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You know, I think I misunderstood the question. You are talking about the image transfer being performed by the FEI software, rather than copying a file via SMB? If so, then almost certainly nothing to do with your hardware at all. Just poor software design
in handling the network transfer by FEI.
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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="http://www.bcm.edu/biochem" class="">www.bcm.edu/biochem</a>)<br class="">
Academic Director, CryoEM Core (<a href="http://cryoem.bcm.edu" class="">cryoem.bcm.edu</a>)<br class="">
Co-Director CIBR Center (<a href="http://www.bcm.edu/research/cibr" class="">www.bcm.edu/research/cibr</a>)<br class="">
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<div class="">On Oct 18, 2018, at 1:29 PM, Matthias Wolf <<a href="mailto:matthias.wolf@oist.jp" class="">matthias.wolf@oist.jp</a>> wrote:</div>
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This email is not from a BCM Source. Only click links or open attachments you know are safe.</b></font><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class=""></span>
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Hi Gene,</div>
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Don't bother with the inadequate FEI microscope PC and its gigabit network.</div>
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For proper performance, you have 2 options:<br class="">
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<li class="">get FEI's storage server and frame saving hardware (CMTS) with dedicated 10Gbit/s upload. It'll cost you $$$. Needs Win7 on the scope PC.<br class="">
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</li><li class="">set up Greg McMullans brilliant Falcon frame capture, which uses a beam splitter (fiber optical tap) to duplicate the raw camera signal and capture it on a dedicated linux PC with fast SSD. Total investment ~3k US$. This works on older Win XP systems,
but Greg has also written code for Win7 (FEI changes something in the Falcon data protocol upon upgrade to Win7). You may want to look up Chen Xu's "falcon hacking" page at Brandeis on Internet Waybackmachine. That way, the FEI system is completely bypassed
and your movie frames will be happily saved on the capture PC before you even get an image in TIA. I have done this with good success for several years until option 1 was installed in the course of a Win7+Falcon3 upgrade. You must obtain specific Solarflare
NICs for Greg's code to work and should follow his instructions to the letter (but best don't bother him and go with option 1)!</li></ol>
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Image size is 16 Mpixel * 14bit/pixel. At 18 fps, the data rate is ~4 Gb/s.</div>
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Decent hardware can deal with this. The camera can go to 32 fps or even higher, but then everything on the linux O/S must be tuned or you drop frames.</div>
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Without frame capture, you won't get decent performance - both number of frames and frame rate will be severely limited and not up to current standards of cryo-EM movie data collection.</div>
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As Steve wrote, your gigabit switch is unlikely to throttle bandwidth.<br class="">
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But the raw camera data is sent in jumbo packets. Maybe your switch is using standard MTU of 1500?</div>
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You could try changing this to use jumbo packets of 9014 bytes with telnet and the CLI.</div>
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Matthias</div>
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<div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>3dem <<a href="mailto:3dem-bounces@ncmir.ucsd.edu" class="">3dem-bounces@ncmir.ucsd.edu</a>>
on behalf of Eugene Pichkur <<a href="mailto:eugene.pichkur@gmail.com" class="">eugene.pichkur@gmail.com</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Tuesday, October 16, 2018 10:15:00 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span><a href="mailto:3dem@ncmir.ucsd.edu" class="">3dem@ncmir.ucsd.edu</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>[3dem] Falcon II uses only half of the 1Gb/s bandwidth.</font>
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<div dir="auto" class="">Hello 3DEM community,
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<div dir="auto" class="">We've noticed that our Falcon II uses only half of the 1Gbps bandwidth to transfer data from the Camera Support Rack to the Microscope PC (I've attached a screenshot to illustrate the issue). </div>
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<div dir="auto" class="">Microscope PC runs Windows 7 and we are able to get the full frame rate (20fps) from the detector, however, it takes ~20s to transfer a typical movie (40frames, 1.2GB) to the PC which is a very frustrating bottleneck. </div>
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<div dir="auto" class="">Both Falcon II and Ceta are connected through the same 1Gb switch (HPE OfficeConnect 1420 24G 2SFP), so my guess is that the bandwidth is split 50/50. However, during data collection only Falcon II is used which makes this limitation
pointless, not to mention that Falcon II and Ceta can't be used simultaneously. </div>
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<div dir="auto" class="">Does anyone have a workaround or any info on the topic?</div>
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<div dir="auto" class="">Thanks in advance,</div>
<div dir="auto" class="">Eugene Pichkur<br class="">
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<div dir="auto" class=""><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 12.8px;" class="">National Research Centre “Kurchatov Institute”<br class="">
</span><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 10pt;" class="">Akademika Kurchatova, 1, Moscow, </span><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 12.8px;" class="">Russia, </span><span style="color: rgb(34, 34, 34); font-family: arial, sans-serif; font-size: 10pt;" class="">123098</span><br class="">
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<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">3dem
mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="mailto:3dem@ncmir.ucsd.edu" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: 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; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">3dem@ncmir.ucsd.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class="">
<a href="https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=GWA2IF6nkq8sZMXHpp1Xpg&m=OolwFF628X2ftLUpz8Ras6lKj2gYG24ZfiJOoYlUzP0&s=M4xY8AZbUX0K19ncPzZDEjD1hTrbXK6xsaTCOQGNQCk&e=" style="font-family: Helvetica; font-size: 18px; font-style: normal; font-variant-caps: 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; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=GWA2IF6nkq8sZMXHpp1Xpg&m=OolwFF628X2ftLUpz8Ras6lKj2gYG24ZfiJOoYlUzP0&s=M4xY8AZbUX0K19ncPzZDEjD1hTrbXK6xsaTCOQGNQCk&e=</a></div>
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