.gitignore
... ...
@@ -0,0 +1,19 @@
1
+# ignore our secrets files!
2
+secrets.yml
3
+# ignore other types of secrets files:
4
+*.secrets
5
+# Eclipse/PyDev stuff...
6
+.project
7
+.pydevproject
8
+# Emacs backup files...
9
+*~
10
+.\#*
11
+\#*
12
+# Mac OS X stuff...
13
+.DS_Store
14
+._*
15
+# Vim swap files
16
+*.swp
17
+*.swo
18
+
19
+
Home.md
... ...
@@ -0,0 +1,78 @@
1
+## Welcome to the SBGrid Core Wiki
2
+
3
+This site provides information on the services provided by the SBGrid Core Group at Harvard Medical School. We provide Research Computing Systems Admin support to SBGrid Core Member Labs.
4
+
5
+If you are a part of a Member Lab please see the links on the sidebar on the right for information regarding the support, services, and systems we provide for your Lab.
6
+
7
+The Structural Biology Grid at Harvard Medical School (SBGrid) is a computing collaboration of more than 140 X-ray crystallography, NMR and electron microscopy laboratories. We're a support organization that helps more than 50 academic institutions and 3 pharmaceutical companies in 11 countries with their research computing needs. The SBGrid organization is led by Profess or Piotr Sliz and divided into two groups:
8
+
9
+## SBGrid Core (you are here)
10
+
11
+* Design of research computing infrastructure including workstation and server hardware purchase recommendations.
12
+* Configuration, maintenance and support of SBGrid Core member workstations and servers
13
+* Data and network security advice and audits
14
+
15
+## SBGrid Consortium
16
+
17
+* Specialized support of a large collection of structural biology software
18
+* Unified computing environment for all members
19
+* 1st tier support for software bugs and application recommendations
20
+
21
+See the [SBGrid Website](https://www.sbgrid.org)
22
+
23
+## Help
24
+* [Getting Help & Support](boston-cmcd-faqs-and-discussion/getting-help)
25
+
26
+## [Lab Support](boston-cmcd-labs-howtos/)
27
+
28
+* [Bradner Lab DFCI](boston-cmcd-labs-howtos/howto-bradner-lab-dfci)
29
+* [D'Souza Lab Harvard University](boston-cmcd-labs-howtos/howto-d-souza-lab-harvard-university)
30
+* Shared Resources for Labs at [Longwood Center labs DFCI](boston-cmcd-labs-howtos/howto-eck-lab-dfci) including:
31
+ * Dhe-Paganon Lab
32
+ * Eck Lab
33
+ * Fischer Lab
34
+ * Wang Lab
35
+
36
+* [Gaudet Lab Harvard University](boston-cmcd-labs-howtos/howto-gaudet-lab-harvard-university)
37
+* [Heldwein Lab Tufts Univertsity](howto-heldwein-lab-tufts)
38
+* [Kahne Lab Harvard University](boston-cmcd-labs-howtos/howto-kahne-lab-harvard-university)
39
+* [kirchhausen Lab, BCH](boston-cmcd-labs-howtos/howto-kirchhausen-lab-bch)
40
+* [Leschziner Lab Harvard University](boston-cmcd-labs-howtos/howto-leschziner-lab-harvard-university)
41
+* [Miller Lab MGH](boston-cmcd-labs-howtos/howto-miller-lab-mgh)
42
+* [Sliz Lab Harvard Medical School](boston-cmcd-labs-howtos/howto-sliz-lab)
43
+* [Springer Lab BCH](boston-cmcd-labs-howtos/howto-springer-lab-bch)
44
+* [Dhe-Paganon Lab](boston-cmcd-labs-howtos/howto-structural-biol-core-dhe-paganon-lab-dfci)
45
+* [Wei Lab Genzyme](boston-cmcd-labs-howtos/howto-wei-lab)
46
+* [Wucherpfennig Lab DFCI](boston-cmcd-labs-howtos/howto-wucherpfennig-lab-dfci)
47
+
48
+## [FAQ](boston-cmcd-faqs-and-discussion/)
49
+Frequently Answered Questions
50
+
51
+### Account Related
52
+* [Change Your Unix Password](boston-cmcd-faqs-and-discussion/changing-your-account-password)
53
+* [Backups Using Crashplan](boston-cmcd-faqs-and-discussion/crashplan-backups)
54
+* [SBGrid/CMCD VPN](boston-cmcd-faqs-and-discussion/connecting-to-cmcd-vpn)
55
+* [NE CAT Data Collection](boston-cmcd-faqs-and-discussion/data-collection-at-ne-cat)
56
+* [Requesting an Account](boston-cmcd-faqs-and-discussion/new-accounts)
57
+
58
+### Software & Linux/Mac/UNIX
59
+
60
+* [Access Remote Filesystems using SSHFS](boston-cmcd-faqs-and-discussion/sshfs)
61
+* [Firefox Problems on Network Account](boston-cmcd-faqs-and-discussion/troubleshooting-firefox-on-a-network-account)
62
+* [How to Forward Email](boston-cmcd-faqs-and-discussion/forwarding-mail-to-crystal)
63
+* [Linux Remote Access](boston-cmcd-faqs-and-discussion/remote-access-to-linux-computers)
64
+* [OS X (Apple): Find MAC Address](boston-cmcd-faqs-and-discussion/how-to-find-mac-address-on-os-x-gui)
65
+* [Running jobs after you logged off (using Screen)](boston-cmcd-faqs-and-discussion/running-remote-jobs-after-disconnecting)
66
+* [SSH Without a Password](boston-cmcd-faqs-and-discussion/setting-up-passwordless-ssh)
67
+* [SBGrid Software](boston-cmcd-faqs-and-discussion/using-sbgrid-programs)
68
+* [Using Crystal Email](boston-cmcd-faqs-and-discussion/using-your-crystal-harvard-edu-email-address* )
69
+* [Other Resources](boston-cmcd-faqs-and-discussion/other-resources)
70
+
71
+
72
+
73
+
74
+
75
+
76
+
77
+
78
+
_Sidebar.md
... ...
@@ -0,0 +1,15 @@
1
+![SBGrid](./images/sbgrid_small_logo.gif) **[Core Wiki](../Home)**
2
+
3
+##### Help
4
+* [How To Get Help & Support](boston-cmcd-faqs-and-discussion/getting-help)
5
+* [Lab Support](boston-cmcd-labs-howtos/Home)
6
+* [FAQ](boston-cmcd-faqs-and-discussion/Home)
7
+
8
+
9
+
10
+
11
+
12
+
13
+
14
+
15
+
boston-cmcd-faqs-and-discussion/Home.md
... ...
@@ -0,0 +1,23 @@
1
+
2
+# FAQ
3
+Frequently Answered Questions
4
+
5
+## Account Related
6
+* [Change Your Unix Password](changing-your-account-password)
7
+* [Backups Using Crashplan](crashplan-backups)
8
+* [SBGrid/CMCD VPN](connecting-to-cmcd-vpn)
9
+* [NE CAT Data Collection](data-collection-at-ne-cat)
10
+* [Requesting an Account](new-accounts)
11
+
12
+## Software & Linux/Mac/UNIX
13
+
14
+* [Access Remote Filesystems using SSHFS](sshfs)
15
+* [Firefox Problems on Network Account](troubleshooting-firefox-on-a-network-account)
16
+* [How to Forward Email](forwarding-mail-to-crystal)
17
+* [Linux Remote Access](remote-access-to-linux-computers)
18
+* [OS X (Apple): Find MAC Address](how-to-find-mac-address-on-os-x-gui)
19
+* [Running jobs after you logged off (using Screen)](running-remote-jobs-after-disconnecting)
20
+* [SSH Without a Password](setting-up-passwordless-ssh)
21
+* [SBGrid Software](using-sbgrid-programs)
22
+* [Using Crystal Email](using-your-crystal-harvard-edu-email-address* )
23
+* [Other Resources](other-resources)
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/getting-help.md
... ...
@@ -0,0 +1,25 @@
1
+# Getting Help
2
+
3
+Please email 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
+[help@sbgrid.org](mailto:help@sbgrid.org).
20
+
21
+For assistance with the structural biology software, please contact
22
+[bugs@sbgrid.org](mailto:bugs@sbgrid.org).
23
+
24
+It is important that you submit a help request for any SBGrid or IT related issue that you may be having, even if you have easy access to speak with SBGrid personnel.
25
+
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/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
+
boston-cmcd-faqs-and-discussion/using-your-crystal-harvard-edu-email-address.md
... ...
@@ -0,0 +1,36 @@
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
+<http://mail.crystal.harvard.edu> ](http://mail.crystal.harvard.edu) .
8
+
9
+
10
+
11
+You can set a vacation responder in the webmail client by clicking *Personal
12
+Settings* and then clicking the *Vacation* tab.
13
+
14
+
15
+
16
+Crystal email is currently hosted through gmail.
17
+
18
+Gmail cheat sheet: [
19
+<http://downloads.marcofolio.net/useful/cheat_sheets/gmail/gmail.cheat.sheet.pdf>
20
+](http://downloads.marcofolio.net/useful/cheat_sheets/gmail/gmail.cheat.sheet.pdf)
21
+
22
+
23
+
24
+## Configuring a Mail Client for IMAP
25
+
26
+To configure your address in a client such as Mail.app or Thunderbird, use the
27
+following options:
28
+
29
+ * Incoming Mail Server: imap.gmail.com, SSL enabled using port 993
30
+
31
+ * Outgoing Mail Server: smtp.gmail.com, SSL enabled using port 465
32
+
33
+ * Username: yourusername@crystal.harvard.edu
34
+
35
+ * Password: Your Google Apps (crystal) password, this may be different from your CMCD account
36
+
boston-cmcd-labs-howtos/Home.md
... ...
@@ -0,0 +1,24 @@
1
+
2
+# Lab Support
3
+
4
+Support Information for SBGrid Core Supported Labs:
5
+
6
+* [Bradner Lab DFCI](howto-bradner-lab-dfci)
7
+* [D'Souza Lab Harvard University](howto-d-souza-lab-harvard-university)
8
+* Shared Resources for Labs at [Longwood Center labs DFCI](howto-eck-lab-dfci) including:
9
+ * Dhe-Paganon Lab
10
+ * Eck Lab
11
+ * Fischer Lab
12
+ * Wang Lab
13
+
14
+* [Gaudet Lab Harvard University](./howto-gaudet-lab-harvard-university)
15
+* [Heldwein Lab Tufts Univertsity](./howto-heldwein-lab-tufts)
16
+* [Kahne Lab Harvard University](./howto-kahne-lab-harvard-university)
17
+* [kirchhausen Lab, BCH](./howto-kirchhausen-lab-bch)
18
+* [Leschziner Lab Harvard University](./howto-leschziner-lab-harvard-university)
19
+* [Miller Lab MGH](./howto-miller-lab-mgh)
20
+* [Sliz Lab Harvard Medical School](./howto-sliz-lab)
21
+* [Springer Lab BCH](./howto-springer-lab-bch)
22
+* [Dhe-Paganon Lab](./howto-structural-biol-core-dhe-paganon-lab-dfci)
23
+* [Wei Lab Genzyme](./howto-wei-lab)
24
+* [Wucherpfennig Lab DFCI](./howto-wucherpfennig-lab-dfci)
... ...
\ No newline at end of file
boston-cmcd-labs-howtos/_Sidebar.md
... ...
@@ -0,0 +1,6 @@
1
+![SBGrid](../images/sbgrid_small_logo.gif) **[Core Wiki](../Home)**
2
+
3
+##### Help
4
+* [How To Get Help & Support](../boston-cmcd-faqs-and-discussion/getting-help)
5
+* [Lab Support](Home)
6
+* [FAQ](boston-cmcd-faqs-and-discussion/Home)
boston-cmcd-labs-howtos/howto-bradner-lab-dfci.md
... ...
@@ -0,0 +1,50 @@
1
+# HOWTO, Bradner Lab, DFCI
2
+
3
+#Site Overview:
4
+Members of the Bradner Lab at the Dana Farber Cancer Institute have access to
5
+a Linux workstation in the wet lab,  running a large collection of structural
6
+biology software. It shares authentication and data directories and can be
7
+only accessed locally from within the lab.
