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<p>Very cool, thanks Steve. Which do you use? <br>
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Reza Khayat, PhD
<div>Assistant Professor </div>
<div>City College of New York</div>
<div>Department of Chemistry</div>
<div>New York, NY 10031</div>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> 3dem <3dem-bounces@ncmir.ucsd.edu> on behalf of Ludtke, Steven J <sludtke@bcm.edu><br>
<b>Sent:</b> Sunday, February 3, 2019 2:38 PM<br>
<b>To:</b> frankg@bgu.ac.il<br>
<b>Cc:</b> 3dem@ncmir.ucsd.edu<br>
<b>Subject:</b> [EXTERNAL] Re: [3dem] visualization of data from a remote server</font>
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<div>
<div class="">Maybe a quick summary of some of the issues for CryoEM:</div>
<div class=""><br class="">
</div>
<div class="">1) remote X sessions</div>
<div class="">pros: </div>
<div class=""> - simple for any machine with an X-client</div>
<div class="">cons:</div>
<div class=""> - very bandwidth intensive, poor interactivity on slow links</div>
<div class=""> - often requires tricky configuration work to make OpenGL function at all</div>
<div class=""> - openGL badly broken on many clients, and slightly broken on most, not always immediately obvious</div>
<div class=""><br class="">
</div>
<div class="">2) compressed remote X sessions (NX, X2GO, etc.)</div>
<div class="">pros:</div>
<div class=""> - compression gives much improved performance</div>
<div class=""> - may support OpenGL</div>
<div class="">cons:</div>
<div class=""> - historically this has gone through many cycles of working/not working with OpenGL</div>
<div class=""> - compression based on X protocol. Great for things like word-processors, but not great for graphics/image intensive work</div>
<div class=""><br class="">
</div>
<div class="">3) TurboVNC/VirtualGL</div>
<div class="">pros:</div>
<div class=""> - developed by NSF supercomputing centers specifically for remote 3-D display</div>
<div class=""> - sends compressed image data tiles, so all rendering done on the server</div>
<div class=""> - works perfectly almost 100% of the time once configured</div>
<div class=""> - cross-platform client</div>
<div class=""> - server set up on many clusters</div>
<div class=""> - can be tunneled through SSH easily</div>
<div class="">cons:</div>
<div class=""> - rendering done server-side, so more CPU/GPU load on the server (in practice I've never seen a problem)</div>
<div class=""> - needs to be setup on server and client. Root privileges required on server</div>
<div class=""> - X2GO may be more efficient for programs which aren't graphics intensive</div>
<div class=""><br class="">
</div>
<div class="">4) Screen-sharing solutions (TeamViewer and others)</div>
<div class="">pros:</div>
<div class=""> - easy, just works</div>
<div class="">cons:</div>
<div class=""> - usually costs $</div>
<div class=""> - data routed through 3rd party service </div>
<div class=""> - network administrators do NOT like this, as it bypasses established network security and can expose the entire institutional network</div>
<div class=""> - like TurboVNC, involves compression, but may not be under user control (bandwidth sensitive)</div>
<div class=""><br class="">
<div class="">
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<font face="Courier" class=""><span class="" style="font-size:14px">--------------------------------------------------------------------------------------<br class="">
Steven Ludtke, Ph.D. <<a href="mailto:sludtke@bcm.edu" class="">sludtke@bcm.edu</a>> Baylor College of Medicine <br class="">
Charles C. Bell Jr., Professor of Structural Biology<br class="">
Dept. of Biochemistry and Molecular Biology (<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bcm.edu_biochem&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=pGKZRJHtbSTUBufrz74ICbWnAKdmU3oypG4IrnnFSSY&s=OamfHEl523bV4-MxWqYepMxI-LFxkK2ffmDdZSTfp1k&e=" class="">www.bcm.edu/biochem</a>)<br class="">
Academic Director, CryoEM Core (<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__cryoem.bcm.edu&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=pGKZRJHtbSTUBufrz74ICbWnAKdmU3oypG4IrnnFSSY&s=a_7gG6Rjk6Qv82OywEwFwpDKktvdo5PzvAUkIcAsLAs&e=" class="">cryoem.bcm.edu</a>)<br class="">
Co-Director CIBR Center (<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.bcm.edu_research_cibr&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=pGKZRJHtbSTUBufrz74ICbWnAKdmU3oypG4IrnnFSSY&s=7h6DxN3uqbos-PDyaZsMEIf99X3AOkM73WvN1dHaNyQ&e=" class="">www.bcm.edu/research/cibr</a>)<br class="">
