Changes in def9320: ssh using xtal200.harvard.edu and NOT crystal.harvard.edu Remove old DFCI page.

				HMS1-Harrison-Chou-Labs.md
			
          @@ -7,7 +7,7 @@ All SBGrid-supported systems are located on an integrated, private network segme

           To reach this network for access to local resources

          -from an external location, please SSH to **[crystal.harvard.edu](faq-remote-access-to-linux-computers)**. Please review our instructions the following, as you will need to request external SSH access:

          +from an external location, please SSH to **[xtal200.harvard.edu](faq-remote-access-to-linux-computers)**. Please review our instructions the following, as you will need to request external SSH access:

           * [faq-remote-access-to-linux-computers](faq-remote-access-to-linux-computers)

          @@ -76,7 +76,7 @@ If you are not currently a member of this list and wish to be added, contact Pro

           # Accounts

           SBGrid manages two different types of Crystal accounts. For simplicity, we use the same username for both accounts, but each has a different password.  The first gives you access to Linux systems in your lab. The second is used to access your Crystal Gmail and other Google services. 

          -* Linux access - ssh to `crystal.harvard.edu`

          +* Linux access - ssh to `xtal.harvard.edu`

           * Google Account - <https://crystal.harvard.edu/mail>

				HMS2-Hogle-Liao-Sliz-Labs.md
			
          @@ -7,7 +7,7 @@ for assistance with Mac & Windows systems.

           New SBGrid computers need to be registered to access the network.

          -All SBGrid-supported systems are located on an integrated, private network segment. To reach this network for access to local resources from an external location, please ssh to crystal.harvard.edu.

          +All SBGrid-supported systems are located on an integrated, private network segment. To reach this network for access to local resources from an external location, please ssh to xtal200.harvard.edu.

           [[_TOC_]]

				bch1-harrison-chen.md
			
          @@ -4,7 +4,7 @@

           # Overview

           SBGrid provides comprehensive system administration support for all Linux systems for the Harrison and Chen labs at CLS.

          -All computers are located on an integrated network segment that integrates structural biology computers at HMS, BCH, and DFCI. To reach this network for access to local resources from an external location, please ssh to crystal.harvard.edu.

          +All computers are located on an integrated network segment that integrates structural biology computers at HMS, BCH, and DFCI. To reach this network for access to local resources from an external location, please ssh to xtal200.harvard.edu.

           [[_TOC_]]

				bch2-wu-springer-hur.md
			
          @@ -1,7 +1,7 @@

           <!-- --- title: BCH: Wu, Springer, & Hur Labs  -->

           # Overview

          -SBGrid provides comprehensive system administration support for all Linux, Windows, and Mac computers at CLS for the Wu, Springer, and Hur labs. All computers are located on an integrated network segment that integrates structural biology computers at HMS, BCH, and DFCI. To reach this network for access to local resources from an external location, please ssh to **crystal.harvard.edu**.

          +SBGrid provides comprehensive system administration support for all Linux, Windows, and Mac computers at CLS for the Wu, Springer, and Hur labs. All computers are located on an integrated network segment that integrates structural biology computers at HMS, BCH, and DFCI. To reach this network for access to local resources from an external location, please ssh to **xtal200.harvard.edu**.

           [[_TOC_]]

				dfci-eck-fischer-wang-dhepaganon-arthanari-sun.md
			
          @@ -3,7 +3,7 @@

           # Overview

           SBGrid provides comprehensive system administration support for all Linux, Windows, and Mac computers at DFCI. Supported labs include Eck, Dhe-Paganon, Wang, Fischer, and Arthanari. All computers are located on an integrated network segment that integrates structural biology computers at HMS, BCH, and DFCI. 

          -To reach this network for access to local resources from an external location, please ssh to **crystal.harvard.edu**.

          +To reach this network for access to local resources from an external location, please ssh to **xtal200.harvard.edu**.

           [[_TOC_]]

				dfci-eck-fischer-wang-dhepaganon-arthanari.md
			
          @@ -1,117 +0,0 @@

          -<!-- ---title: DFCI: Eck, Dhe-Paganon, Wang, Fischer, Arthanari, & Sun Labs -->

          -

          -# Overview

          -SBGrid provides comprehensive system administration support for all Linux, Windows, and Mac computers at DFCI. Supported labs include Eck, Dhe-Paganon, Wang, Fischer, and Arthanari. All computers are located on an integrated network segment that integrates structural biology computers at HMS, BCH, and DFCI. 

