From gmk at runlevelzero.net  Sat Jun  3 22:09:00 2006
From: gmk at runlevelzero.net (Greg M. Kurtzer)
Date: Sat, 3 Jun 2006 22:09:00 -0700
Subject: [cAos] caos3 development
Message-ID: <20060604050900.GB14645@aries.runlevelzero.net>

The next generation of cAos is in development, here and now!

As some of you also know, we are in a position to receive funding for
development. However our funding backers (myself included) have been
watching our current development emphasis and while we have a very
current and maintained Enlightenment stack, we need to also pay as much
(and even more) attention to our services and security.

To accommodate this, cAos-3 primary emphasis is performance, efficiency,
services and security. Our targeted user-base is clustered systems and
servers for ISP, home and office. Secondary emphasis will include other
more general distribution aspects.

The goal is not only to appeal to our potential funders, but also grow
into an area to which I have heard various complaints that there isn't a
reasonable solution for. While the Linux desktop and general purpose
distributions are very important, they also have been solved very well
by both commercial and non-commercial organizations.

I know everyone is busy, I am as well. However we can not expect to get
backed by individuals or other organizations that see very little
progress where they need it most or significantly grow our user-base. It
is time to focus and get stuff done.

At this time, I have the base self hosting development file system
nearing completion. From here I will need package maintainers,
developers, doc writers, and anyone else that wants to be part of the
development group to contact me. I am open to discussing positions for
not only guru developers and maintainers, but also newcomers that want
to be part of an open source project that many people use.

While cAos-2 was a loosely managed project where contributors come and
go and commit when they have time, cAos-3 will be much more structured
and organized higher emphasis on leadership and chain of command. We
will operate more as a unit and as a team bringing a higher level of
professionalism to the project.

Thus I am looking for people to not only volunteer but also commit to long
term maintenance of various aspects of caos3. We have some very intriguing
opportunities in-front of us and we need to be more aggressive and focused
if we are to reach the next level.

Thanks,
Greg
-- 
Greg M. Kurtzer
http://runlevelzero.net/
http://caosity.org/
http://warewulf-cluster.org/

Do not look anywhere for truth, for all that is needed is to refrain from
allowing concepts to arise.


From astevens at gravitypark.com  Sat Jun  3 22:20:09 2006
From: astevens at gravitypark.com (Arthur Stevens)
Date: Sat, 3 Jun 2006 22:20:09 -0700
Subject: [cAos] caos3 development
References: <20060604050900.GB14645@aries.runlevelzero.net>
Message-ID: <000601c68796$8cb7d5a0$6600a8c0@astevens>

Hallelujah!

I could not agree more. Focusing on horsepower and not the cupholders is by 
far the best decision yet!

Arthur


----- Original Message ----- 
From: "Greg M. Kurtzer" <gmk at runlevelzero.net>
To: <caos at caosity.org>
Sent: Saturday, June 03, 2006 10:09 PM
Subject: [cAos] caos3 development


> The next generation of cAos is in development, here and now!
>
> As some of you also know, we are in a position to receive funding for
> development. However our funding backers (myself included) have been
> watching our current development emphasis and while we have a very
> current and maintained Enlightenment stack, we need to also pay as much
> (and even more) attention to our services and security.
>
> To accommodate this, cAos-3 primary emphasis is performance, efficiency,
> services and security. Our targeted user-base is clustered systems and
> servers for ISP, home and office. Secondary emphasis will include other
> more general distribution aspects.
>
> The goal is not only to appeal to our potential funders, but also grow
> into an area to which I have heard various complaints that there isn't a
> reasonable solution for. While the Linux desktop and general purpose
> distributions are very important, they also have been solved very well
> by both commercial and non-commercial organizations.
>
> I know everyone is busy, I am as well. However we can not expect to get
> backed by individuals or other organizations that see very little
> progress where they need it most or significantly grow our user-base. It
> is time to focus and get stuff done.
>
> At this time, I have the base self hosting development file system
> nearing completion. From here I will need package maintainers,
> developers, doc writers, and anyone else that wants to be part of the
> development group to contact me. I am open to discussing positions for
> not only guru developers and maintainers, but also newcomers that want
> to be part of an open source project that many people use.
>
> While cAos-2 was a loosely managed project where contributors come and
> go and commit when they have time, cAos-3 will be much more structured
> and organized higher emphasis on leadership and chain of command. We
> will operate more as a unit and as a team bringing a higher level of
> professionalism to the project.
>
> Thus I am looking for people to not only volunteer but also commit to long
> term maintenance of various aspects of caos3. We have some very intriguing
> opportunities in-front of us and we need to be more aggressive and focused
> if we are to reach the next level.
>
> Thanks,
> Greg
> -- 
> Greg M. Kurtzer
> http://runlevelzero.net/
> http://caosity.org/
> http://warewulf-cluster.org/
>
> Do not look anywhere for truth, for all that is needed is to refrain from
> allowing concepts to arise.
> _______________________________________________
> cAos mailing list
> cAos at caosity.org
> http://lists.caosity.org/mailman/listinfo/caos
> 




From tmattox at gmail.com  Sun Jun  4 06:22:47 2006
From: tmattox at gmail.com (Tim Mattox)
Date: Sun, 4 Jun 2006 09:22:47 -0400
Subject: [cAos] caos3 development
In-Reply-To: <000601c68796$8cb7d5a0$6600a8c0@astevens>
References: <20060604050900.GB14645@aries.runlevelzero.net>
	<000601c68796$8cb7d5a0$6600a8c0@astevens>
Message-ID: <ea86ce220606040622t124bec43vabb139eeaa9e5b38@mail.gmail.com>

I second the "Hallelujah!" :-)

Although, I may be even less available the rest of June, I should be able to
contribute much more starting sometime in July.  Why you may ask?
First, my wife and I are expecting our first in a week or so...  a girl. :-)
Second, in July I'll be actively working at my new position at Indiana
University in the Open Systems Lab.  I'll need to see what my new boss
thinks about it, but I might be able to work on aspects of cAos-3 part of
my official duties.  Either way, I'm on board.

For those not familiar with the OSL @ IU, they are the the developers of
LAM/MPI and one of the founding members of the Open MPI  Team, both
of which are key software projects to be included in cAos-3, IMHO.
http://www.osl.iu.edu/research.php

On 6/4/06, Arthur Stevens <astevens at gravitypark.com> wrote:
> Hallelujah!
>
> I could not agree more. Focusing on horsepower and not the cupholders is by
> far the best decision yet!
>
> Arthur

-- 
Tim Mattox - tmattox at gmail.com
  http://homepage.mac.com/tmattox/
    I'm a bright... http://www.the-brights.net/


From m.stolte at datadevil.demon.nl  Sun Jun  4 08:34:41 2006
From: m.stolte at datadevil.demon.nl (m.stolte at datadevil.demon.nl)
Date: Sun, 04 Jun 2006 17:34:41 +0200
Subject: [cAos] caos3 development
In-Reply-To: <ea86ce220606040622t124bec43vabb139eeaa9e5b38@mail.gmail.com>
References: <ea86ce220606040622t124bec43vabb139eeaa9e5b38@mail.gmail.com>
Message-ID: <20060604173441.g67sc3zpueck4ogg@www.webmail.nl.demon.net>

Quoting Tim Mattox <tmattox at gmail.com>:

>
> I second the "Hallelujah!" :-)
>
> Although, I may be even less available the rest of June, I should be able to
> contribute much more starting sometime in July.  Why you may ask?
> First, my wife and I are expecting our first in a week or so...  a girl. :-)
> Second, in July I'll be actively working at my new position at Indiana
> University in the Open Systems Lab.  I'll need to see what my new boss
> thinks about it, but I might be able to work on aspects of cAos-3 part of
> my official duties.  Either way, I'm on board.

Good to have you onboard Tim.

>
> For those not familiar with the OSL @ IU, they are the the developers of
> LAM/MPI and one of the founding members of the Open MPI  Team, both
> of which are key software projects to be included in cAos-3, IMHO.
> http://www.osl.iu.edu/research.php

They sound like a must have to include indeed, altough I'm by no means 
a cluster
expert :-)

I'm also going to be available again from july onwards, so hope to see 
you then!

