faq-changing-your-account-password.md
... ...
@@ -0,0 +1,29 @@
1
+# Changing your account password
2
+
3
+Password changes for CMCD accounts can be done using a web-based tool. You should use the appropriate tool for your site:
4
+
5
+## HMS
6
+HMS use this [link](http://cmcd.hms.harvard.edu/changepwd)
7
+
8
+## MCB
9
+
10
+For MCB, please use the passwd command at the terminal to change your
11
+password.
12
+
13
+
14
+## Password Restrictions
15
+Please note the following restrictions. Your new password must:
16
+
17
+* Differ from your account name
18
+* Contain at least one letter
19
+* Contain at least one number
20
+* Contain at least 8 characters
21
+
22
+
23
+If you have forgotten your password, or are otherwise unable to log in, please email us at:
24
+
25
+* [help@sbgrid.org](mailto:help@sbgrid.org?Subject=Password_Help)
26
+
27
+
28
+
29
+
faq-connecting-to-cmcd-vpn.md
... ...
@@ -0,0 +1,40 @@
1
+# Connecting to CMCD VPN
2
+
3
+The first thing you need to do is email the SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org?Subject=VPN_Shared_Secret) for the Shared Secret.
4
+
5
+## Configuration
6
+1. Click on the Apple Menu and select System Preferences
7
+1. Click on Network
8
+1. Unlock the panel by clicking on the padlock and enter the username and password of an admin user.
9
+1. Click on the '+' sign to Create a New Service
10
+1. In the dropdown window enter the following:
11
+ * Interface is **VPN**
12
+ * Type is **L2TP over IPSec**
13
+ * Enter a Service Name, ie: **CMCD VPN**
14
+1. Then *Click* on Create.
15
+1. The Network Window will change and you need to enter the following:
16
+ * Server Address: **vpn.sbgrid.org**
17
+ * Account Name: Enter **your** username.
18
+ * This is the username you use to connect to crystal, and other CMCD
19
+ services.
20
+1. Next Click on **Authentication Settings**
21
+1. In the Window that appears enter the following:
22
+ * Enter your password under *User Authentication*
23
+ * Enter the shared secert that the SBGrid emailed you.
24
+ * Click OK.
25
+1. Check the box **Show VPN status in menu bar**
26
+1. Click Apply.
27
+
28
+## Connect
29
+
30
+
31
+To connect to the VPN, open the VPN menu in the menu bar by clicking on it and and click on *"Connect"*.
32
+
33
+You'll see the word Connecting scroll across, and once the connection is complete a timer will start.
34
+
35
+## Disconnect
36
+
37
+When you want to disconnect from the VPN simply open the VPN menu, and select Disconnect.
38
+
39
+
40
+
faq-crashplan-backups.md
... ...
@@ -0,0 +1,13 @@
1
+# CrashPlan backups (HMS local accounts)
2
+
3
+OS X systems at HMS where data is stored locally (self-administered/local accounts) should be backed up up with CrashPlan through HMS IT.
4
+
5
+
6
+## Setup CrashPlan
7
+1. Install CrashPlan ([instructions](http://ecommons.med.harvard.edu//ec_res/nt/DB23E343-E3B9-4545-AA03-AB756F4DC10D/CPP_Install-Macintosh.pdf) & [software](http://download.crashplan.com/installs/mac/install/CrashPlanPROe/CrashPlanPROe_3.6.3_Mac.dmg))
8
+ * SBGrid registration code  JJRR-RHW7-UHJW-H7JM
9
+ *  Server: ```mybackup.med.harvard.edu```
10
+1. Email your eCommons ID and machine name to [help@sbgrid.org](mailto:help@sbgrid.org?Subject=Crashplan_Setup)
11
+
12
+
13
+
faq-data-collection-at-ne-cat.md
... ...
@@ -0,0 +1,152 @@
1
+# Data Collection at NE-CAT
2
+
3
+Data collection time is allocated by the CMCD Synchrotron Committee. Data
4
+collection time at [NE-CAT](http://necat.chem.cornell.edu/
5
+"http://necat.chem.cornell.edu" ) beamlines C and E are available.
6
+
7
+## Local Liaisons
8
+Please work with your local liaisons to learn more about the procedure and
9
+follow up our instructions very carefully.