          -

          -To reach this network for access to local resources from an external location, please ssh to **crystal.harvard.edu**.

          -

          -[[_TOC_]]

          -

          -# Get Help

          -For general questions, email SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org) and include your name and the name of your lab. 

          -Email questions about your software installation to [bugs@sbgrid.org](mailto:bugs@sbgrid.org). 

          -

          -New lab members should contact [help@sbgrid.org](mailto:help@sbgrid.org) to complete their initial setup.

          -

          -

          -# Email Access

          -Lab members have access to a Crystal email account through Google Apps. If you do not have an account, email [help@sbgrid.org](mailto:help@sbgrid.org) and cc your PI in the request.

          -

          -SBGrid maintains a Google mailing list for labs on the Crystal Google domain upon request. If your lab actively uses the mailing list and you would like your name added to the list, please contact [help@sbgrid.org](mailto:help@sbgrid.org).

          -

          -

          -# Lab Wiki

          -

          -A standalone Confluence server instance (version 5.8) is running on a virtual machine on an SBGrid-hosted VM cluster. 

          -

          -Users with a crystal email account can access the wiki at the PI’s request.

          -

          -To access the lab wiki go to <http://wiki.sbgrid.org> and login with your crystal email.

          -

          -# Computers

          -

          -### Linux

          -

          -Linux computers share authentication and data directories and can  only be accessed locally from within the lab. 

          -

          -Home directories are located at 

          -

          -* `/nfs/<lab initials>/<username> (example: /nfs/mje/eck)` 

          -

          -SBGrid's comprehensive collections of structural biology applications is located in the  /programs directory. All systems are configured with Stereo 3D. 

          -

          -The Ivory workstation, which has 48 cores, can be accessed remotely and is typically used for docking computations and data processing.

          -

          -Please note that your home directories are only visible to your labmates and PI by default. Permissions vary depending on the 

          -nature of the directory or files in question. PIs can request modifications to file permissions to suit the lab's needs.

          -

          -### Mac OS X

          -

          -All Mac computers have local administrative accounts that are specific to the lab members. Each user's home directory is located at

          -

          -* `/Users/<username> (example /Users/eck)`

          -

          -This setup allows users to install and update software without requesting help from SBGrid. Every local account is backed up to CrashPlan. 

          -Any network share, including home directories, are mounted via Samba and require user authentication. 

          -

          -These computers are also connected to the lab printers on the 3rd and 4th floors of Longwood Center.

          -

          -Please contact [help@sbgrid.org](mailto:help@sbgrid.org) to request an account. 

          -

          -### Windows

          -

          -Some lab members use Windows systems as their main computers. These computers are not maintained by SBGrid, however, 

          -SBGrid will make them available on the network.

          -

          -

          -### Data collection and Instrument Control Computers

          -

          -The scanner room has two Linux systems (aqua and plum) that control the x-ray scanner. Windows computers on this network are used for 

          -instrument control and data collection for the RockImager and FPLC systems.

          -

          -

          -## Accessing your Samba shares

          -Macs have local accounts with local home directories. To access your Linux network home directory using Samba (SMB):

          -

          -* Open Finder, click Go, then click 'Go to Server'

          -* Type in the server address: `smb://blacker.in.hwlab`

          -	* Click ‘Connect’.

          -* Enter your Samba username and password (contact SBGrid for SMB account issues).

          -

          -

          -# Data Backups

          -Hourly and daily snapshots are taken of the file server Z file system. Data is replicated to another server in building C on the HMS Quad. 

          -The local home directories of SBGrid-supported Macs are backed up to a Crashplan server located in the SGM Building on the HMS Quad.

          -

          -

          -# Printing

          -A Xerox Phaser 8860 is located on the third floor near the kitchen area. Another inkjet printer is located directly above on the fourth floor. 

          -Email [help@sbgrid.org](mailto:help@sbgrid.org) with any printing problems.

          -

          -

          -# RockImager Setup

          -There are two types of data generated by the imager:

          -

          -* Images: Regular “jpg” image files that are stored directly in the file system on the main file server.

          -* Experimental data: As experiments are created, the data is stored on a “Microsoft SQL Server 2014” database, currently running on a Windows 2012 server.