<br class="">
</span></font><br class="">
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<blockquote type="cite" class="">
<div class="">On Feb 3, 2019, at 1:08 PM, <a href="mailto:frankg@bgu.ac.il" class="">
frankg@bgu.ac.il</a> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><font size="2" class="" style="font-family:Helvetica; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none"><b class="">***CAUTION:***
This email is not from a BCM Source. Only click links or open attachments you know are safe.</b></font><span class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important"></span>
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">Hi,</span></div>
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<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">We recently installed X2Go on our servers using the lightweight XFCE graphical environment.</span></div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">This works very well for us.</span></div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">There are versions of X2Go clients for Linux, W10 and Mac.</span></div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">Gabriel A. Frank,</span></div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)">BGU</span></div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-size:11pt; font-family:Calibri,sans-serif; color:rgb(31,73,125)"> </span></div>
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<b class=""><span class="" style="font-size:11pt; font-family:Calibri,sans-serif">From:</span></b><span class="" style="font-size:11pt; font-family:Calibri,sans-serif"><span class="Apple-converted-space"> </span>3dem [<a href="mailto:3dem-bounces@ncmir.ucsd.edu" class="" style="color:rgb(149,79,114); text-decoration:underline">mailto:3dem-bounces@ncmir.ucsd.edu</a>]<span class="Apple-converted-space"> </span><b class="">On
Behalf Of<span class="Apple-converted-space"> </span></b>Amar Dhananjai Parvate<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span><span lang="HE" dir="RTL" class="">יום א 03 פברואר 2019 20:35</span><br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Michael Elbaum <<a href="mailto:michael.elbaum@weizmann.ac.il" class="" style="color:rgb(149,79,114); text-decoration:underline">michael.elbaum@weizmann.ac.il</a>>;<span class="Apple-converted-space"> </span><a href="mailto:3dem@ncmir.ucsd.edu" class="" style="color:rgb(149,79,114); text-decoration:underline">3dem@ncmir.ucsd.edu</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [3dem] visualization of data from a remote server</span></div>
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<span class="" style="font-family:Calibri,sans-serif">Dear All</span></div>
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<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-family:Calibri,sans-serif">I am very glad to know i am not the only one with remote log in GUI visualization problems and ... even better that ppl on this forum have some solutions. </span></div>
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<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-family:Calibri,sans-serif">Here is what i am trying to do and of course its not working... </span></div>
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<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-family:Calibri,sans-serif">1) My workstation is a linux machine with Centos 7. I can access both single particle and tomography software through my home directory. </span></div>
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<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-family:Calibri,sans-serif">2) I have a Windows 10 laptop where i have installed my institute recommended Putty and Xming client for remote login</span></div>
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<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-family:Calibri,sans-serif">3) While off campus, my VPN works fine, i can log in to my workstation, access home directory and run anything command line properly. </span></div>
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<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<b class=""><span class="" style="font-family:Calibri,sans-serif">4) Issue comes when anything GUI needs to be displayed.<span class="Apple-converted-space"> </span></span></b><span class="" style="font-family:Calibri,sans-serif">I have followed several tutorials