Maarten

>
> On 6/4/06, Arthur Stevens <astevens at gravitypark.com> wrote:
>> Hallelujah!
>>
>> I could not agree more. Focusing on horsepower and not the cupholders is by
>> far the best decision yet!
>>
>> Arthur
>
> --
> Tim Mattox - tmattox at gmail.com
>  http://homepage.mac.com/tmattox/
>    I'm a bright... http://www.the-brights.net/
> _______________________________________________
> cAos mailing list
> cAos at caosity.org
> http://lists.caosity.org/mailman/listinfo/caos
>





From linuxtitan at gmail.com  Sun Jun  4 19:30:46 2006
From: linuxtitan at gmail.com (Stephen Houston)
Date: Sun, 4 Jun 2006 21:30:46 -0500
Subject: [cAos] caos3 development
In-Reply-To: <20060604173441.g67sc3zpueck4ogg@www.webmail.nl.demon.net>
References: <ea86ce220606040622t124bec43vabb139eeaa9e5b38@mail.gmail.com>
	<20060604173441.g67sc3zpueck4ogg@www.webmail.nl.demon.net>
Message-ID: <306818890606041930l1aa2a52bh28e0cb01eb3582b5@mail.gmail.com>

On 6/4/06, m.stolte at datadevil.demon.nl <m.stolte at datadevil.demon.nl> wrote:
>
> Quoting Tim Mattox <tmattox at gmail.com>:
>
> >
> > I second the "Hallelujah!" :-)
> >
> > Although, I may be even less available the rest of June, I should be
> able to
> > contribute much more starting sometime in July.  Why you may ask?
> > First, my wife and I are expecting our first in a week or so...  a girl.
> :-)
> > Second, in July I'll be actively working at my new position at Indiana
> > University in the Open Systems Lab.  I'll need to see what my new boss
> > thinks about it, but I might be able to work on aspects of cAos-3 part
> of
> > my official duties.  Either way, I'm on board.
>
> Good to have you onboard Tim.
>
> >
> > For those not familiar with the OSL @ IU, they are the the developers of
> > LAM/MPI and one of the founding members of the Open MPI  Team, both
> > of which are key software projects to be included in cAos-3, IMHO.
> > http://www.osl.iu.edu/research.php
>
> They sound like a must have to include indeed, altough I'm by no means
> a cluster
> expert :-)
>
> I'm also going to be available again from july onwards, so hope to see
> you then!
>
> Maarten
>
> >
> > On 6/4/06, Arthur Stevens <astevens at gravitypark.com> wrote:
> >> Hallelujah!
> >>
> >> I could not agree more. Focusing on horsepower and not the cupholders
> is by
> >> far the best decision yet!
> >>
> >> Arthur
> >
> > --
> > Tim Mattox - tmattox at gmail.com
> >  http://homepage.mac.com/tmattox/
> >    I'm a bright... http://www.the-brights.net/
> > _______________________________________________
> > cAos mailing list
> > cAos at caosity.org
> > http://lists.caosity.org/mailman/listinfo/caos
> >
>
>
>
> _______________________________________________
> cAos mailing list
> cAos at caosity.org
> http://lists.caosity.org/mailman/listinfo/caos
>

Ok. After consideration, I can really see this project is going somewhere
big. Greg is someone you can definetly put trust in and Arthur is someone
that will beat you up if you don't, so how can I say no? On a more serious
work. Work has begin including some that I have done, and the technology of
caos 3 is going to be really great, boosting our popularity without a
doubt.  This is definetly a project to be involved in.

-- 
Stephen Houston
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From glen at callident.com  Mon Jun  5 12:31:54 2006
From: glen at callident.com (Glen Otero)
Date: Mon, 5 Jun 2006 12:31:54 -0700
Subject: [cAos] caos3 development
In-Reply-To: <20060604050900.GB14645@aries.runlevelzero.net>
References: <20060604050900.GB14645@aries.runlevelzero.net>
Message-ID: <5FAD211E-CC25-48BA-AB6A-0478EBB10337@callident.com>

Greg-

I'd like to help with cAos-3 development, but not sure what the best  
way to contribute is. Any suggestions?

Glen

On Jun 3, 2006, at 10:09 PM, Greg M. Kurtzer wrote:

> The next generation of cAos is in development, here and now!
>
> As some of you also know, we are in a position to receive funding for
> development. However our funding backers (myself included) have been
> watching our current development emphasis and while we have a very
> current and maintained Enlightenment stack, we need to also pay as  
> much
> (and even more) attention to our services and security.
>
> To accommodate this, cAos-3 primary emphasis is performance,  
> efficiency,
> services and security. Our targeted user-base is clustered systems and
> servers for ISP, home and office. Secondary emphasis will include  
> other
> more general distribution aspects.
>
> The goal is not only to appeal to our potential funders, but also grow
> into an area to which I have heard various complaints that there  
> isn't a
> reasonable solution for. While the Linux desktop and general purpose
> distributions are very important, they also have been solved very well
> by both commercial and non-commercial organizations.
>
> I know everyone is busy, I am as well. However we can not expect to  
> get
> backed by individuals or other organizations that see very little
> progress where they need it most or significantly grow our user- 
> base. It
> is time to focus and get stuff done.
>
> At this time, I have the base self hosting development file system
> nearing completion. From here I will need package maintainers,
> developers, doc writers, and anyone else that wants to be part of the
> development group to contact me. I am open to discussing positions for
> not only guru developers and maintainers, but also newcomers that want
> to be part of an open source project that many people use.
>
> While cAos-2 was a loosely managed project where contributors come and
> go and commit when they have time, cAos-3 will be much more structured
> and organized higher emphasis on leadership and chain of command. We
> will operate more as a unit and as a team bringing a higher level of
> professionalism to the project.
>
> Thus I am looking for people to not only volunteer but also commit  
> to long
> term maintenance of various aspects of caos3. We have some very  
> intriguing
> opportunities in-front of us and we need to be more aggressive and  
> focused
> if we are to reach the next level.
>
> Thanks,
> Greg
> -- 
> Greg M. Kurtzer
> http://runlevelzero.net/
> http://caosity.org/
> http://warewulf-cluster.org/
>
> Do not look anywhere for truth, for all that is needed is to  
> refrain from
> allowing concepts to arise.
> _______________________________________________
> cAos mailing list
> cAos at caosity.org
> http://lists.caosity.org/mailman/listinfo/caos
>



From gmk at runlevelzero.net  Mon Jun  5 12:56:31 2006
From: gmk at runlevelzero.net (Greg M. Kurtzer)
Date: Mon, 5 Jun 2006 12:56:31 -0700
Subject: [cAos] caos3 development
In-Reply-To: <ea86ce220606040622t124bec43vabb139eeaa9e5b38@mail.gmail.com>
References: <20060604050900.GB14645@aries.runlevelzero.net>
	<000601c68796$8cb7d5a0$6600a8c0@astevens>
	<ea86ce220606040622t124bec43vabb139eeaa9e5b38@mail.gmail.com>
Message-ID: <20060605195631.GA13146@aries.runlevelzero.net>

On Sun, Jun 04, 2006 at 09:22:47AM -0400, Tim Mattox wrote:
> I second the "Hallelujah!" :-)
> 
> Although, I may be even less available the rest of June, I should be able to
> contribute much more starting sometime in July.  Why you may ask?
> First, my wife and I are expecting our first in a week or so...  a girl. :-)
> Second, in July I'll be actively working at my new position at Indiana
> University in the Open Systems Lab.  I'll need to see what my new boss
> thinks about it, but I might be able to work on aspects of cAos-3 part of
> my official duties.  Either way, I'm on board.

Congratulations, and great news on the position at IU!

We will have multiple ways of installing and building various HPC
applications. This is because while RPM is definatly the easiest and
most commonly used for standard solutions, most clusters and truly high
performance systems are not "standard" (eg. they use custom or
specialized compilers and math libraries). So cAos-3 will also be
putting more focus into our "ports" tree for these applications making
it very simple for people to build or customize many of these packages.

We will need maintainers for both of these. :)

> For those not familiar with the OSL @ IU, they are the the developers of
> LAM/MPI and one of the founding members of the Open MPI  Team, both
> of which are key software projects to be included in cAos-3, IMHO.
> http://www.osl.iu.edu/research.php

Very much so. :)

Thanks, and I look forward to seeing ya in July! :)

> On 6/4/06, Arthur Stevens <astevens at gravitypark.com> wrote:
> > Hallelujah!
> >
> > I could not agree more. Focusing on horsepower and not the cupholders is by
> > far the best decision yet!
> >
> > Arthur
> 
> -- 
> Tim Mattox - tmattox at gmail.com
>   http://homepage.mac.com/tmattox/
>     I'm a bright... http://www.the-brights.net/
> _______________________________________________
> cAos mailing list
> cAos at caosity.org
> http://lists.caosity.org/mailman/listinfo/caos

-- 
Greg M. Kurtzer
http://runlevelzero.net/
http://caosity.org/
http://warewulf-cluster.org/

Do not look anywhere for truth, for all that is needed is to refrain from
allowing concepts to arise.


From gmk at runlevelzero.net  Mon Jun  5 13:22:48 2006
From: gmk at runlevelzero.net (Greg M. Kurtzer)
Date: Mon, 5 Jun 2006 13:22:48 -0700
Subject: [cAos] caos3 development
In-Reply-To: <5FAD211E-CC25-48BA-AB6A-0478EBB10337@callident.com>
References: <20060604050900.GB14645@aries.runlevelzero.net>
	<5FAD211E-CC25-48BA-AB6A-0478EBB10337@callident.com>
Message-ID: <20060605202248.GB13146@aries.runlevelzero.net>

If my memory serves me right,... you just happen to be one of the worlds
leading experts on computational genomics and bio-informatics. :)

Lets start there if that works for you. :)

Can you provide a list of the freely available bio-informatics code that
you would be interested in maintaining and their dependencies (eg. web
based frontends may require, apache2, php5, perl, python, *sql, etc..).

Thanks!