10
+
11
+* DFCI: [Sacha Uljon](mailto:Sacha_Uljon@dfci.harvard.edu?subject=NE-CAT)
12
+* Harvard: [John Janetzko](mailto:j.janetzko@gmail.com?subject=NE-CAT)
13
+* Harrison Laboratory and Children's Hospital: [Daryl
14
+Klein](mailto:klein@crystal.harvard.edu?subject=NE-CAT)
15
+
16
+## Allocation Committee:
17
+
18
+* Professor Piotr Sliz,
19
+* Professor Stephen Harrison,
20
+* Professor Mike Eck
21
+* Rachelle Gaudet.
22
+
23
+## Instructions
24
+If you have any questions about allocation process please make sure to contact
25
+the appropriate parties, as outlined below.
26
+
27
+ 1. Your APS User Access must be current.
28
+ * New users must complete [the APS Central Registration](http://www.aps.anl.gov/Users/Current/ "http://www.aps.anl.gov/Users/Current/" ) several weeks before applying for time.
29
+ * If you have any questions about the registration process please contact the APS User Office, your lab data collection coordinator, your PI, or [Cyndi Salbego from NE-CAT](http://necat.chem.cornell.edu/aboutus/Organization/Staff.htm).
30
+
31
+ 2. You must have a GUP proposal in place and know your GUP number [GUP](https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page "https://beam.aps.anl.gov/pls/apsweb/gup0005.start_page" ).
32
+ * Please work with your PI, your lab data collection coordinator, and Cyndi Salbego from NE-CAT when preparing and submitting your proposal.
33
+
34
+ 3. Please join [the CMCD-NECAT mailing list](http://groups.google.com/group/cmcd-necat "http://groups.google.com/group/cmcd-necat" ) and [subscribe](http://www.google.com/calendar/ical/hkl.hms.harvard.edu_ssi0iek9q640ovukjfnj5nvtsc%40group.calendar.google.com/public/basic.ics) to the CMCD calendar.
35
+ * You should review the mailing list archives to get a better sense of the allocation process and to find out about upcoming trips. You can also view [the CMCD calendar](http://www.google.com/calendar/hosted/hkl.hms.harvard.edu/embed?src=hkl.hms.harvard.edu_ssi0iek9q640ovukjfnj5nvtsc%40group.calendar.google.com&ctz=America/New_York) in your browser.
36
+ * Please note that you will need a google, hkl.hms.harvard.edu _or_ crystal.harvard.edu account to apply for the CMCD mailing list membership.
37
+ * The _application should be done through the mailing list website_, which was mentioned above (please indicate your lab name).
38
+ * Contact [Piotr Sliz](mailto:sliz@hkl.hms.harvard.edu?subject=NE-CAT mailing list) if your mailing list request takes more than 3 days to be approved.
39
+ * The mailing list is used for all trip announcements. You are also welcome to post to this list with general questions that might be of interest to other users.  
40
+
41
+ 4. Approximately two weeks before each trip [ **the registration form**](https://docs.google.com/a/hkl.hms.harvard.edu/forms/d/1wbCu44m9N5KK5lw0C6Qoij3xiI9kn9hjRcNraS0r5So/viewform) will be posted to the mailing list.
42
+ * This form should be completed only after this announcement is made. Users will be given two days to complete the form.
43
+ * **NEW USERS:** If this is your first trip please review the past registrations requests. This will give you a better sense of what is required to complete submission.
44
+ * **ALL USERS:** Please note that the registration form often changes. Questions? Please work with your PI, lab data collection coordinator and your CMCD liaisons. You can also post to the mailing list on comment on this post.
45
+ * **ALL:** Please note that incomplete applications will be rejected without any additional feedback from the allocation committee (HINT: please take time to provide sufficient info in the _Beam Time Application_ field and read all online comments).
46
+
47
+ 5. We usually post the finalized trip schedule within 24 hours after all data collection request are received.
48
+ * If you notice any mistakes in the allocation please contact the data collection coordinators as soon as possible.
49
+
50
+ 6. In preparation for the trip you will need to complete an [ESAF](https://beam.aps.anl.gov/pls/apsweb/esaf0001.start_page "https://beam.aps.anl.gov/pls/apsweb/esaf0001.start_page" ) form.
51
+ * This step should be completed immediately after the allocation is announced. Please contact [Cyndi Salbego](http://necat.chem.cornell.edu/aboutus/Organization/Staff.htm) from NE-CAT with questions.
52
+
53
+ 7. On-site visitors should make travel arrangements.
