From eagles051387 at gmail.com  Tue Jul  1 00:26:15 2008
From: eagles051387 at gmail.com (Jon Aquilina)
Date: Tue Oct  7 01:15:12 2008
Subject: Commodity supercomputing, was: Re: NDAs Re: [Beowulf] Nvidia, cuda,
	tesla and... where's my double floating point?
In-Reply-To: <6D1C4C9B-432F-4547-93F4-391B0847951D@xs4all.nl>
References: <alpine.DEB.1.10.0805021404240.2494@localhost>
	<1210016466.4924.1.camel@Vigor13>
	<B1526F5C-9C28-4C20-916D-EB1890D734D8@xs4all.nl>
	<48551E70.7070507@scalableinformatics.com>
	<4AF41375-3A13-4691-A2A1-D5B853FEC3A4@xs4all.nl>
	<20080615154227.u8fwdpn08ww4c40k@webmail.jpl.nasa.gov>
	<B13D9243-7184-4BEA-B3C9-5FAF8AD0113D@xs4all.nl>
	<6.2.5.6.2.20080616084554.02e4dd18@jpl.nasa.gov>
	<486923D6.8070907@moene.indiv.nluug.nl>
	<6D1C4C9B-432F-4547-93F4-391B0847951D@xs4all.nl>
Message-ID: <a31cd3860807010026i3470663fofaec8ac8cea300f5@mail.gmail.com>

not sure if this applies to all kinds of senarios that clusters are used in
but isnt the more ram you have the better?

On 6/30/08, Vincent Diepeveen <diep@xs4all.nl> wrote:
>
> Toon,
>
> Can you drop a line on how important RAM is for weather forecasting in
> latest type of calculations you're performing?
>
> Thanks,
> Vincent
>
>
> On Jun 30, 2008, at 8:20 PM, Toon Moene wrote:
>
> Jim Lux wrote:
>>
>> Yep.  And for good reason.  Even a big DoD job is still tiny in Nvidia's
>>> scale of operations. We face this all the time with NASA work.
>>>  Semiconductor manufacturers have no real reason to produce special purpose
>>> or customized versions of their products for space use, because they can
>>> sell all they can make to the consumer market. More than once, I've had a
>>> phone call along the lines of this:
>>> "Jim: I'm interested in your new ABC321 part."
>>> "Rep: Great. I'll just send the NDA over and we can talk about it."
>>> "Jim: Great, you have my email and my fax # is..."
>>> "Rep: By the way, what sort of volume are you going to be using?"
>>> "Jim: Oh, 10-12.."
>>> "Rep: thousand per week, excellent..."
>>> "Jim: No, a dozen pieces, total, lifetime buy, or at best maybe every
>>> year."
>>> "Rep: Oh...<dial tone>"
>>> {Well, to be fair, it's not that bad, they don't hang up on you..
>>>
>>
>> Since about a year, it's been clear to me that weather forecasting (i.e.,
>> running a more or less sophisticated atmospheric model to provide weather
>> predictions) is going to be "mainstream" in the sense that every business
>> that needs such forecasts for its operations can simply run them in-house.
>>
>> Case in point:  I bought a $1100 HP box (the obvious target group being
>> teenage downloaders) which performs the HIRLAM limited area model *on the
>> grid that we used until October 2006* in December last year.
>>
>> It's about twice as slow as our then-operational 50-CPU Sun Fire 15K.
>>
>> I wonder what effect this will have on CPU developments ...
>>
>> --
>> Toon Moene - e-mail: toon@moene.indiv.nluug.nl - phone: +31 346 214290
>> Saturnushof 14, 3738 XG  Maartensdijk, The Netherlands
>> At home: http://moene.indiv.nluug.nl/~toon/
>> Progress of GNU Fortran: http://gcc.gnu.org/ml/gcc/2008-01/msg00009.html
>>
>
> _______________________________________________
> Beowulf mailing list, Beowulf@beowulf.org
> To change your subscription (digest mode or unsubscribe) visit
> http://www.beowulf.org/mailman/listinfo/beowulf
>



-- 
Jonathan Aquilina
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From andrew at moonet.co.uk  Tue Jul  1 01:20:56 2008
From: andrew at moonet.co.uk (andrew holway)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] A press release
In-Reply-To: <a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>
	<4863E551.8090802@scalableinformatics.com>
	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>
Message-ID: <f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>

Hi Jon,

We have our own stack which we stick on top of the customers favourite
red hat clone. Usually Scientific Linux.

Here is a bit more about it.

http://www.clustervision.com/products_os.php

We sell as a standalone product and it does quite well. I could even
go so far to say that it is 'stack of choice' in many European
institutions.

We have done a couple of M$ installations too.

Ta

Andy

On Sat, Jun 28, 2008 at 12:09 PM, Jon Aquilina <eagles051387@gmail.com> wrote:
> congrats. just wondering what distro is being used on your clusters?
>
> On Thu, Jun 26, 2008 at 8:52 PM, Joe Landman
> <landman@scalableinformatics.com> wrote:
>>
>> andrew holway wrote:
>>>
>>> http://www.clustervision.com/pr_top500_uk.php
>>
>> cool ... congratulations to ClusterVision!
>>
>> --
>> Joseph Landman, Ph.D
>> Founder and CEO
>> Scalable Informatics LLC,
>> email: landman@scalableinformatics.com
>> web  : http://www.scalableinformatics.com
>>       http://jackrabbit.scalableinformatics.com
>> phone: +1 734 786 8423
>> fax  : +1 866 888 3112
>> cell : +1 734 612 4615
>> _______________________________________________
>> Beowulf mailing list, Beowulf@beowulf.org
>> To change your subscription (digest mode or unsubscribe) visit
>> http://www.beowulf.org/mailman/listinfo/beowulf
>
>
>
> --
> Jonathan Aquilina

From Dan.Kidger at quadrics.com  Tue Jul  1 01:42:59 2008
From: Dan.Kidger at quadrics.com (Dan.Kidger@quadrics.com)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] A press release
In-Reply-To: <f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>
	<4863E551.8090802@scalableinformatics.com>
	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>
	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>
Message-ID: <0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>

>Hi Jon,

>We have our own stack which we stick on top of the customers favourite
>red hat clone. Usually Scientific Linux.
>
>Here is a bit more about it.
>
>http://www.clustervision.com/products_os.php
>
>We sell as a standalone product and it does quite well. I could even
>go so far to say that it is 'stack of choice' in many European
>institutions.

Every throught of getting a job in Sales and Marketing?  :-)


Daniel.


On Sat, Jun 28, 2008 at 12:09 PM, Jon Aquilina <eagles051387@gmail.com> wrote:
> congrats. just wondering what distro is being used on your clusters?
>
> On Thu, Jun 26, 2008 at 8:52 PM, Joe Landman
> <landman@scalableinformatics.com> wrote:
>>
>> andrew holway wrote:
>>>
>>> http://www.clustervision.com/pr_top500_uk.php
>>
>> cool ... congratulations to ClusterVision!
>>
>> --
>> Joseph Landman, Ph.D
>> Founder and CEO
>> Scalable Informatics LLC,


From Dan.Kidger at quadrics.com  Tue Jul  1 01:46:14 2008
From: Dan.Kidger at quadrics.com (Dan.Kidger@quadrics.com)
Date: Tue Oct  7 01:15:12 2008
Subject: Commodity supercomputing, was: Re: NDAs Re: [Beowulf] Nvidia,
	cuda, tesla and... where's my	double floating point?
In-Reply-To: <1214864562.6912.29.camel@Vigor13>
References: <alpine.DEB.1.10.0805021404240.2494@localhost>
	<1210016466.4924.1.camel@Vigor13>
	<B1526F5C-9C28-4C20-916D-EB1890D734D8@xs4all.nl>
	<48551E70.7070507@scalableinformatics.com>
	<4AF41375-3A13-4691-A2A1-D5B853FEC3A4@xs4all.nl>
	<20080615154227.u8fwdpn08ww4c40k@webmail.jpl.nasa.gov>
	<B13D9243-7184-4BEA-B3C9-5FAF8AD0113D@xs4all.nl>
	<6.2.5.6.2.20080616084554.02e4dd18@jpl.nasa.gov>
	<486923D6.8070907@moene.indiv.nluug.nl>
	<1214864562.6912.29.camel@Vigor13>
Message-ID: <0D49B15ACFDF2F46BF90B6E08C90048A04884918AD@quadbrsex1.quadrics.com>

John is correct here.

It is one thing to do long range climate prediction yourself using distributed computing and tweaking the stochastics based on a set of starting conditions, and another to try and work out if it will be sunny next Tuesday.
Weather modelling is a different animal to CP- you need a supply of fresh input data - and a sophisticated infrastructure to harvest , collate, sanitise and feed these numbers into your computer model.

Also with CP you typically run many instances concurrently which takes weeks/months to complete, but with WM, you have maybe 6 hours to run the whole job from start to finish which implies a closely coupled cluster.



Daniel

-------------------------------------------------------------
Dr. Daniel Kidger, Quadrics Ltd.   daniel.kidger@quadrics.com
One Bridewell St.,             Mobile:    +44 (0)779 209 1851
Bristol, BS1 2AA, UK           Office:    +44 (0)117 915 5519
----------------------- www.quadrics.com --------------------




-----Original Message-----
From: beowulf-bounces@beowulf.org [mailto:beowulf-bounces@beowulf.org] On Behalf Of John Hearns
Sent: 30 June 2008 23:23
To: beowulf@beowulf.org
Subject: Re: Commodity supercomputing, was: Re: NDAs Re: [Beowulf] Nvidia, cuda, tesla and... where's my double floating point?

On Mon, 2008-06-30 at 20:20 +0200, Toon Moene wrote:

>
> Since about a year, it's been clear to me that weather forecasting
> (i.e., running a more or less sophisticated atmospheric model to provide
> weather predictions) is going to be "mainstream" in the sense that every
> business that needs such forecasts for its operations can simply run
> them in-house.

Garbage in, garbage out.

By that I mean that the CPU horsepower may be more and more readily
affordable for businesses like that - let's say it is an ice-cream
wholesaler who would like to have a three day forecast to allow stocking
of their outlets with ice cream.
However, the models depend on input from sensor networks - not my area
of expertise, but I should imagine manned and unmanned weather stations,
ocean buoys to measure wave height, satellite sensors.
Do we see such data sources being made freely available, and in real
time (ie not archived data sets)??










_______________________________________________
Beowulf mailing list, Beowulf@beowulf.org
To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf


From eagles051387 at gmail.com  Tue Jul  1 02:28:59 2008
From: eagles051387 at gmail.com (Jon Aquilina)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] A press release
In-Reply-To: <0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>
	<4863E551.8090802@scalableinformatics.com>
	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>
	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>
	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>
Message-ID: <a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>

>We have our own stack which we stick on top of the customers favourite
>red hat clone. Usually Scientific Linux.

does it necessarily have to be a redhat clone. can it also be a debian based
clone?


On 7/1/08, Dan.Kidger@quadrics.com <Dan.Kidger@quadrics.com> wrote:
>
> >Hi Jon,
>
> >We have our own stack which we stick on top of the customers favourite
> >red hat clone. Usually Scientific Linux.
> >
> >Here is a bit more about it.
> >
> >http://www.clustervision.com/products_os.php
> >
> >We sell as a standalone product and it does quite well. I could even
> >go so far to say that it is 'stack of choice' in many European
> >institutions.
>
> Every throught of getting a job in Sales and Marketing?  :-)
>
>
> Daniel.
>
>
> On Sat, Jun 28, 2008 at 12:09 PM, Jon Aquilina <eagles051387@gmail.com>
> wrote:
> > congrats. just wondering what distro is being used on your clusters?
> >
> > On Thu, Jun 26, 2008 at 8:52 PM, Joe Landman
> > <landman@scalableinformatics.com> wrote:
> >>
> >> andrew holway wrote:
> >>>
> >>> http://www.clustervision.com/pr_top500_uk.php
> >>
> >> cool ... congratulations to ClusterVision!
> >>
> >> --
> >> Joseph Landman, Ph.D
> >> Founder and CEO
> >> Scalable Informatics LLC,
>



-- 
Jonathan Aquilina
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From henning.fehrmann at aei.mpg.de  Tue Jul  1 02:36:43 2008
From: henning.fehrmann at aei.mpg.de (Henning Fehrmann)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] automount on high ports
Message-ID: <20080701093643.GA17845@gretchen.aei.uni-hannover.de>

Hello,

we need to automount NFS directories on high ports to increase the number of possible mounts.
Currently, we are limited up to ca 360 mounts.

The NFS-server exports with the option 'insecure' but the mounts still end up on ports <1024 on the client side.

Is there a way to enable automounts on higher ports? How can it be done manually:
mount -t nfs -o ....?

We are using autofs version 5.

Thank you,
Henning

From steve_heaton at exemail.com.au  Tue Jul  1 03:28:40 2008
From: steve_heaton at exemail.com.au (Particle Boy)
Date: Tue Oct  7 01:15:12 2008
Subject: Commodity supercomputing, was: Re: NDAs Re: [Beowulf], Nvidia,
	cuda, tesla and... where's my double floating point?
In-Reply-To: <200807010728.m617S3Uc011226@bluewest.scyld.com>
References: <200807010728.m617S3Uc011226@bluewest.scyld.com>
Message-ID: <486A06D8.2050705@exemail.com.au>

Date: Mon, 30 Jun 2008 23:22:32 +0100
From: John Hearns <john.hearns@streamline-computing.com>

<snip>
 > However, the models depend on input from sensor networks - not my area
 > of expertise, but I should imagine manned and unmanned weather >stations,
 >ocean buoys to measure wave height, satellite sensors.
 >Do we see such data sources being made freely available, and in real
 >time (ie not archived data sets)??


G'day John and all

In a nutshell yes, you can can get sets of initial conditions from 
various agencies around the globe. The NCEP at NOAA is a great resource.

SOO/STRC at UCAR packages WRF EMS with the pointers built right in for 
the various feeds :)

Cheers
Stevo



From eagles051387 at gmail.com  Tue Jul  1 03:38:52 2008
From: eagles051387 at gmail.com (Jon Aquilina)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] open mosix alternative
Message-ID: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>

does anyone know an altenative to openmosix?? would it be worth reviving the
development of the kernel?

-- 
Jonathan Aquilina
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From eagles051387 at gmail.com  Tue Jul  1 03:39:48 2008
From: eagles051387 at gmail.com (Jon Aquilina)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] software for compatible with a cluster
Message-ID: <a31cd3860807010339v65709e83ha5afe47e9e22cc8c@mail.gmail.com>

does anyone know of any rendering software that will work with a cluster?

-- 
Jonathan Aquilina
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From geoff at galitz.org  Tue Jul  1 04:04:48 2008
From: geoff at galitz.org (Geoff Galitz)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] software for compatible with a cluster
In-Reply-To: <a31cd3860807010339v65709e83ha5afe47e9e22cc8c@mail.gmail.com>
References: <a31cd3860807010339v65709e83ha5afe47e9e22cc8c@mail.gmail.com>
Message-ID: <7B82EE52C0DC4879AD6AE8FCA937C63C@geoffPC>

 

 

I know people who use Houdini for this:

 

http://www.sidefx.com/index.php

 

I cannot vouch for how well it works or what is involved, though.

 

 

Geoff Galitz
Blankenheim NRW, Deutschland
http://www.galitz.org

  _____  

From: beowulf-bounces@beowulf.org [mailto:beowulf-bounces@beowulf.org] On
Behalf Of Jon Aquilina
Sent: Dienstag, 1. Juli 2008 12:40
To: Beowulf Mailing List
Subject: [Beowulf] software for compatible with a cluster

 

does anyone know of any rendering software that will work with a cluster?

