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/.
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. After reading few posts http://www.reddit.com/r/linuxquestions/comments/2gbgbg/what_would_be_the_best_linux_distro_for_folding/ 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)