From tbooth at ceh.ac.uk  Wed Oct  1 08:56:41 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 1 Oct 2014 13:56:41 +0100
Subject: [Bio-Linux] Swarm amplicon clustering tool now available on
	Bio-Linux
Message-ID: <1412168201.9151.25.camel@balisaur>

Hi All,

I just added a the "swarm" tool for Amplicon clustering:

https://github.com/torognes/swarm

$ sudo apt-get install swarm

The next release of QIIME will be able to make use of the tool directly,
but if you are doing marker gene analyses and want to try it now then it
is pretty easy to run the tool directly - see the instructions at the
link above.

Cheers,

TIM

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705


From crypticlineage at gmail.com  Tue Oct 14 10:10:53 2014
From: crypticlineage at gmail.com (Vikram Chhatre)
Date: Tue, 14 Oct 2014 10:10:53 -0400
Subject: [Bio-Linux] Fresh install - partitioning?
Message-ID: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>

Hello,

New Bio-Linux user here.  We are getting ready to install v.8 on a Dell
PowerEdge server and wondering if we need to manually create root, home,
boot and swap partitions.  If we go with the default option, what
partitions are created?

We would appreciate any feedback on this matter.

Thanks
Vikram
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From tony.travis at abdn.ac.uk  Thu Oct 16 06:52:31 2014
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 16 Oct 2014 11:52:31 +0100
Subject: [Bio-Linux] Fresh install - partitioning?
In-Reply-To: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
References: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
Message-ID: <543FA36F.1090403@abdn.ac.uk>

On 14/10/14 15:10, Vikram Chhatre wrote:
> Hello,
>
> New Bio-Linux user here.  We are getting ready to install v.8 on a Dell
> PowerEdge server and wondering if we need to manually create root, home,
> boot and swap partitions.  If we go with the default option, what
> partitions are created?

I recommend installing into four partitions:

  /
  swap
  /home
  /work

The "work" directory is where to work on shared projects, because "home"
should be private"

HTH,

  Tony.

--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis


The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.


From crypticlineage at gmail.com  Thu Oct 16 07:03:43 2014
From: crypticlineage at gmail.com (Vikram Chhatre)
Date: Thu, 16 Oct 2014 07:03:43 -0400
Subject: [Bio-Linux] Fresh install - partitioning?
In-Reply-To: <543FA36F.1090403@abdn.ac.uk>
References: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
 <543FA36F.1090403@abdn.ac.uk>
Message-ID: <CAJZnH0mLNgWststPuURtjxk5r+kiyTHV3To+j8vXbR2BcH0FZA@mail.gmail.com>

Hi Tony,

Thanks for your reply.  I have tried going both ways, creating partitions
or having the system do it.  I am ending up with the same error in both
cases.

?The grub efi amd64 signed package failed to install into /target/. Without
the GRUB boot loader, the installed system will not boot.?

The Ubuntu forum search hasn't been too useful with this error.  Do you any
suggestions?

Thanks
Vikram

On Thu, Oct 16, 2014 at 6:52 AM, Tony Travis <tony.travis at abdn.ac.uk> wrote:

> On 14/10/14 15:10, Vikram Chhatre wrote:
> > Hello,
> >
> > New Bio-Linux user here.  We are getting ready to install v.8 on a Dell
> > PowerEdge server and wondering if we need to manually create root, home,
> > boot and swap partitions.  If we go with the default option, what
> > partitions are created?
>
> I recommend installing into four partitions:
>
>   /
>   swap
>   /home
>   /work
>
> The "work" directory is where to work on shared projects, because "home"
> should be private"
>
> HTH,
>
>   Tony.
>
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
>
>
> The University of Aberdeen is a charity registered in Scotland, No
> SC013683.
> Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir.
> SC013683.
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
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From tbooth at ceh.ac.uk  Thu Oct 16 07:17:54 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 16 Oct 2014 12:17:54 +0100
Subject: [Bio-Linux] Fresh install - partitioning?
In-Reply-To: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
References: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
Message-ID: <1413458274.9432.29.camel@balisaur>

Hi Vikram,

In short, the default option will give you one big ext4 partition plus a
swap partition.  This is not necessarily a bad thing nowadays, even on a
server, but if you want to use LVM or RAID or if you want a specific
partitioning layout then the manual partitioner is pretty
straightforward to use.

Cheers,

TIM

On Tue, 2014-10-14 at 15:10 +0100, Vikram Chhatre wrote:
> Hello,
> 
> 
> New Bio-Linux user here.  We are getting ready to install v.8 on a
> Dell PowerEdge server and wondering if we need to manually create
> root, home, boot and swap partitions.  If we go with the default
> option, what partitions are created?  
> 
> 
> We would appreciate any feedback on this matter.
> 
> 
> Thanks
> Vikram

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705


From tbooth at ceh.ac.uk  Thu Oct 16 08:20:01 2014
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 16 Oct 2014 13:20:01 +0100
Subject: [Bio-Linux] Fresh install - partitioning?
In-Reply-To: <CAJZnH0mLNgWststPuURtjxk5r+kiyTHV3To+j8vXbR2BcH0FZA@mail.gmail.com>
References: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
 <543FA36F.1090403@abdn.ac.uk>
 <CAJZnH0mLNgWststPuURtjxk5r+kiyTHV3To+j8vXbR2BcH0FZA@mail.gmail.com>
Message-ID: <1413462001.9432.61.camel@balisaur>

Hi Vikram,

I've seen similar issues before.  I sent the following advice to someone
a while back and it helped, so I'm copying that below for you.  Does it
get you anywhere?

Cheers,

TIM

> The final step that the installer does is to add the Linux bootloader,
> named GRUB, to the system.  One obvious fix is to try and re-run the
> installer, but you can also do this bit manually, as follows:
>
>      1. Boot the Live stick or DVD and "Try Bio-Linux"
>      2. Click the "Home Folder" icon to get the file browser
>      3. Select the Linux partition from the devices list - you will
see
>         "bin boot cdrom ...etc" listed as folders.
>      4. Open a terminal and type the command:  cd /media/*/bin/..
>      5. Then type "ls" and check you see the same folder names as in
3.
>      6. Give the following commands.  Only the last one should print
any
>         output:
>
> sudo mount --bind /dev ./dev
> sudo mount --bind /proc ./proc
> sudo mount --bind /sys ./sys
> sudo chroot .
> df .
>
> Here, you should see the filesystem listed as /dev/sda5 or similar.
It
> could be sda4 or sda6.  The important thing is that it is /dev/sdaN
and
> not /dev/sdbN or /dev/sdcN etc.
>
> If so, we're nearly there - two more commands:
>
> grub-install /dev/sda
> update-grub
>
> Does that make the system boot?  If not, does it give any informative
> errors?