On Mon, Jun 05, 2006 at 12:31:54PM -0700, Glen Otero wrote:
> Greg-
> 
> I'd like to help with cAos-3 development, but not sure what the best  
> way to contribute is. Any suggestions?
> 
> Glen
> 
> On Jun 3, 2006, at 10:09 PM, Greg M. Kurtzer wrote:
> 
> > The next generation of cAos is in development, here and now!
> >
> > As some of you also know, we are in a position to receive funding for
> > development. However our funding backers (myself included) have been
> > watching our current development emphasis and while we have a very
> > current and maintained Enlightenment stack, we need to also pay as  
> > much
> > (and even more) attention to our services and security.
> >
> > To accommodate this, cAos-3 primary emphasis is performance,  
> > efficiency,
> > services and security. Our targeted user-base is clustered systems and
> > servers for ISP, home and office. Secondary emphasis will include  
> > other
> > more general distribution aspects.
> >
> > The goal is not only to appeal to our potential funders, but also grow
> > into an area to which I have heard various complaints that there  
> > isn't a
> > reasonable solution for. While the Linux desktop and general purpose
> > distributions are very important, they also have been solved very well
> > by both commercial and non-commercial organizations.
> >
> > I know everyone is busy, I am as well. However we can not expect to  
> > get
> > backed by individuals or other organizations that see very little
> > progress where they need it most or significantly grow our user- 
> > base. It
> > is time to focus and get stuff done.
> >
> > At this time, I have the base self hosting development file system
> > nearing completion. From here I will need package maintainers,
> > developers, doc writers, and anyone else that wants to be part of the
> > development group to contact me. I am open to discussing positions for
> > not only guru developers and maintainers, but also newcomers that want
> > to be part of an open source project that many people use.
> >
> > While cAos-2 was a loosely managed project where contributors come and
> > go and commit when they have time, cAos-3 will be much more structured
> > and organized higher emphasis on leadership and chain of command. We
> > will operate more as a unit and as a team bringing a higher level of
> > professionalism to the project.
> >
> > Thus I am looking for people to not only volunteer but also commit  
> > to long
> > term maintenance of various aspects of caos3. We have some very  
> > intriguing
> > opportunities in-front of us and we need to be more aggressive and  
> > focused
> > if we are to reach the next level.
> >
> > Thanks,
> > Greg
> > -- 
> > Greg M. Kurtzer
> > http://runlevelzero.net/
> > http://caosity.org/
> > http://warewulf-cluster.org/
> >
> > Do not look anywhere for truth, for all that is needed is to  
> > refrain from
> > allowing concepts to arise.
> > _______________________________________________
> > cAos mailing list
> > cAos at caosity.org
> > http://lists.caosity.org/mailman/listinfo/caos
> >
> 
> _______________________________________________
> cAos mailing list
> cAos at caosity.org
> http://lists.caosity.org/mailman/listinfo/caos

-- 
Greg M. Kurtzer
http://runlevelzero.net/
http://caosity.org/
http://warewulf-cluster.org/

Do not look anywhere for truth, for all that is needed is to refrain from
allowing concepts to arise.


From slaton at OCF.Berkeley.EDU  Mon Jun  5 14:01:17 2006
From: slaton at OCF.Berkeley.EDU (slaton)
Date: Mon, 5 Jun 2006 14:01:17 -0700 (PDT)
Subject: [cAos] caos3 development
In-Reply-To: <20060605195631.GA13146@aries.runlevelzero.net>
References: <20060604050900.GB14645@aries.runlevelzero.net>
	<000601c68796$8cb7d5a0$6600a8c0@astevens>
	<ea86ce220606040622t124bec43vabb139eeaa9e5b38@mail.gmail.com>
	<20060605195631.GA13146@aries.runlevelzero.net>
Message-ID: <Pine.GSO.4.64.0606051303160.20892@apocalypse.OCF.Berkeley.EDU>

Hi Greg,

Allow me to add my congrats as well... :)

I also hope to find a way to help out with cAos3.

Your comment about the increased focus on ports for cAos3 is interesting. 
What will the ports position be w/r/t open source HPC applications built 
with commercial compilers? Would i be welcome to maintain ports built with 
with architecture-specific commercial compilers (e.g., PathScale for 
x86_64, Portland for x86, etc)? Or is this too much of a stretch for an 
open source linux distro...

regards
slaton
 
Slaton Lipscomb
Nogales Lab, Howard Hughes Medical Institute
http://cryoem.berkeley.edu


From gmk at runlevelzero.net  Mon Jun  5 22:21:31 2006
From: gmk at runlevelzero.net (Greg M. Kurtzer)
Date: Mon, 5 Jun 2006 22:21:31 -0700
Subject: [cAos] caos3 development
In-Reply-To: <Pine.GSO.4.64.0606051303160.20892@apocalypse.OCF.Berkeley.EDU>
References: <20060604050900.GB14645@aries.runlevelzero.net>
	<000601c68796$8cb7d5a0$6600a8c0@astevens>
	<ea86ce220606040622t124bec43vabb139eeaa9e5b38@mail.gmail.com>
	<20060605195631.GA13146@aries.runlevelzero.net>
	<Pine.GSO.4.64.0606051303160.20892@apocalypse.OCF.Berkeley.EDU>
Message-ID: <20060606052131.GA13540@aries.runlevelzero.net>

On Mon, Jun 05, 2006 at 02:01:17PM -0700, slaton wrote:
> Hi Greg,
> 
> Allow me to add my congrats as well... :)
> 
> I also hope to find a way to help out with cAos3.

Excellent. :)

> Your comment about the increased focus on ports for cAos3 is interesting. 
> What will the ports position be w/r/t open source HPC applications built 
> with commercial compilers? Would i be welcome to maintain ports built with 
> with architecture-specific commercial compilers (e.g., PathScale for 
> x86_64, Portland for x86, etc)? Or is this too much of a stretch for an 
> open source linux distro...

There are two paths forward. The first is maintaining compiler specific
Makefiles within the ports tree. There is no issue at all to have these
available for each compiler commercial or non-commercial. The ports tree
is responsible for downloading and building the applications (eg. not
binary downloads) and can automatcially provide the correct options to
configure against the specified compilers.

We will check to see if there are any limitations of redistribution of
the binaries produced with these compilers. I seem to remember that the
PGI compilers will (even with -static) dynamically include a PGI
specific library which is under a non-distributable license. Which means
that whoever uses it on the other side may also need to purchase the
compilers (which I think is fair). I don't think this is the case with
Intel's compilers, and I don't remember with Pathscale either. They may
have other (non physical) barriers or restrictions for doing this though.

Distributing the binaries doesn't conflict with any open source ethical
issues of mine, and considering that most of the HPC applications are
BSD licensed, there will not be any application licensing restrictions
(I need to check with the GPL licensed apps, but I think we are clear
there too).

If there are compiler restrictions, we will need to go with the first
option (using the ports tree).

Thanks,
Greg
-- 
Greg M. Kurtzer
http://runlevelzero.net/
http://caosity.org/
http://warewulf-cluster.org/

Do not look anywhere for truth, for all that is needed is to refrain from
allowing concepts to arise.


From glen at callident.com  Tue Jun  6 06:33:14 2006
From: glen at callident.com (Glen Otero)
Date: Tue, 6 Jun 2006 06:33:14 -0700
Subject: [cAos] caos3 development
In-Reply-To: <20060605202248.GB13146@aries.runlevelzero.net>
References: <20060604050900.GB14645@aries.runlevelzero.net>
	<5FAD211E-CC25-48BA-AB6A-0478EBB10337@callident.com>
	<20060605202248.GB13146@aries.runlevelzero.net>
Message-ID: <24EDB547-9533-4603-A818-0C0AE3703C53@callident.com>


On Jun 5, 2006, at 1:22 PM, Greg M. Kurtzer wrote:

> If my memory serves me right,... you just happen to be one of the  
> worlds
> leading experts on computational genomics and bio-informatics. :)
>
> Lets start there if that works for you. :)

Works for me.
>
> Can you provide a list of the freely available bio-informatics code  
> that
> you would be interested in maintaining and their dependencies (eg. web
> based frontends may require, apache2, php5, perl, python, *sql,  
> etc..).

Will do. These packages aren't included in any Linux distro  
(obviously), so how will they be organized within cAos? Will groups  
of other domain-specific packages be compiled as well?