54
+ * Accommodation should be booked in the [APS Guesthouse](http://www.anlgh.org/ "http://www.anlgh.org" ).
55
+
56
+ 8. Register and Ship your crystals (_Failure to follow instructions will results in delivery refusal at APS_):
57
+
58
+> a) Please complete a [ **puck registration
59
+form**](https://docs.google.com/a/hkl.hms.harvard.edu/forms/d/1qgLNDOidIXrgvFSsV6JsM1tcfW_Tdr2CVk2Rfa5kx8A/viewform).
60
+Please make arrangements early and have the form           submitted  by 5PM
61
+on the day before Harvard's data collection starts.
62
+
63
+>
64
+
65
+> b) All dewars and corresponding shippers for the CMCD trips should have a
66
+clear, big label in the following format: HU-PI's Initials-dewar number, e.g.
67
+**HU-SCH-1**, HU-SCH-2, HU-SCH-3 for Harrison lab or HU-PS-1 for Sliz group.
68
+
69
+>
70
+
71
+> c) With many labs traveling please try to consolidate shipping - saves money
72
+and effort on the APS end. Please note that number of pucks indicated on the
73
+schedule represent the _maximum number that will be loaded for your group_.
74
+You can certainly have fewer pucks.
75
+
76
+>
77
+
78
+> d) The final ** packing list for each dewar must be included** in each
79
+shipper. If there are last minute scratches just indicate this on your packing
80
+list. There is no need to email coordinators with this info.
81
+
82
+>
83
+
84
+> e) U sers should include a return FEDEX label inside the case when they
85
+ship. Express saver works best in most cases.
86
+
87
+>
88
+
89
+> f) Dewars should be shipped to APS two business days before your assigned
90
+time using _FEDEX Priority Overnight_ service to :
91
+
92
+>
93
+
94
+> **       K. Rajashankar,  Harvard Consortium.
95
+> ** **      Building 436/NE-CAT
96
+>       9700 South Cass Avenue.
97
+>       Argonne, IL 60439**
98
+
99
+Collecting Data:
100
+
101
+> a) Chicago Time! All schedules are posted using CTZ.
102
+>
103
+
104
+>
105
+
106
+> b) Prepare for the trip. Please review all on-line documentation, which is
107
+available on the NE-CAT website, e.g. [remote data collection
108
+manual](http://necat.chem.cornell.edu/~igor/remote_manual.pdf), [contact
109
+list](http://necat.chem.cornell.edu/userprogram/WebPhonelist.pdf), etc. Make
110
+sure that your remote login credentials are active.
111
+
112
+>
113
+
114
+> b) Remote Webex training sessions are mandatory but can be attended
115
+remotely. Users joining late or skipping assigned training session will be
116
+scratched from the allocation list. **No exceptions.**
117
+
118
+>
119
+
120
+> c) Attendance at puck loading, training and data collection sessions is at
121
+your own risk. **No rearrangements** will be made for missed slots or
122
+equipment failures.
123
+
124
+>
125
+
126
+> d) Attend your data collection session ([login
127
+portal](https://remote.nec.aps.anl.gov:3001/)).
128
+
129
+>
130
+
131
+> e) Transfer your frames to a local directory (please [contact
132
+SBGrid](mailto:help@sbgrid.org?subject=NE-CAT data collection) for additional
133
+instructions. We maintain special directories for diffraction images).
134
+
135
+>
136
+
137
+> f) Complete your End-of-Run form.
138
+
139
+GO-TO-Chicago (GTC) Points
140
+
141
+
142
+
143
+Each trip will be attended on-site by one CMCD laboratory (at least one person
144
+on-site for the duration of 48 hour CMCD data collection slot).
145
+
146
+The lab with
147
+the highest number of GTC points will be required to provide this support. GTC
148
+points are collected based on number of previous NE-CAT shifts (0.5 points per
149
+hour of data collection on E and 0.75 points per hour of data collection on
150
+C).
151
+
152
+
faq-forwarding-mail-to-crystal.md
... ...
@@ -0,0 +1,28 @@
1
+# How to Forward Email
2
+
3
+##How to forward email to your Crystal email address
4
+
5
+To setup mail forwarding on Linux, you should have a .forward file configured in your home directory.