          -

          -The data is accessible on the RockImager PCs and also through the RockMaker software. Formulatrix provides technical support for the instrument and has 

          -remote access for troubleshooting. SBGrid maintains the server configuration.

          -

          -# Site Specific Software

          -

          -### HKL2000

          -Licenses for HKL2000 are limited to one specific system per lab. At DFCI you can use the system named mjel12 to run HKL2000.

          -

          -# Networking and General IT Support

          -There are HMS network switches on the 3rd and 4th floors that connect the labs to SBGrid infrastructure. A new port must be 

          -activated for all new SBGrid-supported systems. Email [help@sbgrid.org](mailto:help@sbgrid.org) with the computer information and 

          -port number and SBGrid will work with DFCI/LC IT support to activate the port. 

          -To report DFCI network problems, or for general computing support, contact the Partners Healthcare Help desk at: 

          -

          -* <http://helpdesk.partners.org/> 

          -

          -*Note*: this link only works from within the Partners network.

          -

          -

          -

				faq-changing-your-account-password.md
			
          @@ -2,7 +2,7 @@

           ## HMS 

          -SSH to crystal.harvard.edu and use the passwd command.

          +SSH to xtal200.harvard.edu and use the passwd command.

           ## MCB

				faq-connecting-to-cmcd-vpn.md
			
          @@ -28,7 +28,7 @@ These instructions are for members using Apple Computers.

           1. Then click on "Connect sbgrid.org"

           [[images/vpn_connect.png]]

           1. Enter your SBGrid username and password

          -1. This is the same as your crystal.harvard.edu ssh login

          +1. This is the same as your xtal200.harvard.edu ssh login

           1. If you receive a warning stating that your computer's apparent public IP hasn't changed - this is normal. 

           Just check "Do not check for IP address changes" box and click OK.

				faq-remote-access-to-linux-computers.md
			
          @@ -29,9 +29,9 @@ exceptions see Table I).

           ### How To SSH

           ssh to:

          -* crystal.harvard.edu

          +* xtal200l.harvard.edu

          -You should only use crystal.harvard.edu if you have told to do so by

          +You should only use xtal200.harvard.edu if you have told to do so by

           SBGrid staff. If you need access please email <help@sbgrid.org>.

           Example syntax for connecting to SSH gateway for Harvard Medical School

          @@ -39,17 +39,17 @@ groups:

           * Non-GUI connection: 

          -``` ssh username@crystal.harvard.edu;```

          +``` ssh username@xtal200.harvard.edu;```

           * GUI (connecting to a linux system): 

          -``` ssh -Y username@crystal.harvard.edu;```

          +``` ssh -Y username@xtal200.harvard.edu;```

           ``` ssh -Y abacus ``` (replace abacus with the name of your workstation.)

           * GUI (slower network connection): 

          -```ssh -Y -C username@crystal.harvard.edu;```

          +```ssh -Y -C username@xtal200.harvard.edu;```

           ```ssh -Y -C abacus;``` (replace abacus with the name of your workstation.)

          @@ -67,7 +67,7 @@ If your site is not included on this list please contact us for further info abo

           ### HMS, CHB, & DFCI Labs: 

          -ssh to crystal.harvard.edu. You cannot run jobs on the gateway host and must ssh to your computer nodes to run jobs.

          +ssh to xtal200.harvard.edu. You cannot run jobs on the gateway host and must ssh to your computer nodes to run jobs.

           ###MCB Labs

           ssh to galactica.mcb.harvard.edu. You can run jobs on the gateway or on orthus.

				faq-running-remote-jobs-after-disconnecting.md
			
          @@ -23,7 +23,7 @@ quit screen session |  `exit`

           ### example `screen` file transfer

          -`localsys> ssh [meyer@crystal.harvard.edu](mailto:meyer@crystal.harvard.edu)`

          +`localsys> ssh [meyer@xtal200.harvard.edu](mailto:meyer@xtal200.harvard.edu)`

           # connect to remote system

           `crystal> screen` # start screen session

          @@ -38,7 +38,7 @@ quit screen session |  `exit`

           ### example `screen` computational job

          -`localsys> ssh [meyer@crystal.harvard.edu](mailto:meyer@crystal.harvard.edu)`

          +`localsys> ssh [meyer@xtal200.harvard.edu](mailto:meyer@xtal200.harvard.edu)`

           # connect to remote gateway system

           `crystal> ssh abacus` # connect to your workstation; replace `abacus` with the

				faq-sshfs.md
			
          @@ -29,7 +29,7 @@ On Linux, if you don't have root or sudo access, you can mount sshfs via a direc