Cheers,

TIM

On Thu, 2014-10-16 at 12:03 +0100, Vikram Chhatre wrote:
> Hi Tony,
> 
> 
> Thanks for your reply.  I have tried going both ways, creating
> partitions or having the system do it.  I am ending up with the same
> error in both cases.
> 
> ?The grub efi amd64 signed package failed to install into /target/.
> Without the GRUB boot loader, the installed system will not boot.?
> 
> 
> The Ubuntu forum search hasn't been too useful with this error.  Do
> you any suggestions?
> 
> 
> Thanks
> Vikram
> 
> On Thu, Oct 16, 2014 at 6:52 AM, Tony Travis <tony.travis at abdn.ac.uk>
> wrote:
>         On 14/10/14 15:10, Vikram Chhatre wrote:
>         > Hello,
>         >
>         > New Bio-Linux user here.  We are getting ready to install
>         v.8 on a Dell
>         > PowerEdge server and wondering if we need to manually create
>         root, home,
>         > boot and swap partitions.  If we go with the default option,
>         what
>         > partitions are created?
>         
>         I recommend installing into four partitions:
>         
>           /
>           swap
>           /home
>           /work
>         
>         The "work" directory is where to work on shared projects,
>         because "home"
>         should be private"
>         
>         HTH,
>         
>           Tony.
>         
>         --
>         Dr. A.J.Travis, University of Aberdeen, Institute of
>         Biological and
>         Environmental Sciences, Cruickshank Building, St. Machar
>         Drive, Aberdeen
>         AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224
>         272 396
>         http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk,
>         skype:ajtravis
>         
>         
>         The University of Aberdeen is a charity registered in
>         Scotland, No SC013683.
>         Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an
>         Alba, ?ir. SC013683.
>         _______________________________________________
>         Bio-Linux mailing list
>         Bio-Linux at nebclists.nerc.ac.uk
>         http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> 
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://nebc.nerc.ac.uk
+44 1491 69 2705


From tony.travis at abdn.ac.uk  Thu Oct 16 08:34:03 2014
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 16 Oct 2014 13:34:03 +0100
Subject: [Bio-Linux] Fresh install - partitioning?
In-Reply-To: <CAJZnH0mLNgWststPuURtjxk5r+kiyTHV3To+j8vXbR2BcH0FZA@mail.gmail.com>
References: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
 <543FA36F.1090403@abdn.ac.uk>
 <CAJZnH0mLNgWststPuURtjxk5r+kiyTHV3To+j8vXbR2BcH0FZA@mail.gmail.com>
Message-ID: <543FBB3B.1020705@abdn.ac.uk>

On 16/10/14 12:03, Vikram Chhatre wrote:
> Hi Tony,
>
> Thanks for your reply.  I have tried going both ways, creating
> partitions or having the system do it.  I am ending up with the same
> error in both cases.
>
> ?The grub efi amd64 signed package failed to install into /target/.
> Without the GRUB boot loader, the installed system will not boot.?
>
> The Ubuntu forum search hasn't been too useful with this error.  Do you
> any suggestions?

Hi, Vikram.

My colleague recently had a problem installing Bio-Linux 8 on an EFI
Windows laptop and it turned out to be that Ubuntu detected EFI and
installed "grub-efi" instead of "grub-pc". However, he was booting
Windows in 'legacy' MBR mode and "grub-install" failed. After a bit of
poking around, I realised why it was not working and did what Tim
described to install "grub-pc" in a chroot, then "grub-install" and
rebooted successfully. I think Ubuntu and EFI works OK, unless you are
booting Windows in 'legacy' MBR mode.

HTH,

  Tony.

--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis


The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.


From crypticlineage at gmail.com  Thu Oct 16 08:46:45 2014
From: crypticlineage at gmail.com (Vikram Chhatre)
Date: Thu, 16 Oct 2014 08:46:45 -0400
Subject: [Bio-Linux] Fresh install - partitioning?
In-Reply-To: <543FBB3B.1020705@abdn.ac.uk>
References: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
 <543FA36F.1090403@abdn.ac.uk>
 <CAJZnH0mLNgWststPuURtjxk5r+kiyTHV3To+j8vXbR2BcH0FZA@mail.gmail.com>
 <543FBB3B.1020705@abdn.ac.uk>
Message-ID: <CAJZnH0mOQWGFtz69tcnSEj5aPkEkoiJU8+iF2+U_zWU2ta+nbw@mail.gmail.com>

Tim and Tony -

I have been booting through UEFI boot mode.  It's been a while since I
installed linux and it seems I have completely missed out on the EFI and
UEFI developments.

Let me give Tim's tutorial for grub install a shot and get back to you.

Thank you
Vikram


On Thu, Oct 16, 2014 at 8:34 AM, Tony Travis <tony.travis at abdn.ac.uk> wrote:

> On 16/10/14 12:03, Vikram Chhatre wrote:
> > Hi Tony,
> >
> > Thanks for your reply.  I have tried going both ways, creating
> > partitions or having the system do it.  I am ending up with the same
> > error in both cases.
> >
> > ?The grub efi amd64 signed package failed to install into /target/.
> > Without the GRUB boot loader, the installed system will not boot.?
> >
> > The Ubuntu forum search hasn't been too useful with this error.  Do you
> > any suggestions?
>
> Hi, Vikram.
>
> My colleague recently had a problem installing Bio-Linux 8 on an EFI
> Windows laptop and it turned out to be that Ubuntu detected EFI and
> installed "grub-efi" instead of "grub-pc". However, he was booting
> Windows in 'legacy' MBR mode and "grub-install" failed. After a bit of
> poking around, I realised why it was not working and did what Tim
> described to install "grub-pc" in a chroot, then "grub-install" and
> rebooted successfully. I think Ubuntu and EFI works OK, unless you are
> booting Windows in 'legacy' MBR mode.
>
> HTH,
>
>   Tony.
>
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
>
>
> The University of Aberdeen is a charity registered in Scotland, No
> SC013683.
> Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir.
> SC013683.
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
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From raonyguimaraes at gmail.com  Thu Oct 16 09:04:36 2014
From: raonyguimaraes at gmail.com (=?ISO-8859-1?Q?Raony_Guimaraes_Corr=EAa_Do_Carmo_Lisboa_Cardenas?=)
Date: Thu, 16 Oct 2014 10:04:36 -0300
Subject: [Bio-Linux] Fresh install - partitioning?
In-Reply-To: <543FBB3B.1020705@abdn.ac.uk>
References: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
 <543FA36F.1090403@abdn.ac.uk>
 <CAJZnH0mLNgWststPuURtjxk5r+kiyTHV3To+j8vXbR2BcH0FZA@mail.gmail.com>
 <543FBB3B.1020705@abdn.ac.uk>
Message-ID: <CALenahk4ivT8C2LQ+ZCaO81=0riXec9Mi3XMsDU7as=KAxcBtA@mail.gmail.com>

Hello All!