-- 
Jonathan Aquilina 

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From eagles051387 at gmail.com  Tue Jul  1 04:26:38 2008
From: eagles051387 at gmail.com (Jon Aquilina)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] software for compatible with a cluster
In-Reply-To: <7B82EE52C0DC4879AD6AE8FCA937C63C@geoffPC>
References: <a31cd3860807010339v65709e83ha5afe47e9e22cc8c@mail.gmail.com>
	<7B82EE52C0DC4879AD6AE8FCA937C63C@geoffPC>
Message-ID: <a31cd3860807010426q1be3b70fm8e8e44e06927b9f7@mail.gmail.com>

reason i am asking is because i would like to setup a rendering cluster and
provide rendering services. does this also work for 3d animated movies that
require rendering or does one need somethin entierly different for that?

On 7/1/08, Geoff Galitz <geoff@galitz.org> wrote:
>
>
>
>
>
> I know people who use Houdini for this:
>
>
>
> http://www.sidefx.com/index.php
>
>
>
> I cannot vouch for how well it works or what is involved, though.
>
>
>
>
>
> Geoff Galitz
> Blankenheim NRW, Deutschland
> http://www.galitz.org
>  ------------------------------
>
> *From:* beowulf-bounces@beowulf.org [mailto:beowulf-bounces@beowulf.org] *On
> Behalf Of *Jon Aquilina
> *Sent:* Dienstag, 1. Juli 2008 12:40
> *To:* Beowulf Mailing List
> *Subject:* [Beowulf] software for compatible with a cluster
>
>
>
> does anyone know of any rendering software that will work with a cluster?
>
> --
> Jonathan Aquilina
>



-- 
Jonathan Aquilina
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From gerry.creager at tamu.edu  Tue Jul  1 04:59:03 2008
From: gerry.creager at tamu.edu (Gerry Creager)
Date: Tue Oct  7 01:15:12 2008
Subject: Commodity supercomputing, was: Re: NDAs Re: [Beowulf] Nvidia,
	cuda,	tesla and... where's my	double floating point?
In-Reply-To: <48694BD5.5090303@moene.indiv.nluug.nl>
References: <alpine.DEB.1.10.0805021404240.2494@localhost>	<1210016466.4924.1.camel@Vigor13>	<B1526F5C-9C28-4C20-916D-EB1890D734D8@xs4all.nl>	<48551E70.7070507@scalableinformatics.com>	<4AF41375-3A13-4691-A2A1-D5B853FEC3A4@xs4all.nl>	<20080615154227.u8fwdpn08ww4c40k@webmail.jpl.nasa.gov>	<B13D9243-7184-4BEA-B3C9-5FAF8AD0113D@xs4all.nl>	<6.2.5.6.2.20080616084554.02e4dd18@jpl.nasa.gov>
	<486923D6.8070907@moene.indiv.nluug.nl> <48693DCA.3010903@tamu.edu>
	<48694BD5.5090303@moene.indiv.nluug.nl>
Message-ID: <486A1C07.9050208@tamu.edu>

Toon Moene wrote:
> Gerry Creager wrote:
> 
>> I'm running WRF on ranger, the 580 TF Sun cluster at utexas.edu.  I 
>> can complete the WRF single domain run, using 384 cores in ~30 min 
>> wall clock time.  At the WRF Users Conference last week, the number of 
>> folks I talked to running WRF on workstations or "operationally" on 
>> 16-64 core clusters was impressive.  I suspect a lot of desktop 
>> weather forecasting will, as you suggest, become the norm.  The 
>> question, then, is: Are we looking at an enterprise where everyone 
>> with a gaming machine thinks they understand the model well enough to 
>> try predicting the weather, or are some still in awe of Lorenz' 
>> hypothesis about its complexity?
> 
> This is where I think the pluses of the established meteorological 
> society will be: We know how to establish the quality of meteorological 
> models, how to compare them, how to dive into their parametrizations to 
> figure out the relevant differences and to solve the problems.
> 
> Because we know this, we will be sought after.  However, we will be 
> working inside the industry that needs this knowlegde, and outside 
> academia or institutionalized weather centres.

This is already starting to happen.  However, what I continue to see is 
managers wanting/expecting an absolute answer be generated numerically, 
  and they're paying less attention to the modelers' concerns about the 
"goodness" of the model in certain settings.

As an example, for our evening news programs, we've someone purporting 
to be a meteorologist.  Over the last 10 years, the proportion of folks 
actually trained in meteorology has grown significantly, and talking to 
them one-on-one, they tend to recognize the limitations of the models 
they present.  Yet, rather than saying the temperature tomorrow will be 
in a range from 93-98 deg F (with apologies to our brothers across the 
Pond) they're generally required to say, "96F" because their managers 
believe the public requires an absolute number.

Perhaps, in some industries where statistical analysis is more integral, 
we'll see appropriate use of the data...

gerry
-- 
Gerry Creager -- gerry.creager@tamu.edu
Texas Mesonet -- AATLT, Texas A&M University	
Cell: 979.229.5301 Office: 979.458.4020 FAX: 979.862.3983
Office: 1700 Research Parkway Ste 160, TAMU, College Station, TX 77843

From gerry.creager at tamu.edu  Tue Jul  1 05:13:47 2008
From: gerry.creager at tamu.edu (Gerry Creager)
Date: Tue Oct  7 01:15:12 2008
Subject: Commodity supercomputing, was: Re: NDAs Re: [Beowulf] Nvidia,
	cuda, tesla and... where's my	double floating point?
In-Reply-To: <1214864562.6912.29.camel@Vigor13>
References: <alpine.DEB.1.10.0805021404240.2494@localhost>	<1210016466.4924.1.camel@Vigor13>	<B1526F5C-9C28-4C20-916D-EB1890D734D8@xs4all.nl>	<48551E70.7070507@scalableinformatics.com>	<4AF41375-3A13-4691-A2A1-D5B853FEC3A4@xs4all.nl>	<20080615154227.u8fwdpn08ww4c40k@webmail.jpl.nasa.gov>	<B13D9243-7184-4BEA-B3C9-5FAF8AD0113D@xs4all.nl>	<6.2.5.6.2.20080616084554.02e4dd18@jpl.nasa.gov>	<486923D6.8070907@moene.indiv.nluug.nl>
	<1214864562.6912.29.camel@Vigor13>
Message-ID: <486A1F7B.9080408@tamu.edu>

John Hearns wrote:
> On Mon, 2008-06-30 at 20:20 +0200, Toon Moene wrote:
> 
>> Since about a year, it's been clear to me that weather forecasting 
>> (i.e., running a more or less sophisticated atmospheric model to provide 
>> weather predictions) is going to be "mainstream" in the sense that every 
>> business that needs such forecasts for its operations can simply run 
>> them in-house.
> 
> Garbage in, garbage out.
> 
> By that I mean that the CPU horsepower may be more and more readily
> affordable for businesses like that - let's say it is an ice-cream
> wholesaler who would like to have a three day forecast to allow stocking
> of their outlets with ice cream.
> However, the models depend on input from sensor networks - not my area
> of expertise, but I should imagine manned and unmanned weather stations,
> ocean buoys to measure wave height, satellite sensors.
> Do we see such data sources being made freely available, and in real
> time (ie not archived data sets)??

In the US, at least for academic institutions and hobbyists, surface and 
upper air observations of the sort you describe are generally available 
for incorporation into models for data assimilation.  Models are 
generally forced and bounded using model data from other atmospheric 
models, also available.  As I understand it from colleagues in Europe, 
getting similar data over there is more problemmatical.

> Hopefully on topic the Manchester Guardian newspaper (you all know me
> now for a Guardian reader) is running a "Free Our Data" campaign - to
> pressurise Government to make freely available GIS type data and census
> data which the Government has. I'm personally unconvinced of the
> overwhelming justification for (say) the Ordnance Survey to give all of
> its mapping data away for free.
> http://www.freeourdata.org.uk/

Last summer, in Paris, I had a discussion on this subject with the 
Ordinance Survey's chief cartographer.  It is their intent to free the 
data save reasonable costs of reproduction/maintenance as soon as they 
can establish these.  In the US, this is the norm.  In Texas, where I 
live, there's a site with State basemap data, highly accurate roadway 
data, land-use/land-cover, census, etc. that's just an FTP call away, 
or, if you want to pay roughly $10 per DVD, they'll burn a copy for you 
(cost of personnel for reproduction of the DVD).  Some states have 
deemed their data proprietary.  A lot have locked their data down 
somewhat since 9/11, as our Department of Homeland Security has called 
for restricting access to Critical Infrastructure data.  Note that the 
last listing of Critical Infrastructure for Texas listed some 268 pages 
of delineation, description and justification.  I fear it's been 
updated/expanded since then.  It included banks, cemeteries, schools, 
bridges, water and sewer plants, shopping malls, high-traffic 
motor-ways, refrigerated facilities, supermarkets, gas stations, 
bridges, power transformer and generation sites, power transmission 
lines, petroleum pipelines, and gas stations, to name a few.  There was 
discussion of adding individual residences to the list.  As you can see, 
restricting access to "critical infrastructure" could result in a blank map.
-- 
Gerry Creager -- gerry.creager@tamu.edu
Texas Mesonet -- AATLT, Texas A&M University	
Cell: 979.229.5301 Office: 979.458.4020 FAX: 979.862.3983
Office: 1700 Research Parkway Ste 160, TAMU, College Station, TX 77843

From m.janssens at opencfd.co.uk  Tue Jul  1 05:48:39 2008
From: m.janssens at opencfd.co.uk (Mattijs Janssens)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] open mosix alternative
In-Reply-To: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>
References: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>
Message-ID: <200807011348.39343.m.janssens@opencfd.co.uk>

On Tuesday 01 July 2008 11:38, Jon Aquilina wrote:
> does anyone know an altenative to openmosix?? would it be worth reviving
> the development of the kernel?

maybe

http://www.kerrighed.org

(and that is all I know about it)

Regards,

Mattijs

From geoff at galitz.org  Tue Jul  1 05:50:33 2008
From: geoff at galitz.org (Geoff Galitz)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] open mosix alternative
In-Reply-To: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>
References: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>
Message-ID: <D18932554BC04D5A8EAC3470FE9DAE3D@geoffPC>

 

It seems that much of the effort that was going into openMOSIX is now going
into KVM.

 

http://kvm.qumranet.com/kvmwiki

 

I think the idea is that MOSIX functionality is more easily developed and
deployed in the form of virtual machines than directly at the kernel level.
There are some trade-offs, of course... more overhead being chief among them
but the virtualization model is clearly the overall favorite.  It sure does
beat the heck out of having to track each kernel individually.

 

 

 

 

Geoff Galitz
Blankenheim NRW, Deutschland
http://www.galitz.org

  _____  

From: beowulf-bounces@beowulf.org [mailto:beowulf-bounces@beowulf.org] On
Behalf Of Jon Aquilina
Sent: Dienstag, 1. Juli 2008 12:39
To: Beowulf Mailing List
Subject: [Beowulf] open mosix alternative

 

does anyone know an altenative to openmosix?? would it be worth reviving the
development of the kernel?

-- 
Jonathan Aquilina 

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From mark.kosmowski at gmail.com  Tue Jul  1 05:51:54 2008
From: mark.kosmowski at gmail.com (Mark Kosmowski)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] Re: Beowulf Digest, Vol 53, Issue 1
In-Reply-To: <200807010728.m617S3Ub011226@bluewest.scyld.com>
References: <200807010728.m617S3Ub011226@bluewest.scyld.com>
Message-ID: <c84311bb0807010551v2316ceb3o441b7948f3d2bb7a@mail.gmail.com>

At some point there a cost-benefit analysis needs to be performed.  If
my cluster at peak usage only uses 4 Gb RAM per CPU (I live in
single-core land still and do not yet differentiate between CPU and
core) and my nodes all have 16 Gb per CPU then I am wasting RAM
resources and would be better off buying new machines and physically
transferring the RAM to and from them or running more jobs each
distributed across fewer CPUs.  Or saving on my electricity bill and
powering down some nodes.

As heretical as this last sounds, I'm tempted to throw in the towel on
my PhD studies because I can no longer afford the power to run my
three node cluster at home.  Energy costs may end up being the straw
that breaks this camel's back.

Mark E. Kosmowski

> From: "Jon Aquilina" <eagles051387@gmail.com>

>
> not sure if this applies to all kinds of senarios that clusters are used in
> but isnt the more ram you have the better?
>
> On 6/30/08, Vincent Diepeveen <diep@xs4all.nl> wrote:
> >
> > Toon,
> >
> > Can you drop a line on how important RAM is for weather forecasting in
> > latest type of calculations you're performing?
> >
> > Thanks,
> > Vincent
> >
> >
> > On Jun 30, 2008, at 8:20 PM, Toon Moene wrote:
> >
> > Jim Lux wrote:
> >>
> >> Yep.  And for good reason.  Even a big DoD job is still tiny in Nvidia's
> >>> scale of operations. We face this all the time with NASA work.
> >>>  Semiconductor manufacturers have no real reason to produce special purpose
> >>> or customized versions of their products for space use, because they can
> >>> sell all they can make to the consumer market. More than once, I've had a
> >>> phone call along the lines of this:
> >>> "Jim: I'm interested in your new ABC321 part."
> >>> "Rep: Great. I'll just send the NDA over and we can talk about it."
> >>> "Jim: Great, you have my email and my fax # is..."
> >>> "Rep: By the way, what sort of volume are you going to be using?"
> >>> "Jim: Oh, 10-12.."
> >>> "Rep: thousand per week, excellent..."
> >>> "Jim: No, a dozen pieces, total, lifetime buy, or at best maybe every
> >>> year."
> >>> "Rep: Oh...<dial tone>"
> >>> {Well, to be fair, it's not that bad, they don't hang up on you..
> >>>
> >>
> >> Since about a year, it's been clear to me that weather forecasting (i.e.,
> >> running a more or less sophisticated atmospheric model to provide weather
> >> predictions) is going to be "mainstream" in the sense that every business
> >> that needs such forecasts for its operations can simply run them in-house.
> >>
> >> Case in point:  I bought a $1100 HP box (the obvious target group being
> >> teenage downloaders) which performs the HIRLAM limited area model *on the
> >> grid that we used until October 2006* in December last year.
> >>
> >> It's about twice as slow as our then-operational 50-CPU Sun Fire 15K.
> >>
> >> I wonder what effect this will have on CPU developments ...
> >>
> >> --
> >> Toon Moene - e-mail: toon@moene.indiv.nluug.nl - phone: +31 346 214290
> >> Saturnushof 14, 3738 XG  Maartensdijk, The Netherlands
> >> At home: http://moene.indiv.nluug.nl/~toon/
> >> Progress of GNU Fortran: http://gcc.gnu.org/ml/gcc/2008-01/msg00009.html
> >>
> >
> > _______________________________________________
> > Beowulf mailing list, Beowulf@beowulf.org
> > To change your subscription (digest mode or unsubscribe) visit
> > http://www.beowulf.org/mailman/listinfo/beowulf
> >
>
>
>
> --
> Jonathan Aquilina

From mark.kosmowski at gmail.com  Tue Jul  1 05:53:35 2008
From: mark.kosmowski at gmail.com (Mark Kosmowski)
Date: Tue Oct  7 01:15:12 2008
Subject: Commodity supercomputing, was: Re: NDAs Re: [Beowulf]
Message-ID: <c84311bb0807010553x60f97dc3j3da7e8c882ca7ce9@mail.gmail.com>

And I forgot to change the subject.  Apologies.