           An example of mounting from OSX on your local system is as follows -

           `sudo mkdir -p /sshfs/userdocs`

           `sudo chown -R $USER /sshfs`

          -`/usr/local/bin/sshfs oconnor@crystal.harvard.edu:/nfs/userdocs /sshfs/userdocs -o volname=userdocs,reconnect,ServerAliveInterval=15,ServerAliveCountMax=3,idmap=user,auto_xattr,dev,suid,defer_permissions,noappledouble,noapplexattr,IdentityFile=$HOME/.ssh/sshfs-id_rsa`

          +`/usr/local/bin/sshfs oconnor@xtal200.harvard.edu:/nfs/userdocs /sshfs/userdocs -o volname=userdocs,reconnect,ServerAliveInterval=15,ServerAliveCountMax=3,idmap=user,auto_xattr,dev,suid,defer_permissions,noappledouble,noapplexattr,IdentityFile=$HOME/.ssh/sshfs-id_rsa`

           Basically, your local user needs to own the destination $PATH. We mount one complete filesystem from the remote site(avoids local Apple Finder issues). We give the volume a name (shows mount point on your desktop), add some additional options for server connections, etc. If you are using an [password-less-ssh](faq-setting-up-passwordless-ssh) you would add it's path to the IdentityFile paramater.

          @@ -45,7 +45,7 @@ There is a 'helper' script available that can be used with sshfs_nfs.app for mac

           If the mounts become stuck just rerun to reattach shares.

          -`scp $USER@crystal.harvard.edu:/nfs/staff/shared/sshfs-helper.sh .`

          +`scp $USER@xtal200.harvard.edu:/nfs/staff/shared/sshfs-helper.sh .`

           First run use sudo to create /nfs mount points.

				faq-using-sbgrid-programs.md
			
          @@ -16,7 +16,7 @@ your SSH command, like so:

             1. [user@host ~]$ ssh -Y user@remote-host

           If you have to access your machine through a gateway (i.e., ssh to

          -crystal.harvard.edu, then to a workstation), you can use a command such as:

          +xtal200.harvard.edu, then to a workstation), you can use a command such as:

             1. [user@host ~]$ ssh -t -Y user@remote-host ssh -Y internal-host

				hms3-blacklow-brown-kruse-rapoport.md
			
          @@ -16,7 +16,7 @@ All SBGrid-supported systems are located on an integrated, private

           network segment. 

           To reach this network for access to local resources

          -from an external location, please SSH to **[crystal.harvard.edu](faq-remote-access-to-linux-computers)**. Please review our instructions the following, as you will need to request external SSH access:

          +from an external location, please SSH to **[xtal200.harvard.edu](faq-remote-access-to-linux-computers)**. Please review our instructions the following, as you will need to request external SSH access:

           * [faq-remote-access-to-linux-computers](faq-remote-access-to-linux-computers)

				hms4-cohen-corey-moazed.md
			
          @@ -76,7 +76,7 @@ Support from WQCG is available via:

           The WQCG also completes backups on these machines.

          -One new Linux GPU Workstation is supported and hosted by the SBGrid and backued up by WQCQ. This is system is stored in SBGrid Network Closet in Building C. Lab members have ssh access through crystal to the system which allows them to use the SBGrid software tree to process their data. Any data should be saved in the RAID10 partition and not in the user's home directory. This partition is backed up to HMS storage.

          +One new Linux GPU Workstation is supported and hosted by the SBGrid and backued up by WQCQ. This is system is stored in SBGrid Network Closet in Building C. Lab members have ssh access through xtal200.harvard.edu to the system which allows them to use the SBGrid software tree to process their data. Any data should be saved in the RAID10 partition and not in the user's home directory. This partition is backed up to HMS storage.

           If you need access to the GPU system, please email help@sbgrid.org.