6
+
7
+Add a .forward file to your home directory:
8
+
9
+ 1. cd <your network home directory>    
10
+ * example:
11
+ * ``` cd ~; touch .forward; ```
12
+
13
+Add the following to the .forward file that your just created(using your favorite text editor):
14
+
15
+ 1. <username>@crystal.harvard.edu
16
+ 2. \<username>
17
+
18
+
19
+Make sure the permissions are set correctly on the file:
20
+
21
+ 1. chmod 644 .forward;
22
+
23
+Test the setup and check your inbox on crystal email with this command or by sending and email to it from a different account:
24
+
25
+ 1. mailx -s 'my test email' <username> < /dev/null
26
+
27
+For questions, please contact SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org?Subject=Forward_Email_Help)
28
+
faq-getting-help.md
... ...
@@ -0,0 +1,27 @@
1
+# Getting Help
2
+
3
+Please [help@sbgrid.org](mailto:help@sbgrid.org) us to ask for help! When you email the addresses listed below the emails are forwarded to our Ticketing System which all of can see and ensures that the correct person will help you.
4
+
5
+When you submit a help ticket please include as much information as possible. The following is a list of information that should be useful in any ticket that you submit:
6
+
7
+* Your Lab Name
8
+* State the problem as best you can.
9
+ * Explain what is happening, and explain what you expect to happen when the issue is not present.
10
+* Include the name of the computer you are using.
11
+ * If you are not sure, run the `hostname` command from a Terminal.
12
+* Indicate whether the problem is isolated to a single machine, or if it affects all machines in your lab.
13
+* Include the operating system where applicable (Mac OS X/Linux).
14
+* If the issue is related to a piece of software, include the name of the software and version number.
15
+* If an error message is present, copy and paste the exact error message.
16
+
17
+
18
+To submit a help request, please send email to:
19
+
20
+* [help@sbgrid.org](mailto:help@sbgrid.org).
21
+
22
+For assistance with the structural biology software, please contact:
23
+
24
+* [bugs@sbgrid.org](mailto:bugs@sbgrid.org).
25
+
26
+It is important that you submit a help request for any SBGrid or IT related issue, even if you have easy access to speak with SBGrid personnel.
27
+
faq-how-to-find-mac-address-on-os-x-gui.md
... ...
@@ -0,0 +1,16 @@
1
+# HOWTO: Find MAC address on OS X (GUI)
2
+
3
+Locating your MAC (hardware) address using the OS X GUI.
4
+
5
+* Step 1
6
+
7
+![](../images/how-to-find-mac-address-on-os-x-gui-1.png)
8
+
9
+* Step 2
10
+
11
+![](../images/how-to-find-mac-address-on-os-x-gui-2.png)
12
+
13
+* Step 3
14
+
15
+![](../images/how-to-find-mac-address-on-os-x-gui-3.png)
16
+
faq-new-accounts.md
... ...
@@ -0,0 +1,16 @@
1
+# New Accounts
2
+
3
+## Account Creation
4
+
5
+Requests for user accounts **must** come from a PI or from someone a PI has authorized to perform requests of this nature. In order for SBGrid to create your account, please have your PI send the request to [help@sbgrid.org](mailto:help@sbgrid.org) with the following information:
6
+
7
+ * Your first and last name.
8
+ * Your primary email address
9
+
10
+## Account Deletion
11
+
12
+The PI **must** email [help@sbgrid.org](mailto:help@sbgrid.org) to notify us
13
+when a user leaves the lab.
14
+
15
+At termination, SSH access is disabled. You may request 90-day extension prior to expiration by email (we'll CC: PI). You must set up forwarding email address if account is extended.
16
+
faq-other-resources.md
... ...
@@ -0,0 +1,9 @@
1
+# Other Resources
2
+
3
+Please find more information here:
4
+
5
+ * [SBGrid.org](http://sbgrid.org/software) website
6
+ * list of all applications preninstalled in your computers, and other software related resources.
7
+ * [Unix/Linux tutorial](http://www.ee.surrey.ac.uk/Teaching/Unix/)
8
+ * [Google Apps documentation and howtos](http://learn.googleapps.com/home)
9
+
faq-remote-access-to-linux-computers.md
... ...
@@ -0,0 +1,57 @@
1
+# Remote Access to Linux Computers
2
+Linux computing resources can be accessed from off-campus locations (as well
3
+as different locations on-campus).
4
+
5
+## ssh
6
+
7
+ssh can be used for remote terminal access to your laboratory computers from
8
+home and other sites, as well as for running graphical programs (depending on
9
+your local operating system).
10
+
11
+SSH gateway is an externally accessible computer that can be accessed by ssh (see table below); once connected to the gateway you can use ssh to connect to other workstations in your laboratory.
