From tony.travis at minke-informatics.co.uk  Thu Apr 23 06:22:08 2015
From: tony.travis at minke-informatics.co.uk (Tony Travis)
Date: Thu, 23 Apr 2015 11:22:08 +0100
Subject: [Bio-linux-dev] x2go problems
Message-ID: <5538C7D0.2030903@minke-informatics.co.uk>

Hi, Tim.

I've recently had problems connecting to my Bio-Linux workstation
"wildcat" via an SSH proxy using "x2goclient". The problem is not
confined to "wildcat". Attempting to connect to other Bio-Linux
workstations via the same SSH proxy yield the same error:

> kex error : no match for method server host key algo: server [ssh-rsa,ssh-dss], client [ecdsa-sha2-nistp256]

Direct connections (i.e. not using a proxy) all still work fine and I
can "ssh" through the proxy to "wildcat" without any problems.

I was using the latest PPA version of "x2goclient", but I downgraded it
to the current Ubuntu 'stable' version in case that was the problem:

> ajt at beluga:~$ apt-cache policy x2goclient
> x2goclient:
>   Installed: 4.0.1.1-1ubuntu2
>   Candidate: 4.0.1.1-1ubuntu2
>   Version table:
>  *** 4.0.1.1-1ubuntu2 0
>         500 http://gb.archive.ubuntu.com/ubuntu/ trusty-updates/universe amd64 Packages
>         100 /var/lib/dpkg/status
>      4.0.1.1-1ubuntu1 0
>         500 http://gb.archive.ubuntu.com/ubuntu/ trusty/universe amd64 Packages

It wasn't...

Any ideas?

Thanks,

  Tony.

-- 
Minke Informatics Limited, Registered in Scotland - Company No. SC419028
Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
tel. +44(0)19755 63548                    http://minke-informatics.co.uk
mob. +44(0)7985 078324        mailto:tony.travis at minke-informatics.co.uk


From tbooth at ceh.ac.uk  Thu Apr 23 07:07:57 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 23 Apr 2015 12:07:57 +0100
Subject: [Bio-linux-dev] x2go problems
In-Reply-To: <5538C7D0.2030903@minke-informatics.co.uk>
References: <5538C7D0.2030903@minke-informatics.co.uk>
Message-ID: <1429787277.29817.32.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Tony,

It would help to know where this message is coming from.  Something
wants an ECDSA host key and something doesn't have one.  However, either
of these two somethings could be the client or the server or the proxy.
Can you please look and see what the wildcat log says (sshd logs to
auth.log)?

First thing is, please turn off file sharing in the x2goclient.  In
fact, to be sure, turn off print sharing and sound sharing too.

Also, on wildcat, see if there is an ssh_host_ecdsa_key in /etc/ssh/.
If not, run "sudo ssh-keygen -A" to generate it.  If you have any
control of the proxy then do the same on the proxy host.

Where does that get you?

Cheers,

TIM

On Thu, 2015-04-23 at 11:22 +0100, Tony Travis wrote:
> Hi, Tim.
> 
> I've recently had problems connecting to my Bio-Linux workstation
> "wildcat" via an SSH proxy using "x2goclient". The problem is not
> confined to "wildcat". Attempting to connect to other Bio-Linux
> workstations via the same SSH proxy yield the same error:
> 
> > kex error : no match for method server host key algo: server [ssh-rsa,ssh-dss], client [ecdsa-sha2-nistp256]
> 
> Direct connections (i.e. not using a proxy) all still work fine and I
> can "ssh" through the proxy to "wildcat" without any problems.
> 
> I was using the latest PPA version of "x2goclient", but I downgraded it
> to the current Ubuntu 'stable' version in case that was the problem:
> 
> > ajt at beluga:~$ apt-cache policy x2goclient
> > x2goclient:
> >   Installed: 4.0.1.1-1ubuntu2
> >   Candidate: 4.0.1.1-1ubuntu2
> >   Version table:
> >  *** 4.0.1.1-1ubuntu2 0
> >         500 http://gb.archive.ubuntu.com/ubuntu/ trusty-updates/universe amd64 Packages
> >         100 /var/lib/dpkg/status
> >      4.0.1.1-1ubuntu1 0
> >         500 http://gb.archive.ubuntu.com/ubuntu/ trusty/universe amd64 Packages
> 
> It wasn't...
> 
> Any ideas?
> 
> Thanks,
> 
>   Tony.
> 

