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

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/

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