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

Is the code running in the 'single system' the same running in parallel 
?
Is the software using network efficiently ?
What about network traffic ? It's high ?
Why do you need a layer 3 ? Are cluster's nodes in different network ?
I'm not sure if your problem is network bottleneck.

On 2014-10-14 11:42, suresh kannan wrote:
> 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 [6]
> 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]
>>> [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]
>>> [2]. After reading few posts
>>> 
>> 
> http://www.reddit.com/r/linuxquestions/comments/2gbgbg/what_would_be_the_best_linux_distro_for_folding/
>>> [3]
>>> [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/
>>> [1]
>>> [2]
>>> 
>> 
> http://flakrat.blogspot.kr/2013/04/how-to-compile-gromacs-461-with-openmpi.html
>>> [2]
>>> [3]
>>> 
>> 
> http://www.reddit.com/r/linuxquestions/comments/2gbgbg/what_would_be_the_best_linux_distro_for_folding/
>>> [3]
>> 
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> 
> 
> 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/
> [4] https://mayfirst.org
> [5] 
> https://lists.debian.org/[email protected]
> [6] http://cs.boisestate.edu/%7Eamit/research/beowulf/beowulf-setup.pdf

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