docker -G and non-local groups

So we (like many other labs) store our user identity information in LDAP. I created a docker group in LDAP so that its memberships is valid across our cluster. When I tried to run a docker command, however, I got this error:

Get http:///var/run/docker.sock/v1.20/containers/json: dial unix /var/run/docker.sock: permission denied.
* Are you trying to connect to a TLS-enabled daemon without TLS?
* Is your docker daemon up and running?

Turns out that /var/run/docker.sock was owned by root:root, not root:docker as expected. Running docker in debug mode I saw this message:

DEBU[0000] Warning: could not change group /var/run/docker.sock to docker: Group docker not found 

After a big of poking around and verifying that the group did exist I came across the code in unix_socket.go. To make a longish (lines 41-83) story short, docker relies on libcontainer for its user/group lookups and these parse the /etc/group file, ignoring nsswitch.conf (and thus identity providers like LDAP).

If you use the numeric gid (docker daemon -G 555 for instance) then you get some strange messages in the log (example is from debug mode):

WARN[0000] Could not find GID 555                       
DEBU[0000] 555 group found. gid: 555

but the ownership of the docker Unix socket is set as expected.

How Galaxy resolves dependencies (or not)

There are two parts to building a link between Galaxy and command line bioinformatics tools: the tool XML that specifies a mapping between the Galaxy web user interface and the tool command line and tool dependencies that specify how to source the actual packages that implement the tool's commands. I spent a bit of time today digging into how that second set of components operates as part of my work on SANBI's local Galaxy installation.

Requirements and resolvers

In the tool XML dependencies are specified using <requirement> clauses, for example:

<requirement type="package" version="0.7.10.039ea20639">bwa</requirement>

This is taken from the bwa tool XML that I installed from the toolshed and specifies a particular version of the bwa short read aligner. Not all requirements have a version attached, however - this is from the BAM to BigWig converter, one of the datatype converters that comes with Galaxy (in the lib/galaxy/datatypes/converters directory) and is crucial to the operation of Trackster, the in-Galaxy genome browser:

<requirement type="package">bedtools</requirement>

These dependencies are fed into the dependency manager (DependecyManager in lib/galaxy/tools/deps/__init__.py) which uses various dependency resolvers to generate shell commands that make the dependency available at runtime. These shell commands are passed on to the Galaxy job that actually executes the tool (see the prepare method of JobWrapper).

The default config

Galaxy provides a configuration file, config/dependency_resolvers_conf.xml to configure how the dependency resolvers are used. There is no sample provided but this pull request shows that the default is:

<dependency_resolvers>
  <tool_shed_packages />
  <galaxy_packages />
  <galaxy_packages versionless="true" />
</dependency_resolvers>

These aren't the only available resolvers - there is a homebrew resolver and one (with big warning stickers) that uses Environment Modules - but what is shown above is the default.

A quick note: if all the resolvers fail, you'll see a message such as:

Failed to resolve dependency on 'bedtools', ignoring

in your Galaxy logs (paster.log) and, quite likely, the job depending on that requirement will fail, since the required tool is not in Galaxy's PATH.

Tool Shed Packages resolver

The tool_shed_packages resolver is designed to find packages installed from the Galaxy Toolshed. These are installed in the location specified as tool_dependency_dir in config/galaxy.ini. I'll refer to this location as base_path. Toolshed packages are installed as base_path/toolname/version/toolshed_owner/toolshed_package_name/changeset_revision so for example BLAST+ on our system is base_path/blast+/2.2.31/iuc/package_blast_plus_2_2_31/e36f75574aec at the moment. The tool_shed_packages resolver cannot handle <requirement> clauses without a version number except for when they are referring to type="set_environment", not type="package" requirements. Uhhhhh, ok I'll explain set_environment a bit later. In general, if you want to resolve your dependency through the toolshed, you need to specify a version number.

