<div dir="ltr"><div><div>Thank you very much to all for all your sharings, they will be really useful to us to set everything up.<br><br></div><div>Following your extended comments seems that the best option will probably be to use Slurm and Uprade<br></div><div>all Biolinux to v8, and installing MATE on top. The network will be configured manually. We will probably do<br>all this next week. I'll let you know if we get into big issues; hopefully not! :)<br></div><div><br></div>Best, greetings,<br></div>Xavi<br></div><div class="gmail_extra"><br><div class="gmail_quote">2015-02-05 12:18 GMT+01:00 <span dir="ltr"><<a href="mailto:bio-linux-request@nebclists.nerc.ac.uk" target="_blank">bio-linux-request@nebclists.nerc.ac.uk</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Bio-Linux mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Biolinux8 - Best job scheduler for small cluster?<br>
(Xavier Mart?nez Serrano)<br>
2. Biolinux8 - Is there an installation for "server mode"?<br>
(without X11, just x2go connection) (Xavier Mart?nez Serrano)<br>
3. Re: Biolinux8 - Is there an installation for "server mode"?<br>
(without X11, just x2go connection) (Tony Travis)<br>
4. Re: Biolinux8 - Best job scheduler for small cluster?<br>
(Tony Travis)<br>
5. Re: Biolinux8 - Is there an installation for "server mode"?<br>
(without X11, just x2go connection) (Tim Booth)<br>
6. Re: Biolinux8 - Best job scheduler for small cluster? (Tim Booth)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 5 Feb 2015 08:16:38 +0100<br>
From: Xavier Mart?nez Serrano <<a href="mailto:xmarti6@xtec.cat">xmarti6@xtec.cat</a>><br>
To: <a href="mailto:bio-linux@nebclists.nerc.ac.uk">bio-linux@nebclists.nerc.ac.uk</a><br>
Subject: [Bio-Linux] Biolinux8 - Best job scheduler for small cluster?<br>
Message-ID:<br>
<<a href="mailto:CAPYyywinF97V3eiL_CfZEDE5uS9i_Z0o89d3x_9y_cf4QZ54Xw@mail.gmail.com">CAPYyywinF97V3eiL_CfZEDE5uS9i_Z0o89d3x_9y_cf4QZ54Xw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi,<br>
<br>
We have 4 computers with ~20CPU each in a hospital research group and we<br>
would like to set a cluster with them. Which is the best suitable job<br>
scheduler for us if we are running Biolinux7 in three of them and Biolinux8<br>
in the other?<br>
<br>
We have been looking at common job schedulers like: Slurm, SGE, Condor,<br>
Torque, ... but we wonder which best suits for our small resources, to make<br>
it as easy as possible.<br>
<br>
What can you recommend us?<br>
<br>
Many thanks in advance,<br>
Xavi<br>
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Message: 2<br>
Date: Thu, 5 Feb 2015 08:23:08 +0100<br>
From: Xavier Mart?nez Serrano <<a href="mailto:xmarti6@xtec.cat">xmarti6@xtec.cat</a>><br>
To: <a href="mailto:bio-linux@nebclists.nerc.ac.uk">bio-linux@nebclists.nerc.ac.uk</a><br>
Subject: [Bio-Linux] Biolinux8 - Is there an installation for "server<br>
mode"? (without X11, just x2go connection)<br>
Message-ID:<br>
<<a href="mailto:CAPYyywjGoQ9orbWs5WQq2GJpYvesFY3Adde0z8wRhaWWr%2Bvgzg@mail.gmail.com">CAPYyywjGoQ9orbWs5WQq2GJpYvesFY3Adde0z8wRhaWWr+vgzg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi,<br>
<br>
We are a research group working in metagenomics, and we would like to<br>
install Biolinux8 in a server recently acquired in "server mode", i.e.<br>
whithout X11 enabled, we just need a ssh connection and might be in some<br>
case an x2go connection.<br>
<br>
Is there an option to install Biolinux8 in such mode, revising the<br>
documentation online we could not see it.<br>
<br>
Many thanks,<br>
Xavi<br>
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------------------------------<br>
<br>
Message: 3<br>
Date: Thu, 5 Feb 2015 10:31:22 +0000<br>
From: Tony Travis <<a href="mailto:tony.travis@abdn.ac.uk">tony.travis@abdn.ac.uk</a>><br>
To: <<a href="mailto:bio-linux@nebclists.nerc.ac.uk">bio-linux@nebclists.nerc.ac.uk</a>><br>
Subject: Re: [Bio-Linux] Biolinux8 - Is there an installation for<br>
"server mode"? (without X11, just x2go connection)<br>
Message-ID: <<a href="mailto:54D3467A.8020903@abdn.ac.uk">54D3467A.8020903@abdn.ac.uk</a>><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