12
+
13
+Data processing should not be done on the gateway, for computational jobs
14
+connect through gateway to another workstation and run your jobs there (for
15
+exceptions see Table I).
16
+
17
+Example syntax for connecting to SSH gateway for Harvard Medical School
18
+groups:
19
+
20
+* Non-GUI connection: 
21
+
22
+``` ssh username@crystal.harvard.edu;```
23
+
24
+* GUI (connecting to a linux system): 
25
+
26
+``` ssh -Y username@crystal.harvard.edu;```
27
+
28
+``` ssh -Y abacus ``` (replace abacus with the name of your workstation.)
29
+
30
+* GUI (slower network connection): 
31
+
32
+```ssh -Y -C username@crystal.harvard.edu;```
33
+
34
+```ssh -Y -C abacus;``` (replace abacus with the name of your workstation.)
35
+
36
+ssh is usually installed by default on linux and OS X systems. Terminal App
37
+can be found in your Applications/Utilities folder (when connecting with ```ssh
38
+-Y``` on OS X systems, X11 will start on its own if necessary).
39
+
40
+Please note that external SSH access is deactivated by default. Please contact
41
+ [help@sbgrid.org](mailto:help@sbgrid.org?Subject=Enable_ssh_access)to request remote access for your account.
42
+
43
+## Table I
44
+SSH Gateways are enabled in some of the CMCD laboratories.
45
+
46
+If your site is not included on this list please contact us for further info about remote access.
47
+
48
+|Labs|Gateway|Running jobs on gateway|
49
+| ------------ | :-----------: | -----------: |
50
+|HMS and CHB|crystal.harvard.edu|not allowed |
51
+|DFCI labs|crystal.harvard.edu|not allowed |
52
+| MCB|galactica.mcb.harvard.edu|allowed |
53
+
54
+**Tufts systems** use a VPN instead of a SSH gateway for SSH access.
55
+
56
+
57
+
faq-running-remote-jobs-after-disconnecting.md
... ...
@@ -0,0 +1,60 @@
1
+# Running remote jobs after disconnecting
2
+
3
+## `screen`
4
+
5
+When running long jobs remotely (file transfer, heavy computational jobs,
6
+etc), it's sometimes helpful to be able to start the job and disconnect from
7
+the remote system (while the jobs continues to run).
8
+
9
+`screen` is one tool that can be used to acomplish this. The usual procedure
10
+is to connect to the remote system, start a `screen` session, start the job,
11
+disconnect from the `screen` session, and log-out.
12
+
13
+start session | `screen`
14
+
15
+disconnect from session | `<ctrl-d>` (control + "D")
16
+
17
+re-connect to existing session | `screen -r`
18
+
19
+check for existing sessions | `screen -ls`
20
+
21
+quit screen session | `exit`
22
+
23
+### example `screen` file transfer
24
+
25
+`localsys> ssh [meyer@crystal.harvard.edu](mailto:meyer@crystal.harvard.edu)`
26
+# connect to remote system
27
+
28
+`crystal> screen` # start screen session
29
+
30
+`crystal> scp -r -p meyer@remote_site:~/data/ ~/data/` # start data transfer
31
+
32
+`crystal> <ctrl-d>` # disconnect from screen session
33
+
34
+`crystal> logout` # disconnect from remote system
35
+
36
+`localsys>` # all done
37
+
38
+### example `screen` computational job
39
+
40
+`localsys> ssh [meyer@crystal.harvard.edu](mailto:meyer@crystal.harvard.edu)`
41
+# connect to remote gateway system
42
+
43
+`crystal> ssh abacus` # connect to your workstation; replace `abacus` with the
44
+name of your workstation
45
+
46
+`abacus> screen` # start screen session
47
+
48
+`abacus> ./data_processing_script.sh` # start processing data
49
+
50
+`abacus> <ctrl-d>` # disconnect from screen session
51
+
52
+`abacus> logout` # disconnect from workstation
53
+
54
+`crystal> logout` # disconnect from gateway system
55
+
56
+`localsys>` # all done
57
+
58
+For more information, see [the screen
59
+manual](https://www.gnu.org/software/screen/manual/html_node/index.html).
60
+
faq-setting-up-passwordless-ssh.md
... ...
@@ -0,0 +1,12 @@
1
+# Setting up password-less ssh
2
+ 1. Generate ssh key-pair for local workstation: `ssh-keygen -t rsa` ; accept default options and hit return when prompted for passphrase.
