_Sidebar.md
... ...
@@ -4,6 +4,7 @@
4 4
* [[How To Get Help & Support|faq-getting-help]]
5 5
* [[Remote Access|faqs-remote]]
6 6
* [[FAQ|faqs]]
7
+* [[Crystal Email Spam and Phishing|faq-phishing]]
7 8
8 9
##### HMS Labs
9 10
* [[Harrison & Chou|hms1-harrison-chou-labs]]
... ...
@@ -27,15 +28,3 @@
27 28
* [[Heldwein - Tufts|tufts-heldwein]]
28 29
* [[Miller - MGH|mgh-miller]]
29 30
* [[Wang - Sanofi|sanofi]]
30
-
31
-
32
-
33
-
34
-
35
-
36
-
37
-
38
-
39
-
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-
41
-
faq-home-linux.md
... ...
@@ -1 +1,6 @@
1
-# faq-home-linux
1
+# Linux at home
2
+
3
+## Installing
4
+
5
+We have a custom installer USB/CD image for our supported labs. The install includes sbgrid installer program, pre configured vpn, and the same desktop enviroment currently deployed on most lab systems.
6
+Contact [help@sbgrid.org](mailto:help@sbgrid.org) for access and assistance.
faq-phishing.md
... ...
@@ -0,0 +1,21 @@
1
+# Recieving Phishing and Spam email messages
2
+
3
+## Phishing emails
4
+
5
+Crystal Email is provide GMail. It is important that phishing emails get flagged to limit their impact.
6
+
7
+Please open your email via the web interface.
8
+Open the message.
9
+Next to Reply press the side oprions button
10
+click More
11
+and Report Phishing.
12
+
13
+See the official [Google Instructions](https://support.google.com/mail/answer/8253?hl=en) page.
14
+
15
+Scroll down to 'Report phishing emails'
16
+
17
+## Spam emails
18
+
19
+Open your email via the web interface.
20
+Open the message.
21
+Press the ! in the stop sign button over the message.
faq-remote-X11-beta.md
... ...
@@ -10,7 +10,6 @@ Please [contact us](mailto:help@sbgrid.org) if your SBGrid-supported remote host
10 10
11 11
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'
12 12
13
-
14 13
x2go requires XQuartz - see [faq-using-sbgrid-programs](faq-using-sbgrid-programs) if you do not already have it installed.
15 14
16 15
From the x2go application -
... ...
@@ -27,6 +26,7 @@ You can adjust the desktop size after the session has started.
27 26
## Xpra
28 27
29 28
### macOS (x86_64) to remote Linux workstation
29
+
30 30
[Download](https://xpra.org/dists/osx/x86_64/Xpra.pkg) the installer.
31 31
32 32
### On remote workstation
... ...
@@ -48,6 +48,7 @@ Launch the XPRA gui. Select mode ssh - enter username, host and password info. I
48 48
To end the session on the remote system either tmux a and Ctrl-c or 'xpra stop'
49 49
50 50
#### xpra cli - keep it simple (for more experienced XPRA users)
51
+
51 52
This subsection includes support staff notes is not needed for basic remote work with GUI applications. You need to modify these commands according to your circumstances, *should* you decide to use these commands.
52 53
53 54
On the local Mac OSX system one can open a terminal window and run something like
... ...
@@ -65,7 +66,8 @@ To disconnect, just Ctrl-c from the original terminal window (not the xterm that
65 66
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 in use by the system, like 0 - 5. Pick a higher number up to 999 instead.
66 67
67 68
Note, if you simply close all the windows, including xterm, the remote server is still running:
68
-```
69
+
70
+```bash
69 71
$ ssh oconnor@sch-boltzmann
70 72
$ xpra list
71 73
Found the following xpra sessions:
... ...
@@ -74,7 +76,8 @@ Found the following xpra sessions:
74 76
$ xpra stop :666
75 77
xpra at :666 has exited.
76 78
```
77
-Or if you wanted the session to end when you opened the window:
79
+
80
+Or if you wanted the session to end when you opened the window:
78 81
79 82
`xpra start ssh/oconnor@sch-boltzmann/42 --start-child=xterm --window-close=shutdown`
80 83
... ...