-- 
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://environmentalomics.org/bio-linux
+44 1491 69 2297



From tony.travis at abdn.ac.uk  Thu Apr 23 07:42:26 2015
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 23 Apr 2015 12:42:26 +0100
Subject: [Bio-linux-dev] x2go problems
In-Reply-To: <1429787277.29817.32.camel@wllt1771.nerc-wallingford.ac.uk>
References: <5538C7D0.2030903@minke-informatics.co.uk>
 <1429787277.29817.32.camel@wllt1771.nerc-wallingford.ac.uk>
Message-ID: <5538DAA2.7060305@abdn.ac.uk>

On 23/04/15 12:07, Tim Booth wrote:
> Hi Tony,
>
> It would help to know where this message is coming from.  Something
> wants an ECDSA host key and something doesn't have one.  However, either
> of these two somethings could be the client or the server or the proxy.
> Can you please look and see what the wildcat log says (sshd logs to
> auth.log)?

Hi, Tim.

It came from my "x2goclient" session admin window (screenshot attached).

Looks like the proxy doesn't have an ECDSA key:

> proxy% ls -rtl /etc/ssh
> total 204
> -rw-r--r--   1 root     sys          861 May 24  2005 ssh_config
> -rw-r--r--   1 root     root         231 May 24  2005 ssh_host_rsa_key.pub
> -rw-------   1 root     root         887 May 24  2005 ssh_host_rsa_key
> -rw-r--r--   1 root     root         611 May 24  2005 ssh_host_dsa_key.pub
> -rw-------   1 root     root         668 May 24  2005 ssh_host_dsa_key
> -rw-r--r--   1 root     sys         5108 May 15  2009 sshd_config.20090807
> -rw-r--r--   1 root     sys         5108 May 15  2009 sshd_config
> -rw-r--r--   1 root     sys        88308 May 15  2009 moduli

However, mt laptop "beluga" does:

> ajt at beluga:~$ ls -l /etc/ssh
> total 296
> -rw-r--r-- 1 root root 242091 May 12  2014 moduli
> -rw-r--r-- 1 root root   1690 May 12  2014 ssh_config
> -rw-r--r-- 1 root root   2489 Jun 28  2014 sshd_config
> -rw-r--r-- 1 root root   2489 Jun  5  2013 sshd_config.orig
> -rw------- 1 root root    668 Jun  5  2013 ssh_host_dsa_key
> -rw-r--r-- 1 root root    601 Jun  5  2013 ssh_host_dsa_key.pub
> -rw------- 1 root root    227 Jun  5  2013 ssh_host_ecdsa_key
> -rw-r--r-- 1 root root    173 Jun  5  2013 ssh_host_ecdsa_key.pub
> -rw------- 1 root root    399 Apr 22 23:32 ssh_host_ed25519_key
> -rw-r--r-- 1 root root     93 Apr 22 23:32 ssh_host_ed25519_key.pub
> -rw------- 1 root root    976 Apr 22 23:32 ssh_host_key
> -rw-r--r-- 1 root root    641 Apr 22 23:32 ssh_host_key.pub
> -rw------- 1 root root   1675 Jun  5  2013 ssh_host_rsa_key
> -rw-r--r-- 1 root root    393 Jun  5  2013 ssh_host_rsa_key.pub
> -rw-r--r-- 1 root root    338 Jun 28  2014 ssh_import_id

> First thing is, please turn off file sharing in the x2goclient.  In
> fact, to be sure, turn off print sharing and sound sharing too.

Already had print sharing and sound sharing off - Disabling file sharing
just now makes no difference...