Glen

>
> Thanks!
>
> On Mon, Jun 05, 2006 at 12:31:54PM -0700, Glen Otero wrote:
>> Greg-
>>
>> I'd like to help with cAos-3 development, but not sure what the best
>> way to contribute is. Any suggestions?
>>
>> Glen
>>
>> On Jun 3, 2006, at 10:09 PM, Greg M. Kurtzer wrote:
>>
>>> The next generation of cAos is in development, here and now!
>>>
>>> As some of you also know, we are in a position to receive funding  
>>> for
>>> development. However our funding backers (myself included) have been
>>> watching our current development emphasis and while we have a very
>>> current and maintained Enlightenment stack, we need to also pay as
>>> much
>>> (and even more) attention to our services and security.
>>>
>>> To accommodate this, cAos-3 primary emphasis is performance,
>>> efficiency,
>>> services and security. Our targeted user-base is clustered  
>>> systems and
>>> servers for ISP, home and office. Secondary emphasis will include
>>> other
>>> more general distribution aspects.
>>>
>>> The goal is not only to appeal to our potential funders, but also  
>>> grow
>>> into an area to which I have heard various complaints that there
>>> isn't a
>>> reasonable solution for. While the Linux desktop and general purpose
>>> distributions are very important, they also have been solved very  
>>> well
>>> by both commercial and non-commercial organizations.
>>>
>>> I know everyone is busy, I am as well. However we can not expect to
>>> get
>>> backed by individuals or other organizations that see very little
>>> progress where they need it most or significantly grow our user-
>>> base. It
>>> is time to focus and get stuff done.
>>>
>>> At this time, I have the base self hosting development file system
>>> nearing completion. From here I will need package maintainers,
>>> developers, doc writers, and anyone else that wants to be part of  
>>> the
>>> development group to contact me. I am open to discussing  
>>> positions for
>>> not only guru developers and maintainers, but also newcomers that  
>>> want
>>> to be part of an open source project that many people use.
>>>
>>> While cAos-2 was a loosely managed project where contributors  
>>> come and
>>> go and commit when they have time, cAos-3 will be much more  
>>> structured
>>> and organized higher emphasis on leadership and chain of command. We
>>> will operate more as a unit and as a team bringing a higher level of
>>> professionalism to the project.
>>>
>>> Thus I am looking for people to not only volunteer but also commit
>>> to long
>>> term maintenance of various aspects of caos3. We have some very
>>> intriguing
>>> opportunities in-front of us and we need to be more aggressive and
>>> focused
>>> if we are to reach the next level.
>>>
>>> Thanks,
>>> Greg
>>> -- 
>>> Greg M. Kurtzer
>>> http://runlevelzero.net/
>>> http://caosity.org/
>>> http://warewulf-cluster.org/
>>>
>>> Do not look anywhere for truth, for all that is needed is to
>>> refrain from
>>> allowing concepts to arise.
>>> _______________________________________________
>>> cAos mailing list
>>> cAos at caosity.org
>>> http://lists.caosity.org/mailman/listinfo/caos
>>>
>>
>> _______________________________________________
>> cAos mailing list
>> cAos at caosity.org
>> http://lists.caosity.org/mailman/listinfo/caos
>
> -- 
> Greg M. Kurtzer
> http://runlevelzero.net/
> http://caosity.org/
> http://warewulf-cluster.org/
>
> Do not look anywhere for truth, for all that is needed is to  
> refrain from
> allowing concepts to arise.
> _______________________________________________
> cAos mailing list
> cAos at caosity.org
> http://lists.caosity.org/mailman/listinfo/caos
>



From gmk at runlevelzero.net  Tue Jun  6 13:29:54 2006
From: gmk at runlevelzero.net (Greg M. Kurtzer)
Date: Tue, 6 Jun 2006 13:29:54 -0700
Subject: [cAos] caos3 development
In-Reply-To: <24EDB547-9533-4603-A818-0C0AE3703C53@callident.com>
References: <20060604050900.GB14645@aries.runlevelzero.net>
	<5FAD211E-CC25-48BA-AB6A-0478EBB10337@callident.com>
	<20060605202248.GB13146@aries.runlevelzero.net>
	<24EDB547-9533-4603-A818-0C0AE3703C53@callident.com>
Message-ID: <20060606202954.GA4861@aries.runlevelzero.net>

On Tue, Jun 06, 2006 at 06:33:14AM -0700, Glen Otero wrote:
> 
> On Jun 5, 2006, at 1:22 PM, Greg M. Kurtzer wrote:
> 
> > If my memory serves me right,... you just happen to be one of the  
> > worlds
> > leading experts on computational genomics and bio-informatics. :)
> >
> > Lets start there if that works for you. :)
> 
> Works for me.

Excellent! :)

> > Can you provide a list of the freely available bio-informatics code  
> > that
> > you would be interested in maintaining and their dependencies (eg. web
> > based frontends may require, apache2, php5, perl, python, *sql,  
> > etc..).
> 
> Will do. These packages aren't included in any Linux distro  
> (obviously), so how will they be organized within cAos? Will groups  
> of other domain-specific packages be compiled as well?

Yes, I believe so. Can you give me an example of some of the packages
that you are curious about?

Presently we use group directories and ownerships to allow some people
access to certain parts of the distro's repository. We can do the same
thing here. Maintainers for the dependencies will be decided on by a per
case basis.

They can be installed via predefined profiles and/or system roles.

(does that answer your question?)

Thanks!

-- 
Greg M. Kurtzer
http://runlevelzero.net/
http://caosity.org/
http://warewulf-cluster.org/

Do not look anywhere for truth, for all that is needed is to refrain from
allowing concepts to arise.


From gmk at runlevelzero.net  Mon Jun 12 18:53:02 2006
From: gmk at runlevelzero.net (Greg M. Kurtzer)
Date: Mon, 12 Jun 2006 18:53:02 -0700
Subject: [cAos] caos2 repository updates
Message-ID: <20060613015302.GA18198@aries.runlevelzero.net>

Coming soon to a mirror near you:

current:
   + SRPMS/dia-0.94-4.caos.src.rpm
   + SRPMS/firefox-1.5.0.4-1.caos.src.rpm
   + SRPMS/MySQL-4.1.20-1.caos.src.rpm
   + SRPMS/nagios-2.4-1.caos.src.rpm
   + SRPMS/nmap-4.00-1.caos.src.rpm
   + SRPMS/perl-Authen-SASL-Cyrus-0.12-1.caos.src.rpm
   + SRPMS/perl-RDFStore-0.42-1.caos.src.rpm
   + SRPMS/perl-XML-SAX-0.13-1.caos.src.rpm
   + SRPMS/postfix-2.2.10-2.caos.src.rpm
   + SRPMS/qingy-0.8.0-1.caos.src.rpm
   + SRPMS/scribus-1.3.3.2-1.caos.src.rpm
   + SRPMS/spamassassin-3.1.3-1.caos.src.rpm
   - SRPMS/firefox-1.5.0.3-1.caos.src.rpm
   - SRPMS/openssh-4.2p1-2.caos.src.rpm
   - SRPMS/php5-5.0.5-5.src.rpm
   - SRPMS/postfix-2.2.3-2.caos.src.rpm
   - SRPMS/postfix-2.2.4-1.caos.src.rpm
   - SRPMS/postfix-2.2.5-1.caos.src.rpm
   - SRPMS/postfix-2.2.6-1.caos.src.rpm
   - SRPMS/postfix-2.2.8-1.caos.src.rpm
   - SRPMS/postfix-2.2.9-1.caos.src.rpm
   - SRPMS/postfix-2.2.9-2.caos.src.rpm

stable:
   + SRPMS/firefox-1.5.0.4-1.caos.src.rpm
   + SRPMS/openssh-4.3p2-1.caos.src.rpm
   + SRPMS/perl-Authen-SASL-Cyrus-0.12-1.caos.src.rpm
   + SRPMS/perl-RDFStore-0.42-1.caos.src.rpm
   + SRPMS/perl-XML-SAX-0.13-1.caos.src.rpm
   + SRPMS/php5-5.1.2-7.caos.src.rpm
   + SRPMS/postfix-2.2.10-2.caos.src.rpm
   + SRPMS/qingy-0.8.0-1.caos.src.rpm
   - SRPMS/firefox-1.5.0.3-1.caos.src.rpm
   - SRPMS/openssh-4.2p1-2.caos.src.rpm
   - SRPMS/php5-5.0.5-5.src.rpm
   - SRPMS/postfix-2.2.3-2.caos.src.rpm

-- 
Greg M. Kurtzer
http://runlevelzero.net/
http://caosity.org/
http://warewulf-cluster.org/

Do not look anywhere for truth, for all that is needed is to refrain from
allowing concepts to arise.


From slaton at OCF.Berkeley.EDU  Mon Jun 19 19:53:00 2006
From: slaton at OCF.Berkeley.EDU (slaton)
Date: Mon, 19 Jun 2006 19:53:00 -0700 (PDT)
Subject: [cAos] Problems installing gridengine 5.3
Message-ID: <Pine.GSO.4.64.0606191322510.22173@apocalypse.OCF.Berkeley.EDU>

I'm having a couple of problems installing the Grid Engine 5.3 package 
from repo.