8
+
9
+Research Computing support is provided by SBGrid.  Pl ease contact SBGrid
10
+[here](https://sbgrid.org/help/?tab=contact-us) .
11
+
12
+## Workstations:
13
+
14
+Name|OS|Hardware Configuration|Location|Notes
15
+---|---|---|---|---
16
+jbl1|Sci Linux 5|Intel Core i7 at 3.20GHz. 4 cores. 6GB of RAM. Nvidia Quadro 600.| |Last checked: 11/17/2014
17
+
18
+##Data Backups:
19
+
20
+Backups on the linux workstations are performed on a regular basis by the
21
+research computing group at DFCI. If you have any questions about backups,
22
+need files restored, or have any general issue regarding backups, contact the
23
+Research Computing group via this web page: [Help Me - DFCI Reseach
24
+Computing](http://research4.dfci.harvard.edu/content/helpme) .
25
+
26
+## X-Ray Data Collection:
27
+
28
+Plum and Aqua are workstations designated for data collection, and are located
29
+in the X-Ray room. These machines have custom local software installs to
30
+interact with the Marresearch scanner.
31
+
32
+HKL2000 can be accessed and run on Plum, Aqua, and MJEL12.
33
+
34
+Please contact Mike Eck to obtain guest privileges.
35
+
36
+## Networking and General IT Support:
37
+
38
+To report problems regarding the network at DFCI, or general computing
39
+support, contact the Partners Healthcare Help desk at:
40
+[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only
41
+works from a Partners network connection)
42
+
43
+* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)
44
+* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)
45
+* [Other Resources](http://forums.sbgrid.org/topic/other-resources)
46
+
47
+
48
+
49
+
50
+
boston-cmcd-labs-howtos/howto-d-souza-lab-harvard-university.md
... ...
@@ -0,0 +1,52 @@
1
+# HOWTO, D'Souza Lab, Harvard University
2
+
3
+## Site Overview:
4
+Members of the D’Souza Lab at Harvard University have access to five Linux
5
+workstations running a large collection of structural biology software. These
6
+workstations share authentication and data directories.
7
+
8
+Research Computing support is provided by SBGrid. P lease contact SBGrid
9
+[here](https://sbgrid.org/help/?tab=contact-us) .
10
+
11
+##Workstations:
12
+
13
+
14
+| Name | Operating System | Hardware Configuration|Location|Notes|
15
+|---|---|---|---|---|
16
+|chef|Sci Linux, 6.4|Intel Core i7 CPU at 3.6GHz. 4 Cores. 16G of RAM.|NW 311|09/25/2014|
17
+|clyde|Sci Linux, 6.4|Intel Core i7 CPU at 3.20GHz. 6 Cores. 6G of RAM. Nvidia Quadro 4000|NW 311|09/25/2014|
18
+|jack|Sci Linux, 6.4|Intel Core i7 CPU at 3.6GH. 4 Cores. 16G of RAM. Nvidia GeForce 9600GT. |NW 311 |09/25/2014|
19
+|kenny|Sci Linux, 6.4|Intel Core i7 CPU at 3.20GHz. 6 Cores. 6G of RAM. Nvidia Quadro FX 380.| NW 311 |09/25/2014
20
+|rufus|Sci Linux, 6.4|Intel Core i7 CPU at 3.6GHz. 4 Cores. 16G of RAM.|NW 311|09/25/2014|HKL2000 licensed system.
21
+
22
+##Printers:
23
+
24
+| Name | Model | Location | Notes |
25
+|---|---|---|---|
26
+|carmen|HP LaserJet 4700|Computer Lab|color printer|
27
+|vger|Ricoh Aficio C410|Wet Lab|color printer
28
+
29
+## Data Replication:
30
+
31
+Data is replicated to a secondary server. Snapshots are taken every hour and
32
+kept for 24 hours. Additionally, 7 daily snapshots are kept, 8 weeks, and up
33
+to 12 months. If you need a file restored,  please contact SBGrid
34
+[here](https://sbgrid.org/help/?tab=contact-us) .
35
+
36
+## Remote access:
37
+
38
+SSH access is available through galactica.mcb.harvard.edu . Remote access is
39
+not enabled by default. If you need to access Galactica remotely,  please
40
+contact SBGrid  [here](https://sbgrid.org/help/?tab=contact-us) .
41
+
42
+##Networking and General IT Support:
43
+
44
+To report problems regarding the network at Harvard University, or general
45
+computing support, contact the Harvard University Help desk.
46
+
47
+* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)
48
+* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)
49
+* [Other Resources](http://forums.sbgrid.org/topic/other-resources)
50
+
51
+
52
+
boston-cmcd-labs-howtos/howto-eck-lab-dfci.md
... ...
@@ -0,0 +1,144 @@
1
+# HOWTO, Longwood Center labs, DFCI
2
+
3
+## Site Overview:
4
+
5
+###
6
+
7
+* Eck
8
+* Dhe-Paganon
9
+* Wang
10
+* Fischer
11
+
12
+
13
+Members of these labs at the Dana Farber Cancer Institute have access to
14
+several shared Linux and Mac computers running a large collection of
15
+structural biology software. The Linux computers share authentication and data
16
+directories and can be only accessed locally from within the lab.
17
+
18
+Linux computers are located in the graphics room (fish bowl) on the third
19
+floor and in cubicles on the fourth floor. The X-ray room has two workstations
20
+for data acquisition. Macs are located on lab member’s desks.
21
+
22
+All linux machines are configured for Stereo 3D output.
23
+
24
+Research Computing support is provided by SBGrid - contact them
25
+[here](https://sbgrid.org/help/?tab=contact-us) .
26
+
27
+
28
+## Shared Workstations: (see below)
29
+
30
+
31
+
32
+## Mac Workstations: (see below)
33
+
34
+
35
+
36
+## Home and Data Directories:
37
+
38
+### Linux systems:
39
+
40
+NFS mounted home directories: **/nfs/&lt;PI initials&gt;/&lt;username&gt;**
41
+
42
+NFS mounted synchrotron data:** /synchrotron**
43
+
44
+NFS read only mounted programs tree: **/programs**
45
+
46
+
47
+
48
+### On Mac systems:
49
+
50
+NFS read only mounted home directories: **/nfs/&lt;PI
51
+initials&gt;/&lt;username&gt;**
52
+
53
+NFS read only mounted synchrotron data: **/synchrotron**
54
+
55
+NFS read only mounted programs tree: **/programs**
56
+
57
+SMB read and write mounted home directory:
58
+
59
+To mount your home directory using Samba (SMB):
60
+
61
+\- In Finder, click **Go** then click **'Go to Server'**
62
+
63
+\- Type in server address: **smb://blacker.in.hwlab**
64
+
65
+\- Enter your SMB username and password. (contact SBGrid for SMB account
66
+issues)
67
+
68
+To change your SMB password, use this command on a **linux** system:
69
+
70
+ 1. smbpasswd -R blacker.in.hwlab -U &lt;username&gt;
71
+
72
+
73
+
74
+## Data Backups:
75
+
76
+Fileserver data is snapshotted and also replicated to another server at HMS/C
77
+building. Local iMac accounts are backed up using crashplan.
78
+
79
+## Printing:
80
+
81
+A Xerox Phaser 8860 is located in the third floor near the kitchen area.
82
+Another inkJet printer is located directly above on the fourth floor. If you
83
+are having issues with printing, please contact SBGrid
84
+[here](https://sbgrid.org/help/?tab=contact-us).
85
+
86
+## X-Ray Data Collection:
87
+
88
+Plum and Aqua are workstations designated for data collection, and are located
89
+in the X-Ray room on the third floor. These machines have custom local
90
+software installs to interact with the Marresearch scanner.
91
+
92
+HKL2000 can be accessed and run on Plum, Aqua, mjel14 and sdp2.
93
+
94
+Please contact Mike Eck to obtain guest privileges.
95
+
96
+## Remote Access:
97
+
98
+External SSH access is available at crystal.harvard.edu.
99
+
100
+**Forwarding your red email to Crystal:**
101
+
102
+* Please contact SBGrid help if you have questions about forwarding.
103
+
104
+## Networking and General IT Support:
105
+
106
+To report problems regarding the network at DFCI, or general computing
107
+support, contact the Partners Healthcare Help desk at:
108
+[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only
109
+works from a Partners network connection)
110
+
111
+* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)
112
+* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)
113
+* [Other Resources](http://forums.sbgrid.org/topic/other-resources)
114
+
115
+## Shared Linux Workstations:
116
+
117
+| Name | OS | Hardware Configuration|Location|Notes|
118
+|---|---|---|---|---|
119
+|aqua|Sci Linux 6|Intel Core 2 Duo at 3.33GHz. 2 cores. 1GB or RAM. Nvidia Quadro FX 3700.|X-Ray room(Longwood Center) |Last checked: 13/09/2015, HKL2000 licensed, Works with Marresearch scanner |
120
+|plum|Sci Linux 6 |AMD Athlon 64 Dual Core Processor 4800+. 2 cores. 1GB of RAM.|X-Ray room (Longwood Center)|Last checked: 03/09/2015, HKL2000 licensed, Works with Marresearch scanner |
121
+|mjel11|Sci Linux 6|Intel Core i7 at 3.20GHz. 4 cores. 6 GB of RAM. Nvidia Quadro FX 3800.| Wet lab|Last checked: 03/03/2015|
122
+|mjel12|Sci Linux 6|Intel Core i7 at 3.20GHz. 4 cores. 6 GB of RAM. Nvidia Quadro FX 3800.| Wet lab|Last checked: 03/03/2015, HKL2000 licensed|
123
+|mjel13|Sci Linux 6|Intel Core i7 at 3.20GHz. 4 cores. 6 GB of RAM.| Wet lab|Last checked: 03/03/2015|
124
+|mjel14|Sci Linux 6|Intel Core i7 at 3.20GHz. 4 cores. 32 GB of RAM. Nvidia Quadro 4000.| Graphics room ((Longwood Center)|Last checked: 03/09/2015 \
125
+|mjel15|Sci Linux 6|Intel Core i7 at 3.60GHz. 4 cores. 16 GB of RAM. Nvidia Quadro 4000.| Computer lab|Last checked: 03/04/2015 \
126
+|xrc1|Sci Linux 6|Intel Core Quad at 2.66GHz. 4 cores. 4GB of RAM. Nvidia Quadro FX 1400| Graphics room (Longwood Center)|Last checked: 03/02/2015 \
127
+
128
+## Mac Workstations:
129
+
130
+| Name | OS | Hardware Configuration|Account Backed up| Administrator |
131
+|---|---|---|---|---|
132
+|wood-imac|OSX 10.10.5|iMac10,1, Intel Core 2 Duo 3.06 GHz 2 Cores, Memory: 4 GB, NVIDIA GeForce 9400|Yes|David Wood |
133
+|mje-dwood-imac|OSX 10.5.8|iMac8,1, Intel Core 2 Duo 2.66 GHz 2 Cores, Memory: 2 GB, ATI Radeon HD 2600 Pro, |No|
134
+|jwh-macpro|OSX 10.8.5|MacPro3,1 Quad-Core Intel Xeon 8 Cores, Memory: 10 GB, NVIDIA Quadro FX 5600, |Yes|Jia-Huai |
135
+|yiquns-imac|OSX 10.8.5|iMac11,2, Intel Core i3 3.06 GHz 2 Cores Memory: 4 GB ATI Radeon HD 4670|Yes|SBGrid, (user: hjeon) |
136
+|randalls-imac (broken)|OSX 10.8.5|iMac10,1 Intel Core 2 Duo 3.06 GHz 2 Cores, Memory: 4 GB, NVIDIA GeForce 9400|Yes| Randall McNally |
137
+|mike_eck_macpro|OSX 10.9.4|MacPro3,1 Quad-Core Intel Xeon 8 Cores, Memory: 8GB, NVIDIA Quadro FX 5600|Yes|Mike Eck |
138
+|humayuns-imac|OSX 10.10.1|iMac14,2 Intel Core i5 4 Cores, Memory 16GB, NVIDIA GeForce GT 755M| Yes|Humayun Sharif |
139
+|asher-page-imac|OSX 10.8.5|iMac13,1 Intel Core i5 2.7 GHz 4 Cores, Memory: 8GB,NVIDIA GeForce GT 640M|Yes|Randall McNally |
140
+|li-imac|tbd|tbd|Yes|Qing Li |
141
+|dhcp-155-52-53-43|tbd|tbd| |common iMac (gel reader)|
142
+
143
+
144
+
boston-cmcd-labs-howtos/howto-gaudet-lab-harvard-university.md
... ...