Underneath it all, the tool_shed_packages resolver looks for a file called env.sh provided as part of the packaged tool. This file contains settings that are sourced (i.e. . env.sh) into the job script Galaxy ends up executing.

Galaxy Packages resolver

The galaxy_packages resolver is oriented towards manually installed packages. Note that it is called twice - first with its default - version supporting - form and secondly with versionless="true". The software found by the galaxy_packages resolver is installed under the same base_path as for the tool_shed_packages resolver, but that's where the similarity ends. This resolver looks under base_path/toolname/version by default, so for example base_path/bedtools/2.22. If it finds a bin/ directory in the specified path it will add that to the path Galaxy uses to find binaries. If, however, it finds a file name env.sh it will emit code to source that file. This means that you can use the env.sh script any way you want to add a tool to Galaxy's path. For example, here is our env.sh for bedtools:

#!/bin/sh

if [ -z "$MODULEPATH" ] ; then
  . /etc/profile.d/module.sh
fi

module add bedtools/bedtools-2.20.1

That uses our existing Environment Modules installation to add bedtools to the PATH.

The versionless="true" incarnation of the galaxy_packages resolver works similarly, except that it looks for a symbolic link in base_path/toolname/default, e.g. base_path/bedtools/default. This needs to point to a version numbered directory containing a bin/ subdirectory or env.sh file as above. It is this support for versionless="true" that allows for the resolution of <requirement> specifications with no version.

Supporting versionless requirements

As might not be obvious from the discussion thus far, given the default Galaxy setup, the only way versionless requirements can be satisfied is with a manually installed package with a default link that is resolved with the galaxy_packages resolver. So even if you have the relevant requirement installed via a toolshed package, it will not be used to resolve a versionless requirement: you'd have to make a symlink from base_path/toolname/default to base_path/toolname/version and symlink the env.sh buried within the package's folders to that base_path/toolname/version directory. You could do that, or you could just manually add a env.sh as per the galaxy_packages schema and not install packages through the toolshed.

By the way, the set_environment type of requirement mentioned earlier is related to thing referred to when talking about tool_shed_packages is a special kind of 'package' that simply contains an env.sh script. They are expected to be installed as base_path/environment_settings/toolname/toolshed_owner/toolshed_package_name/changeset_revision and they're the only thing checked for by tool_shed_packages when trying to resolve a versionless requirement.

In Conclusion

If you're read this far, congratulations. I hope this information is useful; after all, everything could change with a wriggle of John Chilton's fingers (wink). Part of the reason that I believe Galaxy dependency resolution is so complicated is that the Galaxy community has been trying to solve the bioinformatics package management problem, something that has bedevilled the community ever since I started working in the field in the 90s.

The problem is this: bioinformatics is a small field of computing. A colleague of mine compared us to a spec of phytoplankton floating in a computing sea and I think he's right. Scientific software is often poorly engineered and most often not well packaged, and keeping up with the myriad ways of installing the software we use, keeping it up to date and having it all work together is dizzyingly hard and time consuming. And there aren't enough hands on the job. Much better resources fields are still trying to solve this problem and its clear that Galaxy is going to try and benefit from that work.

Some of the by-default-unused dependency resolvers try and leverage old (Environment Modules) and new (Homebrew) solutions for dependency management, and with luck and effort (probably more of the latter) things will get better in the future. For our personal Galaxy installation I'm going to probably be doing a bit of manual maintenance and using the galaxy_packages scheme more than packages from the toolshed. I might try and fix up the modules resolver, at least to make it work with what we've got going at SANBI. And hopefully I'll get less confused by those Failed to resolve dependency messages in the future!

How to submit a job to the SANBI computing cluster

I keep trying to finish the documentation about our computing cluster at SANBI and SGE (Sun Grid Engine)1 and how to run jobs. In the meantime, however, here's how to run a job on the cluster at SANBI.

