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Michael Still: The linux.conf.au 2016 Call For Proposals is open!

Mon, 2015-06-01 16:29
The OpenStack community has been well represented at linux.conf.au over the last few years, which I think is reflective of both the growing level of interest in OpenStack in the general Linux community, as well as the fact that OpenStack is one of the largest Python projects around these days. linux.conf.au is one of the region's biggest Open Source conferences, and has a solid reputation for deep technical content.



Its time to make it all happen again, with the linux.conf.au 2016 Call For Proposals opening today! I'm especially keen to encourage talk proposals which are somehow more than introductions to various components of OpenStack. Its time to talk detail about how people's networking deployments work, what container solutions we're using, and how we're deploying OpenStack in the real world to do seriously cool stuff.



The conference is in the first week of February in Geelong, Australia. I'd be happy to chat with anyone who has questions about the CFP process.



Tags for this post: openstack conference linux.conf.au lca2016

Related posts: LCA 2007 Video: CFQ IO; LCA 2006: CFP closes today; I just noticed...; LCA2006 -- CFP opens soon!; I just noticed...; Updated: linux.conf.au 2007 MythTV tutorial homework



Comment

Rusty Russell: Block size: rate of internet speed growth since 2008?

Mon, 2015-06-01 11:29

I’ve been trying not to follow the Great Blocksize Debate raging on reddit.  However, the lack of any concrete numbers has kind of irked me, so let me add one for now.

If we assume bandwidth is the main problem with running nodes, let’s look at average connection growth rates since 2008.  Google lead me to NetMetrics (who seem to charge), and Akamai’s State Of The Internet (who don’t).  So I used the latter, of course:

Akamai’s Average Connection Speed Chart Q4/07 to Q4/14

I tried to pick a range of countries, and here are the results:

Country % Growth Over 7 years Per Annum Australia 348 19.5% Brazil 349 19.5% China 481 25.2% Philippines 258 14.5% UK 333 18.8% US 304 17.2%

 

Countries which had best bandwidth grew about 17% a year, so I think that’s the best model for future growth patterns (China is now where the US was 7 years ago, for example).

If bandwidth is the main centralization concern, you’ll want block growth below 15%. That implies we could jump the cap to 3MB next year, and 15% thereafter. Or if you’re less conservative, 3.5MB next year, and 17% there after.

Sridhar Dhanapalan: Twitter posts: 2015-05-25 to 2015-05-31

Mon, 2015-06-01 00:28

linux.conf.au News: Dates confirmed for #lca2016

Sun, 2015-05-31 22:29
We're thrilled to announce that dates for linux.conf.au 2016 - LCA By the Bay have been confirmed as 1st-5th February 2016 at the wonderful Deakin University Waterfront campus in vibrant Geelong.

Michael Still: Square Rock and Mount Franklin

Thu, 2015-05-28 17:28
I'm not really sure why it took me so long to write this set of walks up -- I think I just got lost in preparations for the most recent OpenStack summit and simply forgot. That said, here they are...



Tony, Steven and I mounted an expedition to Mount Franklin, which is one of the trigs I hadn't been to yet. Its right on the ACT border with NSW, and despite not being a super long walk its verging of inaccessible in winter (think several feet of snow). So, we decided to get it done while we could.



             



Interactive map for this route.



We also tacked on a trip to Square Rock based on the strong recommendation of a good friend. Square Rock has amazing views, highly recommended.



           



Interactive map for this route.



Tags for this post: blog pictures 20150426-square_rock_franklin photo canberra bushwalk trig_point

Related posts: Goodwin trig; Big Monks; Narrabundah trig and 16 geocaches; Cooleman and Arawang Trigs; One Tree and Painter; A walk around Mount Stranger



Comment

Binh Nguyen: Las Vegas Style Food Recipes

Thu, 2015-05-28 04:54
We interrupt our regular blog posts with a word from our sponsor... LOL



Seriously tough, times are tough in Las Vegas so instead of resorting to standard marketing techniques they've been trying to convince food bloggers (including me) to do their work for them... Just look at the condition of the place! Why would I ever want to go there?



http://www.vegas.com/

http://lasvegasrestaurants.com/best-restaurants/

http://www.lasvegas.com/restaurants/



Anyhow, recently someone from Vegas.com (a company that specialises in promoting hotels, restaurants, locations, and other events in Las Vegas) contacted me and asked me to do a take on some of the dishes available in Las Vegas (A copy of the menu is included, https://sites.google.com/site/dtbnguyen/Vegas_EatDrink_v03.pdf)...



