Computing in the Chemistry Department
This part of the appendix gives a brief description a portion of the hardware and software
available for computing in the Chemistry Department. For further information, please contact
the Department’s computing coordinators, Margaret Doll, at margaret_doll@brown.edu.
Margaret will give you a contact to assist you on Window computers, MacIntosh computers, and
web pages. Margaret works on the unix computers and networking. Margaret’s beeper number
only for emergencies is 745-7306. After the beeps dial in a numbers where you can be reached
ended with the ‘#’ sign. Margaret will phone you as soon as possible.
Present computing environment in the Chemistry Department:
Computers available to members of the Chemistry Department include a variety of Window
platforms, MacIntoshes, and UNIX workstations. The computers are located in public clusters,
research rooms, offices, and laboratories throughout the Department. Nearly all of the computers
have network connections giving them access to departmental printers and file servers, on-line
library resources, email, and the World Wide Web.
The Department maintains a cluster of computers in MacMillan 213 for the use of any member
of the Department. MacMillan 213 contains four iMacs, one G3 Mac, a Dell Dimension XPS
R350 and an HP 4050 printer (mm-hp213). An HP LaserJet 4M Plus printer (gc-hp349) and an
iMac with a scanner are located in GeoChem 349. Departmental printers also include an HP
4050 (gc-hp257) in Geochem 257, and an HP 4500 Color printer (gc-hp201-4500) in the main
office; there is a charge of $ .75 a page on the color printer. The HP 4500 Color printer is
normally set up to print on regular printer paper. However, transparencies and glossy paper may
be purchased through the stockroom for the color printer. Use only the transparencies that you
get specifically for the color printer from the stockroom in the color printer.
Most
transparencies will melt around the fuser in the printer. The repair is expensive and timeconsuming.
Do not store your files on the computers within the cluster rooms. The systems are cleaned on a
regular basis.
For backups there are several zip drives attached to iMacs and to the Dell in room 246. The
NMR computers have recordable cds as well.
There are also computers available in MacMillan for teaching. These computers include SUNs
in room 105.
Hardware Care for the Computers:
The University currently provides support for software packages that have been listed in the
sections below. University support means that the packages can be installed on any Windows,
Mac, UNIX box which is currently on the University subnets. Consultants are available in the
CIT building for the software supported on Windows and MacIntoshes. Software consultation is
available through your department computer coordinators on the UNIX computer software.
Members of research groups are also invaluable resources for training in the use of available
software.
The University also provides hardware support for some current models of Windows , current
MacIntoshes, and HP printers owned by the University. Check with the repair shop in the back
of the CIT building or their web pages for a full listing and current repair pricing. Margaret Doll
handles hardware/software problems on Mac and Window computers within the Department.
Hardware support for the UNIX computers within the Department is provided by individual
contracts, by hardware agreements directly with the vendor, or through campus-wide contracts
through the University. Your research advisor or Margaret Doll should be contacted if a UNIX
computer fails. Do not reset or turn off a unix computer unless it is on-fire or making noises like
the disk bearings are shot.
AntiVirus Software: The University provides Norton AntiVirus software for Window and
MacIntosh computers that are connected to our network. Use this software. Make sure that the
software is updated when the application is updated on the server. Set up a weekly schedule on
your computer when new virus definitions will be automatically. Leave your virus scanner on so
that it scans any new files coming on your computer whether via email, web downloads, ftp, etc.
Do a full scan of your disks from time to time. Don’t take a chance on losing your files.
Department Documentation:
Departmental documentation will be maintained on
http://www.chemistry.brown.edu/documents. This is a password protected section of the
departmental web pages. The account is 'chemistry'; the password at the time of this writing is
'education'. This is a new feature of our web pages; documentation will be added as time
permits.
Windows: The Chemistry Department is using a range of Window computers from IBM ATs
running DOS Windows 95/98, NT and 2000. The computers can be equipped with hard disks,
cd players, floppies, and zip drives.
The list of University supported software for Windows can be found on the Application server
and/or http://www.brown.edu/Facilities/CIS/Sofware_Services.
Most of this software runs only if the computer is attached to the Brown Network keyserver. Do
not load any of this software on a cluster computer; ask Margaret Doll to load the software for
you. If you are working in a research group, ask your advisor before adding any software to a
research computer.
To print from a Window computer to a departmental printer log into chemps, our linux print
server. These instructions will be listed in the documents on the Chemistry web pages as
outlined above. If there are additional questions, please email Margaret Doll.
Most Window computers within the Department provide no security for files stored on their hard
disks; anyone who can get to the machine can look at, use, or delete any files on the hard disks.
We are responsible adults who respect the privacy and ownership of files on Department
computers.
You are responsible for backing up your own data via floppies, zip disks, or to your own
computer. chemps can be used as an emergency, temporary backup; you are only allowed to
store 50 Mb of data on this server.