> Also, on wildcat, see if there is an ssh_host_ecdsa_key in /etc/ssh/.
> If not, run "sudo ssh-keygen -A" to generate it.  If you have any
> control of the proxy then do the same on the proxy host.

Already did that ;-)

> Where does that get you?

Not sure - Might be my laptop, because connecting via the same SSH proxy
works from "wildcat" to our local HPC cluster.

Thanks for your advice,

  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.
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From tony.travis at abdn.ac.uk  Thu Apr 23 10:33:25 2015
From: tony.travis at abdn.ac.uk (Tony Travis)
Date: Thu, 23 Apr 2015 15:33:25 +0100
Subject: [Bio-linux-dev] iPlant Atmosphere
Message-ID: <553902B5.10804@abdn.ac.uk>

Hi, Tim.

I've created a Bio-Linux 8 instance on iPlant Atmosphere:

  https://atmo.iplantcollaborative.org

  ID396a5744-87c2-4d3f-ad40-75134482f5ee

I worked around a problem of insufficient space on their default 10GB VM
system volume by mounting /usr on a 20GB partition of an attached volume
instead (I've asked them about getting a 20GB system volume):

> # login to instance
> ajt at beluga:~$ ssh ajtravis at 128.196.64.133
>
> # list available block devices
> ajtravis at vm64-133:~$ lsblk
> NAME   MAJ:MIN RM   SIZE RO TYPE MOUNTPOINT
> vda    253:0    0   9.4G  0 disk /
> vdb    253:16   0    60G  0 disk
> vdc    253:32   0   120G  0 disk
>
> # partition attached volume /dev/vdc
> parted /dev/vdc
> unit MiB
> mklabel msdos
> mkpart primary 1 20GB
> mkpart primary 20GB -0
>
> lsblk
> NAME   MAJ:MIN RM   SIZE RO TYPE MOUNTPOINT
> vda    253:0    0   9.4G  0 disk /
> vdb    253:16   0    60G  0 disk
> vdc    253:32   0   120G  0 disk
> ??vdc1 253:33   0  18.6G  0 part /usr
> ??vdc2 253:34   0 101.4G  0 part
>
>
> # create filesystems
> mkfs -t ext4 /dev/vdc1
> mkfs -t ext4 /dev/vdc2
>
> # move /usr onto attached volume
> mount /dev/vdc1 /mnt
> rsync -axHP /usr/ /mnt/
> mv -i /usr /usr.old
> mkdir /usr
> mount /dev/vdc1 /usr
>
> # update /etc/fstab
> vim /etc/fstab
> ...
> /dev/sda1       /             ext3     defaults       0 0
> /dev/vdc1     /usr          ext4     defaults       0 0
> ...
>
> # reboot to make sure /usr on attached volume is available at boot
> reboot -f
>
> # login again and do Bio-Linux 8 upgrade
> wget -q http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh
>

This is the disk usage after installation:

> ajtravis at vm64-133:~$ df -hT -t ext3 -t ext4
> Filesystem     Type  Size  Used Avail Use% Mounted on
> /dev/vda       ext3  9.3G  3.8G  5.1G  43% /
> /dev/vdc1      ext4   19G  8.9G  8.6G  52% /usr

I can access my Bio-Linux 8 instance via "x2go", which is my preferred
method, but I can't get their web-browser RealVNC client to connect: It
complains that their licence has expired ;-)

I going to use this Bio-Linux 8 instance to try out iPlant Atmosphere
with a view to maybe using it for teaching a Bio-Linux course at UoA.

Do you know anyone else using iPlant Atmosphere (based on OpenStack)?

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 tbooth at ceh.ac.uk  Thu Apr 23 11:09:36 2015
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Thu, 23 Apr 2015 16:09:36 +0100
Subject: [Bio-linux-dev] iPlant Atmosphere
In-Reply-To: <553902B5.10804@abdn.ac.uk>
References: <553902B5.10804@abdn.ac.uk>
Message-ID: <1429801776.29817.51.camel@wllt1771.nerc-wallingford.ac.uk>

Hi Tony,

Thanks for the info.  I'd certainly hope that there was no problem
running upgrade8.sh on any existing 14.04 system (VM or otherwise) but
it's nice to have confirmation it works in iPlant Atmosphere.