More precisely, dishes from the Aria, Caesars Palace, Bellagio, and The Pallazo. I'm going to take a stab at on a take of a few of these dishes in a way that is inexpensive, quick, and hopefully tasty.



http://www.aria.com/

https://www.caesars.com/caesars-palace

http://www.bellagio.com/

http://www.palazzo.com/



The point of these is to also make them more accessible by substituting ingredients as well (A lot of these ingredients quite simply aren't easily available in other parts of the world and to be honest it's hard to be impressed by something you know little about.).



The following three desserts are designed to be eaten like sundaes.



- ice-cream (vanilla, coffee, or rum-raisan will work best for this)

- crushed peanuts or crushed roasted almonds

- chopped up chocolate bar (Snickers, Picnic, or anything which contains nougat/nuts in it's core. Tip - chop it up in a way that the temperature of the ice cream is unlikely to cause it to freeze hard. Texture/perception of the dish can be changed quite a lot by this)(optional)

- strawberries (or another berry) which have been sliced and left in the fridge in a ice/sugar syrup mix (half an hour is enough. We're just trying to get rid of the extreme tartness of many fresh berries)

- a drizzle of caramel/chocolate/coffee sauce

- cocoa/coffee powder (optional)

Scoop ice cream into bowl or cup. Drizzle other ingredients on top.



- ice-cream (vanilla, coffee, or rum-raisan will work best for this)

- raisins which have been drenched in rum overnight

- crushed peanuts or crushed roasted almonds

- drizzle of caramel/chocolate/coffee sauce

- cocoa/coffee powder (optional)

Scoop ice cream into bowl or cup. Drizzle other ingredients on top.



http://www.lifestylefood.com.au/recipes/15383/chocolate-marzipan-cherries

http://www.daringgourmet.com/2014/06/23/how-to-make-marzipan-almond-paste/

http://en.wikipedia.org/wiki/Marzipan

http://www.taste.com.au/recipes/18597/basic+truffles



- ice-cream (vanilla will work best for this)

- some form of cake (can be made or purchased. My preference is towards something darker such as chocolate or coffee flavour. If cooking please cook it so that it is slightly overcooked as it will be mixed with the ice cream. This will stop it from going soggy too quickly and add a bit of texture to the dish).

- some form of alcohol/liquor (we're targetting aroma here. Use whatever you have here but I think rum, cognac, or something else suitably sweet would do well)

Scoop ice cream into bowl or cup. Break up the cake and drop it around in chunks around the ice cream. Drizzle alcohol/liquor around and over the top.



The following is a dessert which is meant to be eaten/drunk like an 'affogato'.

http://en.wikipedia.org/wiki/Affogato

- ice-cream (vanilla will work best for this)

- crushed macaroon biscuits (can be made or purchased. My preference is towards chocolate or coffee flavours. Texture is to be slightly crusty with a chewy interior. Don't bother making the cream if you don't want to)

https://www.howtocookthat.net/public_html/easy-macaron-macaroon-recipe/

http://amazingalmonds.com.au/2012/11/01/almond-macaroons/

- a side drunk of coffee, cappucino, late, Milo (chocolate malt) (I'd probably go for a powdered cappucino/late drink which only requires boiling water to be added to get this done quick and tasty)

- cocoa/coffee powder (optional)

Scoop ice cream into bowl or cup. Drizzle other ingredients on top.



The following is obviously is my take on a deluxe steak sandwich.

- sandwich bread slices

- steak

- onions

- lettuce

- tomatoes

- bacon

- cheese

- egg

- tomato sauce

- balsamic vinegar (optional)

- mayonnaise (optional)

- mustard (optional) 

Toast or grill sandwich slices. Add cheese as first layer. Fry an egg and add this as the next layer. Fry some bacon and add this as the next layer. Fry off steak slices with some onion, garlic, salt, sugar, pepper, and maybe a tiny drop of balsamic vinegar (I would probably caramelise this slightly in a pan to remove some of the tartness before adding it to the sandwich or not add it at all) and add this as the next layer. Slice vegetables and add this as the next layer. Use tomato sauce (mayonnaise and/or mustard are optional depending on your taste) on the top layer as it will stop it from drenching the sandwich prior to your having completing preparing it. Season to taste.



