cb06603ee7321173a1008a9a0cb309accb1e77df
Home.md
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1 | -## Welcome to the SBGrid ARC Wiki |
|
1 | +# Welcome to the SBGrid ARC Wiki |
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2 | 2 | |
3 | 3 | This site provides information on the services provided by the SBGrid Advanced Research Computing Group (ARC) at Harvard Medical School. The SBGrid ARC provides Research Computing Systems support to SBGrid ARC Member Labs. |
4 | 4 | |
... | ... | @@ -21,16 +21,7 @@ The Structural Biology Grid at Harvard Medical School (SBGrid) is a computing co |
21 | 21 | See the [SBGrid Website](https://www.sbgrid.org/) |
22 | 22 | |
23 | 23 | ## Help |
24 | + |
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24 | 25 | * [Getting Help & Support](faq-getting-help) |
25 | 26 | |
26 | 27 | [[include:faqs]] |
27 | - |
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28 | - |
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29 | - |
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30 | - |
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31 | - |
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34 | - |
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35 | - |
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36 | - |
_Sidebar.md
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2 | 2 | |
3 | 3 | ##### Help |
4 | 4 | * [[How To Get Help & Support|faq-getting-help]] |
5 | +* [[Remote Access|faqs-remote]] |
|
5 | 6 | * [[FAQ|faqs]] |
6 | 7 | |
7 | 8 | ##### HMS Labs |
faq-home-linux.md
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1 | +# faq-home-linux |
faq-remote-X11-beta.md
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1 | -## Remote X11 (beta) - x2go and xpra |
|
1 | +# Remote X11 (beta) - x2go and xpra |
|
2 | 2 | |
3 | 3 | In general x2go is easier to use and sufficient for most scenarios. Xpra has better performance and uses less resources. Both clients connect through ssh and are generally faster than ssh -Y. Support for these is beta, x2go is more familiar to the support staff. Most linux systems do not have these tools installed, so you may need to request them. |
4 | 4 | |
5 | 5 | We recommend using x2go. x2go is more familiar to the support staff and it is easier to use. |
6 | 6 | |
7 | -### x2go |
|
7 | +## x2go |
|
8 | + |
|
9 | +### download |
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8 | 10 | |
9 | -#### download |
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10 | 11 | x2go can be downloaded from this page. |
11 | 12 | |
12 | 13 | * <https://wiki.x2go.org/doku.php/download:start> |
13 | 14 | |
14 | 15 | #### Additional Steps |
16 | + |
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15 | 17 | You will need to open System Preferences - Security - General - Temporarily 'Allow from anywhere' open the application, make sure you can reopen it. Then change your security setting back to 'App Store and Identified Developers' |
16 | 18 | |
17 | -For all systems off of the sbgrid network it will be easiest if you use the [cmcd-vpn](faq-connecting-to-cmcd-vpn). |
|
19 | +For all systems off of the sbgrid network it will be easiest if you use the [cmcd-vpn](faq-connecting-to-cmcd-vpn). |
|
18 | 20 | |
19 | 21 | x2go requires XQuartz - see [faq-using-sbgrid-programs](faq-using-sbgrid-programs) if you do not already have it installed. |
20 | 22 | |
21 | -From the x2go application - |
|
23 | +From the x2go application - |
|
22 | 24 | Create a new session |
23 | 25 | Make sure you fill out the following - |
26 | + |
|
24 | 27 | 1. host - the host that you want to connect to. |
25 | 28 | 2. login - your username |
26 | - 3. port - 22 |
|
29 | + 3. port - 22 |
|
27 | 30 | 4. Session type - Mate |
28 | 31 | |
29 | 32 | You can adjust the resolution after the session has started. |
30 | 33 | |
34 | +### Xpra |
|
31 | 35 | |
32 | -### Xpra |
|
33 | 36 | xpra has been described as 'tmux for X11'. It uses x264 encoding. |
34 | 37 | |
35 | 38 | #### OSX to Linux workstation usage |
36 | 39 | |
37 | 40 | For Mac OSX newer than 10.9 the installer is on their downloads page |
38 | -https://www.xpra.org/trac/wiki/Download |
|
41 | +<https://www.xpra.org/trac/wiki/Download> |
|
39 | 42 | |
40 | 43 | GUI version - |
41 | -https://xpra.org/dists/osx/x86_64/Xpra.pkg |
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44 | +<https://xpra.org/dists/osx/x86_64/Xpra.pkg> |
|
42 | 45 | |