@@ -0,0 +1,54 @@
1
+# HOWTO, Gaudet Lab, Harvard University
2
+
3
+## Site Overview:
4
+Members of the Gaudet Lab at Harvard University have access to two graphical
5
+workstations , Pioneer and Cobincho, and a regular workstation ‘Curry’, all
6
+running a large collection of structural biology software. The linux
7
+workstations share authentication and data directories. Pioneer contains a
8
+license for running HKL2000.
9
+
10
+Research Computing support is provided by SBGrid. P lease contact SBGrid
11
+[here](https://sbgrid.org/help/?tab=contact-us) .
12
+
13
+## Workstations:
14
+
15
+|Name|Operating System|Hardware Configuration|Location|Last Checked|Notes|
16
+|---|---|---|---|---|---
17
+|cobincho|CentOS 6.5, |Intel Core i7 CPU at 3.6GHz, 4 Cores. 32 GB of RAM. Nvidia Quadro 4000.|NW 305|10/24/2014
18
+| curry|CentOS 6.5|Intel Core i7 CPU at 2.8GHz, 4 Cores. 2GB of RAM. Nvidia Quadro FX 380. |NW 305|10/27/2014
19
+| pioneer|CentOS 6.4|Intel Core i7 CPU at 3.6GHz, 4 Cores. 32 GB of RAM. Nvidia Quadro 4000.|NW 305|10/24/2014|HKL2000 licensed system.
20
+
21
+## Printers:
22
+
23
+|Name|Model|Location|Notes|
24
+|---|---|---|--- |
25
+|carmen|HP LaserJet 4700|Computer Lab|color printer
26
+|vger|Ricoh Aficio C410|Wet Lab|color printer
27
+
28
+## Using SBGrid programs:
29
+
30
+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
31
+program in the collection by opening up a terminal shell, and typing the name
32
+of the program that you want to run.
33
+
34
+## Data Replication:
35
+
36
+Data is replicated to a secondary server. Snapshots are taken every hour and
37
+kept for 24 hours. Additionally, 7 daily snapshots are kept, 8 weeks, and up
38
+to 12 months. If you need a file restored,  please contact SBGrid
39
+[here](https://sbgrid.org/help/?tab=contact-us) .
40
+
41
+##Remote access:
42
+
43
+SSH access is available through galactica.mcb.harvard.edu . Remote access is
44
+not enabled by default. If you need to access Galactica remotely,  please
45
+contact SBGrid  [here](https://sbgrid.org/help/?tab=contact-us) .
46
+
47
+##Networking and General IT Support:
48
+
49
+To report problems regarding the network at Harvard University, or general
50
+computing support, contact the Harvard University Help desk.
51
+
52
+* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)
53
+* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)
54
+* [Other Resources](http://forums.sbgrid.org/topic/other-resources)
boston-cmcd-labs-howtos/howto-heldwein-lab-tufts.md
... ...
@@ -0,0 +1,45 @@
1
+# HOWTO, Heldwein Lab, Tufts
2
+
3
+## Site Overview:
4
+Members of the Heldwein lab at Tufts University have access to three Linux
5
+computers and a Mac workstation running a large collection of structural
6
+biology software. The Linux computers share authentication and data
7
+directories and can be only accessed locally from within the lab. Lab members
8
+also have access to an HP LaserJet printer. Research Computing support is
9
+provided by SBGrid.  Please contact SBGrid
10
+[here](https://sbgrid.org/help/?tab=contact-us) .
11
+
12
+## WOrkstations
13
+
14
+Name|OS|Hardware Configuration|Location|Notes
15
+---|---|---|---|---
16
+ruby|Sci Linux 6.5| Intel Core i7 at 3.20GHz. 6 cores. 16GB of RAM. Nvidia Quadro 400| |Last checked: 11/13/2014
17
+diamond|CentOS 5| Intel Quad CPU at 2.66GHz. 4 cores. 4GB of RAM. Nvidia GeForce 9600 GT.| |Last checked: 11/13/2014
18
+beryl|CentOS 5| Intel Quad CPU at 2.66GHz. 4 cores. 4GB of RAM. Nvidia GeForce 9600 GT.| |Last checked: 11/13/2014
19
+
20
+## Storage and Backup:
21
+
22
+Backup of /nfs/home, which is hosted via Tufts NAS, are performed by the IT
23
+group at Tufts University.
24
+
25
+## Using SBGrid programs:
26
+
27
+All applications are located in /programs directory and are configured to run
28
+without additional settings.
29
+
30
+Most of the software titles installed in the SBGrid Suite have several
31
+versions available. Typically, we try to provide at least three versions of
32
+each software package, although very old or very new applications may have
33
+fewer versions. To override the default version, follow these instructions.
34
+
35
+Please refer to this [page](http://forums.sbgrid.org/topic/using-sbgrid-
36
+programs) if you need information on how to run SBGrid programs remotely or
37
+locally on your machine.
38
+
39
+## General IT Support:
40
+
41
+Support for office computing is provided by Tufts IT.
42
+
43
+* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)
44
+* [Other Resources](http://forums.sbgrid.org/topic/other-resources)
45
+
boston-cmcd-labs-howtos/howto-kahne-lab-harvard-university.md
... ...
@@ -0,0 +1,35 @@
1
+# HOWTO, Kahne Lab, Harvard University
2
+
3
+# Site Overview:
4
+Members of the Kahne Lab at Harvard University have access to Linux and Mac
5
+workstations running a large collection of structural biology software.
6
+
7
+Research Computing support is provided by SBGrid. P lease contact SBGrid
8
+[here](https://sbgrid.org/help/?tab=contact-us) .
9
+
10
+## Workstations:
11
+
12
+Name|OS|Hardware Configuration|Location|Notes|
13
+---|---|---|---|---|
14
+blain|Sci Linux, 6.5|Intel Xeon CPU at 2.6GHz. 6 cores. 32 GB of RAM.Nvida GeForce GTX 760. || Last checked: 11/03/2014
15
+billy|OS X 10.6.8, |Quad-Core Intel Xeon at 2.8GHz. 4 cores. 3GB of RAM. ATI Radeon HD 5770. | |Last checked: 10/27/2014. HKL2000 licensed machine.
16
+dutch|Sci Linux 6.5|Intel Xeon CPU at 2.6GHz. 6 cores. 32 GB of RAM. Nvida GeForce GTX 760.| |Last checked: 10/27/2014
17
+mac|OS X 10.6.8|Quad-Core Intel Xeon at 2.8GHz. 4 cores. 3GB of RAM. ATI Radeon HD 5770.| |Last checked: 10/27/2014
18
+
19
+## Data Backups:
20
+
21
+TBD
22
+
23
+## Networking and General IT Support:
24
+
25
+To report problems regarding the network at Harvard University, or general
26
+computing support, contact the Harvard University Help desk.
27
+
28
+## Remote access:
29
+
30
+SSH access is available through 128.103.94.191. This accesses the primary
31
+Linux workstation.
32
+
33
+* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)
34
+* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)
35
+* [Other Resources](http://forums.sbgrid.org/topic/other-resources)
boston-cmcd-labs-howtos/howto-kirchhausen-lab-bch.md
... ...
@@ -0,0 +1,69 @@
1
+# HOWTO, Kirchhausen Lab, BCH
2
+
3
+## Site Overview:
4
+Members of the Kirchhausen Lab at the Children’s Hospital Boston have access
5
+to a large collection of structural biology software. Research Computing
6
+support is provided by SBGrid. Please contact them [here
7
+](https://sbgrid.org/help/?tab=contact-us) .
8
+
9
+# Data Backups:
10
+
11
+Full and incremental backups of SBGrid file servers are conducted. This
12
+includes your home and data directories. In general, backups are kept for
13
+three months, and then are stored on physical media for archival purposes. If
14
+you need a file restored,  please contact SBGrid  [here
15
+](https://sbgrid.org/help/?tab=contact-us) .
16
+
17
+## Networking and General IT Support:
18
+
19
+Contact Children’s help desk at (617) 919 4357 or at [
20
+](mailto:help.desk@childrens.harvard.edu) [
21
+](mailto:help.desk@childrens.harvard.edu)[help.desk@childrens.harvard.edu](mailto:help.desk@childrens.harvard.edu)
22
+.
23
+
24
+* [ Using SBGrid programs ](http://forums.sbgrid.org/topic/using-sbgrid-
25
+programs)
26
+*[ Getting help from SBGrid ](http://forums.sbgrid.org/topic/getting-help)
27
+*[ Other Resources ](http://forums.sbgrid.org/topic/other-resources)
28
+
29
+
30
+##Synchronizing working directories between tklab and orchestra**
31
+
32
+### Overview
33
+
34
+The [ data synchronization ](http://forums.sbgrid.org/topic/tklab-data-
35
+synchronization-to-orchestra) process is a one-way synchronization, and files
36
+and directories transfered are no longer writable. For processing, there is a
37
+two-way synchronization of the ` ~/sync ` directory between the ` tklab `
38
+server and ` orchestra ` . Since the ` ~/sync ` directories are in the user's
39
+home directories, users have full ability to create, delete, rename, etc
40
+anything within them without effecting the raw images stored in `
41
+/groups/kirchhausen/datasync ` .
42
+
43
+**Anything outside the ` ~/sync ` directory, including ` .cshrc ` , ` .ssh ` will not be copied to orchestra.**
44
+
45
+### Suggested Working Directory Structure
46
+
47
+Symlinks can be used to keep the processing directories linked to the raw data
48
+directories, without requiring write/delete permissions for data directories.
49
+For example, instead of nstead of creating ` /datasync/Dataset001/process1 ` ,
50
+create a ` ~/sync/Dataset001 ` directory. Within ` ~/sync/Dataset001 ` ,
51
+create a symlink pointing to the images ( ` cd ~/sync/Dataset001 ; ln -s
52
+/groups/kirchhausen/datasync/Dataset001 images ` ).
53
+
54
+### Step by Step
55
+
56
+Setup [ passwordless ssh logins ](http://forums.sbgrid.org/topic/setting-up-
57
+passwordless-ssh) between ` tklab ` and ` orchestra ` before using two-way
58
+sync.
59
+
60
+ 1. Process within the ` ~/sync ` directory, on ` orchestra ` or ` tklab ` .
61
+ 2. When done, or at a checkpoint, initiate synchronization from ` tklab ` : ` unison -auto ` (interactive) or ` unison -batch ` (non-interactive).
62
+
63
+### More details
64
+
65
+Nightly non-interactive synchronization runs will be run from cron.
66
+
67
+If you're curious about unison, more detail is available from the [ project
68
+website ](http://www.cis.upenn.edu/~bcpierce/unison/download.html) .
69
+
boston-cmcd-labs-howtos/howto-leschziner-lab-harvard-university.md
... ...
@@ -0,0 +1,65 @@
1
+# HOWTO, Leschziner Lab, Harvard University
2
+
3
+## Site Overview
4
+Members of the Leschziner Lab at Harvard University have access to 10 Linux
5
+and 2 Mac workstations running a large collection of structural biology
6
+software. The linux workstations share authentication and data directories and
7
+can be only accessed locally from within the computer room.
8
+
9
+Research Computing support is provided by SBGrid - contact them
10
+[here](https://sbgrid.org/help/?tab=contact-us)   .