On 7/1/08, Mark Kosmowski <mark.kosmowski@gmail.com> wrote:
> At some point there a cost-benefit analysis needs to be performed.  If
> my cluster at peak usage only uses 4 Gb RAM per CPU (I live in
> single-core land still and do not yet differentiate between CPU and
> core) and my nodes all have 16 Gb per CPU then I am wasting RAM
> resources and would be better off buying new machines and physically
> transferring the RAM to and from them or running more jobs each
> distributed across fewer CPUs.  Or saving on my electricity bill and
> powering down some nodes.
>
> As heretical as this last sounds, I'm tempted to throw in the towel on
> my PhD studies because I can no longer afford the power to run my
> three node cluster at home.  Energy costs may end up being the straw
> that breaks this camel's back.
>
> Mark E. Kosmowski
>
> > From: "Jon Aquilina" <eagles051387@gmail.com>
>
> >
> > not sure if this applies to all kinds of senarios that clusters are used in
> > but isnt the more ram you have the better?
> >
> > On 6/30/08, Vincent Diepeveen <diep@xs4all.nl> wrote:
> > >
> > > Toon,
> > >
> > > Can you drop a line on how important RAM is for weather forecasting in
> > > latest type of calculations you're performing?
> > >
> > > Thanks,
> > > Vincent
> > >
> > >
> > > On Jun 30, 2008, at 8:20 PM, Toon Moene wrote:
> > >
> > > Jim Lux wrote:
> > >>
> > >> Yep.  And for good reason.  Even a big DoD job is still tiny in Nvidia's
> > >>> scale of operations. We face this all the time with NASA work.
> > >>>  Semiconductor manufacturers have no real reason to produce special purpose
> > >>> or customized versions of their products for space use, because they can
> > >>> sell all they can make to the consumer market. More than once, I've had a
> > >>> phone call along the lines of this:
> > >>> "Jim: I'm interested in your new ABC321 part."
> > >>> "Rep: Great. I'll just send the NDA over and we can talk about it."
> > >>> "Jim: Great, you have my email and my fax # is..."
> > >>> "Rep: By the way, what sort of volume are you going to be using?"
> > >>> "Jim: Oh, 10-12.."
> > >>> "Rep: thousand per week, excellent..."
> > >>> "Jim: No, a dozen pieces, total, lifetime buy, or at best maybe every
> > >>> year."
> > >>> "Rep: Oh...<dial tone>"
> > >>> {Well, to be fair, it's not that bad, they don't hang up on you..
> > >>>
> > >>
> > >> Since about a year, it's been clear to me that weather forecasting (i.e.,
> > >> running a more or less sophisticated atmospheric model to provide weather
> > >> predictions) is going to be "mainstream" in the sense that every business
> > >> that needs such forecasts for its operations can simply run them in-house.
> > >>
> > >> Case in point:  I bought a $1100 HP box (the obvious target group being
> > >> teenage downloaders) which performs the HIRLAM limited area model *on the
> > >> grid that we used until October 2006* in December last year.
> > >>
> > >> It's about twice as slow as our then-operational 50-CPU Sun Fire 15K.
> > >>
> > >> I wonder what effect this will have on CPU developments ...
> > >>
> > >> --
> > >> Toon Moene - e-mail: toon@moene.indiv.nluug.nl - phone: +31 346 214290
> > >> Saturnushof 14, 3738 XG  Maartensdijk, The Netherlands
> > >> At home: http://moene.indiv.nluug.nl/~toon/
> > >> Progress of GNU Fortran: http://gcc.gnu.org/ml/gcc/2008-01/msg00009.html
> > >>
> > >
> > > _______________________________________________
> > > Beowulf mailing list, Beowulf@beowulf.org
> > > To change your subscription (digest mode or unsubscribe) visit
> > > http://www.beowulf.org/mailman/listinfo/beowulf
> > >
> >
> >
> >
> > --
> > Jonathan Aquilina
>

From geoff at galitz.org  Tue Jul  1 05:54:26 2008
From: geoff at galitz.org (Geoff Galitz)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] software for compatible with a cluster
In-Reply-To: <a31cd3860807010426q1be3b70fm8e8e44e06927b9f7@mail.gmail.com>
References: <a31cd3860807010339v65709e83ha5afe47e9e22cc8c@mail.gmail.com>
	<7B82EE52C0DC4879AD6AE8FCA937C63C@geoffPC>
	<a31cd3860807010426q1be3b70fm8e8e44e06927b9f7@mail.gmail.com>
Message-ID: <3CB66E9F377C4961B5457896137EAD1B@geoffPC>

 

That is out of my field of expertise.  Sounds like a question for
professional digital artists.  I can put you in touch some folks that most
likely know the answer to your questions, if you like.

 

Anybody know of any current approaches to this?

 

Geoff Galitz
Blankenheim NRW, Deutschland
http://www.galitz.org

  _____  

From: Jon Aquilina [mailto:eagles051387@gmail.com] 
Sent: Dienstag, 1. Juli 2008 13:27
To: Geoff Galitz
Cc: Beowulf Mailing List
Subject: Re: [Beowulf] software for compatible with a cluster

 

reason i am asking is because i would like to setup a rendering cluster and
provide rendering services. does this also work for 3d animated movies that
require rendering or does one need somethin entierly different for that?

On 7/1/08, Geoff Galitz <geoff@galitz.org> wrote: 

 

 

I know people who use Houdini for this:

 

http://www.sidefx.com/index.php

 

I cannot vouch for how well it works or what is involved, though.

 

 

Geoff Galitz
Blankenheim NRW, Deutschland
http://www.galitz.org <http://www.galitz.org/> 

  _____  

From: beowulf-bounces@beowulf.org [mailto:beowulf-bounces@beowulf.org] On
Behalf Of Jon Aquilina
Sent: Dienstag, 1. Juli 2008 12:40
To: Beowulf Mailing List
Subject: [Beowulf] software for compatible with a cluster

 

does anyone know of any rendering software that will work with a cluster?

-- 
Jonathan Aquilina 




-- 
Jonathan Aquilina 

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From ajt at rri.sari.ac.uk  Tue Jul  1 06:14:38 2008
From: ajt at rri.sari.ac.uk (Tony Travis)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] open mosix alternative
In-Reply-To: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>
References: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>
Message-ID: <486A2DBE.10302@rri.sari.ac.uk>

Jon Aquilina wrote:
> does anyone know an altenative to openmosix?? would it be worth reviving 
> the development of the kernel?

Hello, Jonathan.

I'm still running openMosix (linux-2.4.26-om1) and I did have an attempt 
at porting it to the 2.4.32 kernel so I could use SATA disks, but I 
couldn't get process migration to work. My deb's for rebuilding the 
openMosix kernel under Ubuntu 6.06.1 LTS are at:

	http://bioinformatics.rri.sari.ac.uk/openmosix

We are currently evaluating Kerrighed as an alternative:

	http://www.kerrighed.org

Kerrighed also forms the basis of 'XtreemOS':

	http://www.xtreemos.eu/

Although Kerrighed looks very promising, it is also quite fragile in our 
hands. If one node crashes, you lose the entire cluster. That said, the 
Kerrighed project is extremely well supported and I believe it will be a 
good alternative in the near future. We will continue to run openMosix 
in the short-term, but I may evaluate MOSIX2:

	http://www.mosix.org/

I was, previously, opposed to Mosix on idealogical grounds and loyal to 
Moshe Bar but to be fair to Mosix is now free for non-profit use and the 
source code is available (but not GPL).

Please let me know if you are seriously considering reviving openMosix!

	Tony.
-- 
Dr. A.J.Travis,                     |  mailto:ajt@rri.sari.ac.uk
Rowett Research Institute,          |    http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn,          |   phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK.    |     fax:+44 (0)1224 716687

From landman at scalableinformatics.com  Tue Jul  1 07:00:06 2008
From: landman at scalableinformatics.com (Joe Landman)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] Re: Beowulf Digest, Vol 53, Issue 1
In-Reply-To: <c84311bb0807010551v2316ceb3o441b7948f3d2bb7a@mail.gmail.com>
References: <200807010728.m617S3Ub011226@bluewest.scyld.com>
	<c84311bb0807010551v2316ceb3o441b7948f3d2bb7a@mail.gmail.com>
Message-ID: <486A3866.7030302@scalableinformatics.com>

Mark Kosmowski wrote:
> At some point there a cost-benefit analysis needs to be performed.  If
> my cluster at peak usage only uses 4 Gb RAM per CPU (I live in
> single-core land still and do not yet differentiate between CPU and
> core) and my nodes all have 16 Gb per CPU then I am wasting RAM
> resources and would be better off buying new machines and physically
> transferring the RAM to and from them or running more jobs each
> distributed across fewer CPUs.  Or saving on my electricity bill and
> powering down some nodes.

Possible, though if you do heavy IO even with single core chips, and you 
are running a 64 bit OS, the extra buffer cache is not to be rejected 
lightly.

> 
> As heretical as this last sounds, I'm tempted to throw in the towel on
> my PhD studies because I can no longer afford the power to run my
> three node cluster at home.  Energy costs may end up being the straw
> that breaks this camel's back.

Which country are you in?  You may be able to apply for "free" computing 
resources.   Tera-grid in the US, other similar resources.  Mark Hahn 
might give you pointers for Canada, and the folks at 
Streamline/Clustervision/... might be able to give you pointers for UK/EU.

-- 
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://www.scalableinformatics.com
        http://jackrabbit.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 866 888 3112
cell : +1 734 612 4615

From eagles051387 at gmail.com  Tue Jul  1 07:18:50 2008
From: eagles051387 at gmail.com (Jon Aquilina)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] software for compatible with a cluster
In-Reply-To: <3CB66E9F377C4961B5457896137EAD1B@geoffPC>
References: <a31cd3860807010339v65709e83ha5afe47e9e22cc8c@mail.gmail.com>
	<7B82EE52C0DC4879AD6AE8FCA937C63C@geoffPC>
	<a31cd3860807010426q1be3b70fm8e8e44e06927b9f7@mail.gmail.com>
	<3CB66E9F377C4961B5457896137EAD1B@geoffPC>
Message-ID: <a31cd3860807010718o2586766cobe81f4f215d64afe@mail.gmail.com>

that would be greatly appreciated

On 7/1/08, Geoff Galitz <geoff@galitz.org> wrote:
>
>
>
> That is out of my field of expertise.  Sounds like a question for
> professional digital artists.  I can put you in touch some folks that most
> likely know the answer to your questions, if you like.
>
>
>
> Anybody know of any current approaches to this?
>
>
>
> Geoff Galitz
> Blankenheim NRW, Deutschland
> http://www.galitz.org
>  ------------------------------
>
> *From:* Jon Aquilina [mailto:eagles051387@gmail.com]
> *Sent:* Dienstag, 1. Juli 2008 13:27
> *To:* Geoff Galitz
> *Cc:* Beowulf Mailing List
> *Subject:* Re: [Beowulf] software for compatible with a cluster
>
>
>
> reason i am asking is because i would like to setup a rendering cluster and
> provide rendering services. does this also work for 3d animated movies that
> require rendering or does one need somethin entierly different for that?
>
> On 7/1/08, *Geoff Galitz* <geoff@galitz.org> wrote:
>
>
>
>
>
> I know people who use Houdini for this:
>
>
>
> http://www.sidefx.com/index.php
>
>
>
> I cannot vouch for how well it works or what is involved, though.
>
>
>
>
>
> Geoff Galitz
> Blankenheim NRW, Deutschland
> http://www.galitz.org
>  ------------------------------
>
> *From:* beowulf-bounces@beowulf.org [mailto:beowulf-bounces@beowulf.org] *On
> Behalf Of *Jon Aquilina
> *Sent:* Dienstag, 1. Juli 2008 12:40
> *To:* Beowulf Mailing List
> *Subject:* [Beowulf] software for compatible with a cluster
>
>
>
> does anyone know of any rendering software that will work with a cluster?
>
> --
> Jonathan Aquilina
>
>
>
>
> --
> Jonathan Aquilina
>



-- 
Jonathan Aquilina
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From vanallsburg at hope.edu  Tue Jul  1 07:43:34 2008
From: vanallsburg at hope.edu (Paul Van Allsburg)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] software for compatible with a cluster
In-Reply-To: <a31cd3860807010718o2586766cobe81f4f215d64afe@mail.gmail.com>
References: <a31cd3860807010339v65709e83ha5afe47e9e22cc8c@mail.gmail.com>	<7B82EE52C0DC4879AD6AE8FCA937C63C@geoffPC>	<a31cd3860807010426q1be3b70fm8e8e44e06927b9f7@mail.gmail.com>	<3CB66E9F377C4961B5457896137EAD1B@geoffPC>
	<a31cd3860807010718o2586766cobe81f4f215d64afe@mail.gmail.com>
Message-ID: <486A4296.4050501@hope.edu>

I'd like to do the same, as a project for a group of students...  Please 
keep me in the loop?
Thanks!
Paul

-- 
Paul Van Allsburg       
Computational Science & Modeling Facilitator
Natural Sciences Division,  Hope College
35 East 12th Street
Holland, Michigan 49423
616-395-7292 
http://www.hope.edu/academic/csm/


Jon Aquilina wrote:
> that would be greatly appreciated
>
> On 7/1/08, *Geoff Galitz* <geoff@galitz.org <mailto:geoff@galitz.org>> 
> wrote:
>
>      
>
>     That is out of my field of expertise.  Sounds like a question for
>     professional digital artists.  I can put you in touch some folks
>     that most likely know the answer to your questions, if you like.
>
>      
>
>     Anybody know of any current approaches to this?
>
>      
>
>     Geoff Galitz
>     Blankenheim NRW, Deutschland
>     http://www.galitz.org <http://www.galitz.org/>
>
>     * From: * Jon Aquilina [mailto:eagles051387@gmail.com
>     <mailto:eagles051387@gmail.com>]
>     *Sent:* Dienstag, 1. Juli 2008 13:27
>     *To:* Geoff Galitz
>     *Cc:* Beowulf Mailing List
>     *Subject:* Re: [Beowulf] software for compatible with a cluster
>
>      
>
>     reason i am asking is because i would like to setup a rendering
>     cluster and provide rendering services. does this also work for 3d
>     animated movies that require rendering or does one need somethin
>     entierly different for that?
>
>     On 7/1/08, *Geoff Galitz* <geoff@galitz.org
>     <mailto:geoff@galitz.org>> wrote:
>
>      
>
>      
>
>     I know people who use Houdini for this:
>
>      
>
>     http://www.sidefx.com/index.php
>
>      
>
>     I cannot vouch for how well it works or what is involved, though.
>
>      
>
>      
>
>     Geoff Galitz
>     Blankenheim NRW, Deutschland
>     http://www.galitz.org <http://www.galitz.org/>
>
>     * From: * beowulf-bounces@beowulf.org
>     <mailto:beowulf-bounces@beowulf.org>
>     [mailto:beowulf-bounces@beowulf.org
>     <mailto:beowulf-bounces@beowulf.org>] *On Behalf Of *Jon Aquilina
>     *Sent:* Dienstag, 1. Juli 2008 12:40
>     *To:* Beowulf Mailing List
>     *Subject:* [Beowulf] software for compatible with a cluster
>
>      
>
>     does anyone know of any rendering software that will work with a
>     cluster?
>
>     -- 
>     Jonathan Aquilina
>
>
>
>
>     -- 
>     Jonathan Aquilina
>
>
>
>
> -- 
> Jonathan Aquilina 

From perry at piermont.com  Tue Jul  1 07:44:48 2008
From: perry at piermont.com (Perry E. Metzger)
Date: Tue Oct  7 01:15:12 2008
Subject: Commodity supercomputing, was: Re: NDAs Re: [Beowulf] Nvidia, cuda,
	tesla and... where's my	double floating point?
In-Reply-To: <48694432.4020608@scalableinformatics.com> (Joe Landman's message
	of "Mon\, 30 Jun 2008 16\:38\:10 -0400")
References: <alpine.DEB.1.10.0805021404240.2494@localhost>
	<1210016466.4924.1.camel@Vigor13>
	<B1526F5C-9C28-4C20-916D-EB1890D734D8@xs4all.nl>
	<48551E70.7070507@scalableinformatics.com>
	<4AF41375-3A13-4691-A2A1-D5B853FEC3A4@xs4all.nl>
	<20080615154227.u8fwdpn08ww4c40k@webmail.jpl.nasa.gov>
	<B13D9243-7184-4BEA-B3C9-5FAF8AD0113D@xs4all.nl>
	<6.2.5.6.2.20080616084554.02e4dd18@jpl.nasa.gov>
	<486923D6.8070907@moene.indiv.nluug.nl> <48693DCA.3010903@tamu.edu>
	<48694432.4020608@scalableinformatics.com>
Message-ID: <87d4lxk6jj.fsf@snark.cb.piermont.com>


Joe Landman <landman@scalableinformatics.com> writes:
> I see a curious phenomenon going on in crash simulation and NVH.  We
> see an increasing "decoupling" if you will, between the detailed
> issues of simulation and coding, and the end user using the simulation
> system. That is, the users may know the engineering side, but don't
> seem to grasp the finer aspects of the simulation ... what to take as
> reasonably accurate, and what to grasp might not be.
>
> I don't see this in chemistry, in large part due to many of the users
> also writing their own software.