On 05/02/15 07:23, Xavier Mart?nez Serrano wrote:<br>
> Hi,<br>
><br>
> We are a research group working in metagenomics, and we would like to<br>
> install Biolinux8 in a server recently acquired in "server mode", i.e.<br>
> whithout X11 enabled, we just need a ssh connection and might be in<br>
> some case an x2go connection.<br>
><br>
> Is there an option to install Biolinux8 in such mode, revising the<br>
> documentation online we could not see it.<br>
<br>
Hi, Xavi.<br>
<br>
We run Bio-Linux 8 on servers using Tim's default installation without<br>
any issues. If you want to use Bio-Linux as an "x2go" terminal server,<br>
you will need X11 and the MATE desktop installed anyway. The only real<br>
problem is you have to add the network configuration manually to prevent<br>
network manager from configuring the NIC's dynamically. You can use<br>
"network manager" to statically configure NIC's, but it is intended to<br>
be used to configure NIC's dynamically on laptops or workstations.<br>
<br>
HTH,<br>
<br>
Tony.<br>
<br>
--<br>
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and<br>
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen<br>
AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396<br>
<a href="http://www.abdn.ac.uk" target="_blank">http://www.abdn.ac.uk</a>, mailto:<a href="mailto:tony.travis@abdn.ac.uk">tony.travis@abdn.ac.uk</a>, skype:ajtravis<br>
<br>
<br>
The University of Aberdeen is a charity registered in Scotland, No SC013683.<br>
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.<br>
<br>
<br>
------------------------------<br>
<br>
Message: 4<br>
Date: Thu, 5 Feb 2015 10:46:06 +0000<br>
From: Tony Travis <<a href="mailto:tony.travis@abdn.ac.uk">tony.travis@abdn.ac.uk</a>><br>
To: <<a href="mailto:bio-linux@nebclists.nerc.ac.uk">bio-linux@nebclists.nerc.ac.uk</a>><br>
Cc: Luca Clivio <<a href="mailto:luca.clivio@marionegri.it">luca.clivio@marionegri.it</a>><br>
Subject: Re: [Bio-Linux] Biolinux8 - Best job scheduler for small<br>
cluster?<br>
Message-ID: <<a href="mailto:54D349EE.5050800@abdn.ac.uk">54D349EE.5050800@abdn.ac.uk</a>><br>
Content-Type: text/plain; charset="windows-1252"<br>
<br>
On 05/02/15 07:16, Xavier Mart?nez Serrano wrote:<br>
> Hi,<br>
><br>
> We have 4 computers with ~20CPU each in a hospital research group and<br>
> we would like to set a cluster with them. Which is the best suitable job<br>
> scheduler for us if we are running Biolinux7 in three of them and<br>
> Biolinux8 in the other?<br>
><br>
> We have been looking at common job schedulers like: Slurm, SGE, Condor,<br>
> Torque, ... but we wonder which best suits for our small resources, to<br>
> make it as easy as possible.<br>
><br>
> What can you recommend us?<br>
<br>
Hi, Xavi.<br>
<br>
I've run SGE under Bio-Linux 7, but I would not advocate running a<br>
mixture of Bio-Linux 7 and 8. Tim's Bio-Linux 7-8 upgrade script works<br>
very well and I would recommend upgrading your Bio-Linux 7 machines to<br>
Bio-Linux 8. One thing you might consider looking at is Qlustar:<br>
<br>
<a href="https://qlustar.com/" target="_blank">https://qlustar.com/</a><br>
<br>
They have made some commitment to support Debian/Med and I demo'ed a<br>
version with a Bio-Linux 'Front-end' at last year's Debian-Med Sprint:<br>
<br>
<a href="https://qlustar.com/news/qlustar-demo-debianmed-sprint" target="_blank">https://qlustar.com/news/qlustar-demo-debianmed-sprint</a><br>
<br>
Q-Leap gave a presentation at the recent Debian-Med Sprint, which I<br>
watched on Skype because I couldn't attend the meeting:<br>
<br>
<a href="https://wiki.debian.org/Sprints/2015/DebianMed2015" target="_blank">https://wiki.debian.org/Sprints/2015/DebianMed2015</a><br>
<br>
Maybe Tim can tell you more because he was there. It's pay-for software,<br>
and I have some reservations about their licensing model, but from what<br>
I've seen of it Qlustar is very good cluster software. Q-Leap support<br>
Slurm in particular, but do consider Amdahl's Law:<br>
<br>
<a href="http://en.wikipedia.org/wiki/Amdahl's_law" target="_blank">http://en.wikipedia.org/wiki/Amdahl's_law</a><br>