11
+
12
+
13
+## Workstation** (see comment below)
14
+##Printers** (see comment below)
15
+
16
+
17
+
18
+## Data Replication
19
+
20
+Data is replicated to a secondary server. Snapshots are taken every hour and
21
+kept for 24 hours. Additionally, 7 daily snapshots are kept, 8 weeks, and up
22
+to 12 months. If you need a file restored,  please contact SBGrid
23
+[here](https://sbgrid.org/help/?tab=contact-us) .
24
+
25
+##Remote access:
26
+
27
+SSH access is available through galactica.mcb.harvard.edu . Remote access is
28
+not enabled by default. If you need to access Galactica remotely,  please
29
+contact SBGrid  [here](https://sbgrid.org/help/?tab=contact-us) .
30
+
31
+##Networking and General IT Support:
32
+
33
+To report problems regarding the network at Harvard University, or general
34
+computing support, contact the Harvard University Help desk.
35
+
36
+
37
+* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)
38
+* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)
39
+*[Other Resources](http://forums.sbgrid.org/topic/other-resources)
40
+
41
+
42
+## Workstations:
43
+
44
+Name|Operating System|Hardware Configuration|Location|Notes
45
+---|---|---|---|---
46
+aida|Sci Linux, 6.5|Intel Core i7 CPU at 3.07GHz, 4 cores. 12GB of RAM. Nvidia Quadro 4000.|NW 305|Last checked 10/20/2014
47
+dutchman|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.66GHz, 4 cores. 1GB of RAM. Nvidia Quadro FX 1700.|NW311|Last checked 10/20/2014
48
+fidelio|OSX, 10.6.4|Quad-Core Intel Xeon at 3GHz, 8 cores. 4GB of RAM. Nvidia GeForce 7300 GT.|NW305|Last checked 10/20/2014
49
+figaro|OSX, 10.7.5|Quad-Core Intel Xeon at 3GHz, 8 cores. 4GB of RAM. Nvidia GeForce 7300 GT.|NW 305|Last checked 10/20/2014
50
+giovanni|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.4GHz,4 cores. 1GB of RAM. Nvidia NVS 290.|NW 305|Last checked 10/20/2014
51
+isolde|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.4GHz, 4 cores. 8GB of RAM.Nvidia NVS 290.|NW305|Last checked 10/20/2014
52
+leginon|tbd|tbd|tbd|
53
+leonora|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.4GHz, 4 cores. 8GB of RAM. Nvidia NVS 290.|NW 305|Last checked 10/20/2014
54
+otello|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.66GHz,4 cores. 1GB of RAM. Nvidia Quadro FX 1700.|NW 305|Last checked 10/20/2014
55
+tristan|Sci Linux, 6.5|Intel Core 2 Quad CPU at 2.4GHz,4 cores. 1GB of RAM. Nvidia NVS 290.|NW 305|Last checked 10/20/2014
56
+lothario|Sci Linux, 6.5|Intel Xeon CPU at 2.10GHz.6 cores. 32GB of RAM. 2 x Nvidia Quadro 600.|NW 305|Last checked 10/20/2014
57
+mignon|Sci Linux, 6.5|Intel Xeon CPU at 2.10GHz. 6 cores. 32G of RAM. 2 x Nvidia Quadro 600.|NW 305|Last checked 10/20/2014
58
+
59
+## Printers:
60
+
61
+Name|Model|Location|Notes
62
+---|---|---|---
63
+carmen|HP LaserJet 4700|Computer Lab|color printer
64
+vger|Ricoh Aficio C410|Wet Lab|color printer
65
+
boston-cmcd-labs-howtos/howto-miller-lab-mgh.md
... ...
@@ -0,0 +1,22 @@
1
+# HOWTO, Miller Lab, MGH
2
+
3
+## Site Overview:
4
+Members of the Miller Lab at MGH have remote access to the SBGrid software
5
+tree and can run jobs on Zorin.
6
+
7
+Research Computing support is provided by SBGrid. Pl ease contact SBGrid
8
+[here](https://sbgrid.org/help/?tab=contact-us) .
9
+
10
+## Networking and General IT Support:
11
+
12
+To report problems regarding the network at MGH, or general computing support, contact the Partners Healthcare Help desk at:
13
+[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only
14
+works from a Partners network connection)
15
+
16
+
17
+* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)
18
+* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)
19
+* [Other Resources](http://forums.sbgrid.org/topic/other-resources)
20
+
21
+
22
+
boston-cmcd-labs-howtos/howto-sliz-lab.md
... ...
@@ -0,0 +1,94 @@
1
+# HOWTO, Sliz Lab
2
+
3
+
4
+## Computing Accounts:
5
+
6
+Members of Sliz lab will generally have six computing accounts:
7
+
8
+ * an HKL account for email, calendar and shared documents
9
+ * a local (administrator) account for Mac OS X workstations
10
+ * a CMCD account for login to the Linux workstation, to crystal.harvard.edu and to other Linux workstations at HMS.
11
+ * an HMS account for login to eCommons and to HMS email system.
12
+ * SBGrid account (optional) for software update.
13
+ * DropBox account - this is a business account with unlimited backups and unlimited storage space.
14
+
15
+##Network:
16
+All computers in the lab should be connected to the SBGrid network.
17
+For connecting a personal computer, you will need to email the [MAC
18
+address](http://forums.sbgrid.org/topic/how-to-find-mac-address-on-os-x-gui)
19
+of the ethernet card or adaptor to [help@sbgrid.org](mailto:help@sbgrid.org)
20
+. In order to access SBGrid wi-fi network you will need to email your MAC
21
+address to [help@sbgrid.org](mailto:help@sbgrid.org) and request activation
22
+on the SBGrid wifi network; to connect, authenticate with your CMCD username
23
+and password.
24
+
25
+
26
+
27
+##Printing:
28
+We have two printers in the lab, which are both available from the
29
+SBGrid network. ps-laserjet3000dn is located in the wet lab area, ps-
30
+brother2270 is located in the SBGrid computing room. Printing will not work if
31
+your computer is connected to the HMS Wifi access point (HMS Private or
32
+Public).
33
+
34
+
35
+
36
+##Personal Desktop Computers:
37
+Personal (OS X / Windows?) systems (sch-jlchoi-
38
+imac, ps-wang-macmini, ps-sophia-imac, sb-liz-imac, ps-nozhat-macmini) are
39
+administered by the primary user, with support from SBGrid and HMS/BCMP IT.
40
+
41
+ * SBGrid software will be installed in /programs.
42
+
43
+ * All research data should be backed-up . This is an NIH and HMS regulation.
44
+
45
+ * Visiting Students should use HMS [CrashPlan](http://it.hms.harvard.edu/pg.asp?pn=cpp_backup) for backing up their work directories. (use registration code JJRR-RHW7-UHJW-H7JM).
46
+
47
+ * Postdocs and Graduate Students should always work from a DropBox folder.
48
+
49
+##Software:
50
+
51
+ * personal computers and laptops running OS X can have [SBGrid software installed](http://forums.sbgrid.org/topic/updating-sbgrid-software-on-your-mac-from-sbgrid-central-server)
52
+ * [HMS licensed software](https://rc.hms.harvard.edu/#downloads) (such as ChemOffice or MATLAB)
53
+ * MS office is available on request from [](mailto:bcmpit@hms.harvard.edu)[bcmpit@hms.harvard.edu](mailto:bcmpit@hms.harvard.edu)
54
+ * Geneious: Geneious is preinstalled with SBGrid software collection and Sliz lab has access to a shared database. Please email Piotr for the database login credentials.
55
+ * Please use ReadCube for managing your references and we will purchase a Pro version for your use (Pro supports syncing files between multiple computers).
56
+
57
+#Linux Workstations
58
+Two linux workstations ([schl12][1] and psl2) are fully
59
+administered by SBGrid. ps2 (in the 3rd bay) can dual-boot to Windows 7. To
60
+login to linux systems, use your CMCD credentials. To login to the windows
61
+partition, use the credentials posted over the machine.
62
+
63
+[1]:for consistency, schl12 will be renamed to psl1
64
+
65
+## Instrumentation Computers:
66
+Computers running our FPLCs (PS-FPLC1, PS-FPLC2, PS-FPLC3) are managed by HMS IT and backups are done on a daily basis using CrashPlan. They can print to the laboratory printer.
67
+
68
+Sliz lab also has access to crystallization-room computers (Gryphon
69
+controller, unknown system) Those computers are also managed by HMS IT and
70
+backed-up using CrashPlan.
71
+
72
+
73
+## Support:
74
+
75
+There are several options for support:
76
+
77
+ 1. Please review SBGrid and CMCD support forums on the SBGrid website: forums.sbgrid.org
78
+ 2. For assistance with Linux workstations and SBGrid network please contact SBGrid ( [help@sbgrid.org](mailto:help@sbgrid.org) ). In most cases Pete Meyer or Justin O’Connor will respond to your request.
79
+ 3. For assistance with printing and your personal desktop please contact HMS IT at [bcmpit@hms.harvard.edu](mailto:bcmpit@hms.harvard.edu) . In most cases Peter Cobb will respond to your requests.
80
+ 4. For assistance with the structural biology software please contact [bugs@sbgrid.org](mailto:bugs@sbgrid.org) (Rob and Jason).
81
+
82
+
83
+## Other Resources:
84
+
85
+ * SBGrid.org website
86
+
87
+ * rc.hms.harvard.edu - Harvard Medical School Research Computing Support
88
+
89
+## Communication:
90
+
91
+ * All members of Sliz lab are signed up for the Sliz lab mailing lists and the BCMP mailing lists.
92
+ * You will also receive a copy of SBGrid monthly newsletter.
93
+ * e-mail: Goup members should use hkl.hms.harvard.edu account as the institutional/work email account. You should forward other accounts (e.g. hms.harvard.edu) to HKL.
94
+
boston-cmcd-labs-howtos/howto-springer-lab-bch.md
... ...
@@ -0,0 +1,59 @@
1
+# HOWTO, Springer/Wu/Hur Lab, BCH
2
+
3
+## Site Overview:
4
+Members of the Springer, Wu and Hur Labs at the Children’s Hospital Boston
5
+have access to six Linux workstations; all running SBGrid Software Collection
6
+(see below). The Linux computers share authentication and data directories and
7
+can be accessed remotely by SSH (see
8
+[instructions](http://forums.sbgrid.org/topic/remote-access-to-linux-
9
+computers)).
10
+
11
+Research Computing support is provided by SBGrid - contact them
12
+[here](https://sbgrid.org/help/?tab=contact-us) .
13
+
14
+## Shared Workstations:
15
+
16
+Name|OS|Hardware Configuration|Location|Notes
17
+---|---|---|---|---
18
+tsl1|Sci Linux 6.5|Intel Core i7 at 3.20GHz. 6 cores. 32GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Springer
19
+tsl2|Sci Linux 6.6|Intel Core i7 at 3.20GHz. 6 cores. 32GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Springer
20
+tsl3|Sci Linux 6.6|Intel Core i7 at 3.20GHz. 6 cores. 32GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Springer
21
+tsl4|Sci Linux 6.4|Intel Core i7 at 3.20GHz. 6 cores. 32GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Springer
22
+sun|Sci Linux 6.4|Intel Core Duo CPU at 3.33GHz. 2 cores. 8GB of RAM. Nvidia Quadro FX 3700| CLS 03098|Last checked: 11/19/2014, Owned by Wu
23
+moon|Sci Linux 6.4|Intel Core Duo CPU at 3.33GHz. 2 cores. 8GB of RAM. Nvidia Quadro 4000.| CLS 03098|Last checked: 11/19/2014, Owned by Wu
24
+
25
+## Data Backups:
26
+
27
+Full and incremental backups of SBGrid file servers are conducted. This
28
+includes your home and data directories. In general, backups are kept for
29
+three months, and then are stored on physical media for archival purposes. If
30
+you need a file restored, please contact SBGrid
31
+[here](https://sbgrid.org/help/?tab=contact-us).
32
+
33
+#Printing:
34
+
35
+A Xerox Phaser 6700DN is located in the hallway outside CLS 03098. If you are
36
+having issues with printing,  please contact SBGrid
37
+[here](https://sbgrid.org/help/?tab=contact-us) .
