[3dem] Falcon II uses only half of the 1Gb/s bandwidth.

Tue Oct 16 18:47:22 PDT 2018

Ok, can't comment specifically on the Falcon, but this seems more a computer issue than a camera issue.

Unless you are storing your data on an external drive (USB portable drive or similar) it is almost certainly not the disk speed. Even a cheap spinning platter internal drive can manage 100-120 MB/s sustained write, and most will do ~150 nowadays. The theoretical peak for a 1 Gbps network is 120 MB/s and with overhead, 100 - 110 MB/s is a practical limit for the network. Non-SSD external USB drives (yes, even USB3/C) typically max out at ~50 MB/s.

It is almost certainly not the network switch. There really aren't any half-duplex switches any more, and it looks like the one you have has a 32 Gbps backplane, so should not be a bottleneck.

In most cases, the real issue is the configuration of the shared filesystem on the Windows PC.  The K2 computers have a 10 Gbps port generally used for transfer to the microscope PC, and there, tuning the filesystem parameters (and having a sufficiently fast set of drives on the microscope PC) are critical to getting good throughput. So:

1) no writing directly to shared external drives
2) check your shared filesystem configuration (if that's what you're using to move the images)
3) if you're moving the images some other way (sftp/scp or somesuch), we need to know that to comment

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Steven Ludtke, Ph.D. <sludtke at bcm.edu<mailto:sludtke at bcm.edu>>                      Baylor College of Medicine
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem<http://www.bcm.edu/biochem>)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu<http://cryoem.bcm.edu>)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr<http://www.bcm.edu/research/cibr>)

On Oct 16, 2018, at 8:02 PM, Sargis Dallakyan <sargis at nysbc.org<mailto:sargis at nysbc.org>> wrote:

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Just to break an ice on this topic, what kind of disk is on a PC that you are transferring the data to? It's been mentioned in one of the latest DDN videos<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_watch-3Fv-3DNabTsYl-5FmIQ-26list-3DPLohLhg8SlVmbG8W-5FTFIWQFFhg1LJ0-2Dxf1&d=DwMFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=4ZvqXtesRM4IBU-zUAPbIdFLZVEo1F1tixUiF6vUDKE&s=KUru33P_2mVMifpXMF33Nyz25BpRHmbk-Tg64ZHkg2I&e=> that no matter how big is your bandwidth, you'll be disk IO limited if your storage can't support enough IOPS (https://en.wikipedia.org/wiki/IOPS<https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_IOPS&d=DwMFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=4ZvqXtesRM4IBU-zUAPbIdFLZVEo1F1tixUiF6vUDKE&s=0wiVG1LvTlAYZBXD_HJ_va_utU5R50hVDaW1XSqarA8&e=>). Maybe getting an SSD might solve this bottleneck, if I understand the problem correctly.

Respectfully,
Sargis Dallakyan, PhD - Systems Administrator
National Resource for Automated Molecular Microscopy
Simons Electron Microscopy Center
New York Structural Biology Center
http://emg.nysbc.org/redmine/users/105<https://urldefense.proofpoint.com/v2/url?u=http-3A__emg.nysbc.org_redmine_users_105&d=DwMFAw&c=ZQs-KZ8oxEw0p81sqgiaRA&r=Dk5VoQQ-wINYVssLMZihyC5Dj_sWYKxCyKz9E4Lp3gc&m=4ZvqXtesRM4IBU-zUAPbIdFLZVEo1F1tixUiF6vUDKE&s=DK8kFnGbasHV5hu6_1CAytIhdp2d9bx8DhSXEt0od1U&e=>

Date: Tue, 16 Oct 2018 16:15:00 +0300
From: Eugene Pichkur <eugene.pichkur at gmail.com<mailto:eugene.pichkur at gmail.com>>
To: 3dem at ncmir.ucsd.edu<mailto:3dem at ncmir.ucsd.edu>
Subject: [3dem] Falcon II uses only half of the 1Gb/s bandwidth.
Message-ID:
        <CAJJJP0=9cSHBRxKLOQkaYmqvg3X6Ym4iq-DT_oMCvNYERErr4w at mail.gmail.com<mailto:CAJJJP0=9cSHBRxKLOQkaYmqvg3X6Ym4iq-DT_oMCvNYERErr4w at mail.gmail.com>>
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Hello 3DEM community,

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).

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.

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.

Does anyone have a workaround or any info on the topic?

Thanks in advance,
Eugene Pichkur

National Research Centre ?Kurchatov Institute?
Akademika Kurchatova, 1, Moscow, Russia, 123098
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