MacIntoshes: As with the Windows, this is a computer with minimal security for stored data.
Currently there is not an automatic network backup of any file stored in the USER folder on
most of our MacIntoshes; backups done by the user provide the most security. The University
supports the following list of software on the macs:
The list of University supported software for Macintoshes can be found on the Application server
and/or http://www.brown.edu/Facilities/CIS/Sofware_Services.
Do not load software on any cluster computer; notify Margaret Doll if software is needed on
any departmental computer.
Departmental Software on Windows and MacIntoshes: ChemDraw is available on
computers in MacMillan 213 and the iMac in Geochem 349 as well as within various research
groups throughout the Department. Beilstein is also installed on the computers within the cluster
rooms. Beilstein is also available for any computer within the department; the download link can
be
found
on
the
Brown
software
download
pages
(http://www.brown.edu/Facilities/CIS/Software_Services). AcordexView TIFF is available on
the Mac G3 in MacMillan 213. This software enables the users to view the files from the U.S.
patent office which are displayed by SciFinder Scholar.
Do not copy software from one computer to another; all software must be licensed on each
computer. Any installation of software should be done by the computer coordinators on the
cluster computers or approved by a faculty member on research group computers. Do not
download software from the web especially shareware. Shareware software can easily be
downloaded, but one is supposed to pay a fee for the software’s use. Addition of software to
any computer within the Department is illegal unless you have a receipt of purchase or if the
software is freeware.
UNIX workstations: There are UNIX computers are offices and laboratories; their use is
usually restricted to work for certain research groups.
Candy in GeoChem 255 runs molecular modeling programs Quanta and CHARMm, the
Cambridge Structural Database, CSD, and Autodock. Before a student can use Autodock
software his/her research advisor must sign an agreement that use of the software will
acknowledge in their research papers. Prof. Suggs is the person to see for accounts on this
system.
The GCG, Genetics Computer Group, database is available on enzyme, an SGI computer in
Geochem 425. Enzyme is reserved for use by Prof. Cane’s group.
Jaquar is available on several SGIs. Jaquar offers “chemical accuracy and unprecedented
computational performance for electronic structure calculations.” This software is available to
be installed on any unix computer within the Department. Prof. Doll and Prof. Reiger have it
available on their computers.
NMR experiments run with the use of SGI computers in Geochem 408 and 410 and in
MacMillan 315. See Jim Van Epp for accounts and training on the NMR equipment.
A single-crystal, automated X-ray diffractometer and associated computer programs are
available for obtaining crystal structures at both room and low temperatures. ?? 255 and 408
UNIX computers are also used by the theoretical-physical chemists for programming in C, C++
and Fortran. These computers are used by the research groups of Prof. Doll and Prof. Stratt.
Backups of most of the UNIX computers completed on the weekends. Three backup sets are
maintained at one time. Ask Margaret Doll about backups for the unix computers on which you
are working.
The software for unix computers available through campus agreements are listed on
http://www.brown.edu/Facilities/CIS/Sofware_Services.
Matlab
NAG Matlab
Gateway Generator
Maple V
Maple 6
Splus
Portland Group Inc
Compilers
Data Explorer
NAG ASLI Software
Suite
Visual Numerics
Libraries (IMSL)
Tecplot
Domain License for
Sun compilers
SSH Secure Shell
AIX compilers
- Mathematical manipulations and calculations
- Mathematical manipulations and calculations
- Statistical Package
- for Solaris and linux
- programmable graphics package
- Graphics package
- secure shell is installed on many of the unix computers
There are numerous packages that also come with unix software distribution including media
development, compilers, Mac and WINDOW COMPUTERS translation and communication
packages, plotting routines, and various utilities. See Margaret Doll if you are interested in a
particular package.
chemps: The chemps server is one of several linux servers being used in the Chemistry and
Geological Sciences Departments. It is accessible by Window, MacIntosh and unix computers.
Each member of the Chemistry Department may store files there, transfer files to others, and
gain print access through chemps. Remember there is a 50 Mb limit for all accounts. Refer to
the Department's documentation on the web for instructions on how to make connections to the
server.
Application server: This server is maintained by the Computing and Information Services
Department (CIS) to provide public domain and site-licensed software to Window and
MacIntosh users on campus. On a MacIntosh the Application server is accessible via the
Chooser in the brn_CIS_Services zone. From a Windows computer, an Applications Menu
program presents you with a menu of supported programs which you may install. Contact
Margaret Doll for more information. Most of the software distributed from the Application
server requires attachment of the computer to a campus key server.
WWW server: The Department’s WWW server is a linux computer. The server is used mostly
for course work and for our Department brochure. Students may design pages on the www.chem
which describe their research group or developments within their own research. Ask Margaret
Doll for an account if you wish to add your own web page.
