Re: Beowulf Cluster is very slow. Suggestions needed to increase the speed.

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Hi,

>>>First of all, why do you think network is the bottleneck?

Thank you for your concern.

If i run a specific job in a single system (without parallel) it showed
three months (aprox) time in a quad core processor.  When i did parallel
using four systems it showed October 2015. I was using 100 Mpbs (ip time
router). I have conformed that all the systems uses the processors [using
"top" command]. After that TooMeeK point out i have to use "Gigabit routing
switch supporting layer 3". I dont have that switch in our lab. However, we
had Netgear GS608 1000 Mpbs switch it reduced the time (Feb 2015).
Moreover, I read the link
http://cs.boisestate.edu/~amit/research/beowulf/beowulf-setup.pdf suggested
by TooMeek. They have also suggested that Network switch is important.
Also, I saw few videos in youtube about layer 3 switch capabilities.
Therefore, I am convinced that "Gigabit routing switch supporting layer 3"
will solve this issue.

regards
Suresh





On Tue, Oct 14, 2014 at 4:40 AM, Rogerio Bastos <
[email protected]> wrote:

> First of all, why do you think network is the bottleneck?
> Be sure of this before spend money with network equipments!
>
> On 2014-10-07 00:50, suresh kannan wrote:
>
>> I am an Indian student in suwon, korea. I built a Beowulf cluster
>> (system information below) with four systems in our lab for our
>> simulation work with the help of good tutorials. In those tutorials
>> they have mentioned all the system should have static ip addresses.
>> Unfortunately, in all our labs we have been provided with dynamic ip
>> address[5 ips for 15 members in three separate labs]. I have requested
>> four more ip's from our university system admin. Due to the language
>> problems, i conveyed the requirement through my korean lab mate and i
>> dont know the reason why he denied us the static ip. So i found
>> another way to skip this procedure
>> http://www.reddit.com/r/linuxquestions/comments/
>> 2gubad/why_static_ip_address_is_necessary_for_linux/
>> [1].
>>
>> Someone suggested to use a router (one static ip) and set static ip
>> for the four computers through a router. I did that and it worked.
>> However, the cluster is very slow. For instance If i submit my
>> simulation job in a single computer [4 core processor], it takes 2
>> months to complete a specific job. Although, if i connect 4 systems it
>> shows it take 6 months to complete the same job. It is actually using
>> 10 core processor [3,3,2,2-100% each]. I used TOP command to see how
>> much processor the head and other nodes are using. I have used openMPI
>> to do parallel the systems. I am using GROMACS (Parallelization based
>> on MPI has been part of this software). I followed a parallel
>> configuration for the Gromacs with the help of this tutorial
>> http://flakrat.blogspot.kr/2013/04/how-to-compile-
>> gromacs-461-with-openmpi.html
>> [2]. After reading few posts
>> http://www.reddit.com/r/linuxquestions/comments/
>> 2gbgbg/what_would_be_the_best_linux_distro_for_folding/
>> [3] i suspected the network router might be an issue.
>>
>>
>> Can you suggest me how can i troubleshoot this problem? Some one
>> suggested to use 2 network ports and make linux as a router and use a
>> gigabitswitch to get the speed. However, we dont have 2 network ports
>> system. If this is compulsory i can buy network ports (USB one).
>>
>> Where do i start now?
>>
>> Can i make my head node as a router and use USB network port (for the
>> second network port) and connect to a gigabitswitch (any model
>> suggestion?) to connect other nodes. I dont know much about networking
>> stuffs. It will be helpful if any experts can suggest to troubleshoot
>> this issue.
>>
>> Thank you for your time.
>>
>> regards
>>
>> Suresh
>>
>> System Informations
>> Head node Processor : Intel core i3
>> RAM : 1 GB
>> No. of processor : 4
>> Network cards : 03:00.0 Ethernet controller: Realtek Semiconductor
>> Co., Ltd. RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller
>> (rev 06)
>> System company : Samsung
>> Architecture : x86_64
>> OS flavour : Linux Mint 17 Qiana
>>
>> Node1 Processor : Intel Quad core
>> RAM : 3 GB
>> No. of processor : 4
>> Network cards : 03:00.0 Ethernet controller: Realtek Semiconductor
>> Co., Ltd. RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller
>> (rev 02)
>> System company : TG DREAMSYS
>> Architecture : x86_64
>> OS flavour : Linux Mint 17 Qiana
>>
>> Node2 Processor : Intel core i3
>> RAM : 1 GB
>> No. of processor : 4
>> Network cards : 03:00.0 Ethernet controller: Realtek Semiconductor
>> Co., Ltd. RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller
>> (rev 06)
>> System company : Samsung Architecture : x86_64
>> OS flavour : Linux Mint 17 Qiana
>>
>> Node3 Processor : Intel core i3
>> RAM : 1 GB
>> No. of processor : 2 Network cards : 02:00.0 Ethernet controller :
>> Qualcomm Atheros Attansic L2 Fast Ethernet (rev a0)
>> System company : JOOYONTECH
>> Architecture : x86_64
>> OS flavour : Linux Mint 17 Qiana
>>
>> Router Company : ipTIME N604R
>> Maximum speed : 160Mbps (LAN to WAN)
>>
>> Links:
>> ------
>> [1]
>> http://www.reddit.com/r/linuxquestions/comments/
>> 2gubad/why_static_ip_address_is_necessary_for_linux/
>> [2]
>> http://flakrat.blogspot.kr/2013/04/how-to-compile-
>> gromacs-461-with-openmpi.html
>> [3]
>> http://www.reddit.com/r/linuxquestions/comments/
>> 2gbgbg/what_would_be_the_best_linux_distro_for_folding/
>>
>
> --
>
> My email was sent by May First/People Link
> https://mayfirst.org
>
>
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> To UNSUBSCRIBE, email to [email protected]
> with a subject of "unsubscribe". Trouble? Contact
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> Archive: https://lists.debian.org/40cfbd085315754eb7f15af3a3dfc9
> [email protected]
>
>