38
+
39
+#Remote access:
40
+
41
+Please follow [this link](http://forums.sbgrid.org/topic/remote-access-to-
42
+linux-computers) for details on how to remotely connect to the workstations.
43
+
44
+##Networking and General IT Support:
45
+
46
+Contact Children’s help desk at (617) 919 4357 or at
47
+[](mailto:help.desk@childrens.harvard.edu)[help.desk@childrens.harvard.edu](mailto:help.desk@childrens.harvard.edu)
48
+.
49
+
50
+* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)
51
+* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)
52
+* [Other Resources](http://forums.sbgrid.org/topic/other-resources)
53
+
54
+
55
+
56
+
57
+
58
+
59
+
boston-cmcd-labs-howtos/howto-structural-biol-core-dhe-paganon-lab-dfci.md
... ...
@@ -0,0 +1,68 @@
1
+# HOWTO, Dhe-Paganon Lab, DFCI
2
+
3
+## Site Overview:
4
+
5
+Members of the Dhe-Paganon Lab at the Dana Farber Cancer Institute have access
6
+to a Linux workstation running a large collection of structural biology
7
+software. It shares authentication and data directories.
8
+
9
+Lab members can use SBGrid machines in the Eck lab as well.
10
+
11
+The lab is located at the Longwood Center building.
12
+
13
+Research Computing support is provided by SBGrid.  Pl ease contact SBGrid
14
+[here](https://sbgrid.org/help/?tab=contact-us).
15
+
16
+
17
+## Workstations:
18
+
19
+Name|OS|Hardware Configuration|Location|Notes
20
+---|---|---|---|---
21
+sdp1|Sci Linux 6.5|Intel Core i7 at 3.70GHz. 4 cores. 16 GB or RAM. Nvidia Quadro K4000. | Graphics room (Longwood Center)|Last checked: 03/01/2015
22
+
23
+## Data Backups:
24
+
25
+Backups on the linux workstations are performed on a regular basis by the
26
+research computing group at DFCI. If you have any questions about backups,
27
+need files restored, or have any general issue regarding backups, contact the
28
+Research Computing group via this web page: [Help Me - DFCI Reseach
29
+Computing](http://research4.dfci.harvard.edu/content/helpme) .
30
+
31
+Backups on Macs are managed by SBGrid.  Pl ease contact SBGrid
32
+[here](https://sbgrid.org/help/?tab=contact-us) for more information.
33
+Instructions on how to setup your Mac computer can be found
34
+[here](http://here) .
35
+
36
+##Printing:
37
+
38
+A Xerox Phaser 8860 is available for printing near the admin office. If you
39
+need your workstation configured for printing,  Please contact SBGrid
40
+[here](https://sbgrid.org/help/?tab=contact-us) .
41
+
42
+## X-Ray Data Collection:
43
+
44
+Plum and Aqua are workstations designated for data collection, and are located
45
+in the X-Ray room. These machines have custom local software installs to
46
+interact with the Marresearch scanner.
47
+
48
+HKL2000 can be accessed and run on Plum and Aqua, and mjel12.
49
+
50
+Please contact Mike Eck to obtain guest privileges.
51
+
52
+## Remote Access:
53
+
54
+External SSH access is available at red.dfci.harvard.edu.
55
+
56
+## Networking and General IT Support:
57
+
58
+To report problems regarding the network at DFCI, or general computing
59
+support, contact the Partners Healthcare Help desk at:
60
+[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only
61
+works from a Partners network connection)
62
+
63
+* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)
64
+* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)
65
+* [Other Resources](http://forums.sbgrid.org/topic/other-resources)
66
+
67
+
68
+
boston-cmcd-labs-howtos/howto-wei-lab.md
... ...
@@ -0,0 +1,46 @@
1
+# HOWTO, Wei Lab, Genzyme Corp
2
+
3
+## Site Overview:
4
+
5
+Members of the Wei lab at Genzyme Corporation have access to two Linux
6
+computers running a large collection of structural biology software. Both
7
+computers share authentication and data directories and can be only accessed
8
+locally from within the lab. Research Computing support is provided by
9
+[SBGrid](https://sbgrid.org/) .  Please contact SBGrid
10
+[here](https://sbgrid.org/help/?tab=contact-us) .
11
+
12
+## Backups
13
+
14
+Data backup is performed by the Genzyme IT department.
15
+
16
+## Workstations:
17
+Name|OS|Hardware Configuration|Location|Notes
18
+---|---|---|---|---
19
+montana|CentOS 6.6| | Wei's office |Last checked: 03/02/2015
20
+colorado|Sci Linux 6.6| | Yanfeng's office|Last checked: 03/02/2015
21
+gpenguin|Sci Linux 6.6| | Dana's desk|Last checked: 03/02/2015
22
+
23
+##User Accounts:
24
+To create or delete your account, please refer to this
25
+[page](http://forums.sbgrid.org/topic/new-accounts) . To change your password
26
+please use the yppasswd command on one of the workstations.
27
+
28
+##Using SBGrid programs:
29
+
30
+All applications are located in /programs directory and are configured to run
31
+without additional settings.
32
+
33
+Most of the software titles installed in the SBGrid Suite have several
34
+versions available. Typically, we try to provide at least three versions of
35
+each software package, although very old or very new applications may have
36
+fewer versions. To override the default version, follow these instructions.
37
+
38
+Please refer to this [page](http://forums.sbgrid.org/topic/using-sbgrid-
39
+programs) if you need additional information on how to run SBGrid programs
40
+locally or remotely on your machine.
41
+
42
+* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)
43
+* [Other Resources](http://forums.sbgrid.org/topic/other-resources)
44
+
45
+
46
+
boston-cmcd-labs-howtos/howto-wucherpfennig-lab-dfci.md
... ...
@@ -0,0 +1,63 @@
1
+# HOWTO, Wucherpfennig Lab, DFCI
2
+## Site Overview:
3
+Members of the Wucherpfennig Lab at the Dana Farber Cancer Institute have
4
+access to a Linux workstation in the wet lab,  running a large collection of
5
+structural biology software. It shares authentication and data directories and
6
+can be only accessed locally from within the lab.
7
+
8
+Research Computing support is provided by SBGrid.  Please contact SBGrid
9
+[here](https://sbgrid.org/help/?tab=contact-us) .
10
+
11
+## Using SBGrid programs:
12
+
13
+All applications are located in /programs directory and are configured to run
14
+without additional settings. In most cases, you will easily be able to run any
15
+program in the collection by opening up a terminal shell, and typing the name
16
+of the program that you want to run. Linux applications are installed in the
17
+/programs/i386-linux subdirectory.
18
+
19
+Most of the software titles installed in the SBGrid Suite have several
20
+versions available. Typically, we try to provide at least three versions of
21
+each software package, although very old or very new applications may have
22
+fewer versions. To override the default version, follow [these
23
+instructions](http://forums.sbgrid.org/topic/overriding-software-versions) .
24
+
25
+Please refer to this [page](http://forums.sbgrid.org/topic/using-sbgrid-
26
+programs) if you need information on how to run SBGrid programs remotely or
27
+locally on your machine.
28
+
29
+## Data Backups:
30
+
31
+Backups on the linux workstations are performed on a regular basis by the
32
+research computing group at DFCI. If you have any questions about backups,
33
+need files restored, or have any general issue regarding backups, contact the
34
+Research Computing group via this web page: [Help Me - DFCI Reseach
35
+Computing](http://research4.dfci.harvard.edu/content/helpme) .
36
+
37
+## X-Ray Data Collection:
38
+
39
+Plum and Aqua are workstations designated for data collection, and are located
40
+in the X-Ray room. These machines have custom local software installs to
41
+interact with the Marresearch scanner.
42
+
43
+HKL2000 can be accessed and run on Plum, Aqua and mjel12.
44
+
45
+Please contact Mike Eck to obtain guest privileges.
46
+
47
+
48
+
49
+## Networking and General IT Support:
50
+
51
+To report problems regarding the network at DFCI, or general computing
52
+support, contact the Partners Healthcare Help desk at:
53
+[helpdesk.partners.org](http://helpdesk.partners.org) (Note: this link only
54
+works from a Partners network connection)
55
+
56
+* [Using SBGrid programs](http://forums.sbgrid.org/topic/using-sbgrid-programs)
57
+* [Getting help from SBGrid](http://forums.sbgrid.org/topic/getting-help)
58
+* [Other Resources](http://forums.sbgrid.org/topic/other-resources)
59
+
60
+
61
+
62
+
63
+
consortium-wiki/3d-on-linux.md
... ...
@@ -0,0 +1,128 @@
1
+# 3D on Linux
2
+
3
+## Stereo (3D) for Structural Biology Workstations
4
+
5
+_Last update: October 11, 2013_
6
+
7
+Stereo technology has fully transitioned from using CRT monitors with emitters
8
+and shutter glasses to LCDs with either shutter glasses or passive image
9
+polarization. Whereas CRT stereo technology sprouted from the demands in
10
+engineering and research, LCD stereo is being targeted largely towards the
11
+gaming community. This, combined with the fact that LCD support is relatively
12
+new to the consumer market, means we can't be certain to what extent the
13
+stereo LCD technology will develop for Linux research workstation purposes.
14
+Regardless, we'll continue to test the latest options available and advise
15
+structural biologists that recognize a benefit in stereo 3D imaging.
16
+
17
+### What are our LCD Stereo Options?
18
+
19
+There are two recommended stereo LCD configurations. The technology you choose
20
+is largely dependent on your budget, workstation type (Mac/Linux) and desired
21
+application support.
22
+
23
+
24
+
25
+## Active LCD Stereo
26
+
27
+Active stereo is provided through LCDs that offer a high refresh rate (120Hz).
28
+This allows LCDs to provide a similar stereo experience as the old CRTs. And
29
+like the CRT stereo solution, it requires the purchase of an NVIDIA quadro
30
+card and an emitter/glasses (the NVIDIA 3D Vision kit). This solution is
31
+Linux-only.
32
+
33
+Nvidia maintains a list of monitors compatible with their 3D Vision
34
+technology. [Click here to access their list](http://www.nvidia.com/object/3d-
35
+vision-displays.html "http://www.nvidia.com/object/3d-vision-displays.html" ).
36
+
37
+
38
+### Notes on select 120Hz monitors:
39
+
40
+ * The [Asus VG278H](http://www.asus.com/Display/LCD_Monitors/VG278H/ "http://www.asus.com/Display/LCD_Monitors/VG278H/" ) and VG236H have been working great for us and are our current recommended monitors.
41
+
42
+
43
+
44
+### Required graphics cards:
45
+
46
+ * [NVidia Quadro FX 3700 or higher graphics card](http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html "http://www.nvidia.com/object/quadro_pro_graphics_boards_linux.html" ). Linux support requires the card to have a 3-pin DIN output. According to the NVIDIA driver documentation, you can**not** use USB emitters without the 3-pin cable for Linux stereo. The latest NVIDIA drivers are required for the best Linux support. Newest drivers support dual monitors, where one is in 3D and one in 2D.
47
+
48
+
49
+
50
+### Required emitter/glasses:
51
+
52
+ * [NVIDIA 3D Vision Kit](http://www.nvidia.com/object/product_GeForce_3D_VisionKit_us.html "http://www.nvidia.com/object/product_GeForce_3D_VisionKit_us.html" )
53
+
54
+
55
+
56
+## Passive LCD Stereo
57
+
58
+Passive LCD monitors superimposes two images onto the same screen through
59
+different polarizing filters. As each filter passes only that light which is
60
+similarly polarized and blocks the light polarized in the opposite direction,
61
+each eye sees a different image. Despite its overall lower cost, passive
62
+stereo is qualitatively lower quality than the NVIDIA solution and in stereo
63
+mode, you have half the monitor's vertical resolution available to you due to
64
+the underlying polarization technology. Because it doesn't require specific
65
+graphics cards / drivers, this solution is the only viable stereo for Mac
66
+users.
67
+
68
+We don't have much recent experience with passive monitors as most of our
69
+stereo users on using Linux workstations.