<br>
I'm working with Luca Clivio to install a Qlustar cluster with a<br>
Bio-Linux Front-end at MNI (Mario Negri Institute) in Milan:<br>
<br>
<a href="http://www.marionegri.it/mn/it/index.html" target="_blank">http://www.marionegri.it/mn/it/index.html</a><br>
<br>
Please contact Luca directly if you are interested in this project.<br>
<br>
HTH,<br>
<br>
Tony.<br>
<br>
--<br>
Dr. A.J.Travis, University of Aberdeen, Institute of Biological and<br>
Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen<br>
AB24 3UU, Scotland, UK. tel <a href="tel:%2B44%280%291224%20272700" value="+441224272700">+44(0)1224 272700</a>, fax <a href="tel:%2B44%20%280%291224%20272%20396" value="+441224272396">+44 (0)1224 272 396</a><br>
<a href="http://www.abdn.ac.uk" target="_blank">http://www.abdn.ac.uk</a>, mailto:<a href="mailto:tony.travis@abdn.ac.uk">tony.travis@abdn.ac.uk</a>, skype:ajtravis<br>
<br>
<br>
The University of Aberdeen is a charity registered in Scotland, No SC013683.<br>
Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Thu, 5 Feb 2015 11:02:12 +0000<br>
From: Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
To: Bio-Linux help and discussion <<a href="mailto:bio-linux@nebclists.nerc.ac.uk">bio-linux@nebclists.nerc.ac.uk</a>><br>
Subject: Re: [Bio-Linux] Biolinux8 - Is there an installation for<br>
"server mode"? (without X11, just x2go connection)<br>
Message-ID:<br>
<<a href="mailto:1423134132.23727.117.camel@wllt1771.nerc-wallingford.ac.uk">1423134132.23727.117.camel@wllt1771.nerc-wallingford.ac.uk</a>><br>
Content-Type: text/plain; charset="UTF-8"<br>
<br>
Hi,<br>
<br>
Tony's right - the Bio-Linux ISO is based on the Ubuntu desktop ISO, so<br>
you basically need an X-session to run the installer even if you<br>
subsequently remove X and run the thing headless. It's possible to<br>
strip out the X server packages while still retaining the libraries<br>
needed by MATE for x2go but for simplicity I'd just take out LightDM so<br>
X is present but never started.<br>
<br>
By "add the network configuration manually" this means that if you set<br>
your settings for any network card in /etc/network/interfaces then when<br>
the NM daemon is restarted it will leave that card alone. In my<br>
experience NM now works very well but on a server with fixed network<br>
routing it's just another layer of complexity you don't need. Use the<br>
command "nmcli d" to see what devices NM thinks it is managing.<br>
<br>
Cheers,<br>
<br>
TIM<br>
<br>
On Thu, 2015-02-05 at 10:31 +0000, Tony Travis wrote:<br>
> On 05/02/15 07:23, Xavier Mart?nez Serrano wrote:<br>
> > Hi,<br>
> ><br>
> > We are a research group working in metagenomics, and we would like to<br>
> > install Biolinux8 in a server recently acquired in "server mode", i.e.<br>
> > whithout X11 enabled, we just need a ssh connection and might be in<br>
> > some case an x2go connection.<br>
> ><br>
> > Is there an option to install Biolinux8 in such mode, revising the<br>
> > documentation online we could not see it.<br>
><br>
> Hi, Xavi.<br>
><br>
> We run Bio-Linux 8 on servers using Tim's default installation without<br>
> any issues. If you want to use Bio-Linux as an "x2go" terminal server,<br>
> you will need X11 and the MATE desktop installed anyway. The only real<br>
> problem is you have to add the network configuration manually to prevent<br>
> network manager from configuring the NIC's dynamically. You can use<br>
> "network manager" to statically configure NIC's, but it is intended to<br>
> be used to configure NIC's dynamically on laptops or workstations.<br>
><br>
> HTH,<br>
><br>
> Tony.<br>
><br>
> --<br>
> Dr. A.J.Travis, University of Aberdeen, Institute of Biological and<br>
> Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen<br>
> AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396<br>
> <a href="http://www.abdn.ac.uk" target="_blank">http://www.abdn.ac.uk</a>, mailto:<a href="mailto:tony.travis@abdn.ac.uk">tony.travis@abdn.ac.uk</a>, skype:ajtravis<br>
><br>
><br>
> The University of Aberdeen is a charity registered in Scotland, No SC013683.<br>
