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<p class="MsoNormal"><span lang="DE" style="mso-fareast-language:EN-US">Thanky you Sylvain,
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="mso-fareast-language:EN-US">Added on the to do list, yes I guess we can try with SCP<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">De : </span></b><span style="font-size:12.0pt;color:black">Trepout Sylvain <Sylvain.Trepout@curie.fr><br>
<b>Date : </b>jeudi, 21 décembre 2017 à 15:10<br>
<b>À : </b>Steven Ludtke <sludtke@bcm.edu>, Benoît Zuber <benoit.zuber@ana.unibe.ch><br>
<b>Cc : </b>"3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
<b>Objet : </b>RE: [3dem] Slow connection linux - falcon3 server<o:p></o:p></span></p>
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<p><span style="font-size:12.0pt;color:black">Hi Benoit,<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">CIFS is a specific protocol of SAMBA that has been created to read UNIX mounted drives from Windows machines.<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Since you want to perform file transfer from the opposite direction, you might want to use SAMBA instead of CIFS.<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Though I'm not sure if it will drastically increase the speed.<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Can you use command line operations instead ?<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">SCP should perform much better.<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Best,<o:p></o:p></span></p>
<p><span style="font-size:12.0pt;color:black">Sylvain<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;color:black">----------<br>
Sylvain TREPOUT<br>
Ingénieur de Recherche Inserm<br>
Institut Curie / INSERM U1196<br>
Campus Universitaire d'Orsay, Bat 112<br>
91405 Orsay cedex FRANCE<br>
Phone : +33 1 69 86 31 96<br>
Fax : +33 1 69 07 53 27<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">De :</span></b><span style="color:black"> 3dem <3dem-bounces@ncmir.ucsd.edu> de la part de Ludtke, Steven J <sludtke@bcm.edu><br>
<b>Envoyé :</b> jeudi 21 décembre 2017 14:56:24<br>
<b>À :</b> benoit.zuber@ana.unibe.ch<br>
<b>Cc :</b> 3dem@ncmir.ucsd.edu<br>
<b>Objet :</b> Re: [3dem] Slow connection linux - falcon3 server</span><span style="font-size:12.0pt;color:black">
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Sorry, missed the fast windows -> windows transfer comment in the original message.
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">We went through similar sort of issue when configuring our K2 acquisition computer (windows) to a Linux GPU workstation with 8 drive RAID, also over 10Gb fiber. In our case we were trying to mount
the Linux RAID as a volume on the K2 computer so we could just directly store frames there during acquisition. Similar to your experience we discovered that the performance of the NFS module in Windows is abysmal, even after tuning.
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">Strangely, the approach that gave the best performance was using SMB to share the Linux drive to the Windows machine. I don't remember the final performance numbers (we set this up some time ago),
but I'm pretty sure it was coming in at around 500 MB/s. No other approach we tried gave decent bandwidth.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Courier",serif;color:black">--------------------------------------------------------------------------------------<br>
Steven Ludtke, Ph.D.<br>
Charles C. Bell Jr., Professor of Structural Biology<br>
Dept. of Biochemistry and Molecular Biology (<a href="http://www.bcm.edu/biochem">www.bcm.edu/biochem</a>)
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Co-Director CIBR Center (<a href="http://www.bcm.edu/research/cibr">www.bcm.edu/research/cibr</a>)
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Co-Director National Center For Macromolecular Imaging (<a href="http://ncmi.bcm.edu">ncmi.bcm.edu</a>)
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of Medicine - Houston, TX</span></a><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-top:15.0pt;line-height:15.0pt"><span style="font-size:10.5pt;font-family:"Tahoma",sans-serif;color:#666666">To develop technology for near-atomic resolution structure determination and modeling of molecular nanomachines by
electron cryo-microscopy(cryo-EM), computer reconstruction and structure mining.