1) First there is a "transaction check error" when installing the 5.3p6-8 
package from yum:

$ sudo yum install gridengine
Setting up Install Process
Setting up Repos
core                      100% |=========================|  951 B    00:00     
stable                    100% |=========================| 1.1 kB    00:00     
Reading repository metadata in from local files
core      : ################################################## 167/167
stable    : ################################################## 1562/1562
Parsing package install arguments
Resolving Dependencies
--> Populating transaction set with selected packages. Please wait.
---> Package gridengine.x86_64 0:5.3p6-8.caos set to be updated
--> Running transaction check
--> Processing Dependency: pdksh for package: gridengine
--> Processing Dependency: warewulf for package: gridengine
--> Processing Dependency: /bin/ksh for package: gridengine
--> Restarting Dependency Resolution with new changes.
--> Populating transaction set with selected packages. Please wait.
---> Package warewulf.x86_64 0:2.6.2-1 set to be updated
--> Running transaction check
--> Processing Dependency: warewulf-tools = 2.6.2-1 for package: warewulf
--> Processing Dependency: perl-Unix-Syslog for package: warewulf
--> Processing Dependency: perl(Unix::Syslog) for package: warewulf
--> Running transaction check

Dependencies Resolved
Transaction Listing:
  Install: gridengine.x86_64 0:5.3p6-8.caos - stable

Performing the following to resolve dependencies:
  Install: warewulf.x86_64 0:2.6.2-1 - stable
Total download size: 5.8 MB
Is this ok [y/N]: y
Downloading Packages:
(1/2): gridengine-5.3p6-8 100% |=========================| 4.5 MB    00:06     
(2/2): warewulf-2.6.2-1.x 100% |=========================| 1.3 MB    00:02     
Running Transaction Test
Finished Transaction Test
Transaction Check Error:   file /usr/share/man/man5/complex.5.gz from 
install of gridengine-5.3p6-8.caos conflicts with file from package 
man-pages-1.66-2


Looks like both gridengine and the basic man package include a COMPLEX(5) 
manpage. I don't think this is as simple as just renaming the existing 
(man-pages pkg) file, is it? I imagine i'd also have to edit something 
like a spec file used for srpms, but i'm not familiar enough with yum to 
know where this information is. Thanks for any suggestions.


2) Second problem has more to do with how my cluster is set up. I have a 
master/admin node which is responsible for booting the cluster nodes 
(Warewulf of course ;) and various other sundry server roles. There are no 
user logins on this machine. There is a second, login/interactive node 
which the users log into to access the cluster. So the warewulf master 
node has the full warewulf-package and warewulf-tools, whereas the login 
node only has the warewulf-tools package installed.

It appears that the caos gridengine package needs to run on the warewulf 
master, since it's flagged as a prerequisite. However there is no separate 
gridengine-tools sort of package containing the user tools, correct? 
Therefore i don't see how my users will have access to any of the 
gridengine user commands. There is of course the gridengine-node package, 
which i've installed to VNFS -- perhaps i should have checked this to see 
if it includes the user programs, in which case i will just install this 
as well onto my login node.... 

Thanks for any insights...

slaton

Slaton Lipscomb
Nogales Lab, Howard Hughes Medical Institute
http://cryoem.berkeley.edu


From S.walsh at nerdvana.com.au  Fri Jun 23 04:45:32 2006
From: S.walsh at nerdvana.com.au (Nerdvana - Steve Walsh)
Date: Fri, 23 Jun 2006 21:45:32 +1000
Subject: [cAos] Postfix segfaults on Caos 2.2
In-Reply-To: <20060613015302.GA18198@aries.runlevelzero.net>
Message-ID: <FAEALJLFFJCKIEBGIIEHOENAEKAA.S.walsh@nerdvana.com.au>

Hi Folks

I've got an Intel EM64T box that exhibits the odd behaviour of Segfaulting
when attempting smtp transactions. It's a standard  postfix.x86_64
0:2.2.10-2 package out of the stable repository, with only very basic
configuration. If I try a telnet to localhost, it fails first time, then
accepts the connection for a period of time. After a certain period of time
(obvious some time out value), it will exhibit the same issues. Needless to
say, emails are bouncing to the box.

[root at mail ~]# telnet localhost 25
Trying 127.0.0.1...
Connected to localhost.
Escape character is '^]'.
Connection closed by foreign host.
[root at mail ~]# telnet localhost 25
Trying 127.0.0.1...
Connected to localhost.
Escape character is '^]'.


/var/log/messages shows the following

Jun 24 04:41:15 praetorian postfix: Stopping postfix: succeeded
Jun 24 04:41:15 praetorian postfix: Starting postfix: succeeded
Jun 24 04:41:49 praetorian kernel: smtpd[3656]: segfault at 00002aaaaabbfdf0
rip 00002aaaaaab1191 rsp 00007ffffffc4960 error 7

/var/log/maillog shows

Jun 24 04:41:15 praetorian postfix/postfix-script: starting the Postfix mail
system
Jun 24 04:41:15 praetorian postfix/master[3645]: daemon started -- version
2.2.10, configuration /etc/postfix
Jun 24 04:41:49 praetorian postfix/master[3645]: warning: process
/usr/libexec/postfix/smtpd pid 3656 killed by signal 11
Jun 24 04:41:49 praetorian postfix/master[3645]: warning:
/usr/libexec/postfix/smtpd: bad command startup -- throttling

I'm at a bit of a loss where to start looking. It's a very standard Caos 2.2
box with LAMP config and one or two other things, but nothing that I can see
would be causing it.

Hoping someone can shed some light on the matter

Steve





From slaton at OCF.Berkeley.EDU  Fri Jun 23 13:10:42 2006
From: slaton at OCF.Berkeley.EDU (slaton)
Date: Fri, 23 Jun 2006 13:10:42 -0700 (PDT)
Subject: [cAos] Problems installing gridengine 5.3
Message-ID: <Pine.GSO.4.64.0606231308150.20165@apocalypse.OCF.Berkeley.EDU>

(resent as list was down for a couple of days...)

I'm having a couple of problems installing the Grid Engine 5.3 package 
from repo.

1) First there is a "transaction check error" when installing the 5.3p6-8 
package from yum:

$ sudo yum install gridengine
Setting up Install Process
Setting up Repos
core                      100% |=========================|  951 B    00:00     
stable                    100% |=========================| 1.1 kB    00:00     
Reading repository metadata in from local files
core      : ################################################## 167/167
stable    : ################################################## 1562/1562
Parsing package install arguments
Resolving Dependencies
--> Populating transaction set with selected packages. Please wait.
---> Package gridengine.x86_64 0:5.3p6-8.caos set to be updated
--> Running transaction check
--> Processing Dependency: pdksh for package: gridengine
--> Processing Dependency: warewulf for package: gridengine
--> Processing Dependency: /bin/ksh for package: gridengine
--> Restarting Dependency Resolution with new changes.
--> Populating transaction set with selected packages. Please wait.
---> Package warewulf.x86_64 0:2.6.2-1 set to be updated
--> Running transaction check
--> Processing Dependency: warewulf-tools = 2.6.2-1 for package: warewulf
--> Processing Dependency: perl-Unix-Syslog for package: warewulf
--> Processing Dependency: perl(Unix::Syslog) for package: warewulf
--> Running transaction check

Dependencies Resolved
Transaction Listing:
  Install: gridengine.x86_64 0:5.3p6-8.caos - stable

Performing the following to resolve dependencies:
  Install: warewulf.x86_64 0:2.6.2-1 - stable
Total download size: 5.8 MB
Is this ok [y/N]: y
Downloading Packages:
(1/2): gridengine-5.3p6-8 100% |=========================| 4.5 MB    00:06     
(2/2): warewulf-2.6.2-1.x 100% |=========================| 1.3 MB    00:02     
Running Transaction Test
Finished Transaction Test
Transaction Check Error:   file /usr/share/man/man5/complex.5.gz from 
install of gridengine-5.3p6-8.caos conflicts with file from package 
man-pages-1.66-2


Looks like both gridengine and the basic man package include a COMPLEX(5) 
manpage. I don't think this is as simple as just renaming the existing 
(man-pages pkg) file, is it? I imagine i'd also have to edit something 
like a spec file used for srpms, but i'm not familiar enough with yum to 
know where this information is. Thanks for any suggestions.


2) Second problem has more to do with how my cluster is set up. I have a 
master/admin node which is responsible for booting the cluster nodes, 
Warewulf of course, and a few other sundry server roles. There are no user 
logins on this machine. There is a second, login/interactive node which 
the users log into to access the cluster and also run serial jobs. So the 
warewulf master node has the full warewulf-package and warewulf-tools, 
whereas the login node only has the warewulf-tools package installed.

It appears that the caos gridengine package needs to run on the warewulf 
master, since it's flagged as a prerequisite. However there is no separate 
gridengine-tools sort of package containing the user tools, correct? 
Therefore i don't see how my users will have access to any of the 
gridengine user commands. There is of course the gridengine-node package, 
which i've installed to VNFS -- perhaps I just need to install this on 
my login node as well? So there may be no problem here after all, i'm just 
unfamiliar with SGE.

Thanks for any insights...

slaton

Slaton Lipscomb
Nogales Lab, Howard Hughes Medical Institute
http://cryoem.berkeley.edu


From glen at callident.com  Sun Jun 25 15:27:06 2006
From: glen at callident.com (Glen Otero)
Date: Sun, 25 Jun 2006 15:27:06 -0700
Subject: [cAos] caos3 development
In-Reply-To: <20060606202954.GA4861@aries.runlevelzero.net>
References: <20060604050900.GB14645@aries.runlevelzero.net>
	<5FAD211E-CC25-48BA-AB6A-0478EBB10337@callident.com>
	<20060605202248.GB13146@aries.runlevelzero.net>
	<24EDB547-9533-4603-A818-0C0AE3703C53@callident.com>
	<20060606202954.GA4861@aries.runlevelzero.net>
Message-ID: <A7AF8724-4B1A-447A-BAFC-93FEB2D9C526@callident.com>


On Jun 6, 2006, at 1:29 PM, Greg M. Kurtzer wrote:

> On Tue, Jun 06, 2006 at 06:33:14AM -0700, Glen Otero wrote:
>>
>> On Jun 5, 2006, at 1:22 PM, Greg M. Kurtzer wrote:
>>
>>> If my memory serves me right,... you just happen to be one of the
>>> worlds
>>> leading experts on computational genomics and bio-informatics. :)
>>>
>>> Lets start there if that works for you. :)
>>
>> Works for me.
>
> Excellent! :)
>
>>> Can you provide a list of the freely available bio-informatics code
>>> that
>>> you would be interested in maintaining and their dependencies  
>>> (eg. web
>>> based frontends may require, apache2, php5, perl, python, *sql,
>>> etc..).
>>
>> Will do. These packages aren't included in any Linux distro
>> (obviously), so how will they be organized within cAos? Will groups
>> of other domain-specific packages be compiled as well?
>
> Yes, I believe so. Can you give me an example of some of the packages
> that you are curious about?