           ### Mac

...	...	@@ -29,9 +29,9 @@ exceptions see Table I).
29	29	### How To SSH
30	30	ssh to:
31	31
32		-* crystal.harvard.edu
	32	+* xtal200l.harvard.edu
33	33
34		-You should only use crystal.harvard.edu if you have told to do so by
	34	+You should only use xtal200.harvard.edu if you have told to do so by
35	35	SBGrid staff. If you need access please email <help@sbgrid.org>.
36	36
37	37	Example syntax for connecting to SSH gateway for Harvard Medical School
...	...	@@ -39,17 +39,17 @@ groups:
39	39
40	40	* Non-GUI connection:
41	41
42		-``` ssh username@crystal.harvard.edu;```
	42	+``` ssh username@xtal200.harvard.edu;```
43	43
44	44	* GUI (connecting to a linux system):
45	45
46		-``` ssh -Y username@crystal.harvard.edu;```
	46	+``` ssh -Y username@xtal200.harvard.edu;```
47	47
48	48	``` ssh -Y abacus ``` (replace abacus with the name of your workstation.)
49	49
50	50	* GUI (slower network connection):
51	51
52		-```ssh -Y -C username@crystal.harvard.edu;```
	52	+```ssh -Y -C username@xtal200.harvard.edu;```
53	53
54	54	```ssh -Y -C abacus;``` (replace abacus with the name of your workstation.)
55	55
...	...	@@ -67,7 +67,7 @@ If your site is not included on this list please contact us for further info abo
67	67
68	68	### HMS, CHB, & DFCI Labs:
69	69
70		-ssh to crystal.harvard.edu. You cannot run jobs on the gateway host and must ssh to your computer nodes to run jobs.
	70	+ssh to xtal200.harvard.edu. You cannot run jobs on the gateway host and must ssh to your computer nodes to run jobs.
71	71
72	72	###MCB Labs
73	73	ssh to galactica.mcb.harvard.edu. You can run jobs on the gateway or on orthus.

...	...	@@ -29,7 +29,7 @@ On Linux, if you don't have root or sudo access, you can mount sshfs via a direc
29	29	An example of mounting from OSX on your local system is as follows -
30	30	`sudo mkdir -p /sshfs/userdocs`
31	31	`sudo chown -R $USER /sshfs`
32		-`/usr/local/bin/sshfs oconnor@crystal.harvard.edu:/nfs/userdocs /sshfs/userdocs -o volname=userdocs,reconnect,ServerAliveInterval=15,ServerAliveCountMax=3,idmap=user,auto_xattr,dev,suid,defer_permissions,noappledouble,noapplexattr,IdentityFile=$HOME/.ssh/sshfs-id_rsa`
	32	+`/usr/local/bin/sshfs oconnor@xtal200.harvard.edu:/nfs/userdocs /sshfs/userdocs -o volname=userdocs,reconnect,ServerAliveInterval=15,ServerAliveCountMax=3,idmap=user,auto_xattr,dev,suid,defer_permissions,noappledouble,noapplexattr,IdentityFile=$HOME/.ssh/sshfs-id_rsa`
33	33
34	34	Basically, your local user needs to own the destination $PATH. We mount one complete filesystem from the remote site(avoids local Apple Finder issues). We give the volume a name (shows mount point on your desktop), add some additional options for server connections, etc. If you are using an [password-less-ssh](faq-setting-up-passwordless-ssh) you would add it's path to the IdentityFile paramater.
35	35
...	...	@@ -45,7 +45,7 @@ There is a 'helper' script available that can be used with sshfs_nfs.app for mac
45	45
46	46	If the mounts become stuck just rerun to reattach shares.
47	47
48		-`scp $USER@crystal.harvard.edu:/nfs/staff/shared/sshfs-helper.sh .`
	48	+`scp $USER@xtal200.harvard.edu:/nfs/staff/shared/sshfs-helper.sh .`
49	49
50	50	First run use sudo to create /nfs mount points.
51	51

...	...	@@ -76,7 +76,7 @@ Support from WQCG is available via:
76	76
77	77	The WQCG also completes backups on these machines.
78	78
79		-One new Linux GPU Workstation is supported and hosted by the SBGrid and backued up by WQCQ. This is system is stored in SBGrid Network Closet in Building C. Lab members have ssh access through crystal to the system which allows them to use the SBGrid software tree to process their data. Any data should be saved in the RAID10 partition and not in the user's home directory. This partition is backed up to HMS storage.
	79	+One new Linux GPU Workstation is supported and hosted by the SBGrid and backued up by WQCQ. This is system is stored in SBGrid Network Closet in Building C. Lab members have ssh access through xtal200.harvard.edu to the system which allows them to use the SBGrid software tree to process their data. Any data should be saved in the RAID10 partition and not in the user's home directory. This partition is backed up to HMS storage.
80	80	If you need access to the GPU system, please email help@sbgrid.org.
81	81
82	82	### Mac