43 | 46 | For command line usage please us the 'pkg' installer located here - |
44 | -https://xpra.org/dists/osx/x86_64/Xpra.pkg |
|
47 | +<https://xpra.org/dists/osx/x86_64/Xpra.pkg> |
|
45 | 48 | |
46 | 49 | #### xpra gui |
47 | 50 | |
48 | 51 | On remote system - copy xpra-launch.sh to your home folder and ./xpra-launch.sh or useone of the lines below. |
49 | 52 | |
50 | 53 | #### Full desktop |
54 | + |
|
51 | 55 | tmux new-session -d -s "xpra-desktop" "xpra start-desktop --start=mate-session :$((10 + RANDOM % 999)) --pulseaudio=no --daemon=no" |
52 | 56 | |
53 | 57 | #### Minimal termial window |
58 | + |
|
54 | 59 | tmux new-session -d -s "xpra-terminal" "xpra start --start=mate-terminal :$((10 + RANDOM % 999)) --pulseaudio=no --daemon=no" |
55 | 60 | |
56 | 61 | #### open xpra gui |
62 | + |
|
57 | 63 | Select mode ssh - enter username, host and password info. If there is only one xpra session it will automatically connect to it. You can also save that info to a config file and launch that after. |
58 | 64 | |
59 | 65 | To end the session on the remote system either tmux a and Ctrl-c or 'xpra stop' |
60 | 66 | |
61 | -### xpra cli - keep it simple. |
|
67 | +### xpra cli - keep it simple |
|
62 | 68 | |
63 | 69 | On your local Mac OSX system open a terminal window and run |
64 | 70 | `xpra start ssh/oconnor@sch-boltzmann/42 --start-child=xterm` |
... | ... | @@ -68,8 +74,8 @@ With this one command you should have a remote xterm window come up. From there |
68 | 74 | To disconnect, just ^c from the original terminal window(not the xterm that you connected to), or if you connect from another system it will automatically detach. |
69 | 75 | |
70 | 76 | reattach to attach - |
71 | - |
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72 | -`xpra attach ssh/oconnor@sch-boltzmann/42` |
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77 | + |
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78 | +`xpra attach ssh/oconnor@sch-boltzmann/42` |
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73 | 79 | |
74 | 80 | Note the number 42. You need to pick a number that someone else on the system is not using. Do not use a low number that could be inuse by the system like 0 - 5, instead pick a higher number up to 999. |
75 | 81 | |
... | ... | @@ -82,12 +88,12 @@ Found the following xpra sessions: |
82 | 88 | `xpra stop :666` |
83 | 89 | xpra at :666 has exited. |
84 | 90 | |
85 | -Or if you wantesd the session to end when you opened the window - |
|
91 | +Or if you wantesd the session to end when you opened the window - |
|
86 | 92 | `xpra start ssh/oconnor@sch-boltzmann/42 --start-child=xterm --window-close=shutdown` |
87 | 93 | |
88 | 94 | For all systems off of the sbgrid network it will be easiest if you use the [cmcd-vpn](faq-connecting-to-cmcd-vpn). |
89 | 95 | |
90 | -### Troubleshooting tips. |
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96 | +### Troubleshooting tips |
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91 | 97 | |
92 | 98 | Ideally you would have already set up [SSH with keys](faq-setting-up-key-based-ssh) |
93 | 99 | |
... | ... | @@ -95,7 +101,7 @@ Make sure you can ssh to the host without error. You should not need to type 'ye |
95 | 101 | |
96 | 102 | Press enter one time - is it waiting for password input? |
97 | 103 | |
98 | -connect to the remote host and type - |
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104 | +connect to the remote host and type - |
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99 | 105 | `xpra list` |
100 | 106 | |
101 | 107 | If there is an active session you can connect to it via `xpra attach ssh/user@host/42' from your client. |
... | ... | @@ -104,7 +110,7 @@ There could be an active session with no windows open. Stop the session and star |
104 | 110 | 'xpra stop :42` |
105 | 111 | |
106 | 112 | Try to launch a session from the host in a tmux or screen session on the remote server - |
107 | -`ssh user@myhost" |
|
113 | +`ssh user@myhost` |
|
108 | 114 | `tmux` |
109 | 115 | `xpra start :617 --daemon=no --start-child=xterm` |
110 | 116 | You should see a line that that contains `xpra is ready.` |
faq-ssh-tips.md
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1 | +# faq-ssh-tips |
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2 | + |
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3 | +## Use tmux or screen |
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4 | + |
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5 | +## Make a tunnel |