I'm using Biolinux (first 7 and now 8) in a Poweredge T710 for almost 3.5
years already. I like it's performance a lot!

I have 2 disks of 3TB in Raid-0 where i run Biolinux 8, Postgresql 9.4 and
all the other things I need running really fast!

My configs are:

- 24 cores, 112 GB of ram
- 4 disks with 3TB, 4 disks with 2TB

Raid:

2 disks in raid0
2 disks in raid 1
4 disks in raid 5 (with hot swap enabled!)

Partitions:

  / (raid 0 )
  /swap (raid 0 )
  /home (raid 0 )
  /backup (raid 1)
  /projects (raid 5)

Since I'm using raid 0 for the system (/, /home and etc) I made LVM
snapshots of my root partition just in case everything will blow out some
day.

Oh, and I also have periodic backups of the databases with pg_dump, cron
and rsync!

Let me know how I could help :)


_____________________________________________

Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas
PhD Student in Bioinformatics

email: raonyguimaraes at gmail.com
skype/gtalk: raonyguimaraes
phone: +55 31 93404152

Laboratory of Clinical Genomics
UFMG School of Medicine
Federal University of Minas Gerais - UFMG
Av. Prof. Alfredo Balena, 190, Sala 321
Belo Horizonte, Brazil 30130-100
_____________________________________________

On Thu, Oct 16, 2014 at 9:34 AM, Tony Travis <tony.travis at abdn.ac.uk> wrote:

> On 16/10/14 12:03, Vikram Chhatre wrote:
> > Hi Tony,
> >
> > Thanks for your reply.  I have tried going both ways, creating
> > partitions or having the system do it.  I am ending up with the same
> > error in both cases.
> >
> > "The grub efi amd64 signed package failed to install into /target/.
> > Without the GRUB boot loader, the installed system will not boot."
> >
> > The Ubuntu forum search hasn't been too useful with this error.  Do you
> > any suggestions?
>
> Hi, Vikram.
>
> My colleague recently had a problem installing Bio-Linux 8 on an EFI
> Windows laptop and it turned out to be that Ubuntu detected EFI and
> installed "grub-efi" instead of "grub-pc". However, he was booting
> Windows in 'legacy' MBR mode and "grub-install" failed. After a bit of
> poking around, I realised why it was not working and did what Tim
> described to install "grub-pc" in a chroot, then "grub-install" and
> rebooted successfully. I think Ubuntu and EFI works OK, unless you are
> booting Windows in 'legacy' MBR mode.
>
> HTH,
>
>   Tony.
>
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
>
>
> The University of Aberdeen is a charity registered in Scotland, No
> SC013683.
> Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir.
> SC013683.
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
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From tony.travis at abdn.ac.uk  Thu Oct 16 09:53:32 2014
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 16 Oct 2014 14:53:32 +0100
Subject: [Bio-Linux] Fresh install - partitioning?
In-Reply-To: <CALenahk4ivT8C2LQ+ZCaO81=0riXec9Mi3XMsDU7as=KAxcBtA@mail.gmail.com>
References: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
 <543FA36F.1090403@abdn.ac.uk>
 <CAJZnH0mLNgWststPuURtjxk5r+kiyTHV3To+j8vXbR2BcH0FZA@mail.gmail.com>
 <543FBB3B.1020705@abdn.ac.uk>
 <CALenahk4ivT8C2LQ+ZCaO81=0riXec9Mi3XMsDU7as=KAxcBtA@mail.gmail.com>
Message-ID: <543FCDDC.3050608@abdn.ac.uk>

On 16/10/14 14:04, Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas wrote:
> Hello All!
>
> I'm using Biolinux (first 7 and now 8) in a Poweredge T710 for almost
> 3.5 years already. I like it's performance a lot!
>
> I have 2 disks of 3TB in Raid-0 where i run Biolinux 8, Postgresql 9.4
> and all the other things I need running really fast!
> [...]

Hi, Raony.

RAID0 is quite risky because if *any* of your disk fail you will lose
everything!

I would use RAID10 instead or use two of your disks in RAID1 and backup
onto the third single disk. Disk capacity is important, of course, but
you risk losing everything unless you are backing up your RAID0 onto
external or network disks.

If you *really* want to live dangerously, you might try out Btrfs!

I'm running Bio-Linux 8 on an 8-disk Btrfs RAID10 on my personal
Bio-Linux workstation and it performs very well. I've been doing
disaster-recovery testing and it all seems to work very well. The only
real problem is that you can't swap on a Btrfs filesystem, but you can
mount a file on a loop device and swap on that instead.

I think Btrfs is the future :-)

Bye,

  Tony.

--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis


The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.


From raonyguimaraes at gmail.com  Thu Oct 16 10:08:56 2014
From: raonyguimaraes at gmail.com (=?ISO-8859-1?Q?Raony_Guimaraes_Corr=EAa_Do_Carmo_Lisboa_Cardenas?=)
Date: Thu, 16 Oct 2014 11:08:56 -0300
Subject: [Bio-Linux] Fresh install - partitioning?
In-Reply-To: <543FCDDC.3050608@abdn.ac.uk>
References: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
 <543FA36F.1090403@abdn.ac.uk>
 <CAJZnH0mLNgWststPuURtjxk5r+kiyTHV3To+j8vXbR2BcH0FZA@mail.gmail.com>
 <543FBB3B.1020705@abdn.ac.uk>
 <CALenahk4ivT8C2LQ+ZCaO81=0riXec9Mi3XMsDU7as=KAxcBtA@mail.gmail.com>
 <543FCDDC.3050608@abdn.ac.uk>
Message-ID: <CALenahmfMrMjC877s_yjBCDM6tSQRRQZ8fbDogg5eHS-BXijTA@mail.gmail.com>

You are not the first person who says about btrfs Tony. Thank you, I will
definitely give a try on the next few weeks on this.