...	...	@@ -7,7 +7,7 @@ All SBGrid-supported systems are located on an integrated, private network segme
7	7
8	8
9	9	To reach this network for access to local resources
10		-from an external location, please SSH to [crystal.harvard.edu](faq-remote-access-to-linux-computers). Please review our instructions the following, as you will need to request external SSH access:
	10	+from an external location, please SSH to [xtal200.harvard.edu](faq-remote-access-to-linux-computers). Please review our instructions the following, as you will need to request external SSH access:
11	11
12	12	* [faq-remote-access-to-linux-computers](faq-remote-access-to-linux-computers)
13	13
...	...	@@ -76,7 +76,7 @@ If you are not currently a member of this list and wish to be added, contact Pro
76	76	# Accounts
77	77	SBGrid manages two different types of Crystal accounts. For simplicity, we use the same username for both accounts, but each has a different password. The first gives you access to Linux systems in your lab. The second is used to access your Crystal Gmail and other Google services.
78	78
79		-* Linux access - ssh to `crystal.harvard.edu`
	79	+* Linux access - ssh to `xtal.harvard.edu`
80	80	* Google Account - <https://crystal.harvard.edu/mail>
81	81
82	82

...	...	@@ -7,7 +7,7 @@ for assistance with Mac & Windows systems.
7	7
8	8	New SBGrid computers need to be registered to access the network.
9	9
10		-All SBGrid-supported systems are located on an integrated, private network segment. To reach this network for access to local resources from an external location, please ssh to crystal.harvard.edu.
	10	+All SBGrid-supported systems are located on an integrated, private network segment. To reach this network for access to local resources from an external location, please ssh to xtal200.harvard.edu.
11	11
12	12	[[_TOC_]]
13	13

...	...	@@ -4,7 +4,7 @@
4	4	# Overview
5	5	SBGrid provides comprehensive system administration support for all Linux systems for the Harrison and Chen labs at CLS.
6	6
7		-All computers are located on an integrated network segment that integrates structural biology computers at HMS, BCH, and DFCI. To reach this network for access to local resources from an external location, please ssh to crystal.harvard.edu.
	7	+All computers are located on an integrated network segment that integrates structural biology computers at HMS, BCH, and DFCI. To reach this network for access to local resources from an external location, please ssh to xtal200.harvard.edu.
8	8
9	9	[[_TOC_]]
10	10

...	...	@@ -1,7 +1,7 @@
1	1	<!-- --- title: BCH: Wu, Springer, & Hur Labs -->
2	2
3	3	# Overview
4		-SBGrid provides comprehensive system administration support for all Linux, Windows, and Mac computers at CLS for the Wu, Springer, and Hur labs. All computers are located on an integrated network segment that integrates structural biology computers at HMS, BCH, and DFCI. To reach this network for access to local resources from an external location, please ssh to crystal.harvard.edu.
	4	+SBGrid provides comprehensive system administration support for all Linux, Windows, and Mac computers at CLS for the Wu, Springer, and Hur labs. All computers are located on an integrated network segment that integrates structural biology computers at HMS, BCH, and DFCI. To reach this network for access to local resources from an external location, please ssh to xtal200.harvard.edu.
5	5
6	6	[[_TOC_]]
7	7

...	...	@@ -3,7 +3,7 @@
3	3	# Overview
4	4	SBGrid provides comprehensive system administration support for all Linux, Windows, and Mac computers at DFCI. Supported labs include Eck, Dhe-Paganon, Wang, Fischer, and Arthanari. All computers are located on an integrated network segment that integrates structural biology computers at HMS, BCH, and DFCI.
5	5
6		-To reach this network for access to local resources from an external location, please ssh to crystal.harvard.edu.
	6	+To reach this network for access to local resources from an external location, please ssh to xtal200.harvard.edu.
7	7
8	8	[[_TOC_]]
9	9