Firstly, the structure of the cluster. Our storage, for now, is provided by a storage server and shared across the whole cluster. This means that your home directory and the /cip0 storage area is shared across the whole cluster. We still need to implement better research data management practices but you should do your work in a scratch directory and store your results in your research directory. I'm not going to talk more about that now because the system is in flux.

Secondly, the cluster has a number of compute nodes and a single submit node. The submit node is queue00.sanbi.ac.za, so log in there to submit your job. It is a smallish virtual machine, so don't run anything substantial on the submit node!

So lets's imagine that you want to run a tool like fastqc on the cluster. First, is the tool available? We use a system called environment modules to manage the available software. This allows us to install software in a central place and just add the relevant environment variables to run the tool you need. The module avail command lists available commands, so module avail 2>&1 |grep fastqc will show us that fastqc is indeed available.

Next we need a working directory (e.g. /cip0/scratch/pvh) and a script that will run the command. Here is a little script (lets imagine it is called run_fastqc.sh):

#!/bin/sh

. /etc/profile.d/module.sh

module add fastqc

if [ ! -d out ] ; then
    mkdir out
fi

fastqc -t 1 -out `pwd`/out -f fastq data.fastq

The . /etc/profile.d/module.sh ensures that the module command is available. The module add fastqc adds the path to fastqc so that it is available to our script. You can use module add outside a script if you want to examine how to run a command. It also sets a variable, FASTQC_HOME, pointing to where the command is installed, so you can ls $FASTQC_HOME to see if there is perhaps a README or other useful data in that directory.

Then fastqc needs you to create the output directory, it won't do it itself, so the script does that, creating a directory under the current directory, named out. Now you need to send the script to the cluster's scheduler:

qsub -wd $(pwd) -q all.q -N myfastqc run_fastqc.sh

This will send run_fastqc.sh to the scheduler and tell it to run it on all.q (which happens to be the default queue) with the job named myfastqc. This queue has a time limit of 8 hours, so if you need to run for longer than that you need a -q long.q. The long.q queue has no time limit but fewer CPUs available. The -wd flags sets the job's working directory, in this example the directory you are in when you submit the job.

You can check the status of your job with qstat. Job output is, by default, written into the working directory in two files, one for stderr and the other for stdout.

There's much more to say about the cluster and the use of the qsub, qstat, qacct and qhost commands, but this should be enough to get you started with your first cluster job. The rest will have to wait till I've got time to write more extensive documentation.

Footnotes

Sun Grid Engine is part of the Grid Engine family of job schedulers that has undergone complex evolution over the last years due to Sun's takeover by Oracle and the subsequent forking of the codebase. See the Grid Engine Wiki for details. Back to text

Adventures in Galaxy output collections

For the Galaxy IUC Tools and Collections codefest we (the SANBI software developers) decided to take on what we thought would be a simple job: make the bamtools_split tool output a dataset collection instead of multiple datasets. So here's the output clause of the old (multiple datasets) version of bamtools_split:

  <outputs>
    <data format="txt" name="report" label="BAMSplitter Run" hidden="true">
      <discover_datasets pattern="split_bam\.(?P&lt;designation&gt;.+)\.bam" ext="bam" visible="true"/>
    </data>
  </outputs> 

and this needed to change to:

  <outputs>
    <collection name="report" type="list" label="BAMSplitter Run">
        <discover_datasets pattern="split_bam\.(?P&lt;designation&gt;.+)\.bam" ext="bam"/>
    </collection>
  </outputs>

In other words, the <data> element just gets changed to a <collection> element and the <discover_datasets> element remains essentially the same. So we did this change and everything ran fine except: the output collection was empty. Why?

Lots of debugging followed, based on a fresh checkout of the Galaxy codebase. We discovered that the crucial function here is collect_dynamic_collections() in the galaxy.tools.parameters.output_collect module. This is called by the finish() method of the Jobclass, via the Toolclass' method of the same name.