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Baylor College of Medicine <br>
<a href="mailto:sludtke@bcm.edu">sludtke@bcm.edu</a></span><span style="font-size:12.0pt;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black">On Dec 21, 2017, at 6:32 AM,
<a href="mailto:benoit.zuber@ana.unibe.ch">benoit.zuber@ana.unibe.ch</a> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">Hi Steve,</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">Thanks for your reply. It has 12 disks in RAID (not sure what type). I don’t think this is the problem since when we connect another windows machine to it, files can be transfered
high speed in both directions.<span class="apple-converted-space"> </span></span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">Benoit</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><b><span style="font-size:12.0pt;color:black">De :<span class="apple-converted-space"> </span></span></b><span style="font-size:12.0pt;color:black">Steven Ludtke <<a href="mailto:sludtke@bcm.edu">sludtke@bcm.edu</a>><br>
<b>Date :<span class="apple-converted-space"> </span></b>jeudi, 21 décembre 2017 à 14:06<br>
<b>À :<span class="apple-converted-space"> </span></b>Benoît Zuber <<a href="mailto:benoit.zuber@ana.unibe.ch">benoit.zuber@ana.unibe.ch</a>><br>
<b>Cc :<span class="apple-converted-space"> </span></b>"<a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a>" <<a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a>><br>
<b>Objet :<span class="apple-converted-space"> </span></b>Re: [3dem] Slow connection linux - falcon3 server</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">Hi Benoit,<span class="apple-converted-space"> </span><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">what sort of storage is being used to store the files in question on the FEI server? Your description sounds like the files being transferred are on a single 'spinning platter' hard drive,
which will generally max out in data I/O at 150-200 MB/s. Most machines used for storing high bandwidth data will either use a RAID 5/6 array of traditional hard drive (which can achieve 1000-2000 MB/s depending on the number of drives) or high speed SSDs
which will max out at ~600 MB/s on a standard SATA bus, but can achieve 1000-3000 MB/s if alternative interfaces are used.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.5pt;font-family:"Courier",serif;color:black">--------------------------------------------------------------------------------------<br>
Steven Ludtke, Ph.D.<br>
Charles C. Bell Jr., Professor of Structural Biology<br>
Dept. of Biochemistry and Molecular Biology (<a href="http://www.bcm.edu/biochem"><span style="color:purple">www.bcm.edu/biochem</span></a>)<br>
Co-Director CIBR Center (<a href="http://www.bcm.edu/research/cibr"><span style="color:purple">www.bcm.edu/research/cibr</span></a>)<br>
Co-Director National Center For Macromolecular Imaging (<a href="http://ncmi.bcm.edu/"><span style="color:purple">ncmi.bcm.edu</span></a>)<br>
Baylor College of Medicine <br>
<a href="mailto:sludtke@bcm.edu"><span style="color:purple">sludtke@bcm.edu</span></a></span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">On Dec 21, 2017, at 4:19 AM,<span class="apple-converted-space"> </span><a href="mailto:benoit.zuber@ana.unibe.ch"><span style="color:purple">benoit.zuber@ana.unibe.ch</span></a><span class="apple-converted-space"> </span>wrote:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><b><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:black;background:white">***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.</span></b><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">Dear all</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">We have a linux workstation connected directly through fiber optics to the so-called FEI server, i.e. the computer where Falcon3 saves frames, which runs under Windows. Strangely,
file transfer from linux to windows is fast (600 MB/s) whereas file transfer from windows to linux is slow (160 MB/s). We have tried mounting the windows drive on linux through cifs or nfs, as well as mounting the linux drive on windows through nfs and we
always get the same result.</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">We also tested windows to windows (we connected another windows machine to the fei server) : fast both ways. And we tested linux to linux : fast both ways</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">We tested network speed using iperf, and it is high in either direction. It is only when we transfer files that we have problems.</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">Any suggestion welcome.</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">Thanks</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">Benoit</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">-- <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">Prof. Benoît Zuber</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">University of Bern</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">Institute of Anatomy</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">Baltzerstrasse 2</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black">Postfach 922<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">3000 Bern 9</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black"> </span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span lang="DE" style="color:black">+41 31 631 84 40</span><span style="color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:13.5pt;font-family:"Helvetica",sans-serif;color:black;background:white">_______________________________________________</span><span style="font-size:13.5pt;font-family:"Helvetica",sans-serif;color:black"><br>
<span style="background:white">3dem mailing list</span><br>
</span><span style="color:black"><a href="mailto:3dem@ncmir.ucsd.edu"><span style="font-size:13.5pt;font-family:"Helvetica",sans-serif;color:#954F72;background:white">3dem@ncmir.ucsd.edu</span></a></span><span style="font-size:13.5pt;font-family:"Helvetica",sans-serif;color:black"><br>
</span><span style="color:black"><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=iM30kDS0pjLFsoGLC5GUR_9aRscO2JMiBlLeuLAqe-k&s=c228ksyoRZn9VrDIqrz1-8wQz_j3mEiCm-er4g6mrFE&e="><span style="font-size:13.5pt;font-family:"Helvetica",sans-serif;color:#954F72;background:white">https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.ncmir.ucsd.edu_mailman_listinfo_3dem&d=DwICAg&c=ZQs-KZ8oxEw0p81sqgiaRA&r=GWA2IF6nkq8sZMXHpp1Xpg&m=iM30kDS0pjLFsoGLC5GUR_9aRscO2JMiBlLeuLAqe-k&s=c228ksyoRZn9VrDIqrz1-8wQz_j3mEiCm-er4g6mrFE&e=</span></a><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;color:black"><o:p> </o:p></span></p>
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