EMBOSS-3.0.0-2.bio.src.rpm
R-2.1.0-1.bio.src.rpm
R-Bioconductor-1.6-1.bio.src.rpm
R-DBI-0.1.9-3.bio.src.rpm
R-Hmisc-3.0.6-2.bio.src.rpm
R-RMySQL-0.5.5-2.bio.src.rpm
R-acepack-1.3.2.1-5.bio.src.rpm
R-gdata-2.0.7-3.bio.src.rpm
R-gmodels-2.0.7-2.bio.src.rpm
R-gplots-2.0.7-3.bio.src.rpm
R-gregmisc-2.0.8-6.bio.src.rpm
R-gtools-2.0.7-2.bio.src.rpm
ViennaRNA-1.5-4.bio.src.rpm
biopython-1.30-2.bio.src.rpm
clustalx-1.83-5.bio.src.rpm
gibbs-9.95-3.bio.src.rpm
glimpse-4.18.0-1.rhfc2.bio.src.rpm
grace-5.1.18-1.bio.src.rpm
hmmer-2.3.2-5.bio.src.rpm
libgc-6.6-0.src.rpm
mafft-5.531-1.bio.src.rpm
mcl-4.314-1.bio.src.rpm
mfold-3.1.2-3.bio.src.rpm
ncbi-toolbox-6.1.20050605-1.bio.src.rpm
netcdf-3.5.1-3.bio.src.rpm
paml-3.14-1.rhfc2.bio.src.rpm
pdflib-lite-6.0.0p1-5.bio.src.rpm
perl-AcePerl-1.87-3.bio.src.rpm
perl-Bioperl-1.4-4.bio.src.rpm
perl-DB_File-1.810-1.bio.src.rpm
perl-Data-Stag-0.07-1.bio.src.rpm
perl-Data-Table-1.42-0.bio.1.src.rpm
perl-File-Temp-0.14-3.bio.src.rpm
perl-Graph-0.20105-0.bio.1.src.rpm
perl-Heap-0.71-0.bio.1.src.rpm
perl-IO-Socket-SSL-0.96-1.bio.src.rpm
perl-IO-String-1.05-3.bio.src.rpm
perl-MIME-Base64-3.05-1.bio.src.rpm
perl-MLDBM-2.01-1.bio.src.rpm
perl-Math-Derivative-0.01-2.bio.src.rpm
perl-Math-Spline-0.01-2.bio.src.rpm
perl-PBS-0.19-1.bio.src.rpm
perl-SOAP-Lite-0.60-2.bio.src.rpm
perl-SVG-Graph-0.01-3.bio.src.rpm
perl-Spreadsheet-WriteExcel-2.11-2.bio.src.rpm
perl-Statistics-Descriptive-2.6-2.bio.src.rpm
perl-Text-Shellwords-1.07-2.bio.src.rpm
perl-Tree-DAG_Node-1.04-2.bio.src.rpm
perl-XML-LibXSLT-1.57-1.bio.src.rpm
perl-tfbs-0.5.0-4.bio.src.rpm
primer3-1.0.0-2.bio.src.rpm
renderPM-0.99.20041122-1.bio.src.rpm
reportlab-1_19-2.bio.src.rpm
t-coffee-2.03-1.bio.src.rpm
tdl-1.5.2-1.rhfc2.bio.src.rpm
tkdiff-4.1-1.bio.src.rpm

There are a few others.

Glen


>
> Presently we use group directories and ownerships to allow some people
> access to certain parts of the distro's repository. We can do the same
> thing here. Maintainers for the dependencies will be decided on by  
> a per
> case basis.
>
> They can be installed via predefined profiles and/or system roles.
>
> (does that answer your question?)
>
> Thanks!
>
> -- 
> Greg M. Kurtzer
> http://runlevelzero.net/
> http://caosity.org/
> http://warewulf-cluster.org/
>
> Do not look anywhere for truth, for all that is needed is to  
> refrain from
> allowing concepts to arise.
> _______________________________________________
> cAos mailing list
> cAos at caosity.org
> http://lists.caosity.org/mailman/listinfo/caos
>



From benjamin at py-soft.co.uk  Mon Jun 26 04:16:23 2006
From: benjamin at py-soft.co.uk (Benjamin Donnachie)
Date: Mon, 26 Jun 2006 12:16:23 +0100
Subject: [cAos] caos3 development
In-Reply-To: <20060604050900.GB14645@aries.runlevelzero.net>
References: <20060604050900.GB14645@aries.runlevelzero.net>
Message-ID: <449FC207.7080203@py-soft.co.uk>

Greg M. Kurtzer wrote:
> To accommodate this, cAos-3 primary emphasis is performance, efficiency,
> services and security. Our targeted user-base is clustered systems and
> servers for ISP, home and office. Secondary emphasis will include other
> more general distribution aspects.

What are your thoughts on SELinux?

After almost falling foul of the recent coppermine vulnerability (having
just patched to avoid one!), I feel that cAos-3 should incorporate it in
order to meet its security goals.

> Thus I am looking for people to not only volunteer but also commit to long
> term maintenance of various aspects of caos3. We have some very intriguing
> opportunities in-front of us and we need to be more aggressive and focused
> if we are to reach the next level.

Are there any updates on this?  I've been distracted by other things,
and other projects, but I'd like to help out.

Take care,

Ben


From astevens at gravitypark.com  Mon Jun 26 12:12:35 2006
From: astevens at gravitypark.com (Arthur Stevens)
Date: Mon, 26 Jun 2006 12:12:35 -0700
Subject: [cAos] caos3 development
References: <20060604050900.GB14645@aries.runlevelzero.net>
	<449FC207.7080203@py-soft.co.uk>
Message-ID: <001001c69954$7c101850$6600a8c0@astevens>

I personally would recommend not using SELinux and use openwall or grsec as 
well as others. Offer SELinux support, but don't cater to it from the get 
go. It really does not help as much as some of the other options imho.

We are working on a new kernel for v3 and I think you will like the new 
added security options/features. We should hopefully be replacing postfix 
with qmail and some other security related conversions as well.

Arthur
----- Original Message ----- 
From: "Benjamin Donnachie" <benjamin at py-soft.co.uk>
To: "Community Assembled OS" <caos at caosity.org>
Sent: Monday, June 26, 2006 4:16 AM
Subject: Re: [cAos] caos3 development


> Greg M. Kurtzer wrote:
>> To accommodate this, cAos-3 primary emphasis is performance, efficiency,
>> services and security. Our targeted user-base is clustered systems and
>> servers for ISP, home and office. Secondary emphasis will include other
>> more general distribution aspects.
>
> What are your thoughts on SELinux?
>
> After almost falling foul of the recent coppermine vulnerability (having
> just patched to avoid one!), I feel that cAos-3 should incorporate it in
> order to meet its security goals.
>
>> Thus I am looking for people to not only volunteer but also commit to 
>> long
>> term maintenance of various aspects of caos3. We have some very 
>> intriguing
>> opportunities in-front of us and we need to be more aggressive and 
>> focused
>> if we are to reach the next level.
>
> Are there any updates on this?  I've been distracted by other things,
> and other projects, but I'd like to help out.
>
> Take care,
>
> Ben
> _______________________________________________
> cAos mailing list
> cAos at caosity.org
> http://lists.caosity.org/mailman/listinfo/caos
> 




From mej at caosity.org  Mon Jun 26 13:48:24 2006
From: mej at caosity.org (Michael Jennings)
Date: Mon, 26 Jun 2006 16:48:24 -0400
Subject: [cAos] Postfix segfaults on Caos 2.2
In-Reply-To: <FAEALJLFFJCKIEBGIIEHOENAEKAA.S.walsh@nerdvana.com.au>
References: <20060613015302.GA18198@aries.runlevelzero.net>
	<FAEALJLFFJCKIEBGIIEHOENAEKAA.S.walsh@nerdvana.com.au>
Message-ID: <20060626204824.GA19672@kainx.org>

On Friday, 23 June 2006, at 21:45:32 (+1000),
Nerdvana - Steve Walsh wrote:

> I've got an Intel EM64T box that exhibits the odd behaviour of
> Segfaulting when attempting smtp transactions. It's a standard
> postfix.x86_64 0:2.2.10-2 package out of the stable repository, with
> only very basic configuration.

