bch2-wu-springer-hur.md
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@@ -23,6 +23,9 @@ The Linux computers share authentication and data directories and can only be ac
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The systems named venus, mercury, and mars have GPUs installed and are used for data processing. These systems can be accessed remotely.
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Please note that your home directories are only visible to your labmates and PI by default. Permissions vary depending on the nature of the directory or files in question. PIs can request modifications to file permissions to suit the lab's needs.
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+# Wu Lab Software
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+Cryosparc is installed on Venus. Cryosparc is installed and running on Venus. It is accessible via a web interface, please email [help@sbgrid.org](mailto:help@sbgrid.org) to ask how to access it.
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+
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# Data Backups
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Full and incremental backups are made of SBGrid file servers, including your home and data directories. These backups are usually kept for three months. If you need a file restored, please contact us at [help@sbgrid.org](mailto:help@sbgrid.org).
faq-data-collection-at-ne-cat.md
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@@ -10,7 +10,7 @@ collection time at [NE-CAT](http://necat.chem.cornell.edu/
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Please work with your local liaisons to learn more about the procedure and
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follow up our instructions very carefully.
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-* DFCI: [Sacha Uljon](mailto:Sacha_Uljon@dfci.harvard.edu?subject=NE-CAT)
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+* DFCI: [David Heppner](mailto:heppner@crystal.harvard.edu?subject=NE-CAT)
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* Harvard: [John Janetzko](mailto:j.janetzko@gmail.com?subject=NE-CAT)
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* Harrison Laboratory and Children's Hospital: [Kevin McCarthy](mailto:mccarthy@crystal.harvard.edu?subject=NE-CAT)
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faq-remote-X11-beta.md
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@@ -1,17 +1,17 @@
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-# Remote X11 (beta) - x2go and xpra
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+## Remote X11 (beta) - x2go and xpra
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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.
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-We recommend using x2go. x2go is more familiar to the support staff and it is easier ti use.
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+We recommend using x2go. x2go is more familiar to the support staff and it is easier to use.
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-# x2go
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+### x2go
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-## download
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+#### download
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x2go can be downloaded from this page.
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https://wiki.x2go.org/doku.php/download:start
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-## Additional Steps
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+#### Additional Steps
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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'
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For all systems off of the sbgrid network it will be easiest if you use the [cmcd-vpn](faq-connecting-to-cmcd-vpn).
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@@ -29,21 +29,36 @@ Make sure you fill out the following -
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You can adjust the resolution after the session has started.
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-# Xpra
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+### Xpra
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+xpra has been described as 'tmux for X11'. It uses x264 encoding.
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-xpra has been described as 'tmux for X11' and we are evaluating its usefullness.
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-
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-## OSX to Linux workstation usage
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+#### OSX to Linux workstation usage
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For Mac OSX newer than 10.9 the installer is on their downloads page
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https://www.xpra.org/trac/wiki/Download
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-For our usage please us the 'pkg' installer located here -
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+GUI version -
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+https://xpra.org/dists/osx/x86_64/Xpra.pkg
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+
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+For command line usage please us the 'pkg' installer located here -
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https://xpra.org/dists/osx/x86_64/Xpra.pkg
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-The other version is built around a gui that we are not covering for now.
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+#### xpra gui
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+
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+On remote system - copy xpra-launch.sh to your home folder and ./xpra-launch.sh or useone of the lines below.
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+
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+#### Full desktop
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+tmux new-session -d -s "xpra-desktop" "xpra start-desktop --start=mate-session :$((10 + RANDOM % 999)) --pulseaudio=no --daemon=no"
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+
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+#### Minimal termial window
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+tmux new-session -d -s "xpra-terminal" "xpra start --start=mate-terminal :$((10 + RANDOM % 999)) --pulseaudio=no --daemon=no"
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+
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+#### open xpra gui
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+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.
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+
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+To end the session on the remote system either tmux a and Ctrl-c or 'xpra stop'
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-### xpra, keep it simple!
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+### xpra cli - keep it simple.
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On your local Mac OSX system open a terminal window and run
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`xpra start ssh/oconnor@sch-boltzmann/42 --start-child=xterm`
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@@ -52,7 +67,7 @@ With this one command you should have a remote xterm window come up. From there
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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.
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-So to reattach to attach -
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+reattach to attach -
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`xpra attach ssh/oconnor@sch-boltzmann/42`
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@@ -67,19 +82,12 @@ Found the following xpra sessions:
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`xpra stop :666`
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xpra at :666 has exited.
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-Or one might have run
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+Or if you wantesd the session to end when you opened the window -
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`xpra start ssh/oconnor@sch-boltzmann/42 --start-child=xterm --window-close=shutdown`
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-,but if you accidentally close the window everything will close.
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For all systems off of the sbgrid network it will be easiest if you use the [cmcd-vpn](faq-connecting-to-cmcd-vpn).
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-If you are more linux saavy you can try tunneling your connections as well for exapmle -
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-
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-'ssh -L 4444:ja-gpu1:22 -N oconnor@crystal.harvard.edu'
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-open a new terminal and then -
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-`xpra start ssh/oconnor@localhost:4444/617 --start-child=xterm --window-close=shutdown`
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-
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-## Troubleshooting tips.
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+### Troubleshooting tips.
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Ideally you would have already set up [SSH Without a Password](faq-setting-up-passwordless-ssh)
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@@ -95,23 +103,13 @@ If there is an active session you can connect to it via `xpra attach ssh/user@ho
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There could be an active session with no windows open. Stop the session and start again.
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'xpra stop :42`
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-Lastly try to launch a session from the host in a tmux or screen session on the remote server -
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+Try to launch a session from the host in a tmux or screen session on the remote server -
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`ssh user@myhost"
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`tmux`
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`xpra start :617 --daemon=no --start-child=xterm`
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You should see a line that that contains `xpra is ready.`
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-Detach with CTRL-b - d keys and then you can attach from your own system like so
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+Detach with CTRL-b - d keys and then you can attach from your own system
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`xpra attach ssh/oconnor@sch-boltzmann/617`
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-The launching from within a tmux or screen session might be easier to experiment with other flags like "start-desktop"
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-`xpra start-desktop --start=mate-session :618 --daemon=no'
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-
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See Also
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`man xpra'
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-
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-There are a lot of features, but for our usage keep it simple.
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-
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-## xpra via https
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-
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-Work in progress - Not currently functional.
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-
hu1-gaudet-dsouza.md
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@@ -44,6 +44,7 @@ Snapshots of the Linux filesystems are taken every hour and kept for 24 hours on
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and up to 12 months. Data is also replicated to a secondary server. If you need a file restored, please contact [help@sbgrid.org](mailto:help@sbgrid.org).
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# Software
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+
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## NMRViewJ for D’Souza Lab
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To use nmrviewj you need the NMRViewj configuration files that Victoria created.
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