I will also benchmark read/write speeds with 4 disks in raid 10 against 2
disks in raid 0.

I will leave my /swap in ext4 for now since I barely used it.

Kind regards!

_____________________________________________

Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas
PhD Student in Bioinformatics

email: raonyguimaraes at gmail.com
skype/gtalk: raonyguimaraes
phone: +55 31 93404152

Laboratory of Clinical Genomics
UFMG School of Medicine
Federal University of Minas Gerais - UFMG
Av. Prof. Alfredo Balena, 190, Sala 321
Belo Horizonte, Brazil 30130-100
_____________________________________________

On Thu, Oct 16, 2014 at 10:53 AM, Tony Travis <tony.travis at abdn.ac.uk>
wrote:

> On 16/10/14 14:04, Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas wrote:
> > Hello All!
> >
> > I'm using Biolinux (first 7 and now 8) in a Poweredge T710 for almost
> > 3.5 years already. I like it's performance a lot!
> >
> > I have 2 disks of 3TB in Raid-0 where i run Biolinux 8, Postgresql 9.4
> > and all the other things I need running really fast!
> > [...]
>
> Hi, Raony.
>
> RAID0 is quite risky because if *any* of your disk fail you will lose
> everything!
>
> I would use RAID10 instead or use two of your disks in RAID1 and backup
> onto the third single disk. Disk capacity is important, of course, but
> you risk losing everything unless you are backing up your RAID0 onto
> external or network disks.
>
> If you *really* want to live dangerously, you might try out Btrfs!
>
> I'm running Bio-Linux 8 on an 8-disk Btrfs RAID10 on my personal
> Bio-Linux workstation and it performs very well. I've been doing
> disaster-recovery testing and it all seems to work very well. The only
> real problem is that you can't swap on a Btrfs filesystem, but you can
> mount a file on a loop device and swap on that instead.
>
> I think Btrfs is the future :-)
>
> Bye,
>
>   Tony.
>
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
>
>
> The University of Aberdeen is a charity registered in Scotland, No
> SC013683.
> Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir.
> SC013683.
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
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From jm at iehinc.com  Thu Oct 16 11:30:52 2014
From: jm at iehinc.com (James Mategko)
Date: Thu, 16 Oct 2014 08:30:52 -0700
Subject: [Bio-Linux] Fresh install - partitioning?
In-Reply-To: <CALenahmfMrMjC877s_yjBCDM6tSQRRQZ8fbDogg5eHS-BXijTA@mail.gmail.com>
References: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
 <543FA36F.1090403@abdn.ac.uk>
 <CAJZnH0mLNgWststPuURtjxk5r+kiyTHV3To+j8vXbR2BcH0FZA@mail.gmail.com>
 <543FBB3B.1020705@abdn.ac.uk>
 <CALenahk4ivT8C2LQ+ZCaO81=0riXec9Mi3XMsDU7as=KAxcBtA@mail.gmail.com>
 <543FCDDC.3050608@abdn.ac.uk>
 <CALenahmfMrMjC877s_yjBCDM6tSQRRQZ8fbDogg5eHS-BXijTA@mail.gmail.com>
Message-ID: <543FE4AC.2090502@iehinc.com>

Hi All,

   The following calculator is very helpful when planning arrays: 
http://www.raid-calculator.com/default.aspx

I use RAID 5 most of the time since I tend to work with my datasets in 
memory rather then write intermediate steps to disk. I'm planning on 
moving to RAID 10 when larger capacity HP ProLiant compatible HDDs/SSDs 
come down in price.

Best Regards,
- James

On 10/16/2014 7:08 AM, Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas 
wrote:
> You are not the first person who says about btrfs Tony. Thank you, I 
> will definitely give a try on the next few weeks on this.
>
> I will also benchmark read/write speeds with 4 disks in raid 10 
> against 2 disks in raid 0.
>
> I will leave my /swap in ext4 for now since I barely used it.
>
> Kind regards!
>
> _____________________________________________
>
> Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas
> PhD Student in Bioinformatics
>
> email: raonyguimaraes at gmail.com <mailto:raonyguimaraes at gmail.com>
> skype/gtalk: raonyguimaraes
> phone: +55 31 93404152
>
> Laboratory of Clinical Genomics
> UFMG School of Medicine
> Federal University of Minas Gerais - UFMG
> Av. Prof. Alfredo Balena, 190, Sala 321
> Belo Horizonte, Brazil 30130-100
> _____________________________________________
>
> On Thu, Oct 16, 2014 at 10:53 AM, Tony Travis <tony.travis at abdn.ac.uk 
> <mailto:tony.travis at abdn.ac.uk>> wrote:
>
>     On 16/10/14 14:04, Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas
>     wrote:
>     > Hello All!
>     >
>     > I'm using Biolinux (first 7 and now 8) in a Poweredge T710 for
>     almost
>     > 3.5 years already. I like it's performance a lot!
>     >
>     > I have 2 disks of 3TB in Raid-0 where i run Biolinux 8,
>     Postgresql 9.4
>     > and all the other things I need running really fast!
>     > [...]
>
>     Hi, Raony.
>
>     RAID0 is quite risky because if *any* of your disk fail you will lose
>     everything!
>
>     I would use RAID10 instead or use two of your disks in RAID1 and
>     backup
>     onto the third single disk. Disk capacity is important, of course, but
>     you risk losing everything unless you are backing up your RAID0 onto
>     external or network disks.
>
>     If you *really* want to live dangerously, you might try out Btrfs!
>
>     I'm running Bio-Linux 8 on an 8-disk Btrfs RAID10 on my personal
>     Bio-Linux workstation and it performs very well. I've been doing
>     disaster-recovery testing and it all seems to work very well. The only
>     real problem is that you can't swap on a Btrfs filesystem, but you can
>     mount a file on a loop device and swap on that instead.
>
>     I think Btrfs is the future :-)
>
>     Bye,
>
>       Tony.
>
>     --
>     Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
>     Environmental Sciences, Cruickshank Building, St. Machar Drive,
>     Aberdeen
>     AB24 3UU, Scotland, UK. tel +44(0)1224 272700
>     <tel:%2B44%280%291224%20272700>, fax +44 (0)1224 272 396
>     <tel:%2B44%20%280%291224%20272%20396>
>     http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk
>     <mailto:tony.travis at abdn.ac.uk>, skype:ajtravis
>
>
>     The University of Aberdeen is a charity registered in Scotland, No
>     SC013683.
>     Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba,
>     ?ir. SC013683.
>     _______________________________________________
>     Bio-Linux mailing list
>     Bio-Linux at nebclists.nerc.ac.uk <mailto:Bio-Linux at nebclists.nerc.ac.uk>
>     http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
>
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux


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From tony.travis at abdn.ac.uk  Thu Oct 16 12:03:44 2014
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 16 Oct 2014 17:03:44 +0100
Subject: [Bio-Linux] Fresh install - partitioning?
In-Reply-To: <543FE4AC.2090502@iehinc.com>
References: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
 <543FA36F.1090403@abdn.ac.uk>
 <CAJZnH0mLNgWststPuURtjxk5r+kiyTHV3To+j8vXbR2BcH0FZA@mail.gmail.com>
 <543FBB3B.1020705@abdn.ac.uk>
 <CALenahk4ivT8C2LQ+ZCaO81=0riXec9Mi3XMsDU7as=KAxcBtA@mail.gmail.com>
 <543FCDDC.3050608@abdn.ac.uk>
 <CALenahmfMrMjC877s_yjBCDM6tSQRRQZ8fbDogg5eHS-BXijTA@mail.gmail.com>
 <543FE4AC.2090502@iehinc.com>
Message-ID: <543FEC60.5090500@abdn.ac.uk>

On 16/10/14 16:30, James Mategko wrote:
> Hi All,
>
>   The following calculator is very helpful when planning arrays:
> http://www.raid-calculator.com/default.aspx
>
> I use RAID 5 most of the time since I tend to work with my datasets in
> memory rather then write intermediate steps to disk. I'm planning on
> moving to RAID 10 when larger capacity HP ProLiant compatible HDDs/SSDs
> come down in price.

Hi, James.

RAID5 is risky with large disks because there is a significant chance of
a second disk failing during a rebuild after a single disk failure. This
is especially true if all your disk are the same make and bought at the
same time. RAID6 is now recommenced instead of RAID5 because it can
survive a double-disk failure. However, as I said, I think Btrfs is a
better alternative now BUT Btrfs RAID6 is highly *experimental* even
thought Btrfs RAID0, 1, 10 is more or less ready for production use.

You might be interested in this:

> http://www.oaktable.net/content/baarf-battle-against-any-raid-5

Bye,

  Tony.

--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis


The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.


From Jason.Bramwell at defra.gsi.gov.uk  Thu Oct 16 11:33:28 2014
From: Jason.Bramwell at defra.gsi.gov.uk (Bramwell, Jason (NCS))
Date: Thu, 16 Oct 2014 16:33:28 +0100
Subject: [Bio-Linux] Fresh install - partitioning?
In-Reply-To: <543FE4AC.2090502@iehinc.com>
References: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
 <543FA36F.1090403@abdn.ac.uk>
 <CAJZnH0mLNgWststPuURtjxk5r+kiyTHV3To+j8vXbR2BcH0FZA@mail.gmail.com>
 <543FBB3B.1020705@abdn.ac.uk>
 <CALenahk4ivT8C2LQ+ZCaO81=0riXec9Mi3XMsDU7as=KAxcBtA@mail.gmail.com>
 <543FCDDC.3050608@abdn.ac.uk>
 <CALenahmfMrMjC877s_yjBCDM6tSQRRQZ8fbDogg5eHS-BXijTA@mail.gmail.com>
 <543FE4AC.2090502@iehinc.com>
Message-ID: <BAD9EF24BE0C8140847F231A462B49D005E8EABF@SAMC4V1.DEMETER.ZEUS.GSI.GOV.UK>

Nice little tool but no RAID10 on there <sad face>

 

Regards

Jason Bramwell

 

From: James Mategko [mailto:jm at iehinc.com] 
Sent: 16 October 2014 16:31
To: bio-linux at nebclists.nerc.ac.uk
Subject: Re: [Bio-Linux] Fresh install - partitioning?

 

Hi All, 

  The following calculator is very helpful when planning arrays: http://www.raid-calculator.com/default.aspx 

I use RAID 5 most of the time since I tend to work with my datasets in memory rather then write intermediate steps to disk. I'm planning on moving to RAID 10 when larger capacity HP ProLiant compatible HDDs/SSDs come down in price. 

Best Regards, 
- James 

On 10/16/2014 7:08 AM, Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas wrote:

	You are not the first person who says about btrfs Tony. Thank you, I will definitely give a try on the next few weeks on this.
	
	I will also benchmark read/write speeds with 4 disks in raid 10 against 2 disks in raid 0.
	
	I will leave my /swap in ext4 for now since I barely used it.
	
	Kind regards!

	
	

	_____________________________________________
	
	Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas
	PhD Student in Bioinformatics
	
	email: raonyguimaraes at gmail.com
	skype/gtalk: raonyguimaraes
	phone: +55 31 93404152

	 

	Laboratory of Clinical Genomics
	UFMG School of Medicine

	Federal University of Minas Gerais - UFMG
	Av. Prof. Alfredo Balena, 190, Sala 321
	Belo Horizonte, Brazil 30130-100
	_____________________________________________

	 

	On Thu, Oct 16, 2014 at 10:53 AM, Tony Travis <tony.travis at abdn.ac.uk> wrote:

	On 16/10/14 14:04, Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas wrote:
	> Hello All!
	>
	> I'm using Biolinux (first 7 and now 8) in a Poweredge T710 for almost
	> 3.5 years already. I like it's performance a lot!
	>
	> I have 2 disks of 3TB in Raid-0 where i run Biolinux 8, Postgresql 9.4
	> and all the other things I need running really fast!
	> [...]
	
	Hi, Raony.
	
	RAID0 is quite risky because if *any* of your disk fail you will lose
	everything!
	
	I would use RAID10 instead or use two of your disks in RAID1 and backup
	onto the third single disk. Disk capacity is important, of course, but
	you risk losing everything unless you are backing up your RAID0 onto
	external or network disks.
	
	If you *really* want to live dangerously, you might try out Btrfs!
	
