must be at least 8 characters long (longer is better), and should include mix of CAPS and lower-case letters, numbers, and any of the following characters:
{ } [ ] , . < > ; : ' " ? / | \ ` ~ ! @ # $ % ^ & * ( ) _ - + =
Passwords should not be dictionary-based. Substituting numbers and punctuation for vowels no longer tricks password crack software - intersperse numbers, letters and special characters so that the result doesn't resemble a word. If you would rather have a complex password generated for you, our password generator web page can generate a random and complex password up to 14 characters long: Online Complex Password Generator.
I forgot my password – how do I get it reset?
Contact the FASCS HelpDesk at 6-2727.
How do I get an email account?
Email is automatically included with an LSDiv Domain User Account. One of the fields on this form (“How will you receive email?”) indicates your email preference – simply specify “MCB email” [eventually we will have LSDiv, CSB, and other departments listed]. We can forward LSDiv email to other mail servers; please indicate where to forward email, if that’s what you want.
How large can my mailbox be?
The default is 500MB. This can be increased on request.
What network attached storage is available, and how can I use it?
Life Sciences Division’s NAS is an EMC Celerra (more information on the EMC is available here). Space on the EMC costs $1500/TB/year. Incremental backups are done nightly, full backups on the weekends, and backups are kept for two months. This document explains how to mount or map the EMC volumes.
What happened to atavachron, gossamer, titan and titan2?
These are the nicknames of previous NAS's; the new NAS responds to all of these names. Most labs will be able to map their EMC volume using one of these names.
Where is the DNA Sequencing Facility?
The Sequencing Facility is located in Biolabs 3094.
How can I get a Sequencing Account?
If you already have a Domain User Account, and want to add DNA Sequencing, use this link. If you don’t yet have a Domain User Account, apply here and click the “yes” button next to the question “I need access to the MCB DNA Sequencing Facility.” Additional information on the Sequencing Facility is available here.
Where is my DNA Sequencing data stored?
Sequencing Data is stored in user folders on the EMC. On the PC, this is mapped as \\lsdivfs3\dna\username; on a Mac, it’s smb://lsdivfs3/dna/username.
How can I get access to the Imaging Center?
Contact Dave Smith [dmsmith [-at-] fas [dot] harvard [dot] edu] in the Imaging Center for training, and Jennifer Xie [jxie [-at-] mcb [dot] harvard [dot] edu] in the Financial Office to get your 33-digit chargeline into the database.
A lot of your documents say “Call the FASCS Helpdesk at 6-2727” – why is that?
FASCS provides Desktop Support and front-line HelpDesk services for MCB; the FASCS HelpDesk also generates all support request tickets for LSDiv Research Computing.
Where are the department calendars?
Biological Anthropology || CBS || CCB || CSB (formerly CGR) || MCB || OEB || Psychology
If any of these links breaks, please notify our WebMaster [webmaster [-at-] mcb [dot] harvard [dot] edu], and until the link is fixed, try the “parent” page and look for “News and Events”.
How can I get access to an instrument in the FAS Center for Systems Biology?
Request a “Calcium” account from Claire Reardon [claire [-at-] cgr [dot] harvard [dot] edu]; once you have that, login here.
What software is available to analyze my data?
Some of the analysis tools on the Bauer Core Linux cluster are listed here. Other analysis software is available through FAS and UIS - you need a Harvard PIN to access both of these sites:
Can I get custom programming to manipulate my data?
The FAS Center for Systems Biology offers custom programming. More information is available here.
I want to buy a new computer - what are my options?
The Technology Services web page (which requires a Harvard PIN) is the place to order a Mac or a Lenovo computer; if you want to order a Dell, go here.
Where are the online directories?
Biological Anthropology || CBS || CCB || CSB (formerly CGR) || MCB || OEB || Psychology
How can I send email to people listed on the MCB Directory web page?
The MCB directory has a link, “emailer” on each group’s directory page; by default all members are selected, but you can remove names from the list by clicking in a name’s check box. Then click on one of the “Open Email window” links on the page.
You can always reach us at the following email address: support [-at-] lsdiv [dot] harvard [dot] edu
or by calling our central Life Sciences help desk at 6-2727