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<div dir=3D"ltr"><div><div>Hi,<br><br>&gt;&gt;&gt;First of all, why do you =
think network is the bottleneck?<br><br><span class=3D"im">Thank you for yo=
ur concern.</span><br></div><br>If i run a specific job in a single system =
(without parallel) it showed three months (aprox) time in a quad core proce=
ssor.=C2=A0 When i did parallel using four systems it showed October 2015. =
I was using 100 Mpbs (ip time router). I have conformed that all the system=
s uses the processors [using &quot;top&quot; command]. After that TooMeeK p=
oint out i have to use &quot;Gigabit routing switch supporting layer 3&quot=
;. I dont have that switch in our lab. However, we had Netgear GS608 1000 M=
pbs switch it reduced the time (Feb 2015). Moreover, I read the link <a hre=
f=3D"http://cs.boisestate.edu/%7Eamit/research/beowulf/beowulf-setup.pdf" t=
arget=3D"_blank">http://cs.boisestate.edu/~amit/research/beowulf/beowulf-se=
tup.pdf</a> suggested by TooMeek. They have also suggested that Network swi=
tch is important.=C2=A0 Also, I saw few videos in youtube about layer 3 swi=
tch capabilities. Therefore, I am convinced that &quot;Gigabit routing swit=
ch supporting layer 3&quot; will solve this issue.<br><br></div><div>regard=
s<br></div><div>Suresh<br></div><div><br><div><br><br><br></div></div></div=
><div class=3D"gmail_extra"><br><div class=3D"gmail_quote">On Tue, Oct 14, =
2014 at 4:40 AM, Rogerio Bastos <span dir=3D"ltr">&lt;<a href=3D"mailto:wri=
[email protected]" target=3D"_blank">[email protected]</=
a>&gt;</span> wrote:<br><blockquote class=3D"gmail_quote" style=3D"margin:0=
 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">First of all, why do=
 you think network is the bottleneck?<br>
Be sure of this before spend money with network equipments!<span class=3D""=
><br>
<br>
On 2014-10-07 00:50, suresh kannan wrote:<br>
</span><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-=
left:1px #ccc solid;padding-left:1ex"><span class=3D"">
I am an Indian student in suwon, korea. I built a Beowulf cluster<br>
(system information below) with four systems in our lab for our<br>
simulation work with the help of good tutorials. In those tutorials<br>
they have mentioned all the system should have static ip addresses.<br>
Unfortunately, in all our labs we have been provided with dynamic ip<br>
address[5 ips for 15 members in three separate labs]. I have requested<br>
four more ip&#39;s from our university system admin. Due to the language<br=
>
problems, i conveyed the requirement through my korean lab mate and i<br>
dont know the reason why he denied us the static ip. So i found<br>
another way to skip this procedure<br>
<a href=3D"http://www.reddit.com/r/linuxquestions/comments/2gubad/why_stati=
c_ip_address_is_necessary_for_linux/" target=3D"_blank">http://www.reddit.c=
om/r/<u></u>linuxquestions/comments/<u></u>2gubad/why_static_ip_address_<u>=
</u>is_necessary_for_linux/</a><br></span>
[1].<span class=3D""><br>
<br>
Someone suggested to use a router (one static ip) and set static ip<br>
for the four computers through a router. I did that and it worked.<br>
However, the cluster is very slow. For instance If i submit my<br>
simulation job in a single computer [4 core processor], it takes 2<br>
months to complete a specific job. Although, if i connect 4 systems it<br>
shows it take 6 months to complete the same job. It is actually using<br>
10 core processor [3,3,2,2-100% each]. I used TOP command to see how<br>
much processor the head and other nodes are using. I have used openMPI<br>
to do parallel the systems. I am using GROMACS (Parallelization based<br>
on MPI has been part of this software). I followed a parallel<br>
configuration for the Gromacs with the help of this tutorial<br>
<a href=3D"http://flakrat.blogspot.kr/2013/04/how-to-compile-gromacs-461-wi=