	I'm running Bio-Linux 8 on an 8-disk Btrfs RAID10 on my personal
	Bio-Linux workstation and it performs very well. I've been doing
	disaster-recovery testing and it all seems to work very well. The only
	real problem is that you can't swap on a Btrfs filesystem, but you can
	mount a file on a loop device and swap on that instead.
	
	I think Btrfs is the future :-)
	
	Bye,

	
	  Tony.
	
	--
	Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
	Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
	AB24 3UU, Scotland, UK. tel +44(0)1224 272700 <tel:%2B44%280%291224%20272700> , fax +44 (0)1224 272 396 <tel:%2B44%20%280%291224%20272%20396> 
	http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
	
	
	The University of Aberdeen is a charity registered in Scotland, No SC013683.
	Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.
	_______________________________________________
	Bio-Linux mailing list
	Bio-Linux at nebclists.nerc.ac.uk
	http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux

	 

	
	
	
	

	_______________________________________________
	Bio-Linux mailing list
	Bio-Linux at nebclists.nerc.ac.uk
	http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux






 
Department for Environment, Food and Rural Affairs (Defra)

This email and any attachments is intended for the named recipient only. If you have received it in error you have no authority to use, disclose,
store or copy any of its contents and you should destroy it and inform the sender. 
Whilst this email and associated attachments will have been checked for known viruses whilst within Defra systems we can accept no responsibility once it has left our systems.
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From raonyguimaraes at gmail.com  Thu Oct 16 13:26:39 2014
From: raonyguimaraes at gmail.com (=?ISO-8859-1?Q?Raony_Guimaraes_Corr=EAa_Do_Carmo_Lisboa_Cardenas?=)
Date: Thu, 16 Oct 2014 14:26:39 -0300
Subject: [Bio-Linux] Fresh install - partitioning?
In-Reply-To: <BAD9EF24BE0C8140847F231A462B49D005E8EABF@SAMC4V1.DEMETER.ZEUS.GSI.GOV.UK>
References: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
 <543FA36F.1090403@abdn.ac.uk>
 <CAJZnH0mLNgWststPuURtjxk5r+kiyTHV3To+j8vXbR2BcH0FZA@mail.gmail.com>
 <543FBB3B.1020705@abdn.ac.uk>
 <CALenahk4ivT8C2LQ+ZCaO81=0riXec9Mi3XMsDU7as=KAxcBtA@mail.gmail.com>
 <543FCDDC.3050608@abdn.ac.uk>
 <CALenahmfMrMjC877s_yjBCDM6tSQRRQZ8fbDogg5eHS-BXijTA@mail.gmail.com>
 <543FE4AC.2090502@iehinc.com>
 <BAD9EF24BE0C8140847F231A462B49D005E8EABF@SAMC4V1.DEMETER.ZEUS.GSI.GOV.UK>
Message-ID: <CALenahnOFEW+s3jdMA2yFtsTxCN9G+gZ0eZyXVWShjR9quCkEA@mail.gmail.com>

They make a bit a confusion between RAID 10 (1+0) and RAID 0+1 (Mirror of
stripes).
Main difference between RAID 10 vs RAID 01

   - Performance on both RAID 10 and RAID 01 will be the same.
   - ...
   - So, given a choice between RAID 10 and RAID 01, always choose RAID 10.

http://www.thegeekstuff.com/2011/10/raid10-vs-raid01/

_____________________________________________

Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas
PhD Student in Bioinformatics

email: raonyguimaraes at gmail.com
skype/gtalk: raonyguimaraes
phone: +55 31 93404152

Laboratory of Clinical Genomics
UFMG School of Medicine
Federal University of Minas Gerais - UFMG
Av. Prof. Alfredo Balena, 190, Sala 321
Belo Horizonte, Brazil 30130-100
_____________________________________________

On Thu, Oct 16, 2014 at 12:33 PM, Bramwell, Jason (NCS) <
Jason.Bramwell at defra.gsi.gov.uk> wrote:

> Nice little tool but no RAID10 on there <sad face>
>
>
>
> Regards
>
> Jason Bramwell
>
>
>
> *From:* James Mategko [mailto:jm at iehinc.com]
> *Sent:* 16 October 2014 16:31
> *To:* bio-linux at nebclists.nerc.ac.uk
> *Subject:* Re: [Bio-Linux] Fresh install - partitioning?
>
>
>
> Hi All,
>
>   The following calculator is very helpful when planning arrays:
> http://www.raid-calculator.com/default.aspx
>
> I use RAID 5 most of the time since I tend to work with my datasets in
> memory rather then write intermediate steps to disk. I'm planning on moving
> to RAID 10 when larger capacity HP ProLiant compatible HDDs/SSDs come down
> in price.
>
> Best Regards,
> - James
>
> On 10/16/2014 7:08 AM, Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas
> wrote:
>
> You are not the first person who says about btrfs Tony. Thank you, I will
> definitely give a try on the next few weeks on this.
>
> I will also benchmark read/write speeds with 4 disks in raid 10 against 2
> disks in raid 0.
>
> I will leave my /swap in ext4 for now since I barely used it.
>
> Kind regards!
>
>
> _____________________________________________
>
> Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas
> PhD Student in Bioinformatics
>
> email: raonyguimaraes at gmail.com
> skype/gtalk: raonyguimaraes
> phone: +55 31 93404152
>
>
>
> Laboratory of Clinical Genomics
> UFMG School of Medicine
>
> Federal University of Minas Gerais - UFMG
> Av. Prof. Alfredo Balena, 190, Sala 321
> Belo Horizonte, Brazil 30130-100
> _____________________________________________
>
>
>
> On Thu, Oct 16, 2014 at 10:53 AM, Tony Travis <tony.travis at abdn.ac.uk>
> wrote:
>
> On 16/10/14 14:04, Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas wrote:
> > Hello All!
> >
> > I'm using Biolinux (first 7 and now 8) in a Poweredge T710 for almost
> > 3.5 years already. I like it's performance a lot!
> >
> > I have 2 disks of 3TB in Raid-0 where i run Biolinux 8, Postgresql 9.4
> > and all the other things I need running really fast!
> > [...]
>
> Hi, Raony.
>
> RAID0 is quite risky because if *any* of your disk fail you will lose
> everything!
>
> I would use RAID10 instead or use two of your disks in RAID1 and backup
> onto the third single disk. Disk capacity is important, of course, but
> you risk losing everything unless you are backing up your RAID0 onto
> external or network disks.
>
> If you *really* want to live dangerously, you might try out Btrfs!
>
> I'm running Bio-Linux 8 on an 8-disk Btrfs RAID10 on my personal
> Bio-Linux workstation and it performs very well. I've been doing
> disaster-recovery testing and it all seems to work very well. The only
> real problem is that you can't swap on a Btrfs filesystem, but you can
> mount a file on a loop device and swap on that instead.
>
> I think Btrfs is the future :-)
>
> Bye,
>
>
>   Tony.
>
> --
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
>
>
> The University of Aberdeen is a charity registered in Scotland, No
> SC013683.
> Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir.
> SC013683.
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
>
>
>
>
> _______________________________________________
>
> Bio-Linux mailing list
>
> Bio-Linux at nebclists.nerc.ac.uk
>
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
>
>
>
>
> Department for Environment, Food and Rural Affairs (Defra)
>
> This email and any attachments is intended for the named recipient only.
> If you have received it in error you have no authority to use, disclose,
> store or copy any of its contents and you should destroy it and inform the
> sender.
> Whilst this email and associated attachments will have been checked for
> known viruses whilst within Defra systems we can accept no responsibility
> once it has left our systems.
> Communications on Defra's computer systems may be monitored and/or
> recorded to secure the effective operation of the system and for other
> lawful purposes.
>
> _______________________________________________
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>
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From raonyguimaraes at gmail.com  Thu Oct 16 13:31:32 2014
From: raonyguimaraes at gmail.com (=?ISO-8859-1?Q?Raony_Guimaraes_Corr=EAa_Do_Carmo_Lisboa_Cardenas?=)
Date: Thu, 16 Oct 2014 14:31:32 -0300
Subject: [Bio-Linux] Fresh install - partitioning?
In-Reply-To: <CALenahnOFEW+s3jdMA2yFtsTxCN9G+gZ0eZyXVWShjR9quCkEA@mail.gmail.com>
References: <CAJZnH0mY3wNUm4reZkP=ZGfUfKKE4dY0kS95wCO=2p5eceR0JA@mail.gmail.com>
 <543FA36F.1090403@abdn.ac.uk>
 <CAJZnH0mLNgWststPuURtjxk5r+kiyTHV3To+j8vXbR2BcH0FZA@mail.gmail.com>
 <543FBB3B.1020705@abdn.ac.uk>
 <CALenahk4ivT8C2LQ+ZCaO81=0riXec9Mi3XMsDU7as=KAxcBtA@mail.gmail.com>
 <543FCDDC.3050608@abdn.ac.uk>
 <CALenahmfMrMjC877s_yjBCDM6tSQRRQZ8fbDogg5eHS-BXijTA@mail.gmail.com>
 <543FE4AC.2090502@iehinc.com>
 <BAD9EF24BE0C8140847F231A462B49D005E8EABF@SAMC4V1.DEMETER.ZEUS.GSI.GOV.UK>
 <CALenahnOFEW+s3jdMA2yFtsTxCN9G+gZ0eZyXVWShjR9quCkEA@mail.gmail.com>
Message-ID: <CALenahkj_YmtpWXs=DEwEUCMFAzDiMzLd19ZD313GT-FTwFBBg@mail.gmail.com>

This looks good!

https://www.icc-usa.com/raid-calculator/

_____________________________________________

Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas
PhD Student in Bioinformatics

email: raonyguimaraes at gmail.com
skype/gtalk: raonyguimaraes
phone: +55 31 93404152

Laboratory of Clinical Genomics
UFMG School of Medicine
Federal University of Minas Gerais - UFMG
Av. Prof. Alfredo Balena, 190, Sala 321
Belo Horizonte, Brazil 30130-100
_____________________________________________

On Thu, Oct 16, 2014 at 2:26 PM, Raony Guimaraes Corr?a Do Carmo Lisboa
Cardenas <raonyguimaraes at gmail.com> wrote:

> They make a bit a confusion between RAID 10 (1+0) and RAID 0+1 (Mirror of
> stripes).
> Main difference between RAID 10 vs RAID 01
>
>    - Performance on both RAID 10 and RAID 01 will be the same.
>    - ...
>    - So, given a choice between RAID 10 and RAID 01, always choose RAID
>    10.
>
> http://www.thegeekstuff.com/2011/10/raid10-vs-raid01/
>
> _____________________________________________
>
> Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas
> PhD Student in Bioinformatics
>
> email: raonyguimaraes at gmail.com
> skype/gtalk: raonyguimaraes
> phone: +55 31 93404152
>
> Laboratory of Clinical Genomics
> UFMG School of Medicine
> Federal University of Minas Gerais - UFMG
> Av. Prof. Alfredo Balena, 190, Sala 321
> Belo Horizonte, Brazil 30130-100
> _____________________________________________
>
> On Thu, Oct 16, 2014 at 12:33 PM, Bramwell, Jason (NCS) <
> Jason.Bramwell at defra.gsi.gov.uk> wrote:
>
>> Nice little tool but no RAID10 on there <sad face>
>>
>>
>>
>> Regards
>>
>> Jason Bramwell
>>
>>
>>
>> *From:* James Mategko [mailto:jm at iehinc.com]
>> *Sent:* 16 October 2014 16:31
>> *To:* bio-linux at nebclists.nerc.ac.uk
>> *Subject:* Re: [Bio-Linux] Fresh install - partitioning?
>>
>>
>>
>> Hi All,
>>
>>   The following calculator is very helpful when planning arrays:
>> http://www.raid-calculator.com/default.aspx
>>
>> I use RAID 5 most of the time since I tend to work with my datasets in
>> memory rather then write intermediate steps to disk. I'm planning on moving
>> to RAID 10 when larger capacity HP ProLiant compatible HDDs/SSDs come down
>> in price.
>>
>> Best Regards,
>> - James
>>
>> On 10/16/2014 7:08 AM, Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas
>> wrote:
>>
>> You are not the first person who says about btrfs Tony. Thank you, I will
>> definitely give a try on the next few weeks on this.
>>
>> I will also benchmark read/write speeds with 4 disks in raid 10 against 2
>> disks in raid 0.
>>
>> I will leave my /swap in ext4 for now since I barely used it.
>>
>> Kind regards!
>>
>>
>> _____________________________________________
>>
>> Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas
>> PhD Student in Bioinformatics
>>
>> email: raonyguimaraes at gmail.com
>> skype/gtalk: raonyguimaraes
>> phone: +55 31 93404152
>>
>>
>>
>> Laboratory of Clinical Genomics
>> UFMG School of Medicine
>>
>> Federal University of Minas Gerais - UFMG
>> Av. Prof. Alfredo Balena, 190, Sala 321
>> Belo Horizonte, Brazil 30130-100
>> _____________________________________________
>>
>>
>>
>> On Thu, Oct 16, 2014 at 10:53 AM, Tony Travis <tony.travis at abdn.ac.uk>
>> wrote:
>>
>> On 16/10/14 14:04, Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas wrote:
>> > Hello All!
>> >
>> > I'm using Biolinux (first 7 and now 8) in a Poweredge T710 for almost
>> > 3.5 years already. I like it's performance a lot!
>> >
>> > I have 2 disks of 3TB in Raid-0 where i run Biolinux 8, Postgresql 9.4
>> > and all the other things I need running really fast!
>> > [...]
>>
>> Hi, Raony.
>>
>> RAID0 is quite risky because if *any* of your disk fail you will lose
>> everything!
>>
>> I would use RAID10 instead or use two of your disks in RAID1 and backup
>> onto the third single disk. Disk capacity is important, of course, but
>> you risk losing everything unless you are backing up your RAID0 onto
>> external or network disks.
>>
>> If you *really* want to live dangerously, you might try out Btrfs!
>>
>> I'm running Bio-Linux 8 on an 8-disk Btrfs RAID10 on my personal
>> Bio-Linux workstation and it performs very well. I've been doing
>> disaster-recovery testing and it all seems to work very well. The only
>> real problem is that you can't swap on a Btrfs filesystem, but you can
>> mount a file on a loop device and swap on that instead.
>>
>> I think Btrfs is the future :-)
>>
>> Bye,
>>
>>
>>   Tony.
>>
>> --
>> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
>> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
>> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
>> http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis
>>
>>
>> The University of Aberdeen is a charity registered in Scotland, No
>> SC013683.
>> Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir.
>> SC013683.
>> _______________________________________________
>> Bio-Linux mailing list
>> Bio-Linux at nebclists.nerc.ac.uk
>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>>
>>
>>
>>
>>
>>
>> _______________________________________________
>>
>> Bio-Linux mailing list
>>
>> Bio-Linux at nebclists.nerc.ac.uk
>>
>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>>
>>
>>
>>
>>
>>
>> Department for Environment, Food and Rural Affairs (Defra)
>>
>> This email and any attachments is intended for the named recipient only.
>> If you have received it in error you have no authority to use, disclose,
>> store or copy any of its contents and you should destroy it and inform
>> the sender.
>> Whilst this email and associated attachments will have been checked for
>> known viruses whilst within Defra systems we can accept no responsibility
>> once it has left our systems.
>> Communications on Defra's computer systems may be monitored and/or
>> recorded to secure the effective operation of the system and for other
>> lawful purposes.
>>
>> _______________________________________________
>> Bio-Linux mailing list
>> Bio-Linux at nebclists.nerc.ac.uk
>> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>>
>>
>
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From ramen5in at yahoo.co.in  Mon Oct 20 00:46:02 2014
From: ramen5in at yahoo.co.in (Dr. R. N. Sarma)
Date: Mon, 20 Oct 2014 12:46:02 +0800
Subject: [Bio-Linux] Printer problem
Message-ID: <1413780362.91121.YahooMailNeo@web193002.mail.sg3.yahoo.com>

I have connected my HPLajerjet P1007, but no printout is comming. How to rectify the problem?

The divise URI is 'hp:/usb/HP_LaserJet_P1007?serial=EC0FYA1'
The nkae and model (as shown by prpoertity) is: HP LaserJet P1007 Foomatic/foo2xqx (recommended)
 

*****************************************************************
Dr. R. N. Sarma
Professor
Department of Plant Breeding and Genetics 
Assam Agricultural University 
Jorhat- 785 013, Assam, INDIA 
Phone:
 0376-2310526(O), 2311333 (R);09435350529 (M); Fax:0376-2310831, 2340101 
Web: www.aau.ac.in
*****************************************************************
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From tony.travis at abdn.ac.uk  Mon Oct 20 05:02:47 2014
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Mon, 20 Oct 2014 10:02:47 +0100
Subject: [Bio-Linux] Printer problem
In-Reply-To: <1413780362.91121.YahooMailNeo@web193002.mail.sg3.yahoo.com>
References: <1413780362.91121.YahooMailNeo@web193002.mail.sg3.yahoo.com>
Message-ID: <5444CFB7.1000707@abdn.ac.uk>

On 20/10/14 05:46, Dr. R. N. Sarma wrote:
> I have connected my HPLajerjet P1007, but no printout is comming. How to
> rectify the problem?
>
> The divise URI is 'hp:/usb/HP_LaserJet_P1007?serial=EC0FYA1'
> The nkae and model (as shown by prpoertity) is: HP LaserJet P1007
> Foomatic/foo2xqx (recommended)

Hi, Ramen.

Was the printer detected automatically, or did you select it from a list?

Bye,

  Tony.

--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis


The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.


From tony.travis at abdn.ac.uk  Mon Oct 20 05:12:08 2014
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Mon, 20 Oct 2014 10:12:08 +0100
Subject: [Bio-Linux] Printer problem
In-Reply-To: <1413780362.91121.YahooMailNeo@web193002.mail.sg3.yahoo.com>
References: <1413780362.91121.YahooMailNeo@web193002.mail.sg3.yahoo.com>
Message-ID: <5444D1E8.2080204@abdn.ac.uk>

On 20/10/14 05:46, Dr. R. N. Sarma wrote:
> I have connected my HPLajerjet P1007, but no printout is comming. How to
> rectify the problem?
>
> The divise URI is 'hp:/usb/HP_LaserJet_P1007?serial=EC0FYA1'
> The nkae and model (as shown by prpoertity) is: HP LaserJet P1007
> Foomatic/foo2xqx (recommended)

Hi, Ramen.

The version of "HPLIP" in Ubuntu 14.04 LTS does not support all HP
printers. I use this instead for my HP 'all-in-one' printer/scanner:

  http://sourceforge.net/projects/hplip/

[This is an Ubuntu issue, not a problem with Bio-Linux]

HTH,

  Tony.

--
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396
http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis


The University of Aberdeen is a charity registered in Scotland, No SC013683.
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.