On the contrary. I know computational chemistry specialists who
worry about users of the common commercial software (Gaussian,
Jaguar, etc.) not knowing what to believe and what not to
believe in the output.

Since I've seen people in synthetic organic labs running the
simulation software to design possible synthetic pathways without
understanding the software, I think this worry is perfectly valid. The
overwhelming majority of users are not computational chemists at all
-- they're ordinary organic chemists, and they don't have a good gut
feel for what the limitations of the tools are.

I know of very few users of computational chemistry software who roll
their own. Try reading the computational chemistry mailing lists for a
little while, or reading the journals, and you'll get a feel for what
the average user is like. There might be a lot of people writing
software out there, but there are vastly more who just want to get
answers and don't understand how the programs work at all.


Perry
-- 
Perry E. Metzger		perry@piermont.com

From perry at piermont.com  Tue Jul  1 07:53:06 2008
From: perry at piermont.com (Perry E. Metzger)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] automount on high ports
In-Reply-To: <20080701093643.GA17845@gretchen.aei.uni-hannover.de> (Henning
	Fehrmann's message of "Tue\, 1 Jul 2008 11\:36\:43 +0200")
References: <20080701093643.GA17845@gretchen.aei.uni-hannover.de>
Message-ID: <878wwlk65p.fsf@snark.cb.piermont.com>


Henning Fehrmann <henning.fehrmann@aei.mpg.de> writes:
> we need to automount NFS directories on high ports to increase the
> number of possible mounts. Currently, we are limited up to ca 360 mounts.

A TCP socket is a 4-tuple of localhost:localport:remotehost:remoteport

A given localhost:localport pair can speak to an unlimted array of
remotehost:remoteport sets. For example, in theory, your SMTP port can
get connections from up to 2^32 different hosts on each of 2^16
different sockets from each, for a total space of 2^48 connections to
a single local socket number. This in no way restricts how many
connections can come in to another port, either, because a given
socket is again the full 4-tuple -- if you have an SSH port, it too
can get 2^48 connections.

Now, there is this (odd) convention that only root can open a socket
below 1024, so hosts "trust" (what a bad idea) sockets under that
number. You can still, however, get up to 1023 connections from any
given remote host to a given local host's port.

Thus, your problem sounds rather odd. There is no obvious reason you
should be limited to 360 connections.

Perhaps your problem is not what you think it is at all. Could you
explain it in more detail?

-- 
Perry E. Metzger		perry@piermont.com

From ajt at rri.sari.ac.uk  Tue Jul  1 08:31:48 2008
From: ajt at rri.sari.ac.uk (Tony Travis)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] open mosix alternative
In-Reply-To: <D18932554BC04D5A8EAC3470FE9DAE3D@geoffPC>
References: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>
	<D18932554BC04D5A8EAC3470FE9DAE3D@geoffPC>
Message-ID: <486A4DE4.1090807@rri.sari.ac.uk>

Geoff Galitz wrote:
> [...]
> I think the idea is that MOSIX functionality is more easily developed 
> and deployed in the form of virtual machines than directly at the kernel 
> level.  There are some trade-offs, of course... more overhead being 
> chief among them but the virtualization model is clearly the overall 
> favorite.  It sure does beat the heck out of having to track each kernel 
> individually.

Hello, Geoff.

MOSIX functionality is mainly about load-balancing between independent 
kernels, and avoiding severe memory depletion by migrating processes 
between kernels. In fact (open)MOSIX implements an SMP-like model, but 
with a high-latency interconect (usually GBit ethernet). There is no 
need to 'track' kernels, because the oM HPC extension does it for you.

The principle objective of SSI computing is to use many small machines 
as if they are one big one. This is the opposite of virtualisation which 
uses one (or a few) BIG machines like a lot of small ones. It does this 
by virtually separating the kernels. There is some confusion about this 
because it *is* very convenient to teach about or develop and test SSI 
software on virtual compute nodes if you don't have a lot of real nodes, 
but it defeats the purpose of SSI to use this approach in production.

You might be interested to know that one reason Moshe Bar gave when he 
announced the end of the openMosix project was that SMP is now so cheap 
that SSI clustering less of a factor in computing:

	http://sourceforge.net/forum/forum.php?forum_id=715406

I'm not sure I agree - I still find openMosix useful, and I'll continue 
using it on our Beowulf here until I find a better alternative.

	Tony.
-- 
Dr. A.J.Travis,                     |  mailto:ajt@rri.sari.ac.uk
Rowett Research Institute,          |    http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn,          |   phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK.    |     fax:+44 (0)1224 716687

From tjrc at sanger.ac.uk  Tue Jul  1 08:40:27 2008
From: tjrc at sanger.ac.uk (Tim Cutts)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] automount on high ports
In-Reply-To: <878wwlk65p.fsf@snark.cb.piermont.com>
References: <20080701093643.GA17845@gretchen.aei.uni-hannover.de>
	<878wwlk65p.fsf@snark.cb.piermont.com>
Message-ID: <DC7CE5D8-16C9-48B6-AE5B-83481B80F4D3@sanger.ac.uk>


On 1 Jul 2008, at 3:53 pm, Perry E. Metzger wrote:

>
> Henning Fehrmann <henning.fehrmann@aei.mpg.de> writes:
>> we need to automount NFS directories on high ports to increase the
>> number of possible mounts. Currently, we are limited up to ca 360  
>> mounts.
>
> A TCP socket is a 4-tuple of localhost:localport:remotehost:remoteport
>
> A given localhost:localport pair can speak to an unlimted array of
> remotehost:remoteport sets. For example, in theory, your SMTP port can
> get connections from up to 2^32 different hosts on each of 2^16
> different sockets from each, for a total space of 2^48 connections to
> a single local socket number. This in no way restricts how many
> connections can come in to another port, either, because a given
> socket is again the full 4-tuple -- if you have an SSH port, it too
> can get 2^48 connections.
>
> Now, there is this (odd) convention that only root can open a socket
> below 1024, so hosts "trust" (what a bad idea) sockets under that
> number. You can still, however, get up to 1023 connections from any
> given remote host to a given local host's port.
>
> Thus, your problem sounds rather odd. There is no obvious reason you
> should be limited to 360 connections.
>
> Perhaps your problem is not what you think it is at all. Could you
> explain it in more detail?

Certainly on my systems where I use the am-utils automounter, I find  
the limit on the number of simultaneously mounted filesystems is more  
in the region of 1500.  I've been desperately trying to reduce the  
number of NFS filesystems we have though.  Currently our automount map  
has about 600 entries, I think.

Tim


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From perry at piermont.com  Tue Jul  1 08:48:47 2008
From: perry at piermont.com (Perry E. Metzger)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] automount on high ports
In-Reply-To: <DC7CE5D8-16C9-48B6-AE5B-83481B80F4D3@sanger.ac.uk> (Tim Cutts's
	message of "Tue\, 1 Jul 2008 16\:40\:27 +0100")
References: <20080701093643.GA17845@gretchen.aei.uni-hannover.de>
	<878wwlk65p.fsf@snark.cb.piermont.com>
	<DC7CE5D8-16C9-48B6-AE5B-83481B80F4D3@sanger.ac.uk>
Message-ID: <87od5hip0g.fsf@snark.cb.piermont.com>


Tim Cutts <tjrc@sanger.ac.uk> writes:
> Certainly on my systems where I use the am-utils automounter, I find
> the limit on the number of simultaneously mounted filesystems is more
> in the region of 1500.

And that's doubtless not from TCP port issues but because of other
kinds of resources being limited.

> I've been desperately trying to reduce the number of NFS filesystems
> we have though.  Currently our automount map has about 600 entries,
> I think.

Sometimes that's reasonable. I've seen large sites where everyone has
a workstation in front of them and all of the thousands of users get
their home dir automounted when they sit in front of a box and log
in. However, one notes that in such a situation, the automount maps
have thousands or tens of thousands of entries, but any given machine
generally only is mounting a few file systems.

-- 
Perry E. Metzger		perry@piermont.com

From kilian at stanford.edu  Tue Jul  1 08:49:42 2008
From: kilian at stanford.edu (Kilian CAVALOTTI)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] open mosix alternative
In-Reply-To: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>
References: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>
Message-ID: <200807010849.42415.kilian@stanford.edu>

Hi Jon,

On Tuesday 01 July 2008 03:38:52 am Jon Aquilina wrote:
> does anyone know an altenative to openmosix?? 

You may want to check out OpenSSI: http://www.openssi.org

As its name says, that's a SSI clustering solution, with unified process 
namespace, full process migration, load-balancing, single root 
filesystem, etc. A complete list of features is available at: 
http://wiki.openssi.org/go/Features

Cheers,
-- 
Kilian

From henning.fehrmann at aei.mpg.de  Tue Jul  1 09:47:47 2008
From: henning.fehrmann at aei.mpg.de (Henning Fehrmann)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] automount on high ports
In-Reply-To: <878wwlk65p.fsf@snark.cb.piermont.com>
References: <20080701093643.GA17845@gretchen.aei.uni-hannover.de>
	<878wwlk65p.fsf@snark.cb.piermont.com>
Message-ID: <20080701164747.GA15901@gretchen.aei.uni-hannover.de>

On Tue, Jul 01, 2008 at 10:53:06AM -0400, Perry E. Metzger wrote:
> 
> Henning Fehrmann <henning.fehrmann@aei.mpg.de> writes:
> > we need to automount NFS directories on high ports to increase the
> > number of possible mounts. Currently, we are limited up to ca 360 mounts.
> 
> 
> Thus, your problem sounds rather odd. There is no obvious reason you
> should be limited to 360 connections.
> 
> Perhaps your problem is not what you think it is at all. Could you
> explain it in more detail?

I guess it has also something to do with the automounter. I am not able
to increase this number. 
But even if the automounter would handle more we need to be able to 
use higher ports: 
netstat shows always ports below 1024.

tcp        0      0 client:941         server:nfs

We need to mount up to 1400 nfs exports.

Cheers
Henning

From hahn at mcmaster.ca  Tue Jul  1 09:51:32 2008
From: hahn at mcmaster.ca (Mark Hahn)
Date: Tue Oct  7 01:15:12 2008
Subject: [Beowulf] A press release
In-Reply-To: <a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>
	<4863E551.8090802@scalableinformatics.com>
	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>
	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>
	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>
	<a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0807011245400.21872@coffee.psychology.mcmaster.ca>

>> We have our own stack which we stick on top of the customers favourite
>> red hat clone. Usually Scientific Linux.
>
> does it necessarily have to be a redhat clone. can it also be a debian based
> clone?

but why?  is there some concrete advantage to using Debian?
I've never understood why Debian users tend to be very True Believer,
or what it is that hooks them.

From prentice at ias.edu  Tue Jul  1 10:20:32 2008
From: prentice at ias.edu (Prentice Bisbal)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <Pine.LNX.4.64.0807011245400.21872@coffee.psychology.mcmaster.ca>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>	<4863E551.8090802@scalableinformatics.com>	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>	<a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>
	<Pine.LNX.4.64.0807011245400.21872@coffee.psychology.mcmaster.ca>
Message-ID: <486A6760.5010006@ias.edu>

Mark Hahn wrote:
>>> We have our own stack which we stick on top of the customers favourite
>>> red hat clone. Usually Scientific Linux.
>>
>> does it necessarily have to be a redhat clone. can it also be a debian
>> based
>> clone?
> 
> but why?  is there some concrete advantage to using Debian?
> I've never understood why Debian users tend to be very True Believer,
> or what it is that hooks them.

And the Debian users can say the same thing about Red Hat users. Or SUSE
users.  And if any still exist, the Slackware users could say the same
thing about the both of them. But then the Slackware users could also
point out that the first Linux distro was Slackware, so they are using
the one true Linux distro...

If you want to have a religious war about which distro to use, go
somewhere else. I'm sure there are plenty of mailing lists and
newsgroups where I'm sure that happens every day.

This is a mailing list about beowulf clusters, and the last time I
checked, you can create clusters using any Linux distribution you like,
or even non-Linux operating systems, such as IRIX, Solaris, etc.

--
Prentice

From landman at scalableinformatics.com  Tue Jul  1 10:46:01 2008
From: landman at scalableinformatics.com (Joe Landman)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <486A6760.5010006@ias.edu>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>	<4863E551.8090802@scalableinformatics.com>	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>	<a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>	<Pine.LNX.4.64.0807011245400.21872@coffee.psychology.mcmaster.ca>
	<486A6760.5010006@ias.edu>
Message-ID: <486A6D59.7020704@scalableinformatics.com>



Prentice Bisbal wrote:
> Mark Hahn wrote:

[...]

> If you want to have a religious war about which distro to use, go
> somewhere else. I'm sure there are plenty of mailing lists and
> newsgroups where I'm sure that happens every day.

Hmmm.... for me, its all about the kernel.  Thats 90+% of the battle. 
Some distros use good kernels, some do not.  I won't mention who I think 
is in the latter category.

FWIW:  we tend to build systems and place our own kernel on them. 
Basically we want them to work, and not be surprised by bad things, like 
crashes due to 4k stacks or backported (mis)features.  We also want them 
to have updated drivers, and NFS/file system bits.

> This is a mailing list about beowulf clusters, and the last time I
> checked, you can create clusters using any Linux distribution you like,
> or even non-Linux operating systems, such as IRIX, Solaris, etc.

With all due respect, I think Mark knows what this list is about.

There are lots of folks out there using Fedora, RHEL, Ubuntu, Debian, 
SuSE, ...