@@ -101,13 +104,15 @@ There could be an active session with no windows open. Stop the session and star
101 104
`xpra stop :42`
102 105
103 106
Launch a session from the host in a tmux or screen session on the remote server:
107
+
108
+```bash
109
+ssh user@myhost
110
+tmux
111
+xpra start :617 --daemon=no --start-child=xterm
104 112
```
105
-$ ssh user@myhost
106
-$ tmux
107
-$ xpra start :617 --daemon=no --start-child=xterm
108
-```
113
+
109 114
You should see a line that that contains `xpra is ready.`
110
-Detach with CTRL-b - d keys and then you can attach from your own system
115
+Detach with CTRL-b - d keys and then you can attach from your own system
111 116
`xpra attach ssh/oconnor@sch-boltzmann/617`
112 117
113 118
See Also
faq-remote-access-to-linux-computers.md
... ...
@@ -1,9 +1,10 @@
1 1
# Remote Access to Linux Computers
2
+
2 3
Linux computing resources can be accessed from off-campus locations (as well
3 4
as different locations on-campus).
4 5
[[_TOC_]]
5 6
6
-## SSH
7
+## SSH
7 8
8 9
### Request External SSH Access
9 10
... ...
@@ -14,6 +15,7 @@ locally and SSH from your workstation in the Lab to others systems
14 15
that we manage for you.
15 16
16 17
### Overview
18
+
17 19
SSH can be used for remote command-line access to your laboratory computers from
18 20
home and other sites, as well as for running graphical programs (depending on
19 21
your local operating system).
... ...
@@ -27,6 +29,7 @@ connect through gateway to another workstation and run your jobs there (for
27 29
exceptions see Table I).
28 30
29 31
### How To SSH
32
+
30 33
ssh to:
31 34
32 35
* xtal200.harvard.edu
... ...
@@ -34,42 +37,54 @@ ssh to:
34 37
You should only use xtal200.harvard.edu if you have told to do so by
35 38
SBGrid staff. If you need access please email <help@sbgrid.org>.
36 39
40
+On Apple systems we reccommend using Terminal App, found in your Applications/Utilities folder. Also see [SBGrid Software](faq-using-sbgrid-programs).
41
+On Windows systems we know of Xming, vcxsvr, WSL, and MobaXterm. We do not currently support or have a preference for usage.
42
+
37 43
Example syntax for connecting to SSH gateway for Harvard Medical School
38 44
groups:
39 45
40
-* Non-GUI connection: 
41
-
42
-``` ssh username@xtal200.harvard.edu;```
46
+* Non-GUI connection:
43 47
44
-* GUI (connecting to a linux system): 
48
+```bash
49
+ssh username@xtal200.harvard.edu;
50
+```
45 51
46
-``` ssh -Y username@xtal200.harvard.edu;```
52
+* GUI (connecting to a linux system):
47 53
48
-``` ssh -Y abacus ``` (replace abacus with the name of your workstation.)
54
+```bash
55
+ssh -Y username@xtal200.harvard.edu;
56
+```
49 57
50
-* GUI (slower network connection): 
58
+```bash
59
+ssh -Y abacus
60
+``` (replace abacus with the name of your workstation.)
51 61
52
-```ssh -Y -C username@xtal200.harvard.edu;```
62
+* GUI (slower network connection):
53 63
54
-```ssh -Y -C abacus;``` (replace abacus with the name of your workstation.)
64
+```bash
65
+ssh -Y -C username@xtal200.harvard.edu
66
+```
67
+
68
+```bash
69
+ssh -Y -C abacus
70
+``` (replace abacus with the name of your workstation.)
55 71
56
-ssh is usually installed by default on linux and OS X systems. Terminal App
57
-can be found in your Applications/Utilities folder (when connecting with ```ssh
58
--Y``` on OS X systems, X11 will start on its own if necessary).
59 72
60 73
Please note that external SSH access is deactivated by default. Please contact
61 74
[help@sbgrid.org](mailto:help@sbgrid.org?Subject=Enable_ssh_access) to request remote access for your account.