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6 | + |
|
7 | +## do we need this |
faq-zoom.md
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1 | +# Zoom |
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2 | + |
|
3 | +## Client Download |
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4 | + |
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5 | +Client for multiple platforms can be downloaded from |
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6 | + |
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7 | +<https://zoom.us/support/download> |
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8 | + |
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9 | +## Hosting a meeting |
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10 | + |
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11 | +Depending on your institution you may have access to a free account to host your own meetings. |
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12 | + |
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13 | +[HMS Zoom]<https://harvard.zoom.us/> Click Sign in. |
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14 | +[HHMI Zoom]<https://hhmi.okta.com/app/UserHome> Click Zoom App box. |
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15 | +[BCH Zoom]<https://bostonchildrens.zoom.us> Click Sign in. |
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16 | + |
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17 | +Take note of your Host Key, this will allow you to become the host of the meeting. It will give you additional controls to record for example. |
faqs-remote.md
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1 | +## Working Remotly |
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2 | + |
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3 | +* [Access Remote Filesystems using SSHFS](faq-sshfs) |
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4 | +* [Linux Remote Access](faq-remote-access-to-linux-computers) |
|
5 | +* [Zoom usage](faq-zoom) |
|
6 | +* [SBGrid/CMCD VPN](faq-connecting-to-cmcd-vpn) |
|
7 | +* [Installing Linux at home](faq-home-linux) |
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8 | +* [SSH tips and tricks](faq-ssh-tips) |
|
9 | + |
faqs.md
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1 | 1 | |
2 | -## [FAQ](faqs) |
|
2 | +# [FAQ](faqs) |
|
3 | + |
|
3 | 4 | Frequently Answered Questions |
4 | 5 | |
5 | -### Account Related |
|
6 | +[[include: faqs-remote]] |
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7 | + |
|
8 | +## Account Related |
|
9 | + |
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6 | 10 | * [Change Your Unix Password](faq-changing-your-account-password) |
7 | -* [Backups Using Crashplan](faq-crashplan-backups) |
|
11 | +* [Backups Using Crashplan](faq-crashplan-backups) |
|
8 | 12 | * [SBGrid/CMCD VPN](faq-connecting-to-cmcd-vpn) |
9 | 13 | * [Requesting an Account](faq-new-accounts) |
10 | 14 | * [EM Systems Access](faq-em-facility) |
11 | 15 | |
12 | -### Software & Linux/Mac/UNIX |
|
16 | +## Software & Linux/Mac/UNIX |
|
13 | 17 | |
14 | 18 | * [Access Remote Filesystems using SSHFS](faq-sshfs) |
15 | -* [Firefox Problems on Network Account](faq-troubleshooting-firefox-on-a-network-account) |
|
16 | -* [How to Forward Email](faq-forwarding-mail-to-crystal) |
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17 | 19 | * [Linux Remote Access](faq-remote-access-to-linux-computers) |
20 | +* [Zoom usage](faq-zoom) |
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21 | +* [Firefox Problems on Network Account](faq-troubleshooting-firefox-on-a-network-account) |
|
22 | +* [How to Forward Email](faq-forwarding-mail-to-crystal) |
|
18 | 23 | * [OS X (Apple): Find MAC Address](faq-how-to-find-mac-address-on-os-x-gui) |
19 | 24 | * [Running jobs after you logged off (using Screen)](faq-running-remote-jobs-after-disconnecting) |
20 | 25 | * [SSH with keys](faq-setting-up-key-based-ssh) |
... | ... | @@ -26,7 +31,8 @@ Frequently Answered Questions |
26 | 31 | * [SGI Dial Box on Linux](faq-dial-boxes-on-linux) |
27 | 32 | * [Other Resources](faq-other-resources) |
28 | 33 | |
29 | -### Research Infrastructure |
|
34 | +## Research Infrastructure |
|
35 | + |
|
30 | 36 | * [Data Collection at NE-CAT](faq-data-collection-at-ne-cat) |
31 | 37 | * [SGM EM Facility](faq-em-facility) |
32 | 38 | * [Moving Data](faq-moving-data) |