[3dem] Slow connection linux - falcon3 server

Kasim Sader kasim.sader at gmail.com
Fri Dec 22 04:01:24 PST 2017


Hi Benoit,
I use the same setup as Steve - Linux SMB shares mounted on (many) windows
machines, and I get 800MB/s from the Gatan PC SSD RAID array (Windows) to
my large Linux storage box. You do need to alter your windows host file
though to point to the IP address, otherwise you cannot unmount the drive
easily (a windows bug).
Best regards,
Kasim


*Dr. Kasim Sader*

Staff Scientist

Operational Lead

Cambridge CryoEM Pharmaceutical Consortium

Thermo Fisher Scientific

Tel +447342882058

kasim.sader at thermofisher.com

Sent from my iPhone

On 21 dec. 2017, at 14:44, <benoit.zuber at ana.unibe.ch> <
benoit.zuber at ana.unibe.ch> wrote:

Thanky you Sylvain,

Added on the to do list, yes I guess we can try with SCP



*De : *Trepout Sylvain <Sylvain.Trepout at curie.fr>
*Date : *jeudi, 21 décembre 2017 à 15:10
*À : *Steven Ludtke <sludtke at bcm.edu>, Benoît Zuber <
benoit.zuber at ana.unibe.ch>
*Cc : *"3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
*Objet : *RE: [3dem] Slow connection linux - falcon3 server



Hi Benoit,



CIFS is a specific protocol of SAMBA that has been created to read UNIX
mounted drives from Windows machines.

Since you want to perform file transfer from the opposite direction, you
might want to use SAMBA instead of CIFS.

Though I'm not sure if it will drastically increase the speed.



Can you use command line operations instead ?

SCP should perform much better.



Best,

Sylvain

----------
Sylvain TREPOUT
Ingénieur de Recherche Inserm
Institut Curie / INSERM U1196
Campus Universitaire d'Orsay, Bat 112
91405 Orsay cedex FRANCE
Phone : +33 1 69 86 31 96 <+33%201%2069%2086%2031%2096>
Fax : +33 1 69 07 53 27 <+33%201%2069%2007%2053%2027>
------------------------------

*De :* 3dem <3dem-bounces at ncmir.ucsd.edu> de la part de Ludtke, Steven J <
sludtke at bcm.edu>
*Envoyé :* jeudi 21 décembre 2017 14:56:24
*À :* benoit.zuber at ana.unibe.ch
*Cc :* 3dem at ncmir.ucsd.edu
*Objet :* Re: [3dem] Slow connection linux - falcon3 server



Sorry, missed the fast windows -> windows transfer comment in the original
message.



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.



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.



------------------------------------------------------------
--------------------------
Steven Ludtke, Ph.D.
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (
www.bcm.edu/biochem)

[image: mage supprimée par l’expéditeur.] <http://www.bcm.edu/biochem>

Biochemistry & Molecular Biology | Baylor College of Medicine | Houston,
Texas <http://www.bcm.edu/biochem>

www.bcm.edu

The overview page for the Department of Biochemistry & Molecular Biology.



Co-Director CIBR Center                                    (
www.bcm.edu/research/cibr)

[image: mage supprimée par l’expéditeur.] <http://www.bcm.edu/research/cibr>

Computational and Integrative Biomedical Research Center | Research |
Baylor College of Medicine | Houston, Texas
<http://www.bcm.edu/research/cibr>

www.bcm.edu

Computational and Integrative Biomedical Research Center



Co-Director National Center For Macromolecular Imaging                  (
ncmi.bcm.edu)

- NCMI CryoEM- Baylor College of Medicine - Houston, TX
<http://ncmi.bcm.edu/>

ncmi.bcm.edu

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.



Baylor College of Medicine
sludtke at bcm.edu



On Dec 21, 2017, at 6:32 AM, benoit.zuber at ana.unibe.ch wrote:



Hi Steve,



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.



Benoit



*De : *Steven Ludtke <sludtke at bcm.edu>
*Date : *jeudi, 21 décembre 2017 à 14:06
*À : *Benoît Zuber <benoit.zuber at ana.unibe.ch>
*Cc : *"3dem at ncmir.ucsd.edu" <3dem at ncmir.ucsd.edu>
*Objet : *Re: [3dem] Slow connection linux - falcon3 server



Hi Benoit,

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.



------------------------------------------------------------
--------------------------
Steven Ludtke, Ph.D.
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (
www.bcm.edu/biochem)
Co-Director CIBR Center                                    (
www.bcm.edu/research/cibr)
Co-Director National Center For Macromolecular Imaging                  (
ncmi.bcm.edu)
Baylor College of Medicine
sludtke at bcm.edu




On Dec 21, 2017, at 4:19 AM, benoit.zuber at ana.unibe.ch wrote:



****CAUTION:*** This email is not from a BCM Source. Only click links or
open attachments you know are safe.*
------------------------------

Dear all



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.



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



We tested network speed using iperf, and it is high in either direction. It
is only when we transfer files that we have problems.



Any suggestion welcome.



Thanks

Benoit



-- 

Prof. Benoît Zuber

University of Bern

Institute of Anatomy

Baltzerstrasse 2

Postfach 922

3000 Bern 9



+41 31 631 84 40 <+41%2031%20631%2084%2040>

_______________________________________________
3dem mailing list
3dem at ncmir.ucsd.edu
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=





_______________________________________________
3dem mailing list
3dem at ncmir.ucsd.edu
https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ncmir.ucsd.edu/pipermail/3dem/attachments/20171222/32ef7c9b/attachment-0001.html>


More information about the 3dem mailing list