3
+ 2. Copy public key (`~/.ssh/id_rsa.pub`) to remote system: `scp ~/.ssh/id_rsa.pub remotesys:~/` If this is the first connection to the remote system, type `yes` to accept the remote system key.
4
+ 3. Login to remote system, configure remote system to trust public key:
5
+
6
+ * `ssh remotesys`
7
+ * create ~/.ssh if it doesn't exist: `mkdir ~/.ssh`
8
+ * `cat ~/id_rsa.pub >> ~/.ssh/authorized_keys`
9
+ * `chmod 700 ~/.ssh`
10
+ * `chmod 640 ~/.ssh/authorized_keys`
11
+ 1. Logout of remote system, and repeat login to check that everything works correctly. If so, `~/id_rsa.pub` can be removed from the remote system.
12
+
faq-sshfs.md
... ...
@@ -0,0 +1,32 @@
1
+# sshfs
2
+
3
+## using sshfs
4
+
5
+Usage does not require administrative privileges.
6
+
7
+### Mounting remote filesystems with sshfs
8
+
9
+`sshfs username@remotesystem:/full/path/to/directory /mount/point`
10
+
11
+For example, `sshfs meyer@schl15:/nfs/userdocs/ps/meyer /sshfs` would use
12
+`schl15` as a host to access the directory `/nfs/userdocs/ps/meyer` (in other
13
+words, that user's NFS home directory).
14
+
15
+### Unmounting remote filesystems
16
+
17
+`umount /sshfs`
18
+
19
+
20
+## Setting up sshfs on OS X (Mac) systems
21
+
22
+Installation requires administrative privileges.
23
+
24
+Prior to installing, you should make sure that [password-less ssh](setting-up-passwordless-ssh.md) is configured correctly between the local system and the remote system.
25
+
26
+
27
+ 1. Download OSXFuse (`dmg`) (`pkg`) from <http://osxfuse.github.io>
28
+ 2. Open OSXFuse `dmg` , run installer
29
+ 3. Download SSHFS (`pkg`) from from <http://osxfuse.github.io>
30
+ 4. Run SSHFS installer `pkg`
31
+ 5. Create a folder to access the remote filesystems (aka a mount point): `mkdir /sshfs/`
32
+
faq-troubleshooting-firefox-on-a-network-account.md
... ...
@@ -0,0 +1,31 @@
1
+# Troubleshooting Firefox on a Network Account
2
+The popular Firefox web Browser isn't written for concurrency within a user
3
+profile. That means that you can have only one open instance of the program
4
+per user. If your account is not local to your machine, you must close all
5
+previous instances before trying to start a new browsing session. On
6
+occassion, Firefox will not start, because previous sessions were not closed
7
+properly (because of a crash or network interruption.)
8
+
9
+##On Mac OS X
10
+**To fix this issue on OS X, please log out, and log back in.
11
+You may also need to delete your parentlock file, located at
12
+~/Library/Application Support/Firefox/Profiles/*.default/.parentlock
13
+
14
+##On Linux
15
+**Before attempting the following steps, please make sure that you are currently logged into only one computer.
16
+Here are some steps to use Firefox, if it becomes locked by mistake:
17
+
18
+ * Remove any application lock files. Typically, these lock files are found in the browser home directory. Just run the following to delete the locks:
19
+
20
+> rm -f ~/.mozilla/firefox/*.default/.parentlock
21
+
22
+>
23
+
24
+> rm -f ~/.mozilla/firefox/*.default/lock
25
+
26
+After you do so, try to run firefox one more time.
27
+
28
+ * In the worst case scenario, you could do this: mv /.mozilla/firefox /.mozilla/firefox_hold (Note: this will completely reset Firefox.) Then start your browser, which will create a new profile. After you do this, you may wish to restore your bookmarks. You can do this via the Firefox menu path Bookmarks/Organize Bookmarks/File/Import (your old bookmarks would be in ~/.mozilla/firefox_hold/…)
29
+
30
+
31
+
faq-using-crystal-google-apps.md
... ...
