USEFUL THINGS TO REMEMBER

USEFUL THINGS TO REMEMBER Your email address is: [email protected] You can also use [email protected] as an easier way to ...
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USEFUL THINGS TO REMEMBER Your email address is: [email protected] You can also use [email protected] as an easier way to remember your email address. To access BCB email: https://roaming.dfci.harvard.edu To access Partners email : https://www.partners.org/email Web site of the department: http://bcb.dfci.harvard.edu (for staff login use biostats/B10stat$) Computing site of the department: http://bcbcomputing.dfci.harvard.edu To manage your Partners password: https://myprofile.partners.org Institute’s web site: https://dfcionline.org Wireless network: phswifi3 (Use Partners userid/password to authenticate) For any computing questions/concerns/issues: [email protected] Off-hour support: (only critical issues) call 617-632-3060

Email Settings for all mail clients (PC, Mac, Linux, Android, iOS) Reading email (IMAP Server): imap.dfci.harvard.edu port 993 using SSL Sending email (SMTP server): pascal.dfci.harvard.edu port 465 using SSL (For all the above use BCB userid/password to authenticate) Useful thunderbird add-ons

Accessing computing resources from home There are 3 main options, depending on what kind of resources you need to connect to.

GoToMyPC If you mainly use your desktop computer for work without

having the need to use the departmental servers, and your desktop is either a PC or a Mac then you need to apply for a GoToMyPC account. When you connect to your Mac or PC, what you see is a real-time image of your computer’s screen; you can work with your files, and programs from anywhere just as if you were at your desk. To apply call helpdesk at 2-3399 and open a ticket to request a GoToMyPC account. You will receive an email with additional instructions.

VPN If you only have one device (laptop) to work with both at work and at

home then you need a VPN account. A Virtual Private Network (VPN) is a network technology that creates a secure network connection over a public network such as the Internet extending connectivity between your laptop and the DFCI networks; your laptop “feels” that is inside Partners space and you do not have to change anything to connect to DFCI resources. To apply for a VPN account, go to https://vpnrequests.partners.org/

ssh ssh is the most flexible method, but requires knowledge of how it works

and it’s only recommended for advanced users! To be able to access a login machine from outside Partners you need to use ssh version 2. For example, ssh ada.dfci.harvard.edu should log you in to ada To be able to access graphical applications, you need to enable “X tunneling” in your ssh client and also have an Xserver started in passive mode on your home . Free PC ssh client at http://www.putty.org/ Free PC ssh client/server and other UNIX utilities (find, grep,X,…) can be found at https://www.cygwin.com/ Download and run the setup.exe, which will be used to choose all the utilities to download. Make sure that you choose all the defaults and everything under openssh. For an X server make sure you choose from the X11 packages the xorg-x11-base along with any dependencies. All Macs have ssh. Recent versions of the OS do not have an X server installed. Using the Finder, go to Applications - Utilities - X11 and follow the instructions to download and install Xquartz. GoToMyPC and VPN are mutually exclusive: You can only get one of the two!

Logging in to a UNIX host Currently we have the following login machines ada noah leo orion santiam sphinx mys monet jaws crunch

LINUX 16Gb LINUX 384Gb LINUX 384Gb LINUX 36Gb LINUX 24Gb SOLARIS SOLARIS SOLARIS SOLARIS SOLARIS

8cores 32cores 32cores 16cores 16cores

(Xeon (Xeon (Xeon (Xeon (Xeon

E5-2603 1.8GHz) E5-2650 2.5MHz) E5-2650 2.0MHz) account E5620 2.4Ghz) E5620 2.4Ghz) IB

If you have a desktop PC, you need to configure your Xserver software (exceed) to be able to run graphical applications. Make sure that exceed runs in “Passive mode”, the setting can be found under “communication settings.”