70
+
71
+### Available Passive LCD Monitors:
72
+
73
+ * LG DM2352D-PZ
74
+ * ASUSVG27AH
75
+
76
+### Previous Passive LCD Monitor Recommendation:
77
+
78
+ * [Zalman ZM-M240W](http://www.zalman.com/eng/product/Product_Read.php?Idx=391) \- The Zalman requires software to be explicitly configured to support the monitor. PyMOL and a few other applications do have support (email us for the latest list of SBGrid software with support).
79
+
80
+### Required graphics card:
81
+
82
+ * No special graphics card is required, so you can use this monitor with Macs as well as Linux workstations.
83
+
84
+### Required emitter/glasses:
85
+
86
+ * No emitter is required for passive LCD stereo. Polarized glasses are included with the monitor.
87
+
88
+## Can We Stick With CRT?
89
+
90
+The problem with CRTs is that they are only available as used/remanufactured
91
+from 3rd party vendors and the Quadro cards required to drive them are
92
+becoming increasingly expensive. That said, if you have a CRT monitor (or can
93
+find one) that's capable of sufficient refresh rates and a Quadro NVIDIA card
94
+with a 3-pin stereo DIN, you can continue to use them for your stereo needs.
95
+
96
+### What you need for CRT stereo:
97
+
98
+ 1. NVidia Quadro FX 3700 graphics card or one of the cards in their “Ultra-High-End” product line. Or, if you search for older models, any Quadro FX with the 3-pin Mini DIN stereo output.
99
+ 2. CRT display capable of at least 100Hz refresh rate @ 1280×1024+. These are becoming very hard to find. The latest model we saw produced with these specs was the ViewSonic G225fB, but it is no longer available. Try searching eBay for ”[SGI 061-0061-001](http://shop.ebay.com/?_nkw=sgi+061-0061-001)”. Visit <http://pymol.sourceforge.net/stereo3d.html> for some more recommendations. Note that at this point, if a CRT has problems or fails, it may be very difficult to replace or repair.
100
+ 3. CRT Stereo emitter and glasses ([http://www.reald.com](http://www.reald.com/ "http://www.reald.com" ): E2 emitter and CrystalEyes 3 glasses)
101
+
102
+
103
+
104
+## Software configuration required
105
+
106
+ 1. Install the latest [NVidia "Linux AMD64"](http://www.nvidia.com/object/unix.html "http://www.nvidia.com/object/unix.html" ) binary drivers
107
+ 2. **For CRT stereo displays only:**
108
+ * Edit the “Screen” section of /etc/X11/xorg.conf to include:
109
+
110
+ Option "Stereo" "3" Option "AllowDFPStereo" "1" Option "UBB" "1"
111
+
112
+ 3. **For LCD stereo displays only:**
113
+ * Edit the “Screen” section of /etc/X11/xorg.conf to include:
114
+
115
+ Option "Stereo" "10" Option "AllowDFPStereo" "1" Option "UBB" "1"
116
+
117
+ 4. Add the following to the end of your xorg.conf:
118
+
119
+ Section "Extensions" Option "Composite" "Disable" EndSection
120
+
121
+
122
+
123
+## For more information
124
+
125
+ * <http://pymolwiki.org/index.php/Stereo_3D_Display_Options>
126
+ * <http://en.wikipedia.org/wiki/LCD_shutter_glasses>
127
+ * <http://en.wikipedia.org/wiki/Polarized_3D_glasses>
128
+
consortium-wiki/data-processing-after-ws-mr.md
... ...
@@ -0,0 +1,71 @@
1
+# Data Processing after WS-MR
2
+
3
+## 1 Verify Results for Search Models
4
+
5
+The first follow-up step for a search model resulting from WSMR is to repeat
6
+MR locally.
7
+
8
+To download one of the search models; first click the "Load Top
9
+100 Hits" button, click one of the yellow circles in the resulting plot, and
10
+then use the download link for the model.
11
+
12
+* * *
13
+![](../images/data-processing-after-ws-mr-1.jpg)
14
+* * *
15
+![](../images/data-processing-after-ws-mr-2.png)
16
+* * *
17
+
18
+A typical input deck (`MR01.in` for this example) for `phaser` would look
19
+something like this (with the paths to your input `MTZ` and `PDB` files
20
+adjusted appropriately):
21
+
22
+
23
+
24
+ ROOT MR01
25
+ MODE MR_AUTO
26
+ HKLIn reflections.mtz
27
+ LABIn F=FP SIGF=SIGFP
28
+ ENSEmble SearchModel PDB model.pdb IDENtity 0.3
29
+ COMPosition PERCENTAGE 0.50
30
+ RESOlution HIGH 3.1
31
+ SEARch ENSEmble SearchModel NUM 1
32
+ SGALternative SELECT ALL
33
+
34
+This can be run with versions of `phaser` distributed with `CCP4` or `PHENIX`
35
+(with `phaser < MR01.in > MR01.out` or `phenix.phaser < MR01.in > MR01.out`
36
+respectively). The statistics (LLG and Z-scores) from local runs may differ
37
+due to differences in `phaser` versions.
38
+
39
+The `SGALternative` card is only necessary if you're checking alternative
40
+space-groups.
41
+
42
+## 2 Expand Search
43
+
44
+WSMR searches for a single copy of the search model - however there may be
45
+multiple copies of the model in the ASU. If so, the next step is the increase
46
+the `NUM` value for the `SEARch` card. When in doubt, it's better to set this
47
+too hight rather than too low - `phaser` will stop when unable to locate
48
+additional copies.
49
+
50
+## 3 Autobuild
51
+
52
+Once MR has been exhausted (no more copies of the search model can be placed),
53
+one possible next step is to use an autobuilder for an initial attempt to
54
+correct the sequence of the model.
55
+
56
+Using the `PHENIX` autobuilder:
57
+
58
+`phenix.autobuild reflections.mtz MR_Results.pdb project.fasta nproc=4 >
59
+AutoBuild01.out`
60
+
61
+The input model (`MR_Results.pdb`) for the autobuilder is the final result
62
+modeles from the initial or expanded MR search.
63
+
64
+The input `MTZ` file should be the original amplitudes (or intensities) used
65
+for searching, _not_ the results from `phaser`. If phaser was run with the
66
+`SGALternative` card, make sure the spacegroup of this `MTZ` matches that of
67
+the search solutions.
68
+
69
+The `nproc=4` option should only be used if there are four (or more) available
70
+cores - when using the `rebuild_in_place` option, `phenix.autobuild` can't
71
+take advantage of more than 4 processors.
consortium-wiki/global-overrides-for-sbgrid-sites.md
... ...
@@ -0,0 +1,51 @@
1
+# Global Overrides for SBGrid sites
2
+
3
+## Administrator Software Blacklist
4
+
5
+Site administrators can prevent the shell initialization files from
6
+configuring software on a host by creating an empty file at
7
+**/programs/local/conf/disabled-hosts/&lt;hostname&gt;**, where
8
+**&lt;hostname&gt;** is the output of the _hostname -s_ command. This is
9
+useful for encouraging users not to run jobs on bastion hosts, file servers,
10
+etc.
11
+
12
+## Administrator Software Version Overrides
13
+
14
+Most of the software titles installed in the SBGrid Suite have several
15
+versions available. Typically, we try to provide at least three versions of
16
+each software package, although very old or very new applications may have
17
+fewer versions.
18
+
19
+There are two methods for site admins to configure version overrides using
20
+files placed in a **/programs/local/conf/** directory.
21
+
22
+### Site-wide Version Overrides
23
+
24
+A file named **site.conf** will be read when any SBGrid shell is initialized
25
+from the installation.
26
+
27
+### Per-host Version Overrides
28
+
29
+A file named **&lt;hostname.conf&gt;**, where **&lt;hostname&gt;** is the
30
+output of the _hostname -s_ command, will be read after the site.conf on the
31
+host matching that hostname.
32
+
33
+### Precedence
34
+
35
+There are three files that will be examined for version overrides during shell
36
+initialization. In order from lowest to highest precedence:
37
+
38
+ * /programs/local/conf/site.conf
39
+
40
+ * /programs/local/conf/&lt;hostname.conf&gt;
41
+
42
+ * $HOME/.sbgrid.conf
43
+
44
+The overrides are reported during shell initialization:
45
+
46
+
47
+ Configuration options in effect for this shell: Variable Setting Configuration SPIDER_L 18.10 site CNS_L 1.21 machine CCP4_L 6.1.2 personal
48
+
49
+See [this
50
+page](https://sbgrid.org/wiki/usage/versions#overriding-software-versions_overriding-default-versions ) for details on the override syntax.
51
+
consortium-wiki/install-sbgrid-software-on-your-Mac-from-the-sbgrid-central-server.md
... ...
@@ -0,0 +1,4 @@
1
+# Install SBGrid software on your Mac from the SBGrid Central Server
2
+
3
+Download instructions as a [PDF](https://dl.dropboxusercontent.com/u/5977164/Laptop_Installation_Script.pdf) presentation
4
+and see the [YouTube tutorial](https://www.youtube.com/watch?v=B1orLccn1GA#t=4m17s), starting at 4'17" for additional information.
... ...
\ No newline at end of file
consortium-wiki/launching-remote-schrodinger-jobs-from-maestro.md
... ...
@@ -0,0 +1,35 @@
1
+# launching remote schrodinger jobs from maestro
2
+
3
+The maestro GUI supports running jobs on remote systems (usually ones with
4
+more computational resources). Setting this up requires 3 things: [setting up
5
+passwordless ssh](../boston-cmcd-faqs-and-discussion/setting-up-passwordless-ssh.md)
6
+to the remote system; configuring `schrodinger.hosts` for the system; and
7
+launching the jobs on the appropriate system.
8
+
9
+## Configuring `schrodinger.hosts`
10
+
11
+The `schrodinger.hosts` file should be located (or created) in your home
12
+directory; in `$HOME/.schrodinger`.
13
+
14
+An example `schrodinger.hosts` file:
15
+
16
+
17
+ name: localhost
18
+ tmpdir: /tmp/
19
+
20
+ # remote system
21
+ name: sbgrid-zorin
22
+ user: my_remote_username
23
+ host: zorin.sbgrid.org
24
+ tmpdir: /tmp
25
+ processors: 32
26
+
27
+## launching jobs on the remote system
28
+
29
+To launch a job on a remote system, the name under "Host" should match the
30
+`name` line for the remote system in your `schrodinger.hosts`.
31
+
32
+
33
+
34
+![](../images/launching-remote-schrodinger-jobs-from-maestro-1.png)
35
+
consortium-wiki/overriding-software-versions.md
... ...
@@ -0,0 +1,81 @@
1
+# Overriding Software Versions
2
+
3
+## Overview
4
+Most of the software titles installed in the SBGrid software collection have
5
+several versions available. We try to provide at least three versions of each
6
+software package, although very old or very new applications may have fewer
7
+versions.
8
+
9
+## Display Available Software Versions
10
+
11
+You can display a list of available software versions for your particular
12
+platform using the  sbgrid utility:  _s_bgrid -l. From a Linux machine, a
13
+search for CCP4 versions looks like this:
14
+
15
+ $ sbgrid -l ccp4 Version information for: /programs/x86_64-linux/ccp4
16
+ Default version: 6.4.0
17
+ In-use version: 6.4.0
18
+ Other available versions: 6.3.0 6.2.0
19
+ Overrides use this shell variable: CCP4_X
20
+
21
+Running sbgrid -L will display the available versions for the three current
22
+platforms (OS X PowerPC and Intel, Linux). The output below uses the gnuplot
23
+application as an example:
24
+
25
+ $ sbgrid -L gnuplot Version information for: /programs/x86_64-linux/gnuplot
26
+ Default version: 4.6.4
27
+ In-use version: 4.6.4
28
+ Other available versions: 4.6.0 4.4.3 4.2.6
29
+ Overrides use this shell variable: GNUPLOT_X
30
+
31
+ Version information for: /programs/i386-linux/gnuplot
32
+ Default version: 4.6.0
33
+ Other available versions: 4.4.3 4.2.6
34
+ Overrides use this shell variable: GNUPLOT_L
35
+
36
+ Version information for: /programs/i386-mac/gnuplot
37
+ Default version: 4.6.4
38
+ Other available versions: 4.4.3 4.2.6 4.6.0
39
+ Overrides use this shell variable: GNUPLOT_M
40
+
41
+## Overriding Default Versions
42
+
43
+To override the default version of a software title, you will need to create
44
+an override file. The shell configuration scripts will read this file and
45
+override the default version.