@@ -0,0 +1,115 @@
1
+# Using Crystal Google Apps
2
+
3
+Users have access to the following Crystal Google apps/sites:
4
+
5
+* [<http://mail.crystal.harvard.edu>](http://mail.crystal.harvard.edu)
6
+* [<http://cal.crystal.harvard.edu>](http://cal.crystal.harvard.edu)
7
+* [<http://docs.crystal.harvard.edu>](http://docs.crystal.harvard.edu)
8
+* [<http://sites.crystal.harvard.edu>](http://sites.crystal.harvard.edu)
9
+
10
+
11
+From the web interface you can switch Applications by clicking on the 3x3
12
+square pattern near your email address (top right):
13
+
14
+![](../images/using-crystal-google-apps-1.png)
15
+
16
+## Crystal Google Calendar:
17
+
18
+* [<http://cal.crystal.harvard.edu>](http://cal.crystal.harvard.edu)
19
+
20
+## Mail Client Setup
21
+To setup mail clients, please refer to this page:
22
+
23
+* [<https://support.google.com/calendar/answer/99358>](https://support.google.com/calendar/answer/99358)
24
+
25
+![](../images/using-crystal-google-apps-2.png)
26
+
27
+## Share Calendar
28
+To share your calendars with other users, please refer to this page:
29
+
30
+* [<https://support.google.com/calendar/answer/37082>](https://support.google.com/calendar/answer/37082)
31
+
32
+![](../images/using-crystal-google-apps-3.png)
33
+
34
+![](../images/using-crystal-google-apps-4.png)
35
+
36
+To remove shared calendars, please refer to this page:
37
+
38
+[<https://support.google.com/calendar/answer/40802>](https://support.google.com/calendar/answer/40802)
39
+
40
+![](../images/using-crystal-google-apps-5.png)
41
+
42
+## Calendar Import
43
+Instead of importing calendars into iCal, etc, go to the manage page:
44
+
45
+* [<https://www.google.com/calendar/syncselect>](https://www.google.com/calendar/syncselect)
46
+
47
+![](../images/using-crystal-google-apps-6.png)
48
+
49
+
50
+## Crystal Google Drive/Docs:
51
+
52
+* [<http://docs.crystal.harvard.edu>](http://docs.crystal.harvard.edu)
53
+
54
+Using google drive tools, you can create and share folders, documents,
55
+spreadsheets, presentations, forms, drawings, etc.
56
+
57
+You can also set permissions for read only, comment, and edit.
58
+
59
+![](../images/using-crystal-google-apps-7.png)
60
+
61
+## Crystal Google Mail:
62
+
63
+[<http://mail.crystal.harvard.edu>](http://mail.crystal.harvard.edu)
64
+
65
+![](../images/using-crystal-google-apps-8.png)
66
+
67
+### Tabs for inbox
68
+
69
+![](../images/using-crystal-google-apps-9.png)
70
+
71
+### IMAP
72
+
73
+IMAP Client general settings -
74
+
75
+ * Incoming server: imap.gmail.com - ssl - port 993
76
+ * Outgoing Server: smtp.gmail.com - ssl - port 465
77
+ * username: [yourusername@crystal.harvard.edu](mailto:yourusername@crystal.harvard.edu)
78
+ * password: yourpassword
79
+
80
+The setup for all major mobile devices is simple - Just add an email account,
81
+type GMail, with
82
+[yourusername@crystal.harvard.edu](mailto:yourusername@crystal.harvard.edu) as
83
+the username.
84
+
85
+
86
+
87
+### Mail Tips:
88
+
89
+#### Multiple Duplicate Drafts
90
+Issues with multiple Drafts on server and duplicates in search results.
91
+Additionally it is good to turn off this folder for IMAP, particularly in
92
+larger accounts.
93
+
94
+Log into the web interface and scroll down on the left, you may need to press
95
+the arrow to expand - select 'Manage labels'. From that page for 'All mail'
96
+setting - uncheck 'show in imap'.
97
+
98
+![](../images/using-crystal-google-apps-10.png)
99
+![](../images/using-crystal-google-apps-11.png)
100
+
101
+#### Filters
102
+
103
+Creating filters: From the web interface check the mail and press more.
104
+The selected mess will already have the senders email address. You can add
105
+attitional filtering if you want. Press ‘create filter with this result. Then
106
+you choose what to do with the message. You can select ‘Choose Label’ and that
107
+is basically a folder.
108
+
109
+![](../images/using-crystal-google-apps-12.png)
110
+![](../images/using-crystal-google-apps-13.png)
111
+![](../images/using-crystal-google-apps-14.png)
112
+
113
+
114
+
115
+
faq-using-sbgrid-programs.md
... ...