UNIX The core operating system consisting of the kernel (computer resources like cpu, memory, io devices) and system calls

Shell: command line interpreter (sh, csh, tcsh, bash, ksh) Special characters in UNIX : , , , , #, “, ‘, `, /, \, &, *

Wildcards: * (0 or more), ? (one), [abe], [1-4] Shell invocation: .login, .cshrc, /usr/skel/cshrc Shell variables: PATH, MANPATH, HOME, USER, PAGER, DISPLAY (do not ever set) Use printenv, or ‘echo $VAR to display the value of a variable (echo $PATH) Useful commands: man, ls, which, cp, mv, rm Other useful commands: df, top, nice, kill, {ctrl-z,fg/bg, jobs, kill%}, redirection (,|), gzip (zcat), tar, find, grep, cat, sort (uniq), cut, paste, awk

Controlling file access file attributes : Read,Write,eXecute (rwx, r=4,w=2,x=1) file agents: owner, group, world By setting the attributes for every agent we completely control the access to a file (dir) “chmod N1N2N3 file” where N1 controls the attributes of the owner, N2 that of the group, and N3 of everyone else.

High Performance Cluster We recently merged the department cluster with the Institute’s research computing cluster to form one cluster To apply for a cluster account : http://bcb.dfci.harvard.edu/cluster/newuserrequest.html To open a support case: http://bcb.dfci.harvard.edu/hpc/

To access the cluster, ssh from within Partners network to one of the 2 submit hosts using your Partners credentials. Submit hosts : rcsgc-s1,2 rcsgc11-32 LINUX 57Gb 10 cores each brsgx1-24 LINUX 48Gb 6 cores (Inter Xeon X5650 2.67GHz) each rcapps2 LINUX 528Gb 32 cores (AMD Opteron 6328) each Storage Please store your files in your /bcb/groupname/username folder Do not use your home directory for storing files other than login files. Once the 200MB is full you will not be able to log in. The cluster is using SGE as the cluster queuing software. There are 3 different queues for program submission:

alllong: Jobs take more than 4 hours to complete allmedium: Jobs take between 2 and 4 hours to complete allshort: Jobs take less that 2 hours to complete Sample Script: #!/bin/bash #$ -cwd #$ -N ProgramName #$ -o /bcb/groupfoldername/username/myfile.out #$ -e /bcb/groupfoldername/username/myfile.error /bin/date How to submit a job Copy the simple script example to a file Submit the file with qsub myprog How to check all job status qstat to check all of your jobs qstat -u "*" to check the status of the cluster States: qw(waiting in the queue), t(transferring to a node, about to start), r(running), h(held back by user), E(error) How to get detailed information on a job during a run qstat -j jobid, where jobid is showed when you check on your job status above How to find out why your job failed Examine /bcb/groupfoldername/username/myfile.out and /bcb/groupfoldername/username/myfile.error to get more information How to delete a job qdel jobid

Other Productivity Tools      

Dropbox slack skype Keepass Evernote Xmarks (browser addon)

Other Services Out-of-office calendar Scan to pdf ftp server (ftp.dfci.harvard.edu, supports anonymous ftp) Rstudio server: http://rstudio.dfci.harvard.edu:8787 (login with BCB credentials)

RStudio is a free and open source integrated development environment for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Terminal Server: arcem.dfci.harvard.edu Windows server that currently has : Office 2010 Adobe Acrobat Pro 9 Adobe Illustrator Adobe Photoshop MiKTEX 2.9 Stata 13 nQuery 3.0

EAST 6 and 5.4 Cytel Studio 11 logXact, statXact GraphPAD Prism 6 Multc Lean Desktop 2.1 To access it please follow instructions from http://bcbcomputing.dfci.harvard.edu/index.php/desktopcomputing/windows-remote-desktop

GPU Computing

We recently acquired our first GPU server. CPUs and GPUs have significantly different architectures that make them better suited to different tasks. A GPU can handle large amounts of data in many streams, performing relatively simple operations on them, but is ill-suited to heavy or complex processing on a single or few streams of data. A CPU is much faster on a per-core basis (in terms of instructions per second) and can perform complex operations on a single or few streams of data more easily, but cannot efficiently handle many streams simultaneously. As a result, GPUs are not suited to handle tasks that do not significantly benefit from or cannot be parallelized, including many common consumer applications such as word processors. Furthermore, GPUs use a fundamentally different architecture; one would have to program an application specifically for a GPU for it to work, and significantly different techniques are required to program GPUs. For more information on the techniques needed, look up NVIDIA's parallel computing language CUDA which has hooks for C, C++, and fortran. Login to the server is by invitation only  (at least in the beginning !)