[Beowulf] 2012 Beowulf Bash

2012-11-12 Thread Douglas Eadline
Lest there be any confusion or doubt, the BASH is located at: Clark Planetarium, 110 South 400 West Two blocks from the convention center Time: 9PM See you there! BTW R-HPC is sponsoring the Hitchhiker towels. They are one of funniest trade show giveaways I have ever seen. They are bound to b

[Beowulf] 2012 Beowulf Bash

2012-11-12 Thread Douglas Eadline
Lest there be any confusion or doubt, the BASH is located at: Clark Planetarium, 110 South 400 West Two blocks from the convention center Time: 9PM See you there! BTW R-HPC is sponsoring the Hitchhiker towels. They are one of funniest trade show giveaways I have ever seen. They are bound to be

Re: [Beowulf] how cluster's storage can be flexible/expandable?

2012-11-12 Thread Duke Nguyen
On 11/13/12 6:11 AM, Vincent Diepeveen wrote: > hi Duke, > > Where do you need a parallel file system for if you have 1 fileserver > in total? Vincent, our purpose is to build a cluster and data center which are flexible and expandable. Based on my own experience on genome research, we will soo

Re: [Beowulf] PXE boot with X7DWT-INF IB onboard card

2012-11-12 Thread Duke Nguyen
On 11/12/12 6:53 PM, Hearns, John wrote: > Hi folks, > > We are still on the way of building our first small-cluster. Right now > we have 16 diskless nodes 8GB RAM on X7DWT-INF and a master also on > > > Also, if you are rolling your own cluster, learn how to configure the IPMI > cards on the mothe

Re: [Beowulf] how cluster's storage can be flexible/expandable?

2012-11-12 Thread Vincent Diepeveen
hi Duke, Where do you need a parallel file system for if you have 1 fileserver in total? On Nov 12, 2012, at 12:26 PM, Duke Nguyen wrote: > On 11/12/12 4:42 PM, Tim Cutts wrote: >> On 12 Nov 2012, at 03:50, Duke Nguyen wrote: >> >>> On 11/9/12 7:26 PM, Bogdan Costescu wrote: On Fri, Nov

Re: [Beowulf] how cluster's storage can be flexible/expandable?

2012-11-12 Thread Duke Nguyen
On 11/12/12 4:42 PM, Tim Cutts wrote: > On 12 Nov 2012, at 03:50, Duke Nguyen wrote: > >> On 11/9/12 7:26 PM, Bogdan Costescu wrote: >>> On Fri, Nov 9, 2012 at 7:19 AM, Christopher Samuel >>> wrote: So JBODs with LVM on top and XFS on top of that could be resized on the fly. You can do

Re: [Beowulf] PXE boot with X7DWT-INF IB onboard card

2012-11-12 Thread Duke Nguyen
On 11/12/12 7:05 PM, Vincent Diepeveen wrote: > You can boot over PXE using normal network cables and boot over the > gigabit ethernet using a cheap ethernet > router. Thanks Vincent. Yes we gonna try that with a gigabyte hub. Just wonder anyone has other experience, for example PXE Boot on this

Re: [Beowulf] PXE boot with X7DWT-INF IB onboard card

2012-11-12 Thread Hearns, John
Hi folks, We are still on the way of building our first small-cluster. Right now we have 16 diskless nodes 8GB RAM on X7DWT-INF and a master also on Also, if you are rolling your own cluster, learn how to configure the IPMI cards on the motherboards (referred to as BMCs also) You use IPMI/BMC

[Beowulf] AMD FirePro S10000 1.5 Tflop double precision

2012-11-12 Thread Vincent Diepeveen
I stumbled upon this: http://www.amd.com/us/products/workstation/graphics/firepro-remote- graphics/S1/Pages/S1.aspx#2 1.5 Tflop double precision card. It quotes it has ECC, yet past few weeks AMD started announcing a lot of things. Is it because they're nearly bankrupt (chapter 11) w