for Putty and Xming, tried loging in to the computer via IP or<span class="Apple-converted-space"> </span><a href="mailto:user@home.edu" class="" style="color:rgb(149,79,114); text-decoration:underline">user@home.edu</a>. Have tried several local hosts for
X11 forwarding... and it doesnt seem to work. </span></div>
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<div class="">
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-family:Calibri,sans-serif">I have even tried to edit the ssh-config file. where the X11 forwarding is turned off by default. </span></div>
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<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-family:Calibri,sans-serif">Basically if i try to open a .mrc file via say 3dmod, i see the file being read in the main window but the connection is refused while displaying the zap window. </span></div>
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<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-family:Calibri,sans-serif"> </span></div>
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<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-family:Calibri,sans-serif">Be glad if anyone can share any solutions on this regard...</span></div>
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<span class="" style="font-family:Calibri,sans-serif"> </span></div>
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<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif">
<span class="" style="font-family:Calibri,sans-serif">P.S. - The Putty+X forwarding worked for my colleague who basically has the same laptop as mine, and we are in the same lab, trying to access the same set of imod GUIs. 🤔</span></div>
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<span class="" style="font-family:Calibri,sans-serif">Amar Parvate</span></div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif; background-color:white">
<span class="" style="font-family:Calibri,sans-serif">Purdue University</span></div>
<div class="" style="margin:0cm 0cm 0.0001pt; font-size:12pt; font-family:"Times New Roman",serif; background-color:white">
<span class="" style="font-family:Calibri,sans-serif">Department of Biological Sciences</span></div>
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<b class=""><span class="" style="font-size:11pt; font-family:Calibri,sans-serif">From:</span></b><span class="" style="font-size:11pt; font-family:Calibri,sans-serif"><span class="Apple-converted-space"> </span>3dem <<a href="mailto:3dem-bounces@ncmir.ucsd.edu" class="" style="color:rgb(149,79,114); text-decoration:underline">3dem-bounces@ncmir.ucsd.edu</a>>
on behalf of Michael Elbaum <<a href="mailto:michael.elbaum@weizmann.ac.il" class="" style="color:rgb(149,79,114); text-decoration:underline">michael.elbaum@weizmann.ac.il</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Sunday, February 3, 2019 10:27 AM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:3dem@ncmir.ucsd.edu" class="" style="color:rgb(149,79,114); text-decoration:underline">3dem@ncmir.ucsd.edu</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>[3dem] visualization of data from a remote server</span></div>
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<span class="" style="font-size:10pt; font-family:Tahoma,sans-serif"><br class="">
Hi all,<br class="">
<br class="">
I'm normally using a powerful server for image processing, and then I look at the data by remote ssh with X forwarding. Recently I upgraded the linux OS on my laptop (to Ubuntu 18.04) and all sorts of programs stopped working this way, including 3dmod. It turned
out to be a much broader problem having to do with OpenGL. Indirect rendering, which is what we need, is turned off by default in newer versions of X. I assume others have encountered such trouble as well. Since it took quite some digging to find a solution
I'm posting it here.<br class="">
<br class="">
For those who boot into a command line interface with a black screen and start an X session manually, (e.g., startx -- :2) the fix is simple.<span class="Apple-converted-space"> </span><br class="">
Edit the file /usr/bin/startx and change the line defaultclientargs="" to defaultclientargs="+iglx"<br class="">
+iglx allows indirect rendering by OpenGL applications.<br class="">
This is not relevant to most of us.<br class="">
<br class="">
For those who boot the computer and expect to see the graphical display right away it's a bit trickier. Ubuntu uses X or Wayland for the graphical interface, depending on the version. The solution I found is only for X, so we have to revert to that first. It's
done in two steps, as root:<br class="">