With our system that runs on VCloud Director (VMWare ESX) I'm able to
have a Bio-Linux base image where you can dynamically change the disk
size on deployment and the root partition ends up being that size, but
it took a good bit of hacking to achieve that.  Unless you start with
everything on LVM then shunting /usr, /var and /home on to larger
partitions is inevitably what you end up doing.

> Do you know anyone else using iPlant Atmosphere (based on OpenStack)?

Nope.

Maybe try the cloudbiolinux list?

Cheers,

TIM

On Thu, 2015-04-23 at 15:33 +0100, Tony Travis wrote:
> Hi, Tim.
> 
> I've created a Bio-Linux 8 instance on iPlant Atmosphere:
> 
>   https://atmo.iplantcollaborative.org
> 
>   ID396a5744-87c2-4d3f-ad40-75134482f5ee
> 
> I worked around a problem of insufficient space on their default 10GB VM
> system volume by mounting /usr on a 20GB partition of an attached volume
> instead (I've asked them about getting a 20GB system volume):
> 
> > # login to instance
> > ajt at beluga:~$ ssh ajtravis at 128.196.64.133
> >
> > # list available block devices
> > ajtravis at vm64-133:~$ lsblk
> > NAME   MAJ:MIN RM   SIZE RO TYPE MOUNTPOINT
> > vda    253:0    0   9.4G  0 disk /
> > vdb    253:16   0    60G  0 disk
> > vdc    253:32   0   120G  0 disk
> >
> > # partition attached volume /dev/vdc
> > parted /dev/vdc
> > unit MiB
> > mklabel msdos
> > mkpart primary 1 20GB
> > mkpart primary 20GB -0
> >
> > lsblk
> > NAME   MAJ:MIN RM   SIZE RO TYPE MOUNTPOINT
> > vda    253:0    0   9.4G  0 disk /
> > vdb    253:16   0    60G  0 disk
> > vdc    253:32   0   120G  0 disk
> > ??vdc1 253:33   0  18.6G  0 part /usr
> > ??vdc2 253:34   0 101.4G  0 part
> >
> >
> > # create filesystems
> > mkfs -t ext4 /dev/vdc1
> > mkfs -t ext4 /dev/vdc2
> >
> > # move /usr onto attached volume
> > mount /dev/vdc1 /mnt
> > rsync -axHP /usr/ /mnt/
> > mv -i /usr /usr.old
> > mkdir /usr
> > mount /dev/vdc1 /usr
> >
> > # update /etc/fstab
> > vim /etc/fstab
> > ...
> > /dev/sda1       /             ext3     defaults       0 0
> > /dev/vdc1     /usr          ext4     defaults       0 0
> > ...
> >
> > # reboot to make sure /usr on attached volume is available at boot
> > reboot -f
> >
> > # login again and do Bio-Linux 8 upgrade
> > wget -q http://nebc.nerc.ac.uk/downloads/bl8_only/upgrade8.sh
> >
> 
> This is the disk usage after installation:
> 
> > ajtravis at vm64-133:~$ df -hT -t ext3 -t ext4
> > Filesystem     Type  Size  Used Avail Use% Mounted on
> > /dev/vda       ext3  9.3G  3.8G  5.1G  43% /
> > /dev/vdc1      ext4   19G  8.9G  8.6G  52% /usr
> 
> I can access my Bio-Linux 8 instance via "x2go", which is my preferred
> method, but I can't get their web-browser RealVNC client to connect: It
> complains that their licence has expired ;-)
> 
> I going to use this Bio-Linux 8 instance to try out iPlant Atmosphere
> with a view to maybe using it for teaching a Bio-Linux course at UoA.
> 
> Do you know anyone else using iPlant Atmosphere (based on OpenStack)?
> 
> 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-dev mailing list
> Bio-Linux-dev at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux-dev

-- 
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://environmentalomics.org/bio-linux
+44 1491 69 2297