The following is more savoury and is obviously meant to be a main meal.

- roasted chicken (can be made or purchased)

- pasta in a white sauce (the 'Bacon and Mushroom Carbonara with Pasta' recipe from, http://dtbnguyen.blogspot.com.au/2015/02/simple-pasta-recipes.html would work well here)

- asparagus

- cheese

- potatoes (use the recipes at, http://dtbnguyen.blogspot.com.au/2015/03/fried-fish-with-butter-fried-potatoes.html or http://dtbnguyen.blogspot.com.au/2012/02/butter-fried-potatoes-with-bacon-bits.html and remove relevant ingredients (bacon, cream, and cheese for me) to suit the dish)

Cook pasta. Fry asparagus with garlic, butter, oil or else blanch it. Put it in a microwave for a few seconds with a slice of cheese on top to give it a bit of extra flavour (optional). Serve with roasted chicken and fried potatoes. Season dish to taste. You may need to serve this dish with a salad as it can be very rich or fatty depending on your interpretation.



http://www.taste.com.au/recipes/8071/basic+roast+chicken

http://www.simplyrecipes.com/recipes/kellers_roast_chicken/

http://www.simplyrecipes.com/recipes/classic_baked_chicken/



http://en.wikipedia.org/wiki/Arroz_con_pollo

http://en.wikipedia.org/wiki/Refried_beans

http://www.foodterms.com/encyclopedia/broccoli-rabe/index.html



http://en.wikipedia.org/wiki/Vin_jaune

http://en.wikipedia.org/wiki/Fleur-de-lis

http://en.wikipedia.org/wiki/Tomatillo

Brendan Scott: brendanscott

Wed, 2015-05-27 17:30

Youtube has done wonders for lots of people, but frankly, my reaction to the vast majority of videos is that they are largely or wholly content free.  Those cases where a visual demonstration actually assists are exceedingly slim (some digital illustration videos for example, but even those don’t necessarily show you what you want). Watching videos of ostensibly informative topics is an exercise in entertainment and almost always a waste of my time.  If you have a transcript at least you can jump around to see if it’s got the info you’re looking for. With videos even if you jump around, you’re still pulling down info at the rate they speak (ie slowly). Next time you watch a documentary count the average number of words spoken in a minute. It’s ridiculously low.

It’s something of a farce that for my CLE requirements I can listen to some 5 year out “senior associate” um and arr through some talk at a firm or do some facile online tutorial (are there other kinds?) and get an hour’s credit, but if I read an entire book by an expert in the area or research the cases myself I get exactly 0 points.



James Purser: So Bill is going to bring a Bill

Tue, 2015-05-26 21:30

So Bill Shorten has announced that he and the Deputy Leader of the Opposition, Tanya Plibersec will be putting a bill to the house to allow Same Sex Marriage.

Honestly I'm torn.

The cynical part of me thinks the whole thing is an exercise in futility. Unless the Coalition allows a free vote amongst its members the bill is doomed to die in the House of Reps. If I was going to be really cynical I'd think this was an attempt to take the wind out of the sails of the greens who were proposing a similar bill to start in the Senate.

On the other hand, this is probably the first sign I've seen of Shorten actually stepping forward on an issue that hasn't been focus grouped to death. SSM doesn't have universal support within the Labor party (hi Joe deBruyn you reactionary old fart), and by putting his name directly on the bill Shorten is showing some leadership at last.

If you support Same Sex marriage, or as it's known in other parts of the world, Marriage, I'd urge you to let your local MP know how you feel. Do it politely, do it succinctly but make sure you do it. 

If you want to find out if your local MP or Senator supports or opposes SSM this site is a great resource

Blog Catagories: same sex marriage

Lev Lafayette: MrBayes HPC Installation

Mon, 2015-05-25 12:30

Mr. Bayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models.

Download, extract. Note that the developers have produced a tarbomb which will require a separate directory created before download. This has been raised as a bug.