46
+
47
+The override file is named .sbgrid.conf and should be found in your `$HOME`
48
+directory. The syntax for overrides is a simple key=value pair. E.G. it should
49
+look like this:
50
+
51
+ APPLICATION_X=1.2
52
+
53
+APPLICATION_X is the name of the application followed by an underscore and the
54
+shorthand initial for the architecture. The last field on the line is the
55
+software version number you want to use. The initials for each software branch
56
+are:
57
+
58
+Software Directory| Shorthand Initial
59
+---|---
60
+powermac | `_P`
61
+x86_64-linux | `_X`
62
+i386-mac | `_M`
63
+
64
+
65
+
66
+To open the overrides file in your default $EDITOR, run this command:_
67
+_sbgrid-overrides -e.
68
+
69
+When you open a new shell, you will see a message about the overridden
70
+version. Note that a site administrator can create site-wide or machine-
71
+specific overrides as well.
72
+
73
+The example output below shows a default version change for CCP4 on Linux:
74
+
75
+ Configuration options in effect for this shell: Variable Setting Configuration CCP4_M 6.3.0 personal
76
+
77
+## Disabling a Software Package
78
+
79
+To disable a specific software package, set its version to “disable” in your
80
+~/.sbgrid.conf file.
81
+
consortium-wiki/preparing-linux-workstation-to-run-sbgrid-software.md
... ...
@@ -0,0 +1,42 @@
1
+# Preparing Linux Workstations to run SBGrid Software
2
+
3
+All Linux machines need installations of a recent version (6.17+) of csh/tcsh. Red Hat Enterprise Linux 6 and other recent distributions usually have an up to date version.
4
+
5
+There are RPMs for Red Hat/CentOS/Scientific Linux 5.x in the software tree in the architecture specific directories:
6
+
7
+* /programs/i386-linux/system/RPMs
8
+* /programs/x86_64-linux/system/RPMs
9
+
10
+## SELinux
11
+SELinux must be disabled.
12
+
13
+## 64-Bit Machines
14
+64-bit machines need a number of 32-bit compatibility packages installed **even when using the 64-bit software branch**.
15
+
16
+This is due to a number of binary-only and legacy packages that are only available as 32-bit applications. Additional fonts for Tcl/Tk, Motif and Xview applications are also encouraged.
17
+
18
+### RHEL/CENTOS/Scientific Linux 5
19
+Packages for RHEL 5 and compatible machines:
20
+
21
+```
22
+yum install glibc.i686 libgcc.i386 libX11.i386 libXaw.i386 libXext.i386 ncurses.i386 redhat-lsb.i386 xorg-x11-fonts-75dpi xorg-x11-fonts-100dpi xorg-x11-fonts-ISO8859-1-75dpi xorg-x11-fonts-ISO8859-1-100dpi xorg-x11-fonts-misc
23
+```
24
+
25
+### RHEL/CENTOS/Scientific Linux 6
26
+Packages for RHEL 6 and compatible machines:
27
+```
28
+yum install glibc.i686 libgcc.i686 libX11.i686 libXaw.i686 libXext.i686 ncurses-libs.i686 redhat-lsb.i686 xorg-x11-fonts-75dpi xorg-x11-fonts-100dpi xorg-x11-fonts-ISO8859-1-75dpi xorg-x11-fonts-ISO8859-1-100dpi xorg-x11-fonts-misc
29
+```
30
+
31
+### Debian/Ubuntu
32
+
33
+The same 32-bit requirement applies for 64-bit Debian and Ubuntu machines. This is supported via the [Multiarch](https://wiki.debian.org/Multiarch/HOWTO "https://wiki.debian.org/Multiarch/HOWTO" ) system.
34
+
35
+You'll need at least the following packages to run most of the software. Please email us if you discover we have left some out.
36
+
37
+```
38
+apt-get install libc6-i386 lsb tcsh gawk libjpeg62 curl libx11-6:i386 libxext6:i386
39
+```
40
+
41
+For more information, please check our wiki page
42
+[here](https://sbgrid.org/wiki/workstation_setup "SBGrid Wiki" ):
consortium-wiki/preparing-macs-for-sbgrid-installation.md
... ...
@@ -0,0 +1,6 @@
1
+# Preparing Macs for SBGrid Installation
2
+
3
+Prior to OS X 10.8, the stock X11 has better compatibility than the Xquartz development version available from MacOSForge.
4
+
5
+With the OS X 10.8 release, X11 is no longer included by Apple, and you'll need to install the latest Xquartz version offered on the MacOSForge site to run X11-based applications.
6
+
consortium-wiki/recommended-hardware.md
... ...
@@ -0,0 +1,16 @@
1
+# Recommended Hardware
2
+
3
+## Linux Workstations
4
+
5
+SBGrid's preferred hardware vendor is [ThinkMate](http://thinkmate.com/
6
+"http://thinkmate.com" ) and we have some [recommended
7
+configurations](http://www.thinkmate.com/sbgrid
8
+"http://www.thinkmate.com/sbgrid" ) for structural biology computing.
9
+
10
+## Apple Workstations
11
+
12
+Any Apple machine can be a capable computer for structural biology. The basic
13
+Apple educational discount is available through their online web store, and
14
+your institution may have negotiated an even better deal with their Apple
15
+representative. SBGrid has several labs that run exclusively on Macs and OS X.
16
+
consortium-wiki/sbgrid-computing-resources.md
... ...
@@ -0,0 +1,8 @@
1
+# SBGrid Computing Resources
2
+
3
+SBGrid currently has a 64 core 512G RAM compute system `heron.sbgrid.org` available to consortium members for use in running computationally intensive
4
+jobs.
5
+
6
+`heron.sbgrid.org` is accessable over `ssh`; please contact use at
7
+[help@sbgrid.org](mailto:help@sbgrid.org) to arrange access.
8
+
consortium-wiki/supported-operating-systems.md
... ...
@@ -0,0 +1,63 @@
1
+# Supported Operating Systems
2
+
3
+The SBGrid Software Suite can run on Linux, OS X and IRIX machines.
4
+
5
+## Linux
6
+
7
+We build and test software under 64-bit Red Hat 6. The majority of our Linux
8
+users are using the Red Hat/CentOS/Scientific Linux or Fedora distributions,
9
+but we also have labs using the software with Ubuntu, Debian and OpenSuSE. We
10
+don't explicitly test the software on these distributions, but it is known to
11
+work, and we will work to resolve problems reported by users of these Linux
12
+distributions.
13
+
14
+We officially support the two most recent releases of Red
15
+Hat/CentOS/Scientific Linux (currently 6 and 7) and the two most recent
16
+releases of Fedora Linux. At this time, only 64-bit versions of linux are
17
+fully supported. As of January 2015, we are no longer updating the 32-bit
18
+software branch, though we will work to resolve reported problems.
19
+
20
+
21
+### Linux Currently Supported
22
+
23
+ * Red Hat Enterprise Linux 6.x and 7.x and the community supported versions: CentOS and Scientific Linux.
24
+ * Fedora releases actively supported by the Fedora community. Check  <https://fedoraproject.org/wiki/Releases>  for the current list.
25
+ * We are no longer building software for RHEL 5.x, but compatible applications will remain in the software tree. We will respond to support requests for these and we will resolve problems where possible. RHEL5 users may not receive the latest versions of software, but RHEL5 systems will continue to be functional and supported with existing titles
26
+
27
+
28
+
29
+## OS X Intel
30
+
31
+We build and test the programs under the most four most recent OS X releases.
32
+
33
+Currently Supported:
34
+
35
+ * OS X Intel 10.9 - 10.11
36
+
37
+## OS X PowerPC
38
+
39
+The OS X PowerPC branch is currently frozen. The applications are stable and
40
+work well on our PowerPC hardware, but they are not being updated.
41
+
42
+Currently Supported:
43
+
44
+ * OS X PowerPC 10.4 - 10.5
45
+
46
+## IRIX
47
+
48
+The IRIX programs branch is currently frozen. The applications are stable and
49
+work well on our SGI hardware, but they are not being updated.
50
+
51
+Currently Supported:
52
+
53
+ * IRIX 6.5.26 + bugfix releases
54
+
55
+
56
+Please check [here](https://sbgrid.org/wiki/ "SBGrid Wiki" ) for the
57
+latest information :
58
+
59
+
60
+* <https://sbgrid.org/wiki/>
61
+
62
+
63
+
consortium-wiki/updating-sbgrid-software-on-your-mac-from-sbgrid-central-server.md
... ...
@@ -0,0 +1,12 @@
1
+### Download instructions as a
2
+[PDF](https://dl.dropboxusercontent.com/u/5977164/Laptop_Installation_Script.pdf)
3
+presentation
4
+
5
+### and
6
+
7
+### see the  [ YouTube
8
+tutorial](https://www.youtube.com/watch?v=B1orLccn1GA&list=PLVetO1F9gm_pYNk5VcwUMfpNWI3xGOM90
9
+"SBGrid TV" ), starting at 4'17" for additional information.
10
+
11
+
12
+
consortium-wiki/updating-sbgrid-software-on-your-mac-from-your-local-server.md
... ...
@@ -0,0 +1,172 @@
1
+# Updating SBGrid software on your mac from your local server
2
+
3
+If you run a machine that is frequently disconnected from the network, like a
4
+laptop, or don't want to set up an NFS-shared software installation, it is
5
+possible to install the software to the hard disk on your local machine.
6
+
7
+There are two scripts in the programs tree that can be used to create a copy
8
+of the software on your local hard disk. The `sbgrid-laptop` script allows you
9
+to select individual applications from the software distribution for
10
+installation on your laptop. By default only the latest version of the
11
+selected applications will be installed. The `localsync` script allows you to
12
+copy an entire operating system software branch to your local machine. This
13
+script can be used on laptops, but each branch is quite large in terms of disk
14
+space usage.
15
+
16
+## Laptop Script
17
+
18
+You can create a customized local installation of the software using the
19
+`sbgrid-laptop` script located at `/programs/share/bin/sbgrid-laptop`. This
20
+script requires you to have an SSH login to a computer that has access to an
21
+SBGrid software installation and will let you specify which packages you want
22
+to install.
23
+
24
+ sbgrid-laptop: a tool for creating a local installation of the
25
+ SBGrid software on a laptop.
26
+
27
+ Usage: sbgrid-laptop [-ituv] [-e list|config]
28
+
29
+ -d Debug mode creates a log file for troubleshooting purposes.
30
+ -e [list|config]
31
+ Edit the software download list.
32
+ -i Initial set up and installation of the SBGrid software.
33
+ -s Re-run SSH key set up process.
34
+ -t Test your current configuration.
35
+ -u Update an existing installation using the current
36
+ configuration.
37
+ -v Verbose option for the file transfer.
38
+
39
+ You need an SSH login to a machine with the SBGrid software installed
40
+ to use this script. The script will create an SSH key and run an SSH
41
+ agent process to handle authentication for the file transfers.
42
+
43
+Copy the script the machine you want to install the software on, and then run
44
+it in install mode: `./sbgrid-laptop -i`. Follow the prompts on the screen to
45
+create your configuration file, your software installation list and to enable
46
+logins using an SSH key for authentication.
47
+
48
+## Sync Script
49
+
50
+There is a script in the programs tree that can be used to copy the
51
+appropriate branch from a shared installation to your laptop or workstation.
52
+
53
+Copy /programs/share/bin/localsync from the machine that has the software to
54
+your home directory on the standalone machine:
55
+
56
+ scp your.server.name:/programs/share/bin/localsync ~/
57
+
58
+Then run the script like this:
59
+
60
+ chmod 755 ~/localsync
61
+ ~/localsync [yourusername@your.server.name](mailto:yourusername@your.server.name)
62
+
63
+The script will prompt you for your sudo (admin) password in order to create
64
+the programs directory, and then it will prompt you for your login password to
65
+the server that hosts your programs installation.