IP addresses: Any new computers, printers, or equipment needing an ip address should be
registered with Margaret Doll (margaret_doll@brown.edu). Send the type of equipment, the
serial number of the equipment, the room in which it will be located, the owner of the equipment,
and a potential name in email to Margaret. She will send you back a registered ip number. This
keeps conflicts off the network.
Names for computers must start with two letters indicating the building in which they are
located; ie. "gc" for Geochem and "mm" for MacMillan. This is followed by three digits for the
room number.
Printers' names start with the two letters indicating the building, followed by “-“, then two
letters indicating the type of printer and then three numbers indicating the room in which it is
located. The Departmental printer in GeoChem 257 is named gc-hp257.
Important IP Addresses:
The gateway for computers in GeoChem is 128.148.68.1
The gateway for computers in MacMillan is 128.148.119.1
The campus nameservers are 128.148.128.9 and 128.148.128.11
The netmask is 255.255.255.0
What everyone should know about using a computer:
Smooth operation of the departmental computer resources depends upon a few good habits of its
users. Do store your files in a folder which has your name on it when using Window and
MacIntosh computers. Do not share accounts on the chemps server or on any UNIX computer.
Do not install any games on any computer within the Department. Do not install any software
for which you do not have a sales receipt unless it is freeware and will help in your research; and
never install in on a cluster computer. Do not copy software from one computer to another. Do
not install software on the public cluster computers; notify a computer coordinator that an
installation should be done. Do not browse through, alter, or destroy someone else files. Misuse
of any computer at the University, may lead to revocation of your right to use the equipment.
Get your network ID and password from CIS after you have your identification card. Go to the
CIT building on the corner of Wayland and Brook. The student consultants in the office to the
left of the entrance of that building will setup your password and Eudora account for email.
Contact Margaret Doll for accounts on the chemps server or any of the research UNIX
computers within the Department after obtaining permission from the research advisor. Use of
the UNIX computers is restricted to research needs.
There are a few words of advice that should be given to (and heeded by) every computer user.
Perhaps the most important of these words is “BACKUP.” If you have data, documents,
programs, or other files that you value stored on the hard disk of a computer, you should have an
up-to-date backup copy of these files stored in another room, or better yet, another building.
Nearly every type of computer in the Department has suffered some hard disk problem over the
past few years that destroyed some of all of the files stored on the machine’s disk. Files can also
be lost because of late-night reflexes. For users with backup, this sort of an event is an
inconvenience; for those without backup, it can be a disaster. Students have lost files containing
crucial work for their dissertations. Talk to members of your group or the computer coordinators
about how to perform backups of your files. The USER files on a few MacIntosh and Window
computers within the Department are backed up across the network. Maintaining your own copy
of important files ensures the fastest restoration of materials.
Aside from performing backups, there are some rules for protecting your data, the computer you
are using, and the general computer community.
1. If you use any computer requiring a login procedure, be sure that your password
cannot be easily guessed. Don’t use a word or phrase in any language for your password; make
it at least seven characters long; and use a character or number somewhere in the password
string.
2. Do not share your computer account. The computer coordinator will be glad to
create necessary accounts.
3. If you are a new user of some type of computer, consult with an experienced user for
important information about operating that machine. Do not shutdown UNIX computers.
4. Do not HOT_SWAP devices on computers.
5. Do not put food or other chemicals in a position where they could spill on the
computer. We have lost several keyboards due to spills. Food and drinks are not allowed in
MacMillan 213 and should not be near the computer equipment in GeoChem 349.
6. Clean out your file regularly. Disk space is a valuable resource and is not
inexhaustible. Clean off files you are no longer using. The Computer Coordinator may from
time clean off files on the Window and Mac computers in MacMillan 213 and GeoChem 349.
He/she may also ask various heavy users of disk space on the UNIX computers, to clean out their
files.
7. Pornography is not allowed on the computers.
8. Stolen software may not be installed.
Suspected misuse of computers will be investigated; the computer coordinator reserves
the right to review and remove any file or program which appears to be inappropriate for a
Departmental computer. Violation rules 2, 7, and 8 may lead to revocation of your computer
privileges.
Where to get help
Help with computers is available from many sources. Fellow students and faculty who use the
same machines and programs that you do can sometimes offer advice or suggestions. Margaret
Doll (margaret_doll@brown.edu), GeoChem 166) is the main source for UNIX and network
consultations. Margaret Doll (Margaret_doll@brown.edu) will take questions on Windows,
MacIntoshes, their software, and web pages. The University also maintains a staff of student and
professional consultants for Windows and MacIntoshes in the CIT center. They can be reached
at x 3-7457 (x 3-7HLP). And lastly you can read the documentation on the Department's web
pages.