Note that more recent versions of MrBayes make much better use of autoconfiguration tools.



cd /usr/local/src/MRBAYES

mkdir mrbayes-3.2.5

cd mrbayes-3.2.5

read more

Sridhar Dhanapalan: Twitter posts: 2015-05-18 to 2015-05-24

Mon, 2015-05-25 00:27

Gary Pendergast: How I Would Solve Plugin Dependencies

Sun, 2015-05-24 14:26

lol, I wouldn’t1.

1. If I absolutely had to, I wouldn’t do it the same as Ryan.

WordPress isn’t (and will never be) Linux

ZYpp is the dependency solver used by OpenSUSE (and its PHP port in Composer), it was born of the need to solve complex dependency trees. The good news is, WordPress doesn’t have the same problem, and we shouldn’t create that problem for ourselves.

One of the most common-yet-complex issues is determining how to handle different version requirements by different packages. If My Amazing Plugin requires WP-API 1.9, but Your Wonderful Plugin requires WP-API 2.0, we have a problem. There are two ways to solve it – Windows solves it by installing multiple versions of the dependency, and loading the correct version for each package. This isn’t a particularly viable option in PHP, because trying to load two different versions of the same code in the same process is not my idea of a fun time.

The second option, which ZYpp solves, is to try and find a mutually compatible version of the dependency that each plugin can use. The biggest problem with this method is that it can’t always find a solution. If there’s no compatible way of installing the libraries, it has to throw back to the user to make the decision. This isn’t a viable option, as 99.999*% worth of users wouldn’t be able to tell the difference between WP-API versions 1.9 and 2.0, and nor should they.

But there’s a third option.

Technical Debt as a Service

Code libraries are, by their nature, developer facing. A user never really needs to know that they exist, in the same way that they don’t need to know about WP_Query. In WordPress Core, we strive for (and often achieve) 100% backwards compatibility between major versions. If we were going to implement plugin dependencies, I would make it a requirement that the code libraries shoulder the same burden: don’t make a user choose between upgrades, just always keep the code backwards compatible. If you need to make architectural changes, include a backwards compatible shim to keep things working nicely.

This intentionally moves the burden of upgrading to the developer, rather than the end user.

What Version?

If we’re going to require library developers to maintain backwards compatibility, we can do away with version requirements (and thus, removing the need for a dependency solver). If a plugin needs a library, it can just specify the library slug.

Better Living Through Auto Updates

If we were to implement plugin dependencies, I think it’d be a great place to introduce auto updates being enable by default. There’s no existing architecture for us to take into account, so we can have this use the current WordPress best practices. On top of that, it’s a step towards enabling auto updates for all Core releases, and it encourages developers to create backwards compatible libraries, because their library will almost certainly be updated before a plugin using it is.

Let’s Wrap This Up

I’m still not convinced plugin dependencies is a good thing to put in Core – it introduces significant complexities to plugin updates, as well as adding another dependency on WordPress.org to Core. But it’s definitely a conversation worth having.

Francois Marier: Usual Debian Server Setup

Sat, 2015-05-23 20:16

I manage a few servers for myself, friends and family as well as for the Libravatar project. Here is how I customize recent releases of Debian on those servers.

Hardware tests apt-get install memtest86+ smartmontools e2fsprogs

Prior to spending any time configuring a new physical server, I like to ensure that the hardware is fine.

To check memory, I boot into memtest86+ from the grub menu and let it run overnight.

Then I check the hard drives using:

smartctl -t long /dev/sdX badblocks -swo badblocks.out /dev/sdX Configuration apt-get install etckeepr git sudo vim

To keep track of the configuration changes I make in /etc/, I use etckeeper to keep that directory in a git repository and make the following changes to the default /etc/etckeeper/etckeeper.conf:

  • turn off daily auto-commits
  • turn off auto-commits before package installs

To get more control over the various packages I install, I change the default debconf level to medium:

dpkg-reconfigure debconf

Since I use vim for all of my configuration file editing, I make it the default editor:

update-alternatives --config editor ssh apt-get install openssh-server mosh fail2ban

Since most of my servers are set to UTC time, I like to use my local timezone when sshing into them. Looking at file timestamps is much less confusing that way.