The collect_dynamic_collections function identifies output collections in a tool's definition and then uses a collection builder to map job output files to a dataset collection type. The collection builder is a factory class defined in galaxy.dataset_collections.builder and each dataset collection type (defined in galaxy.dataset_collections.builder.types) has its own way of moving output elements into the members of a collection type.

Anyway, we traced this code all the way through to the point where it was obvious the dataset collection was being created successfully and then turned to the other Galaxy devs (John Chilton specifically) to ask for help, only to discover that the problem was gone. The dataset collection was somehow populated! It turns out that if your Galaxy tool creates an output dataset collection that has an uncertain number of members (like a list collection) then it is populated asynchronously and you need to refresh the history to see its members - this is known bug.

So that's been quite a learning curve. The final tool is on Github. The collection tag for outputs was introduced above. We haven't explored its pair mode, but check out Peter Briggs' trimmomatic tool which has an option to output as a pair type dataset collection.

In the test section of the tool configuration, you can use a dataset collection like this:

<test>
    <param name="input_bam" ftype="bam" value="bamtools-input1.bam"/>
    <param name="analysis_type_selector" value="-mapped"/>
    <output_collection name="report">
      <element name="MAPPED" file="bamtools-split-MAPPED1.bam" />
      <element name="UNMAPPED" file="bamtools-split-UNMAPPED1.bam" />
    </output_collection>
</test>

The output_collection tag essentially groups outputs together, with each element tag taking the place that of an individual output tag. Each element tag has a name that maps to one of the names identified by the discover_datasets pattern (perhaps index numbers can be used instead of names, I don't know) and can use the test attributes that output provides.

With the tests updated and some suitable sample data in place the tests pass and the tool is ready for a pull request. There was some discussion though on the semantics of this tool... for more go and read the comments on the PR.

A BLAST array job for the SANBI cluster

If you want to query a BLAST database with a large number of input query sequences, you might want to use this script. The easy way to gain speed for a BLAST search is to split the input set of query sequences (using a script such as split_fasta.py or (if the sequences don't contain linebreaks) you can use split or you can use csplit) into multiple parts and run the BLAST search as an array job. For this script, you need a working directory containing these subdirectories:

in/ - a directory containing your split queries in files named *.fasta
out/ - an empty output directory
logs/ - an empty log directory

Tune your splitting for efficiency: if your queries are too small, the time to start running will make the search inefficient. If your queries are too large, the jobs will run too long - remember that the timelimit on the default all.q is 8 hours.

Uljana and I wrote the script below to actually run the array job. If your working directory was, for example, /cip0/research/rosemary/blast and you saved this script as blastplus_array.sh and you have 20 input query files, then you could submit the script with:

qsub -wd /cip0/research/rosemary/blast -t 1-20 blastplus_array.sh

Note that each use can have at most 20 jobs running on the cluster at any one time, so your queries will run in blocks of 20 jobs at a time. The raw source code is available and easier to copy than the listing below. Also note that you probably want to customise the actual BLAST command line (at the end of the script). The one in here was designed to pick up taxonomy information from the local install of the NR database - useful for doing a metagenomic scan.

#!/bin/sh

# requirement:
# working directory with:
# in/ - files named .fasta that are query sequences
# out/ - empty directory to put outputs in
# logs/ - empty directory to put logs in 
#
# qsub with:
# qsub -t 1-2 -wd ./my-work-dir blastplus_array.sh

#$ -o logs/$JOB_NAME.o$JOB_ID.$TASK_ID
#$ -e logs/$JOB_NAME.e$JOB_ID.$TASK_ID


### -----
### define input and output directories

base_dir=`pwd`
in_dir=$base_dir/in
out_dir=$base_dir/out

cd $in_dir

### -----
### get all the file names into a file

filelist=../logs/file_list.txt
ls *.fasta > $filelist

### -----
### access the fasta files by the ${SGE_TASK_ID}

fasta=`awk "NR == ${SGE_TASK_ID} {print}" $filelist` # ${file_list[$counter]}
echo $fasta