1) In the file /etc/gdm3/custom.conf, uncomment (erase the hash) the line #WaylandEnable=false. (In Ubuntu it should be enough to start GNOME in Xorg, which is one of the login options.)<br class="">
2) Create a new file /usr/share/X11/xorg.conf.d/50-iglx.conf:<br class="">
Section "ServerFlags" <span class="Apple-converted-space"> </span><br class="">
Option "AllowIndirectGLX" "on" <span class="Apple-converted-space"> </span><br class="">
Option "IndirectGLX" "on" <span class="Apple-converted-space"> </span><br class="">
EndSection<span class="Apple-converted-space"> </span><br class="">
Reboot and it should work. at your own risk, of course...<br class="">
Other distributions might put these files in different places.<br class="">
<br class="">
Here are some useful resources:<br class="">
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__www.visitusers.org_index.php-3Ftitle-3DRe-2Denabling-5FINdirect-5Fglx-5Fon-5Fyour-5FX-5Fserver&d=DwMGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=qY9gTMBGM37MS6-wNHhwW5WhlSPN9gt1MjWTiO0Y22Y&s=LK4vpKWDMPgF6hj-Tw_TcRRUYUK8yQNvD7g3hS-Wa3o&e=" class="" style="color:rgb(149,79,114); text-decoration:underline">https://www.visitusers.org/index.php?title=Re-enabling_INdirect_glx_on_your_X_server</a><br class="">
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.freedesktop.org_archives_xorg_2016-2DMay_058072.html&d=DwMGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=qY9gTMBGM37MS6-wNHhwW5WhlSPN9gt1MjWTiO0Y22Y&s=qtB13C4ftJryMYlU48WVrGF-Q8ikzbV_TJCEbD-9zWU&e=" class="" style="color:rgb(149,79,114); text-decoration:underline">https://lists.freedesktop.org/archives/xorg/2016-May/058072.html</a><br class="">
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__askubuntu.com_questions_745135_how-2Dto-2Denable-2Dindirect-2Dglx-2Dcontexts-2Diglx-2Din-2Dubuntu-2D14-2D04-2Dlts-2Dwith-2Dnvidia-2Dgfx_747088&d=DwMGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=qY9gTMBGM37MS6-wNHhwW5WhlSPN9gt1MjWTiO0Y22Y&s=dmm1y_NIZbPi1OHVN5WGTrkH8LDK0IFknU-3FYc3Tak&e=" class="" style="color:rgb(149,79,114); text-decoration:underline">https://askubuntu.com/questions/745135/how-to-enable-indirect-glx-contexts-iglx-in-ubuntu-14-04-lts-with-nvidia-gfx/747088</a><br class="">
<br class="">
There seems to be a similar issue with XQuartz on the Mac, which is addressed by reverting to the last version that worked.<br class="">
<br class="">
There was another instruction to add in the file /usr/share/lightdm/lightdm.conf.d/50-xserver-command.conf<br class="">
[SeatDefaults]<br class="">
# Dump core<br class="">
xserver-command=X -core +iglx<br class="">
but this didn't work for me.<br class="">
<br class="">
As for Wayland, typing Xwayland -h shows that the options include +iglx, but I wasn't able to find a config file for passing it startup options.<br class="">
<br class="">
A longer term solution seems to be VirtualGL or TurboVNC. Does anyone have those working with 3dem visualization software?<br class="">
<br class="">
regards,<br class="">
Michael</span></div>
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<span class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">_______________________________________________</span><br class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<span class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none; float:none; display:inline!important">3dem
mailing list</span><br class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="mailto:3dem@ncmir.ucsd.edu" class="" style="color:rgb(149,79,114); text-decoration:underline; font-family:Helvetica; font-size:18px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">3dem@ncmir.ucsd.edu</a><br class="" style="font-family:Helvetica; font-size:18px; font-style:normal; font-weight:normal; letter-spacing:normal; text-align:start; text-indent:0px; text-transform:none; white-space:normal; word-spacing:0px; text-decoration:none">
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=qY9gTMBGM37MS6-wNHhwW5WhlSPN9gt1MjWTiO0Y22Y&s=OOiMvjHx9Um0uPBBumyd_FM2TbKgtQbFuoxED5ii8to&e=" class="" style="color:rgb(149,79,114); text-decoration:underline; font-family:Helvetica; font-size:18px; font-style:normal; font-weight:normal; letter-spacing:normal; orphans:auto; text-align:start; text-indent:0px; text-transform:none; white-space:normal; widows:auto; word-spacing:0px">https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=qY9gTMBGM37MS6-wNHhwW5WhlSPN9gt1MjWTiO0Y22Y&s=OOiMvjHx9Um0uPBBumyd_FM2TbKgtQbFuoxED5ii8to&e=</a></div>
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