I also ensure that the locale I use is available on the server by adding it the list of generated locales:

dpkg-reconfigure locales

Other than that, I harden the ssh configuration and end up with the following settings in /etc/ssh/sshd_config (jessie):

HostKey /etc/ssh/ssh_host_ed25519_key HostKey /etc/ssh/ssh_host_rsa_key HostKey /etc/ssh/ssh_host_ecdsa_key KexAlgorithms curve25519-sha256@libssh.org,ecdh-sha2-nistp521,ecdh-sha2-nistp384,ecdh-sha2-nistp256,diffie-hellman-group-exchange-sha256 Ciphers chacha20-poly1305@openssh.com,aes256-ctr,aes192-ctr,aes128-ctr MACs hmac-sha2-512-etm@openssh.com,hmac-sha2-256-etm@openssh.com,umac-128-etm@openssh.com,hmac-sha2-512,hmac-sha2-256,umac-128@openssh.com UsePrivilegeSeparation sandbox AuthenticationMethods publickey PasswordAuthentication no PermitRootLogin no AcceptEnv LANG LC_* TZ LogLevel VERBOSE AllowGroups sshuser

or the following for wheezy servers:

HostKey /etc/ssh/ssh_host_rsa_key HostKey /etc/ssh/ssh_host_ecdsa_key KexAlgorithms ecdh-sha2-nistp521,ecdh-sha2-nistp384,ecdh-sha2-nistp256,diffie-hellman-group-exchange-sha256 Ciphers aes256-ctr,aes192-ctr,aes128-ctr MACs hmac-sha2-512,hmac-sha2-256

On those servers where I need duplicity/paramiko to work, I also add the following:

KexAlgorithms ...,diffie-hellman-group-exchange-sha1 MACs ...,hmac-sha1

Then I remove the "Accepted" filter in /etc/logcheck/ignore.d.server/ssh (first line) to get a notification whenever anybody successfully logs into my server.

I also create a new group and add the users that need ssh access to it:

addgroup sshuser adduser francois sshuser

and add a timeout for root sessions by putting this in /root/.bash_profile:

TMOUT=600 Security checks apt-get install logcheck logcheck-database fcheck tiger debsums corekeeper apt-get remove john john-data rpcbind tripwire

Logcheck is the main tool I use to keep an eye on log files, which is why I add a few additional log files to the default list in /etc/logcheck/logcheck.logfiles:

/var/log/apache2/error.log /var/log/mail.err /var/log/mail.warn /var/log/mail.info /var/log/fail2ban.log

while ensuring that the apache logfiles are readable by logcheck:

chmod a+rx /var/log/apache2 chmod a+r /var/log/apache2/*

and fixing the log rotation configuration by adding the following to /etc/logrotate.d/apache2:

create 644 root adm

I also modify the main logcheck configuration file (/etc/logcheck/logcheck.conf):

INTRO=0 FQDN=0

Other than that, I enable daily checks in /etc/default/debsums and customize a few tiger settings in /etc/tiger/tigerrc:

Tiger_Check_RUNPROC=Y Tiger_Check_DELETED=Y Tiger_Check_APACHE=Y Tiger_FSScan_WDIR=Y Tiger_SSH_Protocol='2' Tiger_Passwd_Hashes='sha512' Tiger_Running_Procs='rsyslogd cron atd /usr/sbin/apache2 postgres' Tiger_Listening_ValidProcs='sshd|mosh-server|ntpd' General hardening apt-get install harden-clients harden-environment harden-servers apparmor apparmor-profiles apparmor-profiles-extra

While the harden packages are configuration-free, AppArmor must be manually enabled:

perl -pi -e 's,GRUB_CMDLINE_LINUX="(.*)"$,GRUB_CMDLINE_LINUX="$1 apparmor=1 security=apparmor",' /etc/default/grub update-grub Entropy and timekeeping apt-get install haveged rng-tools ntp

To keep the system clock accurate and increase the amount of entropy available to the server, I install the above packages and add the tpm_rng module to /etc/modules.

Preventing mistakes apt-get install molly-guard safe-rm sl

The above packages are all about catching mistakes (such as accidental deletions). However, in order to extend the molly-guard protection to mosh sessions, one needs to manually apply a patch.

Package updates apt-get install apticron unattended-upgrades deborphan debfoster apt-listchanges update-notifier-common aptitude popularity-contest

These tools help me keep packages up to date and remove unnecessary or obsolete packages from servers. On Rackspace servers, a small configuration change is needed to automatically update the monitoring tools.