### -----
### add the blast module and run blast

. /etc/profile.d/module.sh
module add blastplus/default

blastn -query $in_dir/$fasta -db nt -out $out_dir/$fasta.txt -outfmt "6 std slen qlen qcovs qcovhsp staxids sscinames sskingdoms" -soft_masking false -max_target_seqs 3 -evalue 10

OrthoMCL and BLAST: Adventures in the (SANBI) Galaxy

BLAST in Galaxy

Part of my work for the week was to start using Galaxy more extensively at SANBI. I.e. to make it more usable. Last week I wrote an authentication plugin to allow a Galaxy server to authenticate using PAM. This got accepted into the 15.07 release of Galaxy, so I updated our Galaxy server to that release. I had neglected to include the example auth_conf.xml in the code I committed, but working off the example on my laptop I got PAM authentication working as a replacement for the previous HTTP authentication (which also spoke to PAM on the backend). I also took the opportunity to switch our server to using HTTPS using the SANBI wildcard certificate.

My first attempt at a practical use for our server came when I needed to run the BLAST step of the OrthoMCL pipeline. OrthoMCL uses an all-against-all BLAST as its input dataset, and based on the data I had from our colleagues, I had a collection of about 300,000 proteins to BLAST against each other. I started this off as an array job at CHPC but thought I could try and work locally as well, as a proof of concept. (Actually there was a previous step, filtering out poor proteins, but I'll get to that below.) My first attempt at using BLAST hit a bug: "NotFound: cannot find 'files_path' while searching for 'db_opts.histdb.files_path'". This exception was thrown from __build_command_line in Galaxy's lib/galaxy/tools/evaluation.py because the BLAST wrappers use an attribute called files_path instead of extra_files_path. Peter Cock and John Chilton discuss the problem in this Github issue and Peter quickly committed a workaround to the BLAST tools.

Having fixed that, and having prepared the protein set (outside Galaxy), I decided to take a chance on the Galaxy "parallelisation" code. This is enabled through appropriate tags in the tool XML, and in the case of the blastp wrapper splits the query dataset into chunks of 1000 sequences each before submitting jobs (in Galaxy terms, actually tasks, not fully fledged jobs) to the cluster. Unfortunately these are individual jobs, not an array job, because array jobs are only implemented in the still-only-on-the-horizon DRMAA version 2. In any event, our cluster can handle thousands of job submissions so I hit go, saw the history item turn from grey to yellow, and waited. Unfortunately, after a day or so it went red (failed), but by then I was too busy with other stuff to debug it. To be continued...

(As an aside, the BLAST wrapper wraps BLAST+, whereas OrthoMCL uses legacy BLAST. I still need to check that the BLAST wrapper exposes enough flags in order to guarantee equivalence. A useful guide for some of the corresponding flags can be found on this page about ortholog finding).

OrthoMCL in and out of Galaxy

As mentioned previously, I was running BLAST as part of the OrthoMCL pipeline. OrthoMCL uses BLAST, MCL and a database (in the version we use, SQLite3) to compute the orthologs in a set of proteins. The pipeline has two steps before the BLAST stage (orthomclAdjustFasta and orthomclFilterFasta), five between the BLAST and MCL stages and a final step to process the MCL output. Currently I use a Makefile to execute the pipeline but at the GCC2015 Hackathon AJ started work on some wrappers for the steps in the pipeline. There has been previous work on executing OrthoMCL within Galaxy but that ran the entire workflow as a single tool. We want to implement the pipeline as a Galaxy workflow because that way we can (in theory at least) benefit from improvements in how BLAST is executed (e.g. parallelism) or even replace the BLAST step with a similar (but apparently faster) tool such as Diamond. The OrthoMCL pipeline is pretty linear so even given the limited capabilities of workflows in current Galaxy (as discussed by John Chilton at BOSC 2015) creating a OrthoMCL workflow should be pretty easy.