66
+
67
+Here is an example run on my workstation:
68
+
69
+ $ ./localsync [bene@developer.sbgrid.org](mailto:bene@developer.sbgrid.org)
70
+ Running 'sudo mkdir /programs && sudo chown bene /programs'
71
+ [sudo] password for bene:
72
+ Copying the software from the i386-mac branch on your server to your local
73
+ hard disk. Enter your ssh login password below for [bene@developer.sbgrid.org](mailto:bene@developer.sbgrid.org):
74
+
75
+ receiving file list ...
76
+
77
+This will copy the entire branch for your architecture to your local hard
78
+drive. For the OS X branch, this will use approximately 100 GB of disk space.
79
+
80
+You should use a network cable for the initial download, since the download is
81
+fairly large. Subsequent runs of the 'localsync' script are differential; they
82
+will only copy new or changed files, so they can be run over a wireless
83
+connection. The script can be run at any time to make your local installation
84
+match the installation on your local server.
85
+
86
+## Sharing a Software Installation without NFS
87
+
88
+While we recommend that sites export their software installation via NFS to
89
+their workstations, it is possible to use rsync to copy the master
90
+installation to each workstation. This method has the drawback that it
91
+requires manual intervention on the part of the local sysadmin, and updates
92
+will not be instantaneous or simultaneous for all machines.
93
+
94
+On each client machine, you'll need an 'sbgrid' user. That user will have a
95
+passphraseless ssh key that lets it log into the machine that hosts your
96
+primary installation. Each client machine will have a cron job for that sbgrid
97
+user that runs at 2 AM that will sync the programs from the master
98
+installation to the client machine.
99
+
100
+Here is a basic command run down. 'server1' holds the programs installation
101
+and 'client1' is what will be connecting to it.
102
+
103
+* Login as root/administrator on client1
104
+* Create the 'sbgrid' user on client1
105
+* Check the free space on /.
106
+* If there's enough free space, set up the programs directory:
107
+
108
+ ```
109
+ mkdir /programs
110
+ chown -R sbgrid:sbgrid /programs
111
+ ```
112
+
113
+* If there is not enough free space on the root volume, you'll need to find space on a local volume.
114
+* Login as 'sbgrid' on client1.
115
+* Create the passphraseless ssh key:
116
+
117
+ ``` ssh-keygen -d ```
118
+
119
+(hit enter to confirm default file location, no passphrase, etc)
120
+
121
+* Copy the ssh key to server1:
122
+
123
+ ``` cat ~/.ssh/id_dsa.pub | ssh server1 'cat - >> ~/.ssh/authorized_keys' ```
124
+
125
+* Copy the localsync script from server1 to client1. From client1:
126
+
127
+ ``` scp sbgrid@server1:/programs/share/bin/localsync . ```
128
+
129
+(May prompt to accept the host key. If you can't login without a password, the
130
+ssh key stuff above has failed, and you'll need to troubleshoot that.)
131
+&lt;/code&gt; chmod 755 localsync ./localsync sbgrid@server1 &lt;/code&gt;
132
+(This will take a while depending on the speed of the machines/network.)
133
+
134
+* Test the installation
135
+ * tcsh
136
+
137
+ ``` source /programs/sbgrid.cshrc ```
138
+
139
+ * bash
140
+
141
+ ``` source /programs/sbgrid.shrc ```
142
+
143
+(You should get a message like this: )
144
+
145
+
146
+
147
+ Welcome to SBGrid!
148
+ ********************************************************************************
149
+ Your use of the applications contained in the /programs directory constitutes
150
+ acceptance of the terms of the SBGrid License Agreement included in the file
151
+ /programs/share/LICENSE. The applications distributed by SBGrid are licensed
152
+ exclusively to member laboratories of the SBGrid Consortium.
153
+
154
+ To hush this license message, run 'touch ~/.agree2sbgrid'.
155
+ ********************************************************************************
156
+ Please submit bug reports and help requests to: <[bugs@sbgrid.org](mailto:bugs@sbgrid.org)> or
157
+ <[http://sbgrid.org/bugs>](http://sbgrid.org/bugs>)
158
+ This installation last updated: 20110411
159
+ ********************************************************************************
160
+ Total time to initialize: 1 second(s)
161
+
162
+
163
+* Add a cronjob for the updates. As the 'sbgrid' user on client1:
164
+
165
+ ``` echo "0 2 * * * ~/localsync sbgrid@server1" | crontab ```
166
+
167
+* Check the cronjob:
168
+
169
+ ``` crontab -l ```
170
+
171
+You're done!
172
+
images/data-processing-after-ws-mr-1.jpg
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sbgrid-consortium-discussion-forum/coot-stereo-swap.md
... ...
@@ -0,0 +1,5 @@
1
+If the graphics appear swapped or inverted in coot, typing
2
+`switch_stereo_sides()` (python scripting) or `(switch-stereo-sides)` (scheme
3
+scripting) may resolve the problem. If this persists, this can also be set
4
+permanently in your `~/.coot` file.
5
+
sbgrid-consortium-discussion-forum/dial-boxes-on-linux.md
... ...
@@ -0,0 +1,18 @@
1
+It's possible, at least in some cases, to use SGI dial boxes on linux with
2
+`O`.
3
+
4
+## What you need
5
+
6
+ 1. Dial Box
7
+ 2. Power supply for the dial box
8
+ 3. Serial to USB adaptor
9
+ 4. admin access to the system, and awareness that messing around in `/dev` can cause problems.
10
+
11
+## What to do
12
+
13
+ 1. add users to appropriate group for `/dev/tty*` files (`dialout`)
14
+ 2. connect dial box and power supply
15
+ 3. remove `/dev/ttyS0`
16
+ 4. create symlink `ln -s /dev/ttyUSB0 /dev/ttyS0`
17
+ 5. Start `O` , check if dials work.
18
+
sbgrid-consortium-discussion-forum/how-to-become-a-forum-member.md
... ...
@@ -0,0 +1,40 @@
1
+Signing up as a forum member will allow you to automatically receive e-mail
2
+messages when new topics are posted and manage other forum options. In the top
3
+menu bar you will have access to "My Area" option. You will be able to
4
+configure your profile and setup watchlists as well as bookmarks. In addition
5
+you will have access to your posts and will be able to send private messages
6
+to other members. Forum members can be also added to private forums (e.g. NE-
7
+CAT for Boston Area) and become forum moderators.
8
+
9
+
10
+
11
+**There are two ways to join the forums, which are available on this website ([forums.sbgrid.org](http://forums.sbgrid.org)):**
12
+
13
+
14
+
15
+
16
+
17
+A) Using your existing Google, Yahoo or Facebook credentials. You will first
18
+need to select the Sign In button. Then
19
+
20
+select one of three icons, G, Y or F:
21
+![](http://forums.sbgrid.org/viewImage.do?fileId=194535000000017019&forumGroupId=194535000000003001).
22
+Selecting option G will allow you to login with Google or Google Apps
23
+credentials. On the following page please enter your Google, Yahoo or Facebook
24
+credential. If the authorization works you will be redirected to the Forums
25
+page. In the top right corner you should see your name and a Sign Out option.
26
+Finally, in order to join the forums you will need to select the Join Now
27
+button. This is the last step. You will automatically become the forum member.
28
+
29
+
30
+
31
+B) You can also create a separate account for SBGrid Forums membership. On the
32
+login screen select the Join Now option, and then proceed to the Sign Up
33
+screen. Create a new user name and password.
34
+
35
+
36
+
37
+Still having trouble with joining? Please [email
38
+us](mailto:help@sbgrid.org?subject=Problems with joining forums.sbgrid.org)
39
+for further assistance.
40
+
sbgrid-consortium-discussion-forum/new-workstation-setup.md
... ...
@@ -0,0 +1,168 @@
1
+I have CentOS 7 installed working to get SBGrid working on it.
2
+
3
+
4
+
5
+I have followed steps on <https://sbgrid.org/wiki/software/workstation_setup>
6
+
7
+
8
+
9
+Everything went smoothly except ncurses.i686 did not install.
10
+
11
+
12
+
13
+
14
+
15
+> [user@biocvh-00754l programs]$ ls
16
+
17
+>
18
+
19
+> i386-linux l m sbgrid.shrc x
20
+
21
+>
22
+
23
+> i386-mac labcshrc sbgrid.cshrc share x86_64-linux
24
+
25
+>
26
+
27
+> [user@biocvh-00754l programs]$ ./sbgrid.shrc
28
+
29
+>
30
+
31
+> Software Support by SBGrid (www.sbgrid.org)
32
+
33
+>
34
+
35
+>
36
+********************************************************************************
37
+
38
+>
39
+
40
+> Your use of the applications contained in the /programs directory
41
+constitutes
42
+
43
+>
44
+
45
+> acceptance of the terms of the SBGrid License Agreement included in the
46
+file
47
+
48
+>
49
+
50
+> /programs/share/LICENSE. The applications distributed by SBGrid are
51
+licensed
52
+
53
+>
54
+
55
+> exclusively to member laboratories of the SBGrid Consortium.
56
+
57
+>
58
+
59
+> /programs/x86_64-linux/dials/dev-496/dials-dev-496/build/setpaths.sh: line
60
+22: libtbx.find_in_repositories: command not found
61
+
62
+>
63
+
64
+> /programs/x86_64-linux/dials/dev-496/dials-dev-496/build/setpaths.sh: line
65
+22: source: filename argument required
66
+
67
+>
68
+
69
+> source: usage: source filename [arguments]
70
+
71
+>
72
+
73
+> /programs/x86_64-linux/dials/dev-496/dials-dev-496/build/setpaths.sh: line
74
+35: libtbx.path_utility: command not found
75
+
76
+>
77
+
78
+> /programs/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/build/setpaths.sh:
79
+line 9: dirname: No such file or directory
80
+
81
+>
82
+
83
+> /programs/x86_64-linux/phenix/1.10-2155/phenix-1.10-2155/build/setpaths.sh:
84
+line 30: libtbx.path_utility: command not found
85
+
86
+>
87
+
88
+> /programs/share/bin/sbgrid-update-check: line 15: basename: command not
89
+found
90
+
91
+>
92
+
93
+> /programs/share/bin/sbgrid-update-check: line 15: basename: command not
94
+found
95
+
96
+>
97
+
98
+> /programs/share/bin/sbgrid-update-check: line 77: date: command not found
99
+
100
+>
101
+
102
+>
103
+********************************************************************************
104
+
105
+>
106
+
107
+> SBGrid was developed with support from its members, Harvard Medical School,
108
+>
109
+
110
+> HHMI, and NSF. If use of SBGrid compiled software was an important element
111
+>
112
+
113
+> in your publication, please include the following reference in your work:
114
+>
115
+
116
+>
117
+>
118
+
119
+> Software used in the project was installed and configured by SBGrid.
120
+>
121
+
122
+> cite: eLife 2013;2:e01456, Collaboration gets the most out of software.
123
+>
124
+
125
+>
126
+********************************************************************************
127
+
128
+>
129
+
130
+> SBGrid installation last updated: 2016-02-03 .
131
+>
132
+
133
+> Please submit bug reports and help requests to:
134
+>
135
+
136
+> <https://sbgrid.org/help> or [bugs@sbgrid.org](mailto:bugs@sbgrid.org)
137
+>
138
+
139
+>
140
+********************************************************************************
141
+
142
+>
143
+
144
+> ./sbgrid.shrc: line 284: date: command not found
145
+
146
+>
147
+
148
+> [user@biocvh-00754l programs]$ coot
149
+
150
+>
151
+
152
+> bash: coot: command not found...
153
+
154
+>
155
+
156
+> [user@biocvh-00754l programs]$ date
157
+
158
+>
159
+
160
+> Fri Feb 12 11:46:19 CST 2016
161
+
162
+>
163
+
164
+> [user@biocvh-00754l programs]$
165
+
166
+I can start the process but it seems to not see other commands like data that
167
+are installed and working on the system.
168
+