62 75
63 76
## SSH Gateways
77
+
64 78
SSH Gateways are enabled in some of the CMCD laboratories. That means if you are outside of the Lab you can SSH to your lab's network using the SSH hosts listed below:
65 79
66 80
If your site is not included on this list please contact us for further info about remote access.
67 81
68
-### HMS, CHB, & DFCI Labs:
82
+### HMS, CHB, & DFCI Labs
69 83
70 84
ssh to xtal200.harvard.edu. You cannot run jobs on the gateway host and must ssh to your computer nodes to run jobs.
71 85
72
-###MCB Labs
86
+### MCB Labs
87
+
73 88
ssh to galactica.mcb.harvard.edu. You can run jobs on the gateway or on orthus.
74 89
75 90
**MCB**: You cannot ssh to galactica.mcb.harvard.edu if you are inside the MCB or Harvard University network. Instead ssh directly to the system you need to access.
faq-running-remote-jobs-after-disconnecting.md
... ...
@@ -1,54 +1,55 @@
1 1
# Running remote jobs after disconnecting
2
-[[_TOC_]]
3 2
4
-## `screen`
3
+Most of the staff prefers to use tmux, screen is another alternative exampled below.
5 4
6
-When running long jobs remotely (file transfer, heavy computational jobs,
7
-etc), it's sometimes helpful to be able to start the job and disconnect from
8
-the remote system (while the jobs continues to run).
5
+[[_TOC_]]
9 6
10
-`screen` is one tool that can be used to acomplish this. The usual procedure
11
-is to connect to the remote system, start a `screen` session, start the job,
12
-disconnect from the `screen` session, and log-out.
7
+## `tmux`
13 8
14
-start session | `screen`
9
+`tmux` is a newer alternative to `screen`. The same approach is used -
10
+ connect to the remote system, start a `tmux` session, start the job,
11
+disconnect from the `tmux` session, and log-out.
15 12
16
-disconnect from session | `<ctrl-a d>` (control a + "d")
13
+start session | `tmux`
17 14
18
-re-connect to existing session | `screen -r`
15
+disconnect from session | `<ctrl-b d>` (control b + "d")
19 16
20
-check for existing sessions | `screen -ls`
17
+re-connect to existing session | `tmux a`
21 18
22
-quit screen session | `exit`
19
+check for existing sessions | `tmux ls`
23 20
24
-### example `screen` file transfer
21
+quit tmux session | `exit`
22
+
23
+### example `tmux` file transfer
25 24
26 25
`localsys> ssh [meyer@xtal200.harvard.edu](mailto:meyer@xtal200.harvard.edu)`
27
-# connect to remote system
28 26
29
-`crystal> screen` # start screen session
27
+## connect to remote system
28
+
29
+`crystal> tmux` # start tmux session
30 30
31 31
`crystal> scp -r -p meyer@remote_site:~/data/ ~/data/` # start data transfer
32 32
33
-`crystal> <ctrl-a d>` # disconnect from screen session
33
+`crystal> <ctrl-b d>` # disconnect from tmux session
34 34
35 35
`crystal> logout` # disconnect from remote system
36 36
37 37
`localsys>` # all done
38 38
39
-### example `screen` computational job
39
+### example `tmux` computational job
40 40
41 41
`localsys> ssh [meyer@xtal200.harvard.edu](mailto:meyer@xtal200.harvard.edu)`
42
-# connect to remote gateway system
42
+
43
+## connect to remote gateway system
43 44
44 45
`crystal> ssh abacus` # connect to your workstation; replace `abacus` with the
45 46
name of your workstation
46 47
47
-`abacus> screen` # start screen session
48
+`abacus> tmux` # start tmux session
48 49
49 50
`abacus> ./data_processing_script.sh` # start processing data
50 51
51
-`abacus> <ctrl-a d>` # disconnect from screen session
52
+`abacus> <ctrl-b d>` # disconnect from tmux session
52 53
53 54
`abacus> logout` # disconnect from workstation
54 55
... ...
@@ -56,53 +57,58 @@ name of your workstation
56 57
57 58
`localsys>` # all done
58 59
59
-For more information, see [the screen
60
-manual](https://www.gnu.org/software/screen/manual/html_node/index.html).
60
+For more information, see [the tmux homepage](https://github.com/tmux/tmux).