Have you tried rebuilding from the SRPM?

Michael

-- 
Michael Jennings (a.k.a. KainX)  http://www.kainx.org/  <mej at kainx.org>
n + 1, Inc., http://www.nplus1.net/       Author, Eterm (www.eterm.org)
-----------------------------------------------------------------------
 "Don't risk more than you can afford to walk away without."
                                                   -- Rule of Life #39


From S.walsh at nerdvana.com.au  Mon Jun 26 14:48:20 2006
From: S.walsh at nerdvana.com.au (Nerdvana - Steve Walsh)
Date: Tue, 27 Jun 2006 07:48:20 +1000
Subject: [cAos] Postfix segfaults on Caos 2.2
In-Reply-To: <20060626204824.GA19672@kainx.org>
Message-ID: <FAEALJLFFJCKIEBGIIEHGEPPEKAA.S.walsh@nerdvana.com.au>

Hi Michael

yes, I tried rebuilding it from the RPM on the mirror, and got yet more
segfaults. I've pulled the box out of the DC and have it back in my office,
so I can get more aggressive with my testing, I'll let you know what I find.



-----Original Message-----
From: Michael Jennings
Sent: Tuesday, 27 June 2006 6:48 AM
To: caos at caosity.org
Subject: Re: [cAos] Postfix segfaults on Caos 2.2


On Friday, 23 June 2006, at 21:45:32 (+1000),
Nerdvana - Steve Walsh wrote:

> I've got an Intel EM64T box that exhibits the odd behaviour of
> Segfaulting when attempting smtp transactions. It's a standard
> postfix.x86_64 0:2.2.10-2 package out of the stable repository, with
> only very basic configuration.

Have you tried rebuilding from the SRPM?

Michael

--
Michael Jennings (a.k.a. KainX)  http://www.kainx.org/  <mej at kainx.org>
n + 1, Inc., http://www.nplus1.net/       Author, Eterm (www.eterm.org)
-----------------------------------------------------------------------
 "Don't risk more than you can afford to walk away without."
                                                   -- Rule of Life #39
_______________________________________________
cAos mailing list
cAos at caosity.org
http://lists.caosity.org/mailman/listinfo/caos




From gmk at runlevelzero.net  Mon Jun 26 22:54:18 2006
From: gmk at runlevelzero.net (Greg M. Kurtzer)
Date: Mon, 26 Jun 2006 22:54:18 -0700
Subject: [cAos] caos3 development
In-Reply-To: <A7AF8724-4B1A-447A-BAFC-93FEB2D9C526@callident.com>
References: <20060604050900.GB14645@aries.runlevelzero.net>
	<5FAD211E-CC25-48BA-AB6A-0478EBB10337@callident.com>
	<20060605202248.GB13146@aries.runlevelzero.net>
	<24EDB547-9533-4603-A818-0C0AE3703C53@callident.com>
	<20060606202954.GA4861@aries.runlevelzero.net>
	<A7AF8724-4B1A-447A-BAFC-93FEB2D9C526@callident.com>
Message-ID: <20060627055418.GA2054@aries.runlevelzero.net>

Are you thinking these would binary packages or in the ports tree?

Main diff is binary packages would be pretty much locked down to just
gcc, and the ports tree would enable multiple compilers and underlying
libs to be optimized.

On Sun, Jun 25, 2006 at 03:27:06PM -0700, Glen Otero wrote:
> 
> On Jun 6, 2006, at 1:29 PM, Greg M. Kurtzer wrote:
> 
> > On Tue, Jun 06, 2006 at 06:33:14AM -0700, Glen Otero wrote:
> >>
> >> On Jun 5, 2006, at 1:22 PM, Greg M. Kurtzer wrote:
> >>
> >>> If my memory serves me right,... you just happen to be one of the
> >>> worlds
> >>> leading experts on computational genomics and bio-informatics. :)
> >>>
> >>> Lets start there if that works for you. :)
> >>
> >> Works for me.
> >
> > Excellent! :)
> >
> >>> Can you provide a list of the freely available bio-informatics code
> >>> that
> >>> you would be interested in maintaining and their dependencies  
> >>> (eg. web
> >>> based frontends may require, apache2, php5, perl, python, *sql,
> >>> etc..).
> >>
> >> Will do. These packages aren't included in any Linux distro
> >> (obviously), so how will they be organized within cAos? Will groups
> >> of other domain-specific packages be compiled as well?
> >
> > Yes, I believe so. Can you give me an example of some of the packages
> > that you are curious about?
> 
> EMBOSS-3.0.0-2.bio.src.rpm
> R-2.1.0-1.bio.src.rpm
> R-Bioconductor-1.6-1.bio.src.rpm
> R-DBI-0.1.9-3.bio.src.rpm
> R-Hmisc-3.0.6-2.bio.src.rpm
> R-RMySQL-0.5.5-2.bio.src.rpm
> R-acepack-1.3.2.1-5.bio.src.rpm
> R-gdata-2.0.7-3.bio.src.rpm
> R-gmodels-2.0.7-2.bio.src.rpm
> R-gplots-2.0.7-3.bio.src.rpm
> R-gregmisc-2.0.8-6.bio.src.rpm
> R-gtools-2.0.7-2.bio.src.rpm
> ViennaRNA-1.5-4.bio.src.rpm
> biopython-1.30-2.bio.src.rpm
> clustalx-1.83-5.bio.src.rpm
> gibbs-9.95-3.bio.src.rpm
> glimpse-4.18.0-1.rhfc2.bio.src.rpm
> grace-5.1.18-1.bio.src.rpm
> hmmer-2.3.2-5.bio.src.rpm
> libgc-6.6-0.src.rpm
> mafft-5.531-1.bio.src.rpm
> mcl-4.314-1.bio.src.rpm
> mfold-3.1.2-3.bio.src.rpm
> ncbi-toolbox-6.1.20050605-1.bio.src.rpm
> netcdf-3.5.1-3.bio.src.rpm
> paml-3.14-1.rhfc2.bio.src.rpm
> pdflib-lite-6.0.0p1-5.bio.src.rpm
> perl-AcePerl-1.87-3.bio.src.rpm
> perl-Bioperl-1.4-4.bio.src.rpm
> perl-DB_File-1.810-1.bio.src.rpm
> perl-Data-Stag-0.07-1.bio.src.rpm
> perl-Data-Table-1.42-0.bio.1.src.rpm
> perl-File-Temp-0.14-3.bio.src.rpm
> perl-Graph-0.20105-0.bio.1.src.rpm
> perl-Heap-0.71-0.bio.1.src.rpm
> perl-IO-Socket-SSL-0.96-1.bio.src.rpm
> perl-IO-String-1.05-3.bio.src.rpm
> perl-MIME-Base64-3.05-1.bio.src.rpm
> perl-MLDBM-2.01-1.bio.src.rpm
> perl-Math-Derivative-0.01-2.bio.src.rpm
> perl-Math-Spline-0.01-2.bio.src.rpm
> perl-PBS-0.19-1.bio.src.rpm
> perl-SOAP-Lite-0.60-2.bio.src.rpm
> perl-SVG-Graph-0.01-3.bio.src.rpm
> perl-Spreadsheet-WriteExcel-2.11-2.bio.src.rpm
> perl-Statistics-Descriptive-2.6-2.bio.src.rpm
> perl-Text-Shellwords-1.07-2.bio.src.rpm
> perl-Tree-DAG_Node-1.04-2.bio.src.rpm
> perl-XML-LibXSLT-1.57-1.bio.src.rpm
> perl-tfbs-0.5.0-4.bio.src.rpm
> primer3-1.0.0-2.bio.src.rpm
> renderPM-0.99.20041122-1.bio.src.rpm
> reportlab-1_19-2.bio.src.rpm
> t-coffee-2.03-1.bio.src.rpm
> tdl-1.5.2-1.rhfc2.bio.src.rpm
> tkdiff-4.1-1.bio.src.rpm
> 
> There are a few others.
> 
> Glen
> 
> 
> >
> > Presently we use group directories and ownerships to allow some people
> > access to certain parts of the distro's repository. We can do the same
> > thing here. Maintainers for the dependencies will be decided on by  
> > a per
> > case basis.
> >
> > They can be installed via predefined profiles and/or system roles.
> >
> > (does that answer your question?)
> >
> > Thanks!
> >
> > -- 
> > Greg M. Kurtzer
> > http://runlevelzero.net/
> > http://caosity.org/
> > http://warewulf-cluster.org/
> >
> > Do not look anywhere for truth, for all that is needed is to  
> > refrain from
> > allowing concepts to arise.
> > _______________________________________________
> > cAos mailing list
> > cAos at caosity.org
> > http://lists.caosity.org/mailman/listinfo/caos
> >
> 
> _______________________________________________
> cAos mailing list
> cAos at caosity.org
> http://lists.caosity.org/mailman/listinfo/caos

-- 
Greg M. Kurtzer
http://runlevelzero.net/
http://caosity.org/
http://warewulf-cluster.org/

Do not look anywhere for truth, for all that is needed is to refrain from
allowing concepts to arise.