th-openmpi.html" target=3D"_blank">http://flakrat.blogspot.kr/<u></u>2013/0=
4/how-to-compile-<u></u>gromacs-461-with-openmpi.html</a><br></span>
[2]. After reading few posts<br>
<a href=3D"http://www.reddit.com/r/linuxquestions/comments/2gbgbg/what_woul=
d_be_the_best_linux_distro_for_folding/" target=3D"_blank">http://www.reddi=
t.com/r/<u></u>linuxquestions/comments/<u></u>2gbgbg/what_would_be_the_best=
_<u></u>linux_distro_for_folding/</a><br>
[3] i suspected the network router might be an issue.<div><div class=3D"h5"=
><br>
<br>
Can you suggest me how can i troubleshoot this problem? Some one<br>
suggested to use 2 network ports and make linux as a router and use a<br>
gigabitswitch to get the speed. However, we dont have 2 network ports<br>
system. If this is compulsory i can buy network ports (USB one).<br>
<br>
Where do i start now?<br>
<br>
Can i make my head node as a router and use USB network port (for the<br>
second network port) and connect to a gigabitswitch (any model<br>
suggestion?) to connect other nodes. I dont know much about networking<br>
stuffs. It will be helpful if any experts can suggest to troubleshoot<br>
this issue.<br>
<br>
Thank you for your time.<br>
<br>
regards<br>
<br>
Suresh<br>
<br>
System Informations<br>
Head node Processor : Intel core i3<br>
RAM : 1 GB<br>
No. of processor : 4<br>
Network cards : 03:00.0 Ethernet controller: Realtek Semiconductor<br>
Co., Ltd. RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller<br>
(rev 06)<br>
System company : Samsung<br>
Architecture : x86_64<br>
OS flavour : Linux Mint 17 Qiana<br>
<br>
Node1 Processor : Intel Quad core<br>
RAM : 3 GB<br>
No. of processor : 4<br>
Network cards : 03:00.0 Ethernet controller: Realtek Semiconductor<br>
Co., Ltd. RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller<br>
(rev 02)<br>
System company : TG DREAMSYS<br>
Architecture : x86_64<br>
OS flavour : Linux Mint 17 Qiana<br>
<br>
Node2 Processor : Intel core i3<br>
RAM : 1 GB<br>
No. of processor : 4<br>
Network cards : 03:00.0 Ethernet controller: Realtek Semiconductor<br>
Co., Ltd. RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller<br>
(rev 06)<br>
System company : Samsung Architecture : x86_64<br>
OS flavour : Linux Mint 17 Qiana<br>
<br>
Node3 Processor : Intel core i3<br>
RAM : 1 GB<br>
No. of processor : 2 Network cards : 02:00.0 Ethernet controller :<br>
Qualcomm Atheros Attansic L2 Fast Ethernet (rev a0)<br>
System company : JOOYONTECH<br>
Architecture : x86_64<br>
OS flavour : Linux Mint 17 Qiana<br>
<br>
Router Company : ipTIME N604R<br>
Maximum speed : 160Mbps (LAN to WAN)<br>
<br></div></div>
Links:<br>
------<br>
[1]<br>
<a href=3D"http://www.reddit.com/r/linuxquestions/comments/2gubad/why_stati=
c_ip_address_is_necessary_for_linux/" target=3D"_blank">http://www.reddit.c=
om/r/<u></u>linuxquestions/comments/<u></u>2gubad/why_static_ip_address_<u>=
</u>is_necessary_for_linux/</a><br>
[2]<br>
<a href=3D"http://flakrat.blogspot.kr/2013/04/how-to-compile-gromacs-461-wi=
th-openmpi.html" target=3D"_blank">http://flakrat.blogspot.kr/<u></u>2013/0=
4/how-to-compile-<u></u>gromacs-461-with-openmpi.html</a><br>
[3]<br>
<a href=3D"http://www.reddit.com/r/linuxquestions/comments/2gbgbg/what_woul=
d_be_the_best_linux_distro_for_folding/" target=3D"_blank">http://www.reddi=
t.com/r/<u></u>linuxquestions/comments/<u></u>2gbgbg/what_would_be_the_best=
_<u></u>linux_distro_for_folding/</a><br>
</blockquote>
<br>
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My email was sent by May First/People Link<br>
<a href=3D"https://mayfirst.org" target=3D"_blank">https://mayfirst.org</a>=
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Archive: <a href=3D"https://lists.debian.org/40cfbd085315754eb7f15af3a3dfc9=
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<br>
</blockquote></div><br></div>

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