Re: [Beowulf] PXE boot with X7DWT-INF IB onboard card

2012-11-12 Thread Andrew Holway
OR put in a USB thumb drive in each node. It would be somewhat simpler to set up :) 2012/11/12 Andrew Holway > > > > 2012/11/12 Vincent Diepeveen > >> Problem is not the infiniband NIC's. > > > Yes it is. You have to flash the device firmware in order for the BIOS > to recognize it as a boota

Re: [Beowulf] PXE boot with X7DWT-INF IB onboard card

2012-11-12 Thread Vincent Diepeveen
You can boot over PXE using normal network cables and boot over the gigabit ethernet using a cheap ethernet router. On Nov 12, 2012, at 12:33 PM, Duke Nguyen wrote: > Hi folks, > > We are still on the way of building our first small-cluster. Right now > we have 16 diskless nodes 8GB RAM on X7DW

Re: [Beowulf] PXE boot with X7DWT-INF IB onboard card

2012-11-12 Thread Andrew Holway
2012/11/12 Vincent Diepeveen > Problem is not the infiniband NIC's. Yes it is. You have to flash the device firmware in order for the BIOS to recognize it as a bootable device. Yes your a bit screwed for booting over IB but booting over 1GE is perfectly acceptable. 1GE bit rate is not 1000 mil

Re: [Beowulf] PXE boot with X7DWT-INF IB onboard card

2012-11-12 Thread Jörg Saßmannshausen
Hi Duke I cannot answer the first question but I try to give some input for the second one. I would have thought you can boot via the gigabit network and do the NFS-mount via the IB network? You can run TCP-over-IB so the existing infrastructure should work IMHO. My idea is to mount say /usr v

Re: [Beowulf] PXE boot with X7DWT-INF IB onboard card

2012-11-12 Thread Mark Hahn
> * if PXE server with Infiniband is impossible, then it is OK with a > gigabyte connection? Or should we go for 16 disks for these 16 clients booting is rare and almost trivial, IO-wise. there's no reason you shouldn't be able to boot several hundred clients over Gb. __

Re: [Beowulf] PXE boot with X7DWT-INF IB onboard card

2012-11-12 Thread Vincent Diepeveen
Maybe there is a simpler thing going on here. Had you looked at supermicro website whether your motherboard can boot the infiniband? If so you might want to check the bios version of the motherboards and flash them to a newer version that does support booting infiniband over PXE. Probably nee

Re: [Beowulf] PXE boot with X7DWT-INF IB onboard card

2012-11-12 Thread Vincent Diepeveen
Problem is not the infiniband NIC's. You need a motherboard with a bios fixed to boot infiniband over PXE, that's all. So you need to contact Supermicro to fix the bios if it doesn't boot them, if they would be willing to do that. On Nov 12, 2012, at 1:56 PM, Duke Nguyen wrote: > On 11/12/12

[Beowulf] PXE boot with X7DWT-INF IB onboard card

2012-11-12 Thread Duke Nguyen
Hi folks, We are still on the way of building our first small-cluster. Right now we have 16 diskless nodes 8GB RAM on X7DWT-INF and a master also on X7DWT-INF with 120GB disk and 16GB RAM. These boards (X7DWT-INF) has built-in Infiniband Card (Infiniband MT25204 20Gbps Controller), and I hoped

Re: [Beowulf] how cluster's storage can be flexible/expandable?

2012-11-12 Thread Tim Cutts
On 12 Nov 2012, at 03:50, Duke Nguyen wrote: > On 11/9/12 7:26 PM, Bogdan Costescu wrote: >> On Fri, Nov 9, 2012 at 7:19 AM, Christopher Samuel >> wrote: >>> So JBODs with LVM on top and XFS on top of that could be resized on >>> the fly. You can do the same with ext[34] as well (from memory).

Re: [Beowulf] Maker2 genomic software license experience?

2012-11-12 Thread Brendan Moloney
On Fri, Nov 9, 2012 at 7:39 AM, Joe Landman wrote: > Hmmm ... I thought it was an interpreter throughout. Perl and Perl6 are > compiled, Ruby is purely interpreted. Java is compiled (in the same way > Perl is). Pythons performance is much closer to Ruby than Java/Perl. > This is also incorrec