...	...	@@ -1,117 +0,0 @@
1		-<!-- ---title: DFCI: Eck, Dhe-Paganon, Wang, Fischer, Arthanari, & Sun Labs -->
2		-
3		-# Overview
4		-SBGrid provides comprehensive system administration support for all Linux, Windows, and Mac computers at DFCI. Supported labs include Eck, Dhe-Paganon, Wang, Fischer, and Arthanari. All computers are located on an integrated network segment that integrates structural biology computers at HMS, BCH, and DFCI.
5		-
6		-To reach this network for access to local resources from an external location, please ssh to crystal.harvard.edu.
7		-
8		-[[_TOC_]]
9		-
10		-# Get Help
11		-For general questions, email SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org) and include your name and the name of your lab.
12		-Email questions about your software installation to [bugs@sbgrid.org](mailto:bugs@sbgrid.org).
13		-
14		-New lab members should contact [help@sbgrid.org](mailto:help@sbgrid.org) to complete their initial setup.
15		-
16		-
17		-# Email Access
18		-Lab members have access to a Crystal email account through Google Apps. If you do not have an account, email [help@sbgrid.org](mailto:help@sbgrid.org) and cc your PI in the request.
19		-
20		-SBGrid maintains a Google mailing list for labs on the Crystal Google domain upon request. If your lab actively uses the mailing list and you would like your name added to the list, please contact [help@sbgrid.org](mailto:help@sbgrid.org).
21		-
22		-
23		-# Lab Wiki
24		-
25		-A standalone Confluence server instance (version 5.8) is running on a virtual machine on an SBGrid-hosted VM cluster.
26		-
27		-Users with a crystal email account can access the wiki at the PI’s request.
28		-
29		-To access the lab wiki go to <http://wiki.sbgrid.org> and login with your crystal email.
30		-
31		-# Computers
32		-
33		-### Linux
34		-
35		-Linux computers share authentication and data directories and can only be accessed locally from within the lab.
36		-
37		-Home directories are located at
38		-
39		-* `/nfs/<lab initials>/<username> (example: /nfs/mje/eck)`
40		-
41		-SBGrid's comprehensive collections of structural biology applications is located in the /programs directory. All systems are configured with Stereo 3D.
42		-
43		-The Ivory workstation, which has 48 cores, can be accessed remotely and is typically used for docking computations and data processing.
44		-
45		-Please note that your home directories are only visible to your labmates and PI by default. Permissions vary depending on the
46		-nature of the directory or files in question. PIs can request modifications to file permissions to suit the lab's needs.
47		-
48		-### Mac OS X
49		-
50		-All Mac computers have local administrative accounts that are specific to the lab members. Each user's home directory is located at
51		-
52		-* `/Users/<username> (example /Users/eck)`
53		-
54		-This setup allows users to install and update software without requesting help from SBGrid. Every local account is backed up to CrashPlan.
55		-Any network share, including home directories, are mounted via Samba and require user authentication.
56		-
57		-These computers are also connected to the lab printers on the 3rd and 4th floors of Longwood Center.
58		-
59		-Please contact [help@sbgrid.org](mailto:help@sbgrid.org) to request an account.
60		-
61		-### Windows
62		-
63		-Some lab members use Windows systems as their main computers. These computers are not maintained by SBGrid, however,
64		-SBGrid will make them available on the network.
65		-
66		-
67		-### Data collection and Instrument Control Computers
68		-
69		-The scanner room has two Linux systems (aqua and plum) that control the x-ray scanner. Windows computers on this network are used for
70		-instrument control and data collection for the RockImager and FPLC systems.
71		-
72		-
73		-## Accessing your Samba shares
74		-Macs have local accounts with local home directories. To access your Linux network home directory using Samba (SMB):
75		-
76		-* Open Finder, click Go, then click 'Go to Server'
77		-* Type in the server address: `smb://blacker.in.hwlab`
78		- * Click ‘Connect’.
79		-* Enter your Samba username and password (contact SBGrid for SMB account issues).
80		-
81		-
82		-# Data Backups
83		-Hourly and daily snapshots are taken of the file server Z file system. Data is replicated to another server in building C on the HMS Quad.
84		-The local home directories of SBGrid-supported Macs are backed up to a Crashplan server located in the SGM Building on the HMS Quad.
85		-
86		-
87		-# Printing
88		-A Xerox Phaser 8860 is located on the third floor near the kitchen area. Another inkjet printer is located directly above on the fourth floor.
89		-Email [help@sbgrid.org](mailto:help@sbgrid.org) with any printing problems.
90		-
91		-
92		-# RockImager Setup
93		-There are two types of data generated by the imager:
94		-
95		-* Images: Regular “jpg” image files that are stored directly in the file system on the main file server.
96		-* Experimental data: As experiments are created, the data is stored on a “Microsoft SQL Server 2014” database, currently running on a Windows 2012 server.
97		-
98		-The data is accessible on the RockImager PCs and also through the RockMaker software. Formulatrix provides technical support for the instrument and has
99		-remote access for troubleshooting. SBGrid maintains the server configuration.
100		-
101		-# Site Specific Software
102		-
103		-### HKL2000
104		-Licenses for HKL2000 are limited to one specific system per lab. At DFCI you can use the system named mjel12 to run HKL2000.
105		-
106		-# Networking and General IT Support
107		-There are HMS network switches on the 3rd and 4th floors that connect the labs to SBGrid infrastructure. A new port must be
108		-activated for all new SBGrid-supported systems. Email [help@sbgrid.org](mailto:help@sbgrid.org) with the computer information and
109		-port number and SBGrid will work with DFCI/LC IT support to activate the port.
110		-To report DFCI network problems, or for general computing support, contact the Partners Healthcare Help desk at:
111		-
112		-* <http://helpdesk.partners.org/>
113		-
114		-Note: this link only works from within the Partners network.
115		-
116		-
117		-