We generally don't care which distro is used.  Only that the kernel is 
reasonable, stable under load, and supports updated file systems/network 
capability.

Beowulf depends upon good kernels at the end of the day.  You need high 
performance and stability throughout.

-- 
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 734 786 8452
cell : +1 734 612 4615


From thpierce at gmail.com  Tue Jul  1 05:07:22 2008
From: thpierce at gmail.com (Tom Pierce)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] June New York/Jersey HPC users meeting
Message-ID: <25e9e5ad0807010507s74ea33e7p42abeff3d275b5a2@mail.gmail.com>

Dear Dan,

First, you missed a enjoyable meeting with lively discussion, good pub food
and beer. I hope we meet there again in July.

I attended most of the meeting. My memory summarized it:

Sun Grid Engine users were the majority at the meeting ( 60% SGE users, and
40% Torqur/Maui users)

The installations of the two systems are different experiences. With SGE,
you are about "half-done" after you install the system. The installation of
Torque/Maui is more functional right out of the box. Both seem to have
similar functionality when setup.

SGE has Sun developers actively working on it, so the newest versions have
more options.  eg a Flexlm link for license management.

Torque/Maui is open source, and has not been modified as often as SGE has.
Altho cpusets, similar to SGE cpusets, have recently been added.

Torque/Maui has commercial upgrades to Torque/Moab for large sites, or
people who want paid support. (and Moab
supports Flexlm license management).

There seem to be more installations of Torque/Maui than there are of SGE,
but that was just a discussion of perceptions.
However, the history of PBS, up through Torque, means that there are a great
many PBS scripts on the internet for job
submissions of HPC applications.

The discussion of MPI interfaces was ongoing. Neither system seemed to have
an advantage. Torque has the OSC mpiexec script and SGE has some builtin
hooks for MPI. The discussions mentioned Openmpi, LAM, MPICH, GM and no
obvious resolution that one system was more functional or easier than the
other for MPI codes.

At the end, I would call it a "draw".  Torque/Maui easier to setup and lots
of examples vs SGE flexibility and Flexlm license mgt.

Tom


Daniel.Roberts@sanofi-aventis.com wrote:

Anyone have minutes or conclusions to offer from this scheduler smack
down?
Thanks
Dan

-----Original Message-----
From: beowulf-bounces@beowulf.org [mailto:beowulf-bounces@beowulf.org]


If you live or work in the New York/North Jersey Metropolitan area, mark
your calender for this Thursday, June 19th.

The NYCA-HUG (New York City Area HPC Users Group) will be trying to
answer the ultimate question Torque or Sun Grid Engine? We will be
discussing the pros/cons of each scheduler for HPC clusters.
Come and add your experiences, wants, and rants.
Then you decide.
-------------- next part --------------
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From merc4krugger at gmail.com  Tue Jul  1 06:27:44 2008
From: merc4krugger at gmail.com (Krugger)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] automount on high ports
In-Reply-To: <20080701093643.GA17845@gretchen.aei.uni-hannover.de>
References: <20080701093643.GA17845@gretchen.aei.uni-hannover.de>
Message-ID: <fe34ee810807010627y419537d7q74e9b61af789b3b1@mail.gmail.com>

Hi,

Am I understanding it correctly? You want to have more than 360 mounts
in a single NFS client? And you want that client to be run on a
non-privileged port?

What you are doing doesn't make much sense to me, but you can try
adding the option "lockd.udpport=32768 lockd.tcpport=32768" to your
kernel flags so that the kernel puts the daemon lockd that handles NFS
locks at the port you selected in the client side. I don't understand
how changing the port will help you get more mounts in. I would
actually suggest you review the maximum allowed filehandles for each
process.

You will also need and start services manually, something like:
statd -p 32765 -o 32766
mountd -p 32767

If you use modules you need to reconfigure you modules with "options
lockd nlm_udpport=32768 nlm_tcpport=32768" to your /etc/modules.conf

If I am misunderstanding and you are having a maximum of 360 clients
for your NFS server, then maybe you are having a network problem,
because with NFS3 your clients will lose connection to the server when
de UDP starts losing packets due to heavy I/O from the calculations if
both happen on the same network. Maybe NFS v4 might help with TCP
connections or/and some sort of shaping to make sure there is enough
bandwith reservered for NFS to operate properly.

Notice that all have differant ports 32765,32766,32767,32768

Krugger


On Tue, Jul 1, 2008 at 10:36 AM, Henning Fehrmann
<henning.fehrmann@aei.mpg.de> wrote:
> Hello,
>
> we need to automount NFS directories on high ports to increase the number of possible mounts.
> Currently, we are limited up to ca 360 mounts.
>
> The NFS-server exports with the option 'insecure' but the mounts still end up on ports <1024 on the client side.
>
> Is there a way to enable automounts on higher ports? How can it be done manually:
> mount -t nfs -o ....?
>
> We are using autofs version 5.
>
> Thank you,
> Henning
> _______________________________________________
> Beowulf mailing list, Beowulf@beowulf.org
> To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf
>

From vernard at venger.net  Tue Jul  1 08:19:15 2008
From: vernard at venger.net (Vernard Martin)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] software for compatible with a cluster
In-Reply-To: <a31cd3860807010339v65709e83ha5afe47e9e22cc8c@mail.gmail.com>
References: <a31cd3860807010339v65709e83ha5afe47e9e22cc8c@mail.gmail.com>
Message-ID: <486A4AF3.9040108@venger.net>

Jon Aquilina wrote:
> does anyone know of any rendering software that will work with a cluster?
The Big Daddy of them all, Pixar's RenderMan Pro Server is supported 
under Linux and is used by nearly everybody in Hollywood that does 
graphic rendering for movies.  It ain't cheap but its pretty much the 
best there

Check out https://renderman.pixar.com/products/techspecs/index.htm for 
more info.


From gregory.warnes at rochester.edu  Tue Jul  1 09:39:38 2008
From: gregory.warnes at rochester.edu (Gregory Warnes)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] open mosix alternative
In-Reply-To: <200807010849.42415.kilian@stanford.edu>
Message-ID: <C48FD60A.78A5%gregory.warnes@rochester.edu>


Or, of course, the original Mosix project.  Ammon Barak is very amiable and
willing to work with folks.

http://www.mosix.org

-Greg


On 7/1/08 11:49AM , "Kilian CAVALOTTI" <kilian@stanford.edu> wrote:

> Hi Jon,
> 
> On Tuesday 01 July 2008 03:38:52 am Jon Aquilina wrote:
>> > does anyone know an altenative to openmosix??
> 
> You may want to check out OpenSSI: http://www.openssi.org
> 
> As its name says, that's a SSI clustering solution, with unified process
> namespace, full process migration, load-balancing, single root
> filesystem, etc. A complete list of features is available at:
> http://wiki.openssi.org/go/Features
> 
> Cheers,
> --
> Kilian
> _______________________________________________
> Beowulf mailing list, Beowulf@beowulf.org
> To change your subscription (digest mode or unsubscribe) visit
> http://www.beowulf.org/mailman/listinfo/beowulf
> 

-- 
Gregory R. Warnes, Ph.D
Program Director
Center for Computational Arts, Sciences, and Engineering
University of Rochester

Tel: 585-273-2794
Fax: 585-276-2097
Email: gregory.warnes@rochester.edu


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From landman at scalableinformatics.com  Tue Jul  1 11:06:34 2008
From: landman at scalableinformatics.com (Joe Landman)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] open mosix alternative
In-Reply-To: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>
References: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>
Message-ID: <486A722A.3000405@scalableinformatics.com>

Hi Job

Jon Aquilina wrote:
> does anyone know an altenative to openmosix?? would it be worth reviving 
> the development of the kernel?

   OpenMOSIX was all about process migration between different 
independent OSes.  You can still get some of that with Scyld, with 
OpenSSI, and a few others.

   If you prefer more of an SMP model (simpler programming), you should 
look at ScaleMP DSMs.  Some on this list argue the shared memory 
programming is not easier than distributed memory programming, though I 
am not one of them who makes this argument.  It has different 
challenges, costs and benefits than MPI.  It has different limitations. 
  Not so surprisingly, with the advent of many-core units, shared memory 
programming techniques are needed to get good performance within a 
single system.

   Disclosure: We are looking at these units for some of our work.

Joe


-- 
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://www.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 734 786 8452
cell : +1 734 612 4615


From smulcahy at aplpi.com  Tue Jul  1 11:11:23 2008
From: smulcahy at aplpi.com (stephen mulcahy)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <486A6D59.7020704@scalableinformatics.com>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>	<4863E551.8090802@scalableinformatics.com>	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>	<a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>	<Pine.LNX.4.64.0807011245400.21872@coffee.psychology.mcmaster.ca>	<486A6760.5010006@ias.edu>
	<486A6D59.7020704@scalableinformatics.com>
Message-ID: <486A734B.3000701@aplpi.com>

Joe Landman wrote:
> Hmmm.... for me, its all about the kernel.  Thats 90+% of the battle. 
> Some distros use good kernels, some do not.  I won't mention who I think 
> is in the latter category.

> ..

> We generally don't care which distro is used.  Only that the kernel is 
> reasonable, stable under load, and supports updated file systems/network 
> capability.

This information would be most interesting to me and surely others on 
the list .. can you talk about of the distributions that provide "good 
kernels" if not about the others (and hey, theres hundreds of Linux 
distributions out there - http://lwn.net/Distributions/ so we couldn't 
infer the bad ones from your omissions ;)

-stephen

-- 
Stephen Mulcahy, Applepie Solutions Ltd., Innovation in Business Center,
GMIT, Dublin Rd, Galway, Ireland.  +353.91.751262  http://www.aplpi.com
Registered in Ireland, no. 289353 (5 Woodlands Avenue, Renmore, Galway)

From geoff at galitz.org  Tue Jul  1 12:05:54 2008
From: geoff at galitz.org (Geoff Galitz)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] Re:  "hobbyists"
In-Reply-To: <48693A89.3080605@moene.indiv.nluug.nl>
References: <485920D8.2030309@ias.edu>	<6.2.5.6.2.20080618164843.02b1bd30@jpl.nasa.gov>	<Pine.LNX.4.64.0806190840371.4566@lilith.rgb.private.net>	<200806190945.21604.kilian@stanford.edu><485A9520.2080508@scalableinformatics.com>
	<48693A89.3080605@moene.indiv.nluug.nl>
Message-ID: <128FF5A06DBD4D74B8AA8CB6E4EF4B1F@geoffPC>



Ohh...  I was just waiting for the conversation to back to this.  For an
inside perspective:

http://www.spiegel.de/international/europe/0,1518,562315,00.html

Does that make me on-topic?

-geoff



Geoff Galitz
Blankenheim NRW, Deutschland
http://www.galitz.org


-----Original Message-----
From: beowulf-bounces@beowulf.org [mailto:beowulf-bounces@beowulf.org] On
Behalf Of Toon Moene
Sent: Montag, 30. Juni 2008 21:57
To: Joe Landman
Cc: beowulf@beowulf.org
Subject: Re: [Beowulf] Re: "hobbyists"

Joe Landman wrote:

> Tactical nukes (aimed at armies) were on the table for a few of the NATO 
> scenarios involving responses to Soviet invasion of western Europe 
> (based upon some of the historical reading, though I am not sure how 
> serious they were).  The western Europeans were understandably 
> un-enthusiastic about such scenarios.

You bet we were.  I was in the organization of the 400,000+ protest in 
Amsterdam in November. 1981.

Cannon-fodder at a high level ...

-- 
Toon Moene - e-mail: toon@moene.indiv.nluug.nl - phone: +31 346 214290
Saturnushof 14, 3738 XG  Maartensdijk, The Netherlands
At home: http://moene.indiv.nluug.nl/~toon/
Progress of GNU Fortran: http://gcc.gnu.org/ml/gcc/2008-01/msg00009.html
_______________________________________________
Beowulf mailing list, Beowulf@beowulf.org
To change your subscription (digest mode or unsubscribe) visit
http://www.beowulf.org/mailman/listinfo/beowulf


From jan.heichler at gmx.net  Tue Jul  1 12:08:32 2008
From: jan.heichler at gmx.net (Jan Heichler)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>
	<4863E551.8090802@scalableinformatics.com>
	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>
	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>
	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>
	<a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>
Message-ID: <66506789.20080701210832@gmx.net>

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From jan.heichler at gmx.net  Tue Jul  1 12:09:08 2008
From: jan.heichler at gmx.net (Jan Heichler)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>
	<4863E551.8090802@scalableinformatics.com>
	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>
	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>
	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>
Message-ID: <62974595.20080701210908@gmx.net>

Hallo Dan,

Dienstag, 1. Juli 2008, meintest Du:

>>Hi Jon,

>>We have our own stack which we stick on top of the customers favourite
>>red hat clone. Usually Scientific Linux.

>>Here is a bit more about it.

>>http://www.clustervision.com/products_os.php

>>We sell as a standalone product and it does quite well. I could even
>>go so far to say that it is 'stack of choice' in many European
>>institutions.

DKqc> Every throught of getting a job in Sales and Marketing?  :-)

What makes you think that he hasn't that kind of job? ;-)

@Andy: SCNR 

Regards
Jan
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From hahn at mcmaster.ca  Tue Jul  1 12:19:24 2008
From: hahn at mcmaster.ca (Mark Hahn)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <486A6760.5010006@ias.edu>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>
	<4863E551.8090802@scalableinformatics.com>
	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>
	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>
	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>
	<a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>
	<Pine.LNX.4.64.0807011245400.21872@coffee.psychology.mcmaster.ca>
	<486A6760.5010006@ias.edu>
Message-ID: <Pine.LNX.4.64.0807011510530.21872@coffee.psychology.mcmaster.ca>

>>> does it necessarily have to be a redhat clone. can it also be a debian
>>> based
>>> clone?
>>
>> but why?  is there some concrete advantage to using Debian?
>> I've never understood why Debian users tend to be very True Believer,
>> or what it is that hooks them.
>
> And the Debian users can say the same thing about Red Hat users. Or SUSE

very nice!  an excellent parody of the True Believer response.

but I ask again: what are the reasons one might prefer using debian?
really, I'm not criticizing it - I really would like to know why it 
would matter whether someone (such as ClusterVisionOS (tm)) would 
use debian or another distro.

From matt at technoronin.com  Tue Jul  1 12:30:05 2008
From: matt at technoronin.com (Matt Lawrence)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] Re: Beowulf Digest, Vol 53, Issue 1
In-Reply-To: <c84311bb0807010551v2316ceb3o441b7948f3d2bb7a@mail.gmail.com>
References: <200807010728.m617S3Ub011226@bluewest.scyld.com>
	<c84311bb0807010551v2316ceb3o441b7948f3d2bb7a@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0807011428310.4893@oberon.technoronin.com>

On Tue, 1 Jul 2008, Mark Kosmowski wrote:

> As heretical as this last sounds, I'm tempted to throw in the towel on
> my PhD studies because I can no longer afford the power to run my
> three node cluster at home.  Energy costs may end up being the straw
> that breaks this camel's back.

Perhaps you should consider getting time on someone else's cluster.  For 
something that only requires three nodes, there should be quite a number 
of places to run.

-- Matt
It's not what I know that counts.
It's what I can remember in time to use.