61 61
62
-## `tmux`
62
+## `screen`
63 63
64
-`tmux` is a newer alternative to `screen`. The same approach is used -
65
- connect to the remote system, start a `tmux` session, start the job,
66
-disconnect from the `tmux` session, and log-out.
64
+When running long jobs remotely (file transfer, heavy computational jobs,
65
+etc), it's sometimes helpful to be able to start the job and disconnect from
66
+the remote system (while the jobs continues to run).
67 67
68
-start session | `tmux`
68
+`screen` is one tool that can be used to acomplish this. The usual procedure
69
+is to connect to the remote system, start a `screen` session, start the job,
70
+disconnect from the `screen` session, and log-out.
69 71
70
-disconnect from session | `<ctrl-b d>` (control b + "d")
72
+start session | `screen`
71 73
72
-re-connect to existing session | `tmux a`
74
+disconnect from session | `<ctrl-a d>` (control a + "d")
73 75
74
-check for existing sessions | `tmux ls`
76
+re-connect to existing session | `screen -r`
75 77
76
-quit tmux session | `exit`
78
+check for existing sessions | `screen -ls`
77 79
78
-### example `tmux` file transfer
80
+quit screen session | `exit`
81
+
82
+## example `screen` file transfer
79 83
80 84
`localsys> ssh [meyer@xtal200.harvard.edu](mailto:meyer@xtal200.harvard.edu)`
81
-# connect to remote system
82 85
83
-`crystal> tmux ` # start tmux session
86
+### connecting to remote system
87
+
88
+`crystal> screen` # start screen session
84 89
85 90
`crystal> scp -r -p meyer@remote_site:~/data/ ~/data/` # start data transfer
86 91
87
-`crystal> <ctrl-b d>` # disconnect from tmux session
92
+`crystal> <ctrl-a d>` # disconnect from screen session
88 93
89 94
`crystal> logout` # disconnect from remote system
90 95
91 96
`localsys>` # all done
92 97
93
-### example `tmux` computational job
98
+### example `screen` computational job
94 99
95 100
`localsys> ssh [meyer@xtal200.harvard.edu](mailto:meyer@xtal200.harvard.edu)`
96
-# connect to remote gateway system
101
+
102
+### connect to remote system
97 103
98 104
`crystal> ssh abacus` # connect to your workstation; replace `abacus` with the
99 105
name of your workstation
100 106
101
-`abacus> tmux` # start tmux session
107
+`abacus> screen` # start screen session
102 108
103 109
`abacus> ./data_processing_script.sh` # start processing data
104 110
105
-`abacus> <ctrl-b d>` # disconnect from tmux session
111
+`abacus> <ctrl-a d>` # disconnect from screen session
106 112
107 113
`abacus> logout` # disconnect from workstation
108 114
... ...
@@ -110,5 +116,5 @@ name of your workstation
110 116
111 117
`localsys>` # all done
112 118
113
-For more information, see [the tmux homepage](https://github.com/tmux/tmux).
114
-
119
+For more information, see [the screen
120
+manual](https://www.gnu.org/software/screen/manual/html_node/index.html).
faq-sshfs.md
... ...
@@ -2,7 +2,7 @@
2 2
3 3
## Setting up sshfs on OS X (Mac) systems
4 4
5
-Installation requires administrative privileges.
5
+Installation requires administrative privileges.
6 6
7 7
Prior to installing, you should make sure that [you can SSH with keys](faq-setting-up-key-based-ssh)
8 8
... ...
@@ -12,7 +12,6 @@ Prior to installing, you should make sure that [you can SSH with keys](faq-setti
12 12
4. Run SSHFS installer `pkg`
13 13
5. Create a folder to access the remote filesystems (aka a mount point): `mkdir /sshfs/`
14 14
15
-
16 15
### Mounting remote filesystems with sshfs
17 16
18 17
`sshfs username@remotesystem:/full/path/to/directory /mount/point`
... ...
@@ -23,14 +22,13 @@ words, that user's NFS home directory).
23 22
24 23
You should mount sshfs via a directory in your home directory. Just remember to specify the PATH to the directory.