In addition to this, I use the update-notifier-common package along with the following cronjob in /etc/cron.daily/reboot-required:

#!/bin/sh cat /var/run/reboot-required 2> /dev/null || true

to send me a notification whenever a kernel update requires a reboot to take effect.

Handy utilities apt-get install renameutils atool iotop sysstat lsof mtr-tiny

Most of these tools are configure-free, except for sysstat, which requires enabling data collection in /etc/default/sysstat to be useful.

Apache configuration apt-get install apache2-mpm-event

While configuring apache is often specific to each server and the services that will be running on it, there are a few common changes I make.

I enable these in /etc/apache2/conf.d/security:

<Directory /> AllowOverride None Order Deny,Allow Deny from all </Directory> ServerTokens Prod ServerSignature Off

and remove cgi-bin directives from /etc/apache2/sites-enabled/000-default.

I also create a new /etc/apache2/conf.d/servername which contains:

ServerName machine_hostname Mail apt-get install postfix

Configuring mail properly is tricky but the following has worked for me.

In /etc/hostname, put the bare hostname (no domain), but in /etc/mailname put the fully qualified hostname.

Change the following in /etc/postfix/main.cf:

inet_interfaces = loopback-only myhostname = (fully qualified hostname) smtp_tls_security_level = may smtp_tls_protocols = !SSLv2, !SSLv3

Set the following aliases in /etc/aliases:

  • set francois as the destination of root emails
  • set an external email address for francois
  • set root as the destination for www-data emails

before running newaliases to update the aliases database.

Create a new cronjob (/etc/cron.hourly/checkmail):

#!/bin/sh ls /var/mail

to ensure that email doesn't accumulate unmonitored on this box.

Finally, set reverse DNS for the server's IPv4 and IPv6 addresses and then test the whole setup using mail root.

Network tuning

To reduce the server's contribution to bufferbloat I change the default kernel queueing discipline (jessie or later) by putting the following in /etc/sysctl.conf:

net.core.default_qdisc=fq_codel

Lev Lafayette: General Atomic and Molecular Electronic Structure System HPC Installation

Fri, 2015-05-22 17:30

GAMESS (General Atomic and Molecular Electronic Structure System (GAMESS)) is a general ab initio quantum chemistry package. You will need to agree to the license prior to download, which will provide a link to gamess-current.tar.gz

Download and extract, load the environment variables for atlas and gcc.



cd /usr/local/src/

tar gamess-current.tar.gz

cd gamess

module load atlas/3.10.2

module load gcc/4.9.1

read more

Craige McWhirter: Craige McWhirter: How To Resolve a Volume is Busy Error on Cinder With Ceph Block Storage

Fri, 2015-05-22 15:28

When deleting a volume in OpenStack you may sometimes get an error message stating that Cinder was unable to delete the volume because the volume was busy:

2015-05-21 23:31:41.160 16911 ERROR cinder.volume.manager [req-6f77ef4d-bbff-4ff4-8a3e-4c6b264ac5ca \ 04b7cb61dd3f4f2f8f80bbd9833addbd 5903e3bda1e840d492fe79fb840acacc - - -] Cannot delete volume \ f8867d43-bc82-404e-bcf5-6d345c32269e: volume is busy

There are a number of reasons why a volume may be reported by Ceph as busy, however the most common reason in my experience has been that a Cinder client connection has not yet been closed, possibly because a client crashed.

If you were to look at the volume in Cinder, that status is usually available, the record looks in order. When you check Ceph, you'll see that the volume still exists there too.

% cinder show f8867d43-bc82-404e-bcf5-6d345c32269e | grep status | status | available | # rbd -p my.ceph.cinder.pool ls | grep f8867d43-bc82-404e-bcf5-6d345c32269e volume-f8867d43-bc82-404e-bcf5-6d345c32269e

Perhaps there's a lock on this volume. Let's check for locks and then remove them if we find one:

# rbd lock list my.ceph.cinder.pool/volume-f8867d43-bc82-404e-bcf5-6d345c32269e

If there are any locks on the volume, you can use lock remove using the id and locker from the previous command to delete the lock:

# rbd lock remove <image-name> <id> <locker>

What if there are no locks on the volume but you're still unable to delete it from either Cinder or Ceph? Let's check for snapshots:

# rbd -p my.ceph.cinder.pool snap ls volume-f8867d43-bc82-404e-bcf5-6d345c32269e SNAPID NAME SIZE 2072 snapshot-33c4309a-d5f7-4ae1-946d-66ba4f5cdce3 25600 MB

When you attempt to delete that snapshot you will get the following:

# rbd snap rm my.ceph.cinder.pool/volume-f8867d43-bc82-404e-bcf5-6d345c32269e@snapshot-33c4309a-d5f7-4ae1-946d-66ba4f5cdce3 rbd: snapshot 'snapshot-33c4309a-d5f7-4ae1-946d-66ba4f5cdce3' is protected from removal. 2015-05-22 01:21:52.504966 7f864f71c880 -1 librbd: removing snapshot from header failed: (16) Device or resource busy

This reveals that it was the snapshot that was busy and locked all along.

Now we need to unprotect the snapshot:

# rbd snap unprotect my.ceph.cinder.pool/volume-f8867d43-bc82-404e-bcf5-6d345c32269e@snapshot-33c4309a-d5f7-4ae1-946d-66ba4f5cdce3

You should now be able to delete the volume and it's snapshot via Cinder.

Enjoy :-)

Lev Lafayette: JAGS (Just Another Gibbs Sampler) Installation

Thu, 2015-05-21 16:30

JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.



cd /usr/local/src/JAGS

wget http://downloads.sourceforge.net/project/mcmc-jags/JAGS/3.x/Source/JAGS-...

tar xvf JAGS-3.4.0.tar.gz

mv JAGS-3.4.0 jags-3.4.0

cd jags-3.4.0

../config

make

make check

make install

make installcheck

The config script takes the following form



#!/bin/bash

install=$(basename $(pwd) | sed 's%-%/%')

read more

Lev Lafayette: MuTect Installation

Thu, 2015-05-21 16:30

MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.

For complete details, please see the publication in Nature Biotechnology:

Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnology (2013).doi:10.1038/nbt.2514

Download after login.

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Lev Lafayette: PROJ.4 Cartographic Projections library installation

Thu, 2015-05-21 16:30

The PROJ.4 Cartographic Projections library was originally written by Gerald Evenden then of the USGS.

Download, extract, install.



cd /usr/local/src/PROJ

wget http://download.osgeo.org/proj/proj-4.9.1.tar.gz

tar xvf proj-4.9.1.tar.gz

cd proj-4.9.1

../config

make

make check

make install

The config file is a quick executable.



#!/bin/bash

./configure --prefix=/usr/local/$(basename $(pwd) | sed 's#-#/#')

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Lev Lafayette: Geospatial Data Abstraction Library Installation

Thu, 2015-05-21 16:30

GDAL (Geospatial Data Abstraction Library) is a translator library for raster and vector geospatial data formats.

Download, extract, install.



cd /usr/local/src/GDAL

wget http://download.osgeo.org/gdal/1.11.2/gdal-1.11.2.tar.gz

tar gdal-1.11.2.tar.gz

cd gdal-1.11.2

../config

make

make install

The config file is a quick executable.



#!/bin/bash

./configure --prefix=/usr/local/$(basename $(pwd) | sed 's#-#/#')

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Lev Lafayette: Rosetta Proteins with SCons (and jam and cream)

Thu, 2015-05-21 15:30

Rosetta is a library based object-oriented software suite which provides a robust system for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

You'll need a license

Download, extract, load scons, and compile.



cd /usr/local/src/ROSETTA

tar xvf rosetta_src_2015.19.57819_bundle.tgz

cd rosetta_src_2015.19.57819_bundle/main/src

module load scons

scons

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Lev Lafayette: SCons with Modules

Thu, 2015-05-21 15:30

SCons is a software construction tool (build tool, or make tool) implemented in Python, that uses Python scripts as "configuration files" for software builds.



cd /usr/local/src/SCONS

wget http://prdownloads.sourceforge.net/scons/scons-2.3.4.tar.gz

tar xvf scons-2.3.4.tar.gz

cd scons-2.3.4

python setup.py install --prefix=/usr/local/scons/2.3.4

Change to the appropriate modules directory, check for .desc and .version and .base, create a symblink to .base



cd /usr/local/Modules/modulefiles/scons

ln -s .base 2.3.4

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