From hahn at mcmaster.ca  Tue Jul  1 12:25:48 2008
From: hahn at mcmaster.ca (Mark Hahn)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <486A6D59.7020704@scalableinformatics.com>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>
	<4863E551.8090802@scalableinformatics.com>
	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>
	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>
	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>
	<a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>
	<Pine.LNX.4.64.0807011245400.21872@coffee.psychology.mcmaster.ca>
	<486A6760.5010006@ias.edu> <486A6D59.7020704@scalableinformatics.com>
Message-ID: <Pine.LNX.4.64.0807011519460.21872@coffee.psychology.mcmaster.ca>

> Hmmm.... for me, its all about the kernel.  Thats 90+% of the battle. Some 
> distros use good kernels, some do not.  I won't mention who I think is in the 
> latter category.

I was hoping for some discussion of concrete issues.  for instance,
I have the impression debian uses something other than sysvinit - 
does that work out well?  is it a problem getting commercial 
packages (pathscale/pgi/intel compilers, gaussian, etc) to run?

the couple debian people I know tend to have more ideological motives
(which I do NOT impugn, except that I am personally more swayed by 
practical, concrete reasons.)

From landman at scalableinformatics.com  Tue Jul  1 12:53:23 2008
From: landman at scalableinformatics.com (Joe Landman)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <Pine.LNX.4.64.0807011519460.21872@coffee.psychology.mcmaster.ca>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>	<4863E551.8090802@scalableinformatics.com>	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>	<a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>	<Pine.LNX.4.64.0807011245400.21872@coffee.psychology.mcmaster.ca>	<486A6760.5010006@ias.edu>
	<486A6D59.7020704@scalableinformatics.com>
	<Pine.LNX.4.64.0807011519460.21872@coffee.psychology.mcmaster.ca>
Message-ID: <486A8B33.7020600@scalableinformatics.com>

Mark Hahn wrote:
>> Hmmm.... for me, its all about the kernel.  Thats 90+% of the battle. 
>> Some distros use good kernels, some do not.  I won't mention who I 
>> think is in the latter category.
> 
> I was hoping for some discussion of concrete issues.  for instance,
> I have the impression debian uses something other than sysvinit - does 
> that work out well?  is it a problem getting commercial packages 
> (pathscale/pgi/intel compilers, gaussian, etc) to run?

Hi Mark:

   We have multiple Ubuntu servers up, and thus far, no major problems 
... just a few "translational" gotchas.  We have successfully run pgi, 
intel, gaussian, gamess, ... on our Ubuntu units as well as our 
RHEL/Centos, Fedora, ...

> 
> the couple debian people I know tend to have more ideological motives

Yeah ... can't escape this.  I like some of the elements of 
Ubuntu/Debian better than I do RHEL (the network configuration in Debian 
is IMO sane, while in RHEL/Centos/SuSE it is not).  There are some 
aspects that are worse (no /etc/profile.d ... so I add that back in by 
hand ).



> (which I do NOT impugn, except that I am personally more swayed by 
> practical, concrete reasons.)


Building and deploying updated/correct kernels with Ubuntu/Debian is far 
easier (the build is much easier/saner) than with SuSE, RHEL, ...  From 
a pragmatic view, this is what why we have a slight preference for that.

Joe

-- 
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://www.scalableinformatics.com
        http://jackrabbit.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 866 888 3112
cell : +1 734 612 4615

From lindahl at pbm.com  Tue Jul  1 13:01:23 2008
From: lindahl at pbm.com (Greg Lindahl)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] open mosix alternative
In-Reply-To: <486A722A.3000405@scalableinformatics.com>
References: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>
	<486A722A.3000405@scalableinformatics.com>
Message-ID: <20080701200122.GA23583@bx9.net>

On Tue, Jul 01, 2008 at 02:06:34PM -0400, Joe Landman wrote:

>   If you prefer more of an SMP model (simpler programming), you should  
> look at ScaleMP DSMs.  Some on this list argue the shared memory  
> programming is not easier than distributed memory programming,

Gee, and I thought the biggest argument about ScaleMP was that the
previous 50 times the same thing was attempted, it had low
performance.

I'd love to see some benchmarks (other than Stream). So if you do look
at it, please share.

-- greg


From asabigue at fing.edu.uy  Tue Jul  1 13:14:26 2008
From: asabigue at fing.edu.uy (ariel sabiguero yawelak)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] Re: Beowulf Digest, Vol 53, Issue 1
In-Reply-To: <c84311bb0807010551v2316ceb3o441b7948f3d2bb7a@mail.gmail.com>
References: <200807010728.m617S3Ub011226@bluewest.scyld.com>
	<c84311bb0807010551v2316ceb3o441b7948f3d2bb7a@mail.gmail.com>
Message-ID: <486A9022.5070109@fing.edu.uy>

Well Mark, don't give up!
I am not sure which one is your application domain, but if you require 
24x7 computation, then you should not be hosting that at home.
On the other hand, if you are not doing real computation and you just 
have a testbed at home, maybe for debugging your parallel applications 
or something similar, you might be interested in a virtualized solution. 
Several years ago, I used to "debug" some neural networks at home, but 
training sessions (up to two weeks of training) happened at the university.
I would suggest to do something like that.
You can always scale-down your problem in several phases and save the 
complete data-set / problem for THE RUN.

You are not being a heretic there, but suffering energy costs ;-)
In more places that you may believe, useful computing nodes are being 
replaced just because of energy costs. Even in some application domains 
you can even loose computational power if you move from 4 nodes into a 
single quad-core (i.e. memory bandwidth problems). I know it is very 
nice to be able to do everything at home.. but maybe before dropping 
your studies or working overtime to pay the electricity bill, you might 
want to reconsider the fact of collapsing your phisical deploy into a 
single virtualized cluster. (or just dispatch several threads/processes 
in a single system).
If you collapse into a single system you have only 1 mainboard, one HDD, 
one power source, one processor (physically speaking), .... and you can 
achieve almost the performance of 4 systems in one, consuming the power 
of.... well maybe even less than a single one. I don't want to go into 
discussions about performance gain/loose due to the variation of the 
hardware architecture. Invest some bucks (if you haven't done that yet) 
in a good power source. Efficiency of OEM unbranded power sources is 
realy pathetic. may be 45-50% efficiency, while a good power source 
might be 75-80% efficient. Use the energy for computing, not for heating 
your house.
What I mean is that you could consider just collapsing a complete 
"small" cluster into single system. If your application is CPU-bound and 
not I/O bound, VMware Server could be an option, as it is free software 
(unfortunately not open, even tough some patches can be done on the 
drivers). I think it is not possible to publish benchmarking data about 
VMware, but I can tell you that in long timescales, the performance you 
get in the host OS is similar than the one of the guest OS. There are a 
lot of problems related to jitter, from crazy clocks to delays, but if 
your application is not sensitive to that, then you are Ok.
Maybe this is not a solution, but you can provide more information 
regarding your problem before quitting...

my 2 cents....

ariel

Mark Kosmowski escribi?:
> At some point there a cost-benefit analysis needs to be performed.  If
> my cluster at peak usage only uses 4 Gb RAM per CPU (I live in
> single-core land still and do not yet differentiate between CPU and
> core) and my nodes all have 16 Gb per CPU then I am wasting RAM
> resources and would be better off buying new machines and physically
> transferring the RAM to and from them or running more jobs each
> distributed across fewer CPUs.  Or saving on my electricity bill and
> powering down some nodes.
>
> As heretical as this last sounds, I'm tempted to throw in the towel on
> my PhD studies because I can no longer afford the power to run my
> three node cluster at home.  Energy costs may end up being the straw
> that breaks this camel's back.
>
> Mark E. Kosmowski
>
>   
>> From: "Jon Aquilina" <eagles051387@gmail.com>
>>     
>
>   
>> not sure if this applies to all kinds of senarios that clusters are used in
>> but isnt the more ram you have the better?
>>
>> On 6/30/08, Vincent Diepeveen <diep@xs4all.nl> wrote:
>>     
>>> Toon,
>>>
>>> Can you drop a line on how important RAM is for weather forecasting in
>>> latest type of calculations you're performing?
>>>
>>> Thanks,
>>> Vincent
>>>
>>>
>>> On Jun 30, 2008, at 8:20 PM, Toon Moene wrote:
>>>
>>> Jim Lux wrote:
>>>       
>>>> Yep.  And for good reason.  Even a big DoD job is still tiny in Nvidia's
>>>>         
>>>>> scale of operations. We face this all the time with NASA work.
>>>>>  Semiconductor manufacturers have no real reason to produce special purpose
>>>>> or customized versions of their products for space use, because they can
>>>>> sell all they can make to the consumer market. More than once, I've had a
>>>>> phone call along the lines of this:
>>>>> "Jim: I'm interested in your new ABC321 part."
>>>>> "Rep: Great. I'll just send the NDA over and we can talk about it."
>>>>> "Jim: Great, you have my email and my fax # is..."
>>>>> "Rep: By the way, what sort of volume are you going to be using?"
>>>>> "Jim: Oh, 10-12.."
>>>>> "Rep: thousand per week, excellent..."
>>>>> "Jim: No, a dozen pieces, total, lifetime buy, or at best maybe every
>>>>> year."
>>>>> "Rep: Oh...<dial tone>"
>>>>> {Well, to be fair, it's not that bad, they don't hang up on you..
>>>>>
>>>>>           
>>>> Since about a year, it's been clear to me that weather forecasting (i.e.,
>>>> running a more or less sophisticated atmospheric model to provide weather
>>>> predictions) is going to be "mainstream" in the sense that every business
>>>> that needs such forecasts for its operations can simply run them in-house.
>>>>
>>>> Case in point:  I bought a $1100 HP box (the obvious target group being
>>>> teenage downloaders) which performs the HIRLAM limited area model *on the
>>>> grid that we used until October 2006* in December last year.
>>>>
>>>> It's about twice as slow as our then-operational 50-CPU Sun Fire 15K.
>>>>
>>>> I wonder what effect this will have on CPU developments ...
>>>>
>>>> --
>>>> Toon Moene - e-mail: toon@moene.indiv.nluug.nl - phone: +31 346 214290
>>>> Saturnushof 14, 3738 XG  Maartensdijk, The Netherlands
>>>> At home: http://moene.indiv.nluug.nl/~toon/
>>>> Progress of GNU Fortran: http://gcc.gnu.org/ml/gcc/2008-01/msg00009.html
>>>>
>>>>         
>>> _______________________________________________
>>> Beowulf mailing list, Beowulf@beowulf.org
>>> To change your subscription (digest mode or unsubscribe) visit
>>> http://www.beowulf.org/mailman/listinfo/beowulf
>>>
>>>       
>>
>> --
>> Jonathan Aquilina
>>     
> _______________________________________________
> Beowulf mailing list, Beowulf@beowulf.org
> To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf
>
>   

From perry at piermont.com  Tue Jul  1 13:21:55 2008
From: perry at piermont.com (Perry E. Metzger)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] automount on high ports
In-Reply-To: <20080701164747.GA15901@gretchen.aei.uni-hannover.de> (Henning
	Fehrmann's message of "Tue\, 1 Jul 2008 18\:47\:47 +0200")
References: <20080701093643.GA17845@gretchen.aei.uni-hannover.de>
	<878wwlk65p.fsf@snark.cb.piermont.com>
	<20080701164747.GA15901@gretchen.aei.uni-hannover.de>
Message-ID: <87fxqtuzh8.fsf@snark.cb.piermont.com>


Henning Fehrmann <henning.fehrmann@aei.mpg.de> writes:
>> Thus, your problem sounds rather odd. There is no obvious reason you
>> should be limited to 360 connections.
>> 
>> Perhaps your problem is not what you think it is at all. Could you
>> explain it in more detail?
>
> I guess it has also something to do with the automounter. I am not able
> to increase this number. 
> But even if the automounter would handle more we need to be able to 
> use higher ports: 
> netstat shows always ports below 1024.
>
> tcp        0      0 client:941         server:nfs
>
> We need to mount up to 1400 nfs exports.

All NFS clients are connecting to a single port, not to a different
port for every NFS export. You do not need 1400 listening TCP ports on
a server to export 1400 different file systems. Only one port is
needed, whether you are exporting one file system or one million, just
as only one SMTP port is needed whether you are receiving mail from
one client or from one million.

The clients are connecting from ports below 1024 because Berkeley set
up a hack in the original BSD stack so that only root could open ports
below 1024. This way, you could "know" the process on the remote host
was a root process, thus you could feel "secure" [sic]. It doesn't add
any real security any more, but it is also not the cause of any
problem you are experiencing.

We can help you figure this out, but you will have to give a lot more
detail about the problem. Please describe your network setup. How many
servers do you have? How many clients? How many file systems are those
servers exporting? How many is a typical client mounting, and why?
Start there and we can try to move forward.

-- 
Perry E. Metzger		perry@piermont.com

From landman at scalableinformatics.com  Tue Jul  1 13:24:04 2008
From: landman at scalableinformatics.com (Joe Landman)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] open mosix alternative
In-Reply-To: <20080701200122.GA23583@bx9.net>
References: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>	<486A722A.3000405@scalableinformatics.com>
	<20080701200122.GA23583@bx9.net>
Message-ID: <486A9264.5090902@scalableinformatics.com>

Greg Lindahl wrote:
> On Tue, Jul 01, 2008 at 02:06:34PM -0400, Joe Landman wrote:
> 
>>   If you prefer more of an SMP model (simpler programming), you should  
>> look at ScaleMP DSMs.  Some on this list argue the shared memory  
>> programming is not easier than distributed memory programming,
> 
> Gee, and I thought the biggest argument about ScaleMP was that the
> previous 50 times the same thing was attempted, it had low
> performance.

The researchy DSMs had low performance.  That is known.  This one seems 
not to be bad over good IB nets.  You always have latency.  Can't escape 
that.

> I'd love to see some benchmarks (other than Stream). So if you do look
> at it, please share.

If you are serious about this, I'll bug Shai as to what is shareable. 
He does have benchmarks.  The ones I have seen (real applications, not 
microbenchmarks), looked pretty good.  Which is why we are looking at them.

Joe

-- 
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman@scalableinformatics.com
web  : http://www.scalableinformatics.com
        http://jackrabbit.scalableinformatics.com
phone: +1 734 786 8423
fax  : +1 866 888 3112
cell : +1 734 612 4615

From andrew at moonet.co.uk  Tue Jul  1 13:35:29 2008
From: andrew at moonet.co.uk (andrew holway)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <f8b14cb80807011334u5972d937ye85b64f54dd027d@mail.gmail.com>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>
	<4863E551.8090802@scalableinformatics.com>
	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>
	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>
	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>
	<a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>
	<66506789.20080701210832@gmx.net>
	<f8b14cb80807011334u5972d937ye85b64f54dd027d@mail.gmail.com>
Message-ID: <f8b14cb80807011335v4a0e0b39p3851187119e0e788@mail.gmail.com>

> does it necessarily have to be a redhat clone. can it also be a debian based
> clone?

Not at all, If there were demand or a customer with enough cash to
throw at the job then we would of course accommodate his every need.
Considering that it is taking several rather expensive developers
quite a long time to push out the latest incarnation, ClusterVisionOS
4 through beta this cost could be considerable to ensure a stable
environment. I'm no expert in the subtleties of distributions but
maintaining and supporting one to a high enough standard is quite
enough work thanks very much :)

Ta

Andy

From lindahl at pbm.com  Tue Jul  1 13:37:14 2008
From: lindahl at pbm.com (Greg Lindahl)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] open mosix alternative
In-Reply-To: <486A9264.5090902@scalableinformatics.com>
References: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>
	<486A722A.3000405@scalableinformatics.com>
	<20080701200122.GA23583@bx9.net>
	<486A9264.5090902@scalableinformatics.com>
Message-ID: <20080701203713.GB28024@bx9.net>

On Tue, Jul 01, 2008 at 04:24:04PM -0400, Joe Landman wrote:

> If you are serious about this, I'll bug Shai as to what is shareable. He 
> does have benchmarks.  The ones I have seen (real applications, not  
> microbenchmarks), looked pretty good.  Which is why we are looking at 
> them.