...	...	@@ -2,7 +2,7 @@
2	2
3	3	## HMS
4	4
5		-SSH to crystal.harvard.edu and use the passwd command.
	5	+SSH to xtal200.harvard.edu and use the passwd command.
6	6
7	7	## MCB
8	8

...	...	@@ -28,7 +28,7 @@ These instructions are for members using Apple Computers.
28	28	1. Then click on "Connect sbgrid.org"
29	29	[[images/vpn_connect.png]]
30	30	1. Enter your SBGrid username and password
31		-1. This is the same as your crystal.harvard.edu ssh login
	31	+1. This is the same as your xtal200.harvard.edu ssh login
32	32	1. If you receive a warning stating that your computer's apparent public IP hasn't changed - this is normal.
33	33	Just check "Do not check for IP address changes" box and click OK.
34	34

...	...	@@ -23,7 +23,7 @@ quit screen session \| `exit`
23	23
24	24	### example `screen` file transfer
25	25
26		-`localsys> ssh [meyer@crystal.harvard.edu](mailto:meyer@crystal.harvard.edu)`
	26	+`localsys> ssh [meyer@xtal200.harvard.edu](mailto:meyer@xtal200.harvard.edu)`
27	27	# connect to remote system
28	28
29	29	`crystal> screen` # start screen session
...	...	@@ -38,7 +38,7 @@ quit screen session \| `exit`
38	38
39	39	### example `screen` computational job
40	40
41		-`localsys> ssh [meyer@crystal.harvard.edu](mailto:meyer@crystal.harvard.edu)`
	41	+`localsys> ssh [meyer@xtal200.harvard.edu](mailto:meyer@xtal200.harvard.edu)`
42	42	# connect to remote gateway system
43	43
44	44	`crystal> ssh abacus` # connect to your workstation; replace `abacus` with the

...	...	@@ -16,7 +16,7 @@ your SSH command, like so:
16	16	1. [user@host ~]$ ssh -Y user@remote-host
17	17
18	18	If you have to access your machine through a gateway (i.e., ssh to
19		-crystal.harvard.edu, then to a workstation), you can use a command such as:
	19	+xtal200.harvard.edu, then to a workstation), you can use a command such as:
20	20
21	21	1. [user@host ~]$ ssh -t -Y user@remote-host ssh -Y internal-host
22	22

...	...	@@ -16,7 +16,7 @@ All SBGrid-supported systems are located on an integrated, private
16	16	network segment.
17	17
18	18	To reach this network for access to local resources
19		-from an external location, please SSH to [crystal.harvard.edu](faq-remote-access-to-linux-computers). Please review our instructions the following, as you will need to request external SSH access:
	19	+from an external location, please SSH to [xtal200.harvard.edu](faq-remote-access-to-linux-computers). Please review our instructions the following, as you will need to request external SSH access:
20	20
21	21	* [faq-remote-access-to-linux-computers](faq-remote-access-to-linux-computers)
22	22