Introduction to Computing at the Martinos Center Why

Introduction to Computing at the Martinos Center Why. NHow - Sept 20, 2012 • Sam Mehl • Jon Kaiser

Cyclotron MRPET MEG Micro. PET 7 T 4. 7 T 3 T/128 channel 9. 4 T 14 T Connectom 1. 5 T 3 T AC 88 15 T

Harvard University MIT Martinos Center CNY 149, CNY 75, CNY 120, CNY 114 Simches MGH Harvard Medical School Not pictured: Needham Data Center

Data Storage /cluster/<name> Check usage with: clusterquota PACS Bourget (14 Y / 44 T) CDs /space/<computername> findsession & Unpack to Lab owned storage http: //www. freesurfer. net/fswiki/findsession http: //surfer. nmr. mgh. harvard. edu/fswiki/unpacksdcmdir Check usage with: df & du

DATA BACK UP For suggestions on backing up Windows or Macs: http: //help. nmr. mgh. harvard. edu/ > BACKUPS To check the status of your linux backups: https: //www. nmr. mgh. harvard. edu/martinos/user. Info/computer/nmr-secure/list. History. php

Command line terminal (shell) • Windows: putty http: //www. chiark. greenend. org. uk/~sgtatham/putty/download. html • Mac: terminal Applications > Utilities > Terminal • Linux: terminal right-click on the desktop

• Make Your Own Personal Web Page Home Directory • Navigate to your home directory: pwd cd ~<username> cd /homes/11/xmehlsa (‘cd –’ takes you back to the previous directory you were in) • Make a new directory called public_html: mkdir public_html mkdir ~/public_html mkdir /homes/11/xmehlsa/public_html • Navigate inside the public_html directory and create the file index. html: cd public_html touch index. html

• Make Your Own Personal Web Page Text Editors nano, vim, emacs • Edit ~/public_html/index. html • Content you create here is visible online: http: //www. nmr. mgh. harvard. edu/~<username> or http: //www. martinos. org/~<username> • Mind your quota. By default everyone has 2 Gb quota

. cshrc • Find it in your home directory using ls It’s hidden so you’ll need to us ls –a • Make a backup copy of it before you edit cp. cshrc. SAVE • Lets change the prompt so it will display the current directory set prompt = "[%n@%m%~]“ • Improve ls by adding -F

. cshrc • Sourcing the freesurfer environment creates login dependencies. setenv SUBJECTS_DIR /space/michigan/1/users/mehlsa/ source /usr/local/freesurfer/nmr-stable 51 -env • Better to make aliases alias fs-stable source /usr/local/freesurfer/nmr-stable 51 -env alias subj setenv SUBJECTS_DIR /space/michigan/1/users/mehlsa/

Unix Groups • Find out what groups you’re in: groups • Find out what groups someone else is in: groups <username> • List the members of a specific group: ypmatch <groupname> group • Find a user’s username: finger <name> finger <username>

• Unix permissions. Tutorial: http: //www. nmr. mgh. harvard. edu/martinos/user. Info/computer/perms. php [root@anderson scripts]# ls -l run-pasl_withingroup. sh -rw-rw-r-- 1 gcoombs dinahgp 6898 Aug 23 16: 11 run-pasl_withingroup. sh

• Unix permissions. Show permissions: ls –l michigan: xmehlsa[198] ls -l total 12 drwxrwxrwx 3 xmehlsa 4096 Sep 20 08: 52 089763987 drwxrwxrwx 3 xmehlsa 4096 Mar 30 2009 09033011 drwxrwxrwx 3 xmehlsa 4096 Sep 20 08: 51 98234798 Remove permissions for others: chmod –R o-rwx michigan: xmehlsa[207] chmod -R o-rxw. michigan: xmehlsa[208] ls -l total 12 drwxrwx--- 3 xmehlsa 4096 Sep 20 08: 52 089763987 drwxrwx--- 3 xmehlsa 4096 Mar 30 2009 09033011 drwxrwx--- 3 xmehlsa 4096 Sep 20 08: 51 98234798 /usr/pubsw/bin/setgrp michigan: xmehlsa[222] /usr/pubsw/bin/setgrp sysadm * michigan: xmehlsa[223] ls -l total 12 drwxrws--- 3 xmehlsa sysadm 4096 Sep 20 08: 52 089763987 drwxrws--- 3 xmehlsa sysadm 4096 Mar 30 2009 09033011 drwxrws--- 3 xmehlsa sysadm 4096 Sep 20 08: 51 98234798

• Remote Access Tools ssh, screen, NX In order to ssh from outside the Partners firewall, you must use one of the three gateway servers: gate. nmr. mgh. harvard. edu entry. nmr. mgh. harvard. edu door. nmr. mgh. harvard. edu screen –ls screen –r screen –x man screen http: //www. nmr. mgh. harvard. edu/martinos/user. Info/computer/NX/

Martinos Center IT Group help@nmr. mgh. harvard. edu ‣Paul Raines Ph. D (Hired in 2000) ‣Chris Johnson (Hired in 2000) ‣Sam Mehl (Hired in 2004) ‣Alex Ramsdell (Hired in 2011) Not to be confused with the Partners Help Desk (http: //helpdesk. partners. org) *Partners email *Cisco telephones & Network Ports *Insight / Red. Cap / People. Soft / Share. Point / e. Buy

CNY 149 1. 108 ‣How to find us: http: //help. nmr. mgh. harvard. edu > last link on the page has a map.

Support ‣~ 2345 ‘NMR’ login/email accounts since 2004. 960 currently active. ‣~ 580 Desktop Computers Cent. OS Linux (433), Windows (105) Mac OSX (47) ‣~ 714 Laptops registered by users approx 1/3 we encrypted ‣Approx 1800 emails received by help@nmr. mgh. harvard. edu every month.

Where to get help. ‣ 1. Your Lab ‣ 2. http: //help. nmr. mgh. harvard. edu ‣ 3. http: //faq. nmr. mgh. harvard. edu ‣ 4. http: //www. yahoo. com ‣ 5. help@nmr. mgh. harvard. edu

How not to ask for help. Date: Thu, 13 Sep 2012 14: 42: 16 -0400 From: ***** <*******@husky. neu. edu> To: help@nmr. mgh. harvard. edu Subject: NMR account I m having trouble access my NMR account. I was wandering if you can help. Date: Mon, 21 May 2012 09: 33: 35 -0400 From: ***** <*******@nmr. mgh. harvard. edu> To: Help Desk <help@nmr. mgh. harvard. edu> Subject: help! My computer is considerably slow. Is there anything you can do to speed it up? Date: Fri, 13 Feb 2012 12: 05 -0400 From: *******@nmr. mgh. harvard. edu To: help@nmr. mgh. harvard. edu Subject: workstation ‘mirabai’ My linux computer mirabai isn’t working, can someone take a look at it?

How to ask for help. If the computer has a name, what is is? Where is it physically located? What are the details of your problem? What were you doing when the problem occurred? Is the problem constant or intermittent. Is the problem reproducible? Have you attempted mitigation on your own? If so what were the results. If files are involved, what is the full path to the files? If programs are involved, which version? Copy/paste any commands you ran along with any error messages (verbatim). Provide more details than you think matter.