If you look back on this mailing list, you'll see that I asked him for
benchmarks, and he posted stream. Which isn't interesting, because
it's embarrassingly parallel.

-- greg



From hahn at mcmaster.ca  Tue Jul  1 13:44:05 2008
From: hahn at mcmaster.ca (Mark Hahn)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] open mosix alternative
In-Reply-To: <20080701200122.GA23583@bx9.net>
References: <a31cd3860807010338u4b517d3ah685cd9e312eb234e@mail.gmail.com>
	<486A722A.3000405@scalableinformatics.com>
	<20080701200122.GA23583@bx9.net>
Message-ID: <Pine.LNX.4.64.0807011641410.21872@coffee.psychology.mcmaster.ca>

> I'd love to see some benchmarks (other than Stream). So if you do look
> at it, please share.

me too.  in particular, I'd like to see "hot page" performance - 
where a multithreaded program bangs on a heavily write-shared page.

From gerry.creager at tamu.edu  Tue Jul  1 13:57:08 2008
From: gerry.creager at tamu.edu (Gerry Creager)
Date: Tue Oct  7 01:15:13 2008
Subject: Commodity supercomputing, was: Re: NDAs Re: [Beowulf] Nvidia,
	cuda, tesla and... where's my	double floating point?
In-Reply-To: <486A9822.7000902@moene.indiv.nluug.nl>
References: <alpine.DEB.1.10.0805021404240.2494@localhost>	<1210016466.4924.1.camel@Vigor13>	<B1526F5C-9C28-4C20-916D-EB1890D734D8@xs4all.nl>	<48551E70.7070507@scalableinformatics.com>	<4AF41375-3A13-4691-A2A1-D5B853FEC3A4@xs4all.nl>	<20080615154227.u8fwdpn08ww4c40k@webmail.jpl.nasa.gov>	<B13D9243-7184-4BEA-B3C9-5FAF8AD0113D@xs4all.nl>	<6.2.5.6.2.20080616084554.02e4dd18@jpl.nasa.gov>	<486923D6.8070907@moene.indiv.nluug.nl>	<1214864562.6912.29.camel@Vigor13>
	<486A1F7B.9080408@tamu.edu> <486A9822.7000902@moene.indiv.nluug.nl>
Message-ID: <486A9A24.9000800@tamu.edu>

I was at the WRF conf. last week.  A colleague from the Netherlands was 
lamenting that he couldn't get ECMWF data (I don't recall the annual 
cost/year but it was huge).  NOAA/NCEP GFS data are available via FTP 
and regular enough to allow really simple scripting, as well as other 
methods.  I don't understand why folks wouldn't use these data.

As for competing, if our companies are not sufficiently technically 
astute, should we be protecting them from European companies, just 
because the data are free?

Toon Moene wrote:
> Gerry Creager wrote:
> 
>> In the US, at least for academic institutions and hobbyists, surface 
>> and upper air observations of the sort you describe are generally 
>> available for incorporation into models for data assimilation.  Models 
>> are generally forced and bounded using model data from other 
>> atmospheric models, also available.  As I understand it from 
>> colleagues in Europe, getting similar data over there is more 
>> problemmatical.
> 
> Exactly !  And what happens in Europe is that companies take the freely 
> available US data, use it to compete with US companies, and disregard 
> the (meteorological superior) ECMWF data, because it is not free.
> 
> A colleague of mine held some very unpopular talks in Reading, England, 
> about this (according to his figures, 99 % of the meteorological data 
> used in Europe originates from the US).
> 

-- 
Gerry Creager -- gerry.creager@tamu.edu
Texas Mesonet -- AATLT, Texas A&M University	
Cell: 979.229.5301 Office: 979.458.4020 FAX: 979.862.3983
Office: 1700 Research Parkway Ste 160, TAMU, College Station, TX 77843

From eagles051387 at gmail.com  Tue Jul  1 15:53:34 2008
From: eagles051387 at gmail.com (Jon Aquilina)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] software for compatible with a cluster
In-Reply-To: <486A4296.4050501@hope.edu>
References: <a31cd3860807010339v65709e83ha5afe47e9e22cc8c@mail.gmail.com>
	<7B82EE52C0DC4879AD6AE8FCA937C63C@geoffPC>
	<a31cd3860807010426q1be3b70fm8e8e44e06927b9f7@mail.gmail.com>
	<3CB66E9F377C4961B5457896137EAD1B@geoffPC>
	<a31cd3860807010718o2586766cobe81f4f215d64afe@mail.gmail.com>
	<486A4296.4050501@hope.edu>
Message-ID: <a31cd3860807011553l3ff9e85dhc0a7c334b71d15f8@mail.gmail.com>

my idea is more of for my thesis.  if i am goign ot do anything like this.
vernard thanks for the link. whats it like in a cluster environment?

On Tue, Jul 1, 2008 at 4:43 PM, Paul Van Allsburg <vanallsburg@hope.edu>
wrote:

> I'd like to do the same, as a project for a group of students...  Please
> keep me in the loop?
> Thanks!
> Paul
>
> --
> Paul Van Allsburg       Computational Science & Modeling Facilitator
> Natural Sciences Division,  Hope College
> 35 East 12th Street
> Holland, Michigan 49423
> 616-395-7292 http://www.hope.edu/academic/csm/
>
>
> Jon Aquilina wrote:
>
>> that would be greatly appreciated
>>
>> On 7/1/08, *Geoff Galitz* <geoff@galitz.org <mailto:geoff@galitz.org>>
>> wrote:
>>
>>
>>    That is out of my field of expertise.  Sounds like a question for
>>    professional digital artists.  I can put you in touch some folks
>>    that most likely know the answer to your questions, if you like.
>>
>>
>>    Anybody know of any current approaches to this?
>>
>>
>>    Geoff Galitz
>>    Blankenheim NRW, Deutschland
>>    http://www.galitz.org <http://www.galitz.org/>
>>
>>    * From: * Jon Aquilina [mailto:eagles051387@gmail.com
>>    <mailto:eagles051387@gmail.com>]
>>    *Sent:* Dienstag, 1. Juli 2008 13:27
>>    *To:* Geoff Galitz
>>    *Cc:* Beowulf Mailing List
>>    *Subject:* Re: [Beowulf] software for compatible with a cluster
>>
>>
>>    reason i am asking is because i would like to setup a rendering
>>    cluster and provide rendering services. does this also work for 3d
>>    animated movies that require rendering or does one need somethin
>>    entierly different for that?
>>
>>    On 7/1/08, *Geoff Galitz* <geoff@galitz.org
>>    <mailto:geoff@galitz.org>> wrote:
>>
>>
>>
>>    I know people who use Houdini for this:
>>
>>
>>    http://www.sidefx.com/index.php
>>
>>
>>    I cannot vouch for how well it works or what is involved, though.
>>
>>
>>
>>    Geoff Galitz
>>    Blankenheim NRW, Deutschland
>>    http://www.galitz.org <http://www.galitz.org/>
>>
>>    * From: * beowulf-bounces@beowulf.org
>>    <mailto:beowulf-bounces@beowulf.org>
>>    [mailto:beowulf-bounces@beowulf.org
>>    <mailto:beowulf-bounces@beowulf.org>] *On Behalf Of *Jon Aquilina
>>    *Sent:* Dienstag, 1. Juli 2008 12:40
>>    *To:* Beowulf Mailing List
>>    *Subject:* [Beowulf] software for compatible with a cluster
>>
>>
>>    does anyone know of any rendering software that will work with a
>>    cluster?
>>
>>    --    Jonathan Aquilina
>>
>>
>>
>>
>>    --    Jonathan Aquilina
>>
>>
>>
>>
>> --
>> Jonathan Aquilina
>>
>


-- 
Jonathan Aquilina
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From perry at piermont.com  Tue Jul  1 16:23:10 2008
From: perry at piermont.com (Perry E. Metzger)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <486A6760.5010006@ias.edu> (Prentice Bisbal's message of "Tue\,
	01 Jul 2008 13\:20\:32 -0400")
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>
	<4863E551.8090802@scalableinformatics.com>
	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>
	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>
	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>
	<a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>
	<Pine.LNX.4.64.0807011245400.21872@coffee.psychology.mcmaster.ca>
	<486A6760.5010006@ias.edu>
Message-ID: <87bq1hgpep.fsf@snark.cb.piermont.com>


Prentice Bisbal <prentice@ias.edu> writes:
>>> does it necessarily have to be a redhat clone. can it also be a debian
>>> based
>>> clone?
>> 
>> but why?  is there some concrete advantage to using Debian?
>> I've never understood why Debian users tend to be very True Believer,
>> or what it is that hooks them.
>
> And the Debian users can say the same thing about Red Hat users. Or SUSE
> users.  And if any still exist, the Slackware users could say the same
> thing about the both of them. But then the Slackware users could also
> point out that the first Linux distro was Slackware, so they are using
> the one true Linux distro...

Precisely. It pays to allow people to use what they want. Fewer
religious battles that way. Whether one distro or another has an
advantage isn't the point -- people have their own tastes and it
doesn't pay to tell them "no" without good reason.

Perry
-- 
Perry E. Metzger		perry@piermont.com

From perry at piermont.com  Tue Jul  1 16:25:19 2008
From: perry at piermont.com (Perry E. Metzger)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <Pine.LNX.4.64.0807011519460.21872@coffee.psychology.mcmaster.ca>
	(Mark Hahn's message of "Tue\,
	1 Jul 2008 15\:25\:48 -0400 \(EDT\)")
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>
	<4863E551.8090802@scalableinformatics.com>
	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>
	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>
	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>
	<a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>
	<Pine.LNX.4.64.0807011245400.21872@coffee.psychology.mcmaster.ca>
	<486A6760.5010006@ias.edu> <486A6D59.7020704@scalableinformatics.com>
	<Pine.LNX.4.64.0807011519460.21872@coffee.psychology.mcmaster.ca>
Message-ID: <877ic5gpb4.fsf@snark.cb.piermont.com>


Mark Hahn <hahn@mcmaster.ca> writes:
> I was hoping for some discussion of concrete issues.  for instance,
> I have the impression debian uses something other than sysvinit - 
> does that work out well?  is it a problem getting commercial packages
> (pathscale/pgi/intel compilers, gaussian, etc) to run?

It is trivial to port init scripts between different init
systems. They're just short shell scripts, they're utterly readable,
and any sysadmin worth their salt can make the needed changes in a few
minutes. If you have a large cluster, you need such a person anyway.

Perry
-- 
Perry E. Metzger		perry@piermont.com

From perry at piermont.com  Tue Jul  1 16:31:50 2008
From: perry at piermont.com (Perry E. Metzger)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <Pine.LNX.4.64.0807011510530.21872@coffee.psychology.mcmaster.ca>
	(Mark Hahn's message of "Tue\,
	1 Jul 2008 15\:19\:24 -0400 \(EDT\)")
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>
	<4863E551.8090802@scalableinformatics.com>
	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>
	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>
	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>
	<a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>
	<Pine.LNX.4.64.0807011245400.21872@coffee.psychology.mcmaster.ca>
	<486A6760.5010006@ias.edu>
	<Pine.LNX.4.64.0807011510530.21872@coffee.psychology.mcmaster.ca>
Message-ID: <873amtgp09.fsf@snark.cb.piermont.com>


Mark Hahn <hahn@mcmaster.ca> writes:
>>> but why?  is there some concrete advantage to using Debian?
>>> I've never understood why Debian users tend to be very True Believer,
>>> or what it is that hooks them.
>>
>> And the Debian users can say the same thing about Red Hat users. Or SUSE
>
> very nice!  an excellent parody of the True Believer response.

Actually, he was just being reasonable.

> but I ask again: what are the reasons one might prefer using debian?
> really, I'm not criticizing it - I really would like to know why it
> would matter whether someone (such as ClusterVisionOS (tm)) would use
> debian or another distro.

Often it is just a question of what the people using the system are
used to. I often prefer using BSD systems, largely because of certain
technical advantages, but also to a great extent because my first big
Unix boxes were Vaxes running 4.2BSD in the early 1980s and after 25
years with the same flavor of Unix you get used to the way things are
done. It is much the same reason I use Emacs instead of vi -- I
started using Emacs on Tops-20 decades ago and I'm too used to it
now. If you told me I "have" to use vi, things would get ugly, even
though I don't think there is anything wrong with using vi per se.


Perry
-- 
Perry E. Metzger		perry@piermont.com

From perry at piermont.com  Tue Jul  1 16:34:17 2008
From: perry at piermont.com (Perry E. Metzger)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] software for compatible with a cluster
In-Reply-To: <a31cd3860807011553l3ff9e85dhc0a7c334b71d15f8@mail.gmail.com>
	(Jon Aquilina's message of "Wed\, 2 Jul 2008 00\:53\:34 +0200")
References: <a31cd3860807010339v65709e83ha5afe47e9e22cc8c@mail.gmail.com>
	<7B82EE52C0DC4879AD6AE8FCA937C63C@geoffPC>
	<a31cd3860807010426q1be3b70fm8e8e44e06927b9f7@mail.gmail.com>
	<3CB66E9F377C4961B5457896137EAD1B@geoffPC>
	<a31cd3860807010718o2586766cobe81f4f215d64afe@mail.gmail.com>
	<486A4296.4050501@hope.edu>
	<a31cd3860807011553l3ff9e85dhc0a7c334b71d15f8@mail.gmail.com>
Message-ID: <87y74lfabq.fsf@snark.cb.piermont.com>


"Jon Aquilina" <eagles051387@gmail.com> writes:
> my idea is more of for my thesis.

If you're trying to do 3d animation on the cheap and you want
something that's already cluster capable, I'd try Blender. It is open
source and it has already made some reasonable length movies. Not
being an animation type, I know nothing about how nice it is compared
to commercial products, but it is hard to beat the price.

Perry
-- 
Perry E. Metzger		perry@piermont.com

From hahn at mcmaster.ca  Tue Jul  1 22:06:43 2008
From: hahn at mcmaster.ca (Mark Hahn)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <C4904902.79B7%gregory.warnes@rochester.edu>
References: <C4904902.79B7%gregory.warnes@rochester.edu>
Message-ID: <Pine.LNX.4.64.0807020054010.21872@coffee.psychology.mcmaster.ca>

>> I was hoping for some discussion of concrete issues.  for instance,
>> I have the impression debian uses something other than sysvinit -
>> does that work out well?
>>
> Debian uses standard sysvinit-style scripts in /etc/init.d, /etc/rc0.d, ...

thanks.  I guess I was assuming that mainstream debian was like ubuntu.

>>   is it a problem getting commercial
>> packages (pathscale/pgi/intel compilers, gaussian, etc) to run?
>>
> Išve never had any major problems.  Most linux vendors supply both RPMšs and
> .tar.gz installers, and I generally have better luck with the latter, even
> on RPM based systems anyway.

interesting - I wonder why.  the main difference would be that the rpm 
format encodes dependencies...

>> the couple debian people I know tend to have more ideological motives
>> (which I do NOT impugn, except that I am personally more swayed by
>> practical, concrete reasons.)
>>
> My Œconversionš to use of Debian had little to do with ideological motives,
> and a lot more to do with minimizing the amount of time I had to take away
> from my research to support the Linux clusters I was maintaining at the
> time.

again interesting, thanks.  what sorts of things in rpm-based distros 
consumed your time?