From benjamin at py-soft.co.uk  Mon Jun 26 23:10:55 2006
From: benjamin at py-soft.co.uk (Benjamin Donnachie)
Date: Tue, 27 Jun 2006 07:10:55 +0100
Subject: [cAos] caos3 development
Message-ID: <44A0CBEF.2090004@py-soft.co.uk>

Arthur Stevens <astevens at gravitypark.com> wrote:
>We are working on a new kernel for v3 and I think you will like the new 
>added security options/features. We should hopefully be replacing postfix 
>with qmail and some other security related conversions as well.

Sounds interesting...  I've been distracted with other projects lately,
but please let me know if I can help.

Take care,

Ben


From gmk at runlevelzero.net  Tue Jun 27 06:11:15 2006
From: gmk at runlevelzero.net (Greg M. Kurtzer)
Date: Tue, 27 Jun 2006 06:11:15 -0700
Subject: [cAos] Problems installing gridengine 5.3
In-Reply-To: <Pine.GSO.4.64.0606191322510.22173@apocalypse.OCF.Berkeley.EDU>
References: <Pine.GSO.4.64.0606191322510.22173@apocalypse.OCF.Berkeley.EDU>
Message-ID: <20060627131115.GB2054@aries.runlevelzero.net>

On Mon, Jun 19, 2006 at 07:53:00PM -0700, slaton wrote:
> I'm having a couple of problems installing the Grid Engine 5.3 package 
> from repo.

...

> Looks like both gridengine and the basic man package include a COMPLEX(5) 
> manpage. I don't think this is as simple as just renaming the existing 
> (man-pages pkg) file, is it? I imagine i'd also have to edit something 
> like a spec file used for srpms, but i'm not familiar enough with yum to 
> know where this information is. Thanks for any suggestions.

This would require a modification to the SPEC file for the gridengine. I
will look into it. for now, you can quickly work around the problem by
locating the downloaded binary RPM in /var/cache/yum/*/packages/*.rpm
and installing by hand with RPM (rpm -ivh --force /path/to/package.rpm).

> 2) Second problem has more to do with how my cluster is set up. I have a 
> master/admin node which is responsible for booting the cluster nodes 
> (Warewulf of course ;) and various other sundry server roles. There are no 
> user logins on this machine. There is a second, login/interactive node 
> which the users log into to access the cluster. So the warewulf master 
> node has the full warewulf-package and warewulf-tools, whereas the login 
> node only has the warewulf-tools package installed.
> 
> It appears that the caos gridengine package needs to run on the warewulf 
> master, since it's flagged as a prerequisite. However there is no separate 
> gridengine-tools sort of package containing the user tools, correct? 
> Therefore i don't see how my users will have access to any of the 
> gridengine user commands. There is of course the gridengine-node package, 
> which i've installed to VNFS -- perhaps i should have checked this to see 
> if it includes the user programs, in which case i will just install this 
> as well onto my login node.... 

If I understand the problem correctly, the best thing to do is to mount
/sge via NFS onto your interactive nodes and set the appropriate paths
and setup the login node as a submit host.

> Thanks for any insights...

Hope it helps!

-- 
Greg M. Kurtzer
http://runlevelzero.net/
http://caosity.org/
http://warewulf-cluster.org/

Do not look anywhere for truth, for all that is needed is to refrain from
allowing concepts to arise.


From benjamin at py-soft.co.uk  Thu Jun 29 09:46:55 2006
From: benjamin at py-soft.co.uk (Benjamin Donnachie)
Date: Thu, 29 Jun 2006 17:46:55 +0100
Subject: [cAos] caos3 development
In-Reply-To: <20060604050900.GB14645@aries.runlevelzero.net>
References: <20060604050900.GB14645@aries.runlevelzero.net>
Message-ID: <44A403FF.9040306@py-soft.co.uk>

Greg M. Kurtzer wrote:
> To accommodate this, cAos-3 primary emphasis is performance, efficiency,
> services and security. Our targeted user-base is clustered systems and
> servers for ISP, home and office.

I just thought - are there any plans to incorporate the hardened php 
patches from http://www.hardened-php.net ?

Take care,

Ben


From astevens at gravitypark.com  Thu Jun 29 10:28:50 2006
From: astevens at gravitypark.com (Arthur Stevens)
Date: Thu, 29 Jun 2006 10:28:50 -0700
Subject: [cAos] caos3 development
References: <20060604050900.GB14645@aries.runlevelzero.net>
	<44A403FF.9040306@py-soft.co.uk>
Message-ID: <000c01c69ba1$7cecee20$6600a8c0@astevens>

I am currently testing it. Have you used it much by chance?

Arthur (astevens)
----- Original Message ----- 
From: "Benjamin Donnachie" <benjamin at py-soft.co.uk>
To: "Community Assembled OS" <caos at caosity.org>
Sent: Thursday, June 29, 2006 9:46 AM
Subject: Re: [cAos] caos3 development


> Greg M. Kurtzer wrote:
>> To accommodate this, cAos-3 primary emphasis is performance, efficiency,
>> services and security. Our targeted user-base is clustered systems and
>> servers for ISP, home and office.
> 
> I just thought - are there any plans to incorporate the hardened php 
> patches from http://www.hardened-php.net ?
> 
> Take care,
> 
> Ben
> _______________________________________________
> cAos mailing list
> cAos at caosity.org
> http://lists.caosity.org/mailman/listinfo/caos
>



From benjamin at py-soft.co.uk  Thu Jun 29 11:15:37 2006
From: benjamin at py-soft.co.uk (Benjamin Donnachie)
Date: Thu, 29 Jun 2006 19:15:37 +0100
Subject: [cAos] caos3 development
In-Reply-To: <000c01c69ba1$7cecee20$6600a8c0@astevens>
References: <20060604050900.GB14645@aries.runlevelzero.net>	<44A403FF.9040306@py-soft.co.uk>
	<000c01c69ba1$7cecee20$6600a8c0@astevens>
Message-ID: <44A418C9.6000403@py-soft.co.uk>

Arthur Stevens wrote:
> I am currently testing it. Have you used it much by chance?

I'm currently testing it too along with suPHP from 
http://www.suphp.org/, which also looks promising.

I'll let you know how it goes! :)

Ben


From slaton at OCF.Berkeley.EDU  Thu Jun 29 14:04:14 2006
From: slaton at OCF.Berkeley.EDU (slaton)
Date: Thu, 29 Jun 2006 14:04:14 -0700 (PDT)
Subject: [cAos] Problems installing gridengine 5.3
In-Reply-To: <20060627131115.GB2054@aries.runlevelzero.net>
References: <Pine.GSO.4.64.0606191322510.22173@apocalypse.OCF.Berkeley.EDU>
	<20060627131115.GB2054@aries.runlevelzero.net>
Message-ID: <Pine.GSO.4.64.0606281622090.29996@conquest.OCF.Berkeley.EDU>

> > Looks like both gridengine and the basic man package include a 
> > COMPLEX(5) manpage. I don't think this is as simple as just renaming 
> > the existing (man-pages pkg) file, is it? I imagine i'd also have to 
> > edit something like a spec file used for srpms, but i'm not familiar 
> > enough with yum to know where this information is. Thanks for any 
> > suggestions.
> 
> This would require a modification to the SPEC file for the gridengine. I 
> will look into it. for now, you can quickly work around the problem by 
> locating the downloaded binary RPM in /var/cache/yum/*/packages/*.rpm 
> and installing by hand with RPM (rpm -ivh --force /path/to/package.rpm).

Thanks Greg. After (forced) install, the gridengine processes 
automatically started, then immediately bailed:

Starting the SGE processes
gethostbyname() failed: Resource temporarily unavailable
gethostbyname() failed: Resource temporarily unavailable
/etc/rc.d/init.d/rcsge: line 172: [: =: unary operator expected
critical error: unrecoverable error - contact systems manager
/var/tmp/rpm-tmp.25302: line 63: 28663 Aborted                 (core 
dumped) qconf -Ac host 
/var/spool/gridengine/default/qmaster/complexes/host
critical error: unrecoverable error - contact systems manager
/var/tmp/rpm-tmp.25302: line 64: 28664 Aborted                 (core 
dumped) qconf -Ac queue 
/var/spool/gridengine/default/qmaster/complexes/queue
critical error: unrecoverable error - contact systems manager
/var/tmp/rpm-tmp.25302: line 65: 28665 Aborted                 (core 
dumped) qconf -as $HOSTNAME
Don't forget to add /sge to the /etc/exports for your sharedfs networ

Ouch. Apparently gridengine expects to run on a machine with internet 
access. :) I expect there is a workaround, no worries.

> > It appears that the caos gridengine package needs to run on the 
> > warewulf master, since it's flagged as a prerequisite. However there 
> > is no separate gridengine-tools sort of package containing the user 
> > tools, correct? Therefore i don't see how my users will have access to 
> > any of the gridengine user commands. There is of course the 
> > gridengine-node package, which i've installed to VNFS -- perhaps i 
> > should have checked this to see if it includes the user programs, in 
> > which case i will just install this as well onto my login node....
> 
> If I understand the problem correctly, the best thing to do is to mount 
> /sge via NFS onto your interactive nodes and set the appropriate paths 
> and setup the login node as a submit host.

Understood....thanks.

slaton