25 24
26
-
27 25
## OS X (Mac) helpful hints
28 26
29 27
As of OSX 10.15 Catilina we are not recommending to create mounts in the root path or / of the file system.
30 28
31 29
An example of mounting from OSX on your local system is as follows -
32 30
33
-```
31
+```bash
34 32
mkdir ~/userdocs
35 33
/usr/local/bin/sshfs oconnor@xtal200.harvard.edu:/nfs/userdocs /Users/oconnor/userdocs -o volname=userdocs,reconnect,ServerAliveInterval=15,ServerAliveCountMax=3,idmap=user,auto_xattr,dev,suid,defer_permissions,noappledouble,noapplexattr
36 34
```
... ...
@@ -42,7 +40,6 @@ You should mount one complete filesystem from the remote site, so this would be
42 40
On occasion the mount may become stuck or unresponsive you can force unmount via -
43 41
`diskutil umount force /Users/oconnor/userdocs`
44 42
45
-
46 43
## Using helper script
47 44
48 45
We created a 'helper' script available that can be used with sshfs_nfs.app for mac to automount at login. The app is simply a wrapper for sshfs-helper.sh and assumes the script exists in your home folder.
... ...
@@ -53,7 +50,7 @@ If the mounts become stuck just rerun to reattach shares.
53 50
54 51
or copy the whole set -
55 52
56
-```
53
+```bash
57 54
rsync -rlptD $USER@xtal200.harvard.edu:/net/cronus/cmcd1/arc/shared/sbgrid-sshfsfiles.zip .
58 55
```
59 56
... ...
@@ -69,10 +66,7 @@ An example -
69 66
`oconnor@sshfs.sbgrid.org /nfs/userdocs /Users/oconnor/userdocs`
70 67
`jo232@transfer.o2.hms.harvard.edu /home/myfolder /Users/oconnor/o2home`
71 68
72
-<<<<<<< HEAD
73 69
After it is working you can add a shortcut into your dock by navigating to your home folder on your Mac `open ~` and then dragging the sshfs_nfs.app into your dock. If you need to reconnect to the shares just press the app and it will connect or reconnect.
74
-=======
75 70
For additional folders you must create the destination folder like - `mkdir ~/o2home`
76 71
77 72
After it is working you can add a shortcut into your dock by navigating to /Users/Shared/ on your Mac `open /Users/Shared` and then dragging the sshfs_nfs.app into your dock. If you need to reconnect to the shares just press the app and it will connect or reconnect.
78
->>>>>>> 8aa79253b37400a03ebc3816d37b7965d8a64915
faq-zoom.md
... ...
@@ -6,12 +6,16 @@ Client for multiple platforms can be downloaded from
6 6
7 7
<https://zoom.us/support/download>
8 8
9
+The application is free to use and you do not need credentials or a login if you only need to join a meeding and have the meeting ID number.
10
+
9 11
## Hosting a meeting
10 12
11 13
Depending on your institution you may have access to a free account to host your own meetings.
12 14
13 15
[HMS Zoom]<https://harvard.zoom.us/> Click Sign in.
16
+
14 17
[HHMI Zoom]<https://hhmi.okta.com/app/UserHome> Click Zoom App box.
18
+
15 19
[BCH Zoom]<https://bostonchildrens.zoom.us> Click Sign in.
16 20
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.
21
+In the settings options from your instutional page take note of your Host Key, this will allow you to become the host of the meeting. It will give you additional controls to make other participants hosts, co-hosts, mute people, and record for example.
faqs-remote.md
... ...
@@ -1,4 +1,4 @@
1
-## Working Remotely
1
+# Working Remotely
2 2
3 3
* [Access Remote Filesystems using SSHFS](faq-sshfs)
4 4
* [Linux Remote Access](faq-remote-access-to-linux-computers)
... ...
@@ -6,4 +6,5 @@
6 6
* [SBGrid/CMCD VPN](faq-connecting-to-cmcd-vpn)
7 7
* [Installing Linux at home](faq-home-linux)
8 8
* [SSH tips and tricks](faq-ssh-tips)
9
+* [Running jobs after you logged off (using tmux)](faq-running-remote-jobs-after-disconnecting)
9 10
* [Remote control of GUI applications](faq-remote-X11-beta)