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

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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)

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<div dir=3D"ltr">I am an=20
Indian student in suwon, korea. I built a Beowulf cluster (system=20
information below) with four systems in our lab for our simulation work=20
with the help of good tutorials. In those tutorials they have mentioned=20
all the system should have static ip addresses. Unfortunately, in all=20
our labs we have been provided with dynamic ip address[5 ips for 15=20
members in three separate labs]. I have requested four more ip&#39;s from=
=20
our university system admin. Due to the language problems, i conveyed=20
the requirement through my korean lab mate and i dont know the reason=20
why he denied us the static ip. So i found another way to skip this=20
procedure <a href=3D"http://www.reddit.com/r/linuxquestions/comments/2gubad=
/why_static_ip_address_is_necessary_for_linux/" target=3D"_blank">http://ww=
w.reddit.com/r/linuxquestions/comments/2gubad/why_static_ip_address_is_nece=
ssary_for_linux/</a>.=20

<p>Someone suggested to use a router (one static ip) and set static ip=20
for the four computers through a router. I did that and it worked.=20
However, the cluster is very slow. For instance If i submit my=20
simulation job in a single computer [4 core processor], it takes 2=20
months to complete a specific job. Although, if i connect 4 systems it=20
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=20
processor the head and other nodes are using. I have used openMPI to do=20
parallel the systems. I am using GROMACS (Parallelization based on MPI=20
has been part of this software). I followed a parallel configuration for th=
e Gromacs with the help of this tutorial <a href=3D"http://flakrat.blogspot=
.kr/2013/04/how-to-compile-gromacs-461-with-openmpi.html" target=3D"_blank"=
>http://flakrat.blogspot.kr/2013/04/how-to-compile-gromacs-461-with-openmpi=
.html</a>. After reading few posts <a href=3D"http://www.reddit.com/r/linux=
questions/comments/2gbgbg/what_would_be_the_best_linux_distro_for_folding/"=
 target=3D"_blank">http://www.reddit.com/r/linuxquestions/comments/2gbgbg/w=
hat_would_be_the_best_linux_distro_for_folding/</a> i suspected the network=
 router might be an issue.</p>

<p>Can you suggest me how can i troubleshoot this problem? Some one=20
suggested to use 2 network ports and make linux as a router and use a=20
gigabitswitch to get the speed. However, we dont have 2 network ports=20
system. If this is compulsory i can buy network ports (USB one). <br></p><p=
>Where do i start now?</p><p>Can
 i make my head node as a router and use USB network port (for the=20
second network port) and connect to a gigabitswitch (any model=20
suggestion?) to connect other nodes. I dont know much about networking=20
stuffs. It will be helpful if any experts can suggest to troubleshoot=20
this issue.<br></p>

<p>Thank you for your time.</p><p>regards</p><p>Suresh</p><p><br></p><p>Sys=
tem Informations <br></p>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 Co., Ltd.=20
RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller (rev 06) <br>Syst=
em 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 Co., Ltd.=20
RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller (rev 02) <br>Syst=
em company : TG DREAMSYS <br>Architecture : x86_64<br>OS flavour : Linux Mi=
nt 17 Qiana<br><br>Node2 Processor : Intel core i3 <br>RAM : 1 GB <br>No. o=
f processor : 4 <br>Network
 cards : 03:00.0 Ethernet controller: Realtek Semiconductor Co., Ltd.=20
RTL8111/8168/8411 PCI Express Gigabit Ethernet Controller (rev 06) <br>Syst=
em company : Samsung Architecture : x86_64 <br>OS flavour : Linux Mint 17 Q=
iana<br><br>Node3 Processor : Intel core i3 <br>RAM : 1 GB <br>No. of proce=
ssor : 2 Network cards : 02:00.0 Ethernet controller : Qualcomm Atheros Att=
ansic L2 Fast Ethernet (rev a0) <br>System company : JOOYONTECH <br>Archite=
cture : x86_64 <br>OS flavour : Linux Mint 17 Qiana<br><br>Router Company :=
 ipTIME N604R <br>Maximum speed : 160Mbps (LAN to WAN)</div>

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