@@ -0,0 +1,66 @@
1
+# Using SBGrid Programs
2
+All applications are located in **/programs** directory and are configured to run without additional settings. In most cases, you will easily be able to run any program in the collection by opening up a terminal shell, and typing the name of the program that you want to run. Linux applications are installed in the /**programs/i386-linux** subdirectory. Mac applications are installed in the **/programs/i386-mac** subdirectory (for intel macs) or the
3
+**/programs/powermac** subdirectory (for PPC macs).
4
+
5
+Most of the software titles installed in the SBGrid Suite have several
6
+versions available. Typically, we try to provide at least three versions of
7
+each software package, although very old or very new applications may have
8
+fewer versions. To override the default version, follow these instructions.
9
+
10
+## Running GUI Programs Remotely
11
+
12
+It is currently possible to run programs remotely over SSH through a process
13
+called X-forwarding. To accomplish this, you may simply use the -Y flag in
14
+your SSH command, like so:
15
+
16
+ 1. [user@host ~]$ ssh -Y user@remote-host
17
+
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:
20
+
21
+ 1. [user@host ~]$ ssh -t -Y user@remote-host ssh -Y internal-host
22
+
23
+After logging in to the remote host, you may launch programs by running the
24
+command name in a Terminal. With X-forwarding enabled, programs will launch
25
+their user interfaces on your computer, much like they would if you ran the
26
+program locally.
27
+
28
+
29
+_NOTE_: On Mac OS X, you may need to change your display output in order for
30
+certain programs to run correctly. You can do this by opening the X11
31
+preferences, clicking the output tab, and selecting a different option from
32
+the 'Colors:' dropdown (the default is "From Display"). 256 Colors will
33
+emulate an 8-bit color scheme for running applications such as WEB.
34
+
35
+If you need to download a newer version of X11 for OS X, you can find the
36
+binaries here: <http://xquartz.macosforge.org/trac/wiki>
37
+
38
+## Running SBGrid Programs
39
+
40
+Running programs from the SBGrid software tree should be as simple as opening
41
+a Terminal and typing the name of the application you would like to run. You
42
+may see a list of available software packages at:
43
+[http://sbgrid.org/software/](https://sbgrid.org/software/)
44
+
45
+If you are unable to run programs in this manner, you'll need to add the
46
+appropriate lines to your shell configuration. Run echo $SHELL in a terminal
47
+to determine which file you should edit.
48
+
49
+For tcsh, edit your ~/.cshrc file to contain:
50
+
51
+ if ( -e /programs/sbgrid.cshrc ) then
52
+ source /programs/sbgrid.cshrc
53
+ endif
54
+
55
+For bash,** **edit your ~/.bashrc file to contain:
56
+
57
+ if [ -f /programs/sbgrid.shrc ]; then
58
+ . /programs/sbgrid.shrc
59
+ fi
60
+
61
+You may also need to create a .bash_profile with the following contents:
62
+
63
+ if [ -f $HOME/.bashrc ]; then
64
+ . $HOME/.bashrc
65
+ fi
66
+
faq-using-your-crystal-harvard-edu-email-address.md
... ...
@@ -0,0 +1,35 @@
1
+### Using your @crystal.harvard.edu email address
2
+
3
+#### Using webmail
4
+
5
+There is an email associated with your CMCD network account at
6
+&lt;username&gt;@crystal.harvard.edu. You may access the webmail at:
7
+
8
+* <http://mail.crystal.harvard.edu>.
9
+
10
+You can set a vacation responder in the webmail client by clicking *Personal
11
+Settings* and then clicking the *Vacation* tab.
12
+
13
+Crystal email is currently hosted through gmail.
14
+
15
+Gmail cheat sheet:
16
+
17
+* <http://downloads.marcofolio.net/useful/cheat_sheets/gmail/gmail.cheat.sheet.pdf>
18
+
19
+#### Configuring a Mail Client for IMAP
20
+
21
+To configure your address in a client such as Apple's Mail Application or Thunderbird, use the following options:
22
+
23
+ * Incoming Mail Server:
24
+
25
+ * imap.gmail.com
26
+ * SSL enabled using port 993
27
+ * Outgoing Mail Server:
28
+
29
+ * smtp.gmail.com
30
+ * SSL enabled using port 465
31
+ * Username:
32
+ * yourusername@crystal.harvard.edu
33
+ * Password:
34
+ * Your Google Apps (crystal) password, this may be different from your CMCD account
35
+