> Tha Oilthigh Obar Dheathain na charthannas cl?raichte ann an Alba, ?ir. SC013683.<br>
> _______________________________________________<br>
> Bio-Linux mailing list<br>
> <a href="mailto:Bio-Linux@nebclists.nerc.ac.uk">Bio-Linux@nebclists.nerc.ac.uk</a><br>
> <a href="http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux" target="_blank">http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux</a><br>
<br>
--<br>
Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
NERC Environmental Bioinformatics Centre<br>
<br>
Centre for Ecology and Hydrology<br>
Maclean Bldg, Benson Lane<br>
Crowmarsh Gifford<br>
Wallingford, England<br>
OX10 8BB<br>
<br>
<a href="http://environmentalomics.org/bio-linux" target="_blank">http://environmentalomics.org/bio-linux</a><br>
<a href="tel:%2B44%201491%2069%202297" value="+441491692297">+44 1491 69 2297</a><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 6<br>
Date: Thu, 5 Feb 2015 11:18:22 +0000<br>
From: Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
To: Bio-Linux help and discussion <<a href="mailto:bio-linux@nebclists.nerc.ac.uk">bio-linux@nebclists.nerc.ac.uk</a>><br>
Cc: Xavier Mart?nez Serrano <<a href="mailto:xmarti6@xtec.cat">xmarti6@xtec.cat</a>><br>
Subject: Re: [Bio-Linux] Biolinux8 - Best job scheduler for small<br>
cluster?<br>
Message-ID:<br>
<<a href="mailto:1423135102.23727.126.camel@wllt1771.nerc-wallingford.ac.uk">1423135102.23727.126.camel@wllt1771.nerc-wallingford.ac.uk</a>><br>
Content-Type: text/plain; charset="UTF-8"<br>
<br>
Hi Xavi,<br>
<br>
To be honest I don't really know. Hopefully someone on the list will<br>
have some practical experience to share. We use Torqe on a cluster here<br>
at CEH but it's not actually running Bio-Linux and I had no part in<br>
setting it up so I don't know how easy it is to configure.<br>
<br>
I have experience with Condor and I don't think it is what you need at<br>
all. SGE used to be good but Oracle have not looked after it well.<br>
<br>
My guess would be that Slurm is the best answer for you. The latest<br>
version of QIIME recommends it, which is a good sign, and I'm told that<br>
set-up for a small cluster is "very simple". You might well have issues<br>
with running a cluster of Bio-Linux 7 and 8 machines, though, because<br>
the packaged versions of Slurm and of the bioinformatics software will<br>
be different on the different nodes. I'd strongly recommend upgrading<br>
everything to the same version.<br>
<br>
Also, you really should set up a fast shared NFS drive that all the<br>
machines can see. Running a cluster without a shared filesystem is<br>
possible but for most bioinformatics tasks it's highly impractical.<br>
<br>
Cheers,<br>
<br>
TIM<br>
<br>
<br>
<br>
<br>
On Thu, 2015-02-05 at 07:16 +0000, Xavier Mart?nez Serrano wrote:<br>
> Hi,<br>
><br>
> We have 4 computers with ~20CPU each in a hospital research group and<br>
> we would like to set a cluster with them. Which is the best suitable<br>
> job scheduler for us if we are running Biolinux7 in three of them and<br>
> Biolinux8 in the other?<br>
><br>
> We have been looking at common job schedulers like: Slurm, SGE,<br>
> Condor, Torque, ... but we wonder which best suits for our small<br>
> resources, to make it as easy as possible.<br>
><br>
> What can you recommend us?<br>
><br>
> Many thanks in advance,<br>
> Xavi<br>
><br>
<br>
--<br>
Tim Booth <<a href="mailto:tbooth@ceh.ac.uk">tbooth@ceh.ac.uk</a>><br>
NERC Environmental Bioinformatics Centre<br>
<br>
Centre for Ecology and Hydrology<br>
Maclean Bldg, Benson Lane<br>
Crowmarsh Gifford<br>
Wallingford, England<br>
OX10 8BB<br>
<br>
<a href="http://environmentalomics.org/bio-linux" target="_blank">http://environmentalomics.org/bio-linux</a><br>
<a href="tel:%2B44%201491%2069%202297" value="+441491692297">+44 1491 69 2297</a><br>
<br>
<br>
<br>
------------------------------<br>
<br>
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<br>
End of Bio-Linux Digest, Vol 77, Issue 2<br>
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</blockquote></div><br></div>