> Side note, one very nice thing about debian is the ability to upgrade a
> system in-place from one O/S  release to another via
>
>    apt-get dist-upgrade
>
> Much nicer than reinstalling the O/S as seems to be (used to be?) the norm
> with RPM-based systems

I've done major version upgrades using rpm, admittedly in the pre-fedora
days.  it _is_ a nice capability - I'm a little surprised desktop-oriented
distros don't emphasize it...
From tjrc at sanger.ac.uk  Tue Jul  1 22:37:19 2008
From: tjrc at sanger.ac.uk (Tim Cutts)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <486A8B33.7020600@scalableinformatics.com>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>	<4863E551.8090802@scalableinformatics.com>	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>	<f8b14cb80807010120u7ed78c5cl6417a531c37c4cef@mail.gmail.com>	<0D49B15ACFDF2F46BF90B6E08C90048A04884918AC@quadbrsex1.quadrics.com>	<a31cd3860807010228m50366682v128d7002edcae53@mail.gmail.com>	<Pine.LNX.4.64.0807011245400.21872@coffee.psychology.mcmaster.ca>	<486A6760.5010006@ias.edu>
	<486A6D59.7020704@scalableinformatics.com>
	<Pine.LNX.4.64.0807011519460.21872@coffee.psychology.mcmaster.ca>
	<486A8B33.7020600@scalableinformatics.com>
Message-ID: <86A30BE3-3B8E-47C8-8286-D2D7E2C74A40@sanger.ac.uk>


On 1 Jul 2008, at 8:53 pm, Joe Landman wrote:

>> the couple debian people I know tend to have more ideological motives
>
> Yeah ... can't escape this.

Indeed.  Ubuntu is slightly more pragmatic than Debian, as far as the  
ideological stuff goes.

>  I like some of the elements of Ubuntu/Debian better than I do RHEL  
> (the network configuration in Debian is IMO sane, while in RHEL/ 
> Centos/SuSE it is not).  There are some aspects that are worse (no / 
> etc/profile.d ... so I add that back in by hand ).

Here, our clusters all run Debian, but we also have RHAS and SLES  
around when support matrices demand it (Oracle, mainly).

I'd agree that fundamentally it's a case of what you're used to.  We  
stopped using Red Hat widely about four years ago, and the reasons  
(which are probably not valid any more) were:

1)  Not all userland programs were 64-bit file aware.
2)  There were certain features which we just couldn't get to work  
properly on RHAS - a prime example being multipath SAN access.  It  
"just worked" on Debian.
3)  Smooth upgrades from one major release to the next without having  
to reinstall.  While this is probably not important for beowulf nodes,  
it is for more complex servers.

I still prefer Debian's package management system, but that's probably  
because I'm used to it, rather than it inherently being superior.   
yast2 can do pretty much everything that aptitude does, although I  
think aptitude is more amenable to automation through cfengine and the  
like.  There are some very powerful little parts of the packaging  
system, like dpkg-divert, which allows you to replace a file from a  
package with your own, in such a way that it will not be overwritten  
the next time the package is upgraded.  For those of us that need to  
customise our systems that sort of thing is very useful, and saves a  
lot of work down the line.

>> (which I do NOT impugn, except that I am personally more swayed by  
>> practical, concrete reasons.)
>
>
> Building and deploying updated/correct kernels with Ubuntu/Debian is  
> far easier (the build is much easier/saner) than with SuSE,  
> RHEL, ...  From a pragmatic view, this is what why we have a slight  
> preference for that.

I'd agree with that.  Using make-kpkg to build a custom kernel .deb  
which you can then easily deploy to all your machines is a real boon.

At the end of the day, people should use what they're comfortable with.

I don't necessarily buy the support argument; there are some companies  
(Platform, for example) who will support you whichever distro you use;  
all they care about is what kernel version and C library version  
you're running.  I like this attitude and I wish it was more  
widespread amongst proprietary software vendors.

Tim


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From eagles051387 at gmail.com  Tue Jul  1 22:37:21 2008
From: eagles051387 at gmail.com (Jon Aquilina)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] software for compatible with a cluster
In-Reply-To: <87y74lfabq.fsf@snark.cb.piermont.com>
References: <a31cd3860807010339v65709e83ha5afe47e9e22cc8c@mail.gmail.com>
	<7B82EE52C0DC4879AD6AE8FCA937C63C@geoffPC>
	<a31cd3860807010426q1be3b70fm8e8e44e06927b9f7@mail.gmail.com>
	<3CB66E9F377C4961B5457896137EAD1B@geoffPC>
	<a31cd3860807010718o2586766cobe81f4f215d64afe@mail.gmail.com>
	<486A4296.4050501@hope.edu>
	<a31cd3860807011553l3ff9e85dhc0a7c334b71d15f8@mail.gmail.com>
	<87y74lfabq.fsf@snark.cb.piermont.com>
Message-ID: <a31cd3860807012237p4ceae4fbh774e96208edb1c9@mail.gmail.com>

if i use blender how nicely does it work in a cluster?

On Wed, Jul 2, 2008 at 1:34 AM, Perry E. Metzger <perry@piermont.com> wrote:

>
> "Jon Aquilina" <eagles051387@gmail.com> writes:
> > my idea is more of for my thesis.
>
> If you're trying to do 3d animation on the cheap and you want
> something that's already cluster capable, I'd try Blender. It is open
> source and it has already made some reasonable length movies. Not
> being an animation type, I know nothing about how nice it is compared
> to commercial products, but it is hard to beat the price.
>
> Perry
> --
> Perry E. Metzger                perry@piermont.com
>



-- 
Jonathan Aquilina
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From carsten.aulbert at aei.mpg.de  Wed Jul  2 00:26:58 2008
From: carsten.aulbert at aei.mpg.de (Carsten Aulbert)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] automount on high ports
In-Reply-To: <87fxqtuzh8.fsf@snark.cb.piermont.com>
References: <20080701093643.GA17845@gretchen.aei.uni-hannover.de>	<878wwlk65p.fsf@snark.cb.piermont.com>	<20080701164747.GA15901@gretchen.aei.uni-hannover.de>
	<87fxqtuzh8.fsf@snark.cb.piermont.com>
Message-ID: <486B2DC2.9010604@aei.mpg.de>

Hi Perry,

Perry E. Metzger wrote:

> 
> All NFS clients are connecting to a single port, not to a different
> port for every NFS export. You do not need 1400 listening TCP ports on
> a server to export 1400 different file systems. Only one port is
> needed, whether you are exporting one file system or one million, just
> as only one SMTP port is needed whether you are receiving mail from
> one client or from one million.
> 
That's clear and not the problem

> The clients are connecting from ports below 1024 because Berkeley set
> up a hack in the original BSD stack so that only root could open ports
> below 1024. This way, you could "know" the process on the remote host
> was a root process, thus you could feel "secure" [sic]. It doesn't add
> any real security any more, but it is also not the cause of any
> problem you are experiencing.

We might run out of "secure" ports.

> We can help you figure this out, but you will have to give a lot more
> detail about the problem. Please describe your network setup. How many
> servers do you have? How many clients? How many file systems are those
> servers exporting? How many is a typical client mounting, and why?
> Start there and we can try to move forward.
> 

OK, we have 1342 nodes which act as servers as well as clients. Every
node exports a single local directory and all other nodes can mount this.

What we do now to optimize the available bandwidth and IOs is spread
millions of files according to a hash algorithm to all nodes (multiple
copies as well) and then run a few 1000 jobs opening one file from one
box then one file from the other box and so on. With a short autofs
timeout that ought to work. Typically it is possible that a single
process opens about 10-15 files per second, i.e. making 10-15 mounts per
second. With 4 parallel process per node that's 40-60 mounts/second.
With a timeout of 5 seconds we should roughly have 200-300 concurrent
mounts (on average, no idea abut the variance).

Our tests so far have shown that sometimes a node keeps a few mounts
open (autofs4 problems AFAIK) and at some point is not able to mount
more shares. Usually this occurs at about 350 mounts and we are not yet
100% sure if we are running out of secure ports.

All our boxes export now with "insecure" option (NFSv3), but our clients
all connect from a "secure" port, anyone here who might give us a hint
how to force this in Linux?

Thanks a lot

Carsten


From tjrc at sanger.ac.uk  Wed Jul  2 01:19:50 2008
From: tjrc at sanger.ac.uk (Tim Cutts)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] automount on high ports
In-Reply-To: <486B2DC2.9010604@aei.mpg.de>
References: <20080701093643.GA17845@gretchen.aei.uni-hannover.de>	<878wwlk65p.fsf@snark.cb.piermont.com>	<20080701164747.GA15901@gretchen.aei.uni-hannover.de>
	<87fxqtuzh8.fsf@snark.cb.piermont.com>
	<486B2DC2.9010604@aei.mpg.de>
Message-ID: <66EB3DC0-B281-4869-BB8E-A55E577C44FE@sanger.ac.uk>


On 2 Jul 2008, at 8:26 am, Carsten Aulbert wrote:

> OK, we have 1342 nodes which act as servers as well as clients. Every
> node exports a single local directory and all other nodes can mount  
> this.
>
> What we do now to optimize the available bandwidth and IOs is spread
> millions of files according to a hash algorithm to all nodes (multiple
> copies as well) and then run a few 1000 jobs opening one file from one
> box then one file from the other box and so on. With a short autofs
> timeout that ought to work. Typically it is possible that a single
> process opens about 10-15 files per second, i.e. making 10-15 mounts  
> per
> second. With 4 parallel process per node that's 40-60 mounts/second.
> With a timeout of 5 seconds we should roughly have 200-300 concurrent
> mounts (on average, no idea abut the variance).

Please tell me you're not serious!  The overheads of just performing  
the NFS mounts are going to kill you, never mind all the network  
traffic going all over the place.

Since you've distributed the files to the local disks of the nodes,  
surely the right way to perform this work is to schedule the  
computations so that each node works on the data on its own local  
disk, and doesn't have to talk networked storage at all?  Or don't you  
know in advance which files a particular job is going to need?

Tim


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From henning.fehrmann at aei.mpg.de  Wed Jul  2 01:44:58 2008
From: henning.fehrmann at aei.mpg.de (Henning Fehrmann)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] automount on high ports
In-Reply-To: <66EB3DC0-B281-4869-BB8E-A55E577C44FE@sanger.ac.uk>
References: <20080701093643.GA17845@gretchen.aei.uni-hannover.de>
	<878wwlk65p.fsf@snark.cb.piermont.com>
	<20080701164747.GA15901@gretchen.aei.uni-hannover.de>
	<87fxqtuzh8.fsf@snark.cb.piermont.com>
	<486B2DC2.9010604@aei.mpg.de>
	<66EB3DC0-B281-4869-BB8E-A55E577C44FE@sanger.ac.uk>
Message-ID: <20080702084458.GA12879@gretchen.aei.uni-hannover.de>

On Wed, Jul 02, 2008 at 09:19:50AM +0100, Tim Cutts wrote:
> 
> On 2 Jul 2008, at 8:26 am, Carsten Aulbert wrote:
> 
> >OK, we have 1342 nodes which act as servers as well as clients. Every
> >node exports a single local directory and all other nodes can mount this.
> >
> >What we do now to optimize the available bandwidth and IOs is spread
> >millions of files according to a hash algorithm to all nodes (multiple
> >copies as well) and then run a few 1000 jobs opening one file from one
> >box then one file from the other box and so on. With a short autofs
> >timeout that ought to work. Typically it is possible that a single
> >process opens about 10-15 files per second, i.e. making 10-15 mounts per
> >second. With 4 parallel process per node that's 40-60 mounts/second.
> >With a timeout of 5 seconds we should roughly have 200-300 concurrent
> >mounts (on average, no idea abut the variance).
> 
> Please tell me you're not serious!  The overheads of just performing the NFS mounts are going to kill you, never mind all the network traffic going 
> all over the place.
> 
> Since you've distributed the files to the local disks of the nodes, surely the right way to perform this work is to schedule the computations so that 
> each node works on the data on its own local disk, and doesn't have to talk networked storage at all?  Or don't you know in advance which files a 
> particular job is going to need?

Yes, this is the problem. The amount of files is too big to store it
everywhere (few TByte and 50 million files). Mounting a view NFS server does not provide
the bandwidth. 
On the other hand, the coreswitch should be able to handle the flows non
blocking. We think that nfs mounts are the fastest possibility to
distribute the demanded files to the nodes. 

Henning

From tjrc at sanger.ac.uk  Wed Jul  2 01:45:21 2008
From: tjrc at sanger.ac.uk (Tim Cutts)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <Pine.LNX.4.64.0807020054010.21872@coffee.psychology.mcmaster.ca>
References: <C4904902.79B7%gregory.warnes@rochester.edu>
	<Pine.LNX.4.64.0807020054010.21872@coffee.psychology.mcmaster.ca>
Message-ID: <011E261F-94D7-4F1C-AA69-4A008A1DA1E2@sanger.ac.uk>


On 2 Jul 2008, at 6:06 am, Mark Hahn wrote:

>>> I was hoping for some discussion of concrete issues.  for instance,
>>> I have the impression debian uses something other than sysvinit -
>>> does that work out well?
>>>
>> Debian uses standard sysvinit-style scripts in /etc/init.d, /etc/ 
>> rc0.d, ...
>
> thanks.  I guess I was assuming that mainstream debian was like  
> ubuntu.

It's sort of the other way around.  Remember that Ubuntu is based off  
a six-monthly snapshot of Debian's testing track, which is why Hardy  
looks a lot more like the upcoming Debian Lenny than it does like  
Debian Etch.

> interesting - I wonder why.  the main difference would be that the  
> rpm format encodes dependencies...

The difficulty is that many ISVs tend to do a fairly terrible job of  
packaging their applications as RPM's or DEB's, for example creating  
init scripts which don't obey the distribution's policies, or making  
willy-nilly modifications to configuration files all over the place,  
even in other packages (which in the Debian world is a *big* no-no,  
that's why many Debian/Ubuntu packages have now moved to the conf.d  
type of configuration directory, so that other packages can drop in  
little independent snippets of configuration)

I have seen, for example, .deb packages from a Large Company With  
Which We Are All Familiar which essentially attempted to convert your  
system into a Red Hat system by moving all your init scripts around  
and whatnot, so once you'd installed this abomination, you'd totally  
wrecked the ability of many of the main distro packages to be updated  
ever again.  Oh, and of course uninstalling the package didn't put  
anything back the way it had been before.

Like you, I tend to use tarballs if they are available, and if I want  
to turn them into packages I do it myself, and make sure they are  
policy compliant for the distro.

So this, while not a statement in favour of either flavour of distro,  
is definitely a warning to be very wary of what packages that have  
come from sources other than the distro itself might do (which of  
course, you'd be wary of anyway for security reasons).

Tim


-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From ajt at rri.sari.ac.uk  Wed Jul  2 02:23:06 2008
From: ajt at rri.sari.ac.uk (Tony Travis)
Date: Tue Oct  7 01:15:13 2008
Subject: [Beowulf] A press release
In-Reply-To: <Pine.LNX.4.64.0807011510530.21872@coffee.psychology.mcmaster.ca>
References: <f8b14cb80806261130k16c5eed0i208516868bf5104b@mail.gmail.com>	<4863E551.8090802@scalableinformatics.com>	<a31cd3860806280309i26212473o60be0e287c444a85@mail.gmail.com>	<f8b14cb80807010120u7ed78c5cl6417a531