To that end we've now got a Github repository for the tool wrappers. I'm trying to follow the structure that groups like IUC use. AJ's working on orthomclAdjustFasta, so I decided to tackle orthomclFilterFasta, a tool that takes a directory full of FASTA files as input, does some simple filtering and outputs a combined FASTA file. I'm not 100% sure on the requirements for the command line (I need to go back into the code and see how it is executed) so I've got a tool that generates a single shell command in the form:

mkdir inputs && /bin/bash orthomcl_prepare_dataset_for_filter.sh dataset1.dat && /bin/bash orthomcl prepare_dataset_for_filter.sh dataset2.dat && orthomclFilterFasta inputs/ <p1> <p2>

The prepare_dataset_for_filter.sh is just a simple script to take a FASTA file, extract the tag that OrthoMCL uses to identify sets (added by orthomclAdjustFasta) and renames the file according to that tag. The orthomclFilterFasta tool insists that input files end in .fasta and are named according to their tag.

In any event the tool runs fine on a local Galaxy install. The next step is to get tool dependencies right, which is where the stuff in the package directory comes in. Galaxy can install packages for you (in an admin-configurable folder). For a tool the dependencies it needs are specified in a file called tool_dependencies.xml that is in the same folder as the tool XML.

The tool dependencies specify packages to install. For OrthoMCL two new packages have been written (see here, one for OrthoMCL and one for the Perl DBD::SQLite module that it depends on. OrthoMCL in turn depends on Perl and DBD::SQLite. This is done using a repository_dependencies.xml file - I'm still not sure if this is the correct approach, but in any event it follows the guide for simple repository dependencies in Galaxy. One limitation to repository dependencies is that they apparently only work within a single toolshed, so what to do if the package you require is in another toolshed?

Thus far the tool dependency stuff has been tested on a local Galaxy installation. It doesn't work. Directories are created, but they are empty. Further testing and a better testing procedure is needed. Eric Rasche mentioned that Marius van den Beek has some Jenkins based testing framework that uses Docker to create sandboxes, and it is here - so perhaps getting this up and running is a next step.

And then finally, FastOrtho seems like a possibly viable alternative to OrthoMCL. The output seems roughly similar to OrthoMCLs and it is much faster (and as a single tool with no Perl dependencies, easier to package), but as with all new tools in bioinformatics, we'll have to prove that it works well enough to replace OrthoMCL (which is somewhat of a standard in this domain). Well check back in a few weeks for updates...

Mixed HTTP / WordPress authentication with nginx

Our WordPress blog / site network at wp.sanbi.ac.za uses Daniel Westermann-Clark's HTTP Authentication plugin. Despite the scary warning on the plugin's page over at wordpress.org, the setup has worked well for us over the years. The only problem has been allowing external (non-SANBI) users to edit pages. This is something we really need for the annual bioinformatics course website.

After quite a few false starts I realised that the solution is to use passive authentication. I.e. do not force the user to use HTTP authentication but rather make it an optional extra. We use PAM for nginx authentication (via nginx_auth_pam, included in the nginx build in Ubuntu's nginx-full module) and the crucial bit of the nginx config looks like this:

        location /sanbi-login.html {
            auth_pam  "SANBI authentication";
            auth_pam_service_name "nginx";
        }
        # Process only the requests to wp-login and wp-admin
        location ~ /wp-(admin|login|includes|content) {
          try_files $uri $uri/ \1/index.php?args;

          location ~ \.php$ {
             try_files $uri =404;
             include fastcgi_params;
             fastcgi_param REMOTE_USER $remote_user;
             fastcgi_index index.php;
             fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
             fastcgi_pass  php;
             fastcgi_intercept_errors on;
          }
        }

(Full nginx config is here). The nginx server forwards the REMOTE_USER variable to the php5-fpm backend but doesn't actually force HTTP authentication for any of the WordPress content. Instead only a single page is protected with HTTP authentication, and that page simply redirects to the WordPress admin interface. Here's the source of sanbi-login.html:

<html>
<head>
<title>SANBI login</title>
<meta http-equiv="refresh" content="0; url=/wp-admin" />
</head>
<body>
</body>
</html>

This works well because ours is a sub-domain based WordPress network. In the HTTP Authentication plugin settings, we point to the address of the sanbi-login.html page as the login page, so the login page ends up looking like this:

WP login screen.

The Log in with HTTP Authentication takes you to the sanbi-login.html page that requests HTTP Authentication and immediately redirects back to /wp-admin. The login form uses conventional WordPress authentication.

One remaining challenge is how to set this option for all sites in the network. Currently it needs to be configured for each site individually. The setting is stored in the wordpress database in the wp_BLOGNUMBER_options table (where BLOGNUMBER is the number of the blog in the wordpress network) with option_name = 'http_authentication_options', as part of a serialised array. This code suggests how to set an option for all sites in a network but as yet there is no way to do this from the wordpress web interface, and I'm a bit loath to work on the database directly.

Reflections on Big Data, Bioinformatics and the recent UCT/UWC workshop

Monday and Tuesday of this week was largely consumed by a focus on Big Data. First, Ton Engbersen from the IBM/ASTRON Centre for Exascale Technology presented a talk at UCT on microservers, data gravity and microclouds.

The microserver in question is the [DOME](http://www.hpcwire.com/2014/04/10/dome-ibm-research- microserver-freescale/), a system-on-chip based device that crams 128 computers into a 19" 2U rack drawer. Each computer takes up 13cm x 5 cm (and is 6 mm thick) and provides 12 PowerPC cores with up to 48 GB RAM, resulting in a 2U rack with 1536 cores and over 6 TB of RAM. The whole thing is cooled with warm water, an IBM innovation that is currently in use on the SuperMUC supercomputer in Leipzig, read more about its benefits on their page.

The DOME server is being developed to analyse data from the SKA, an exascale computing problem. The SKA is anticipated to generate between 300 to 1500 petabytes of data per year, putting it on the extreme end of scientific enterprises in terms of data volume. While big data is commonly associated with data volume, researchers at IBM identify four V's of big data: volume, velocity, variety and veracity. Volume is straightforward. Velocity speaks to the rate at which new data appears. With the amount of sequence data available in GenBank growing at an exponential rate, both volume and velocity of data threaten to outstrip the ability of bioinformatics centres to analyse data. In terms of integration of data, however, my presentation on the big data of tuberculosis focussed more on the variety and veracity of available data. A survey of the data published alongside research articles in the field shows that much of the variety of data gleaned through bioinformatics experiments is lost or only retained in closed institutional databases (and thus effectively lost to the field). An overview of health data collected as part of the NIH-funded Centre for Predictive Computational Phenotyping illustrates the problem of data veracity: electronic health records for patients are often incomplete and lack the vocabulary researchers require to identify disease presence of progression.

Managing the data collections necessary to study e.g. the global state of TB prevalence and treatment will require digital curation of multiple datasets drawn from experiments performed in a range of domains. As Ton Engbersen pointed out that the growing size of data means that "compared to the cost of moving bytes around, everything else is free" (originally a Jim Gray quote). Add to this the (much more tractable) fact that the skills required to build stores and curate these datasets are unevenly distributed, data collections are set to become "the new oil". Engebersen proposes a solution: micro-clouds that offer the possibility to move code to the data rather than the other way round. Such entities would require a sophisticated cross-institutional authentication framework - almost certainly built on digital certificates - to allow authorised software agents to interface with data. This immediate suggests a set of research priorities to add to SANBI's existing research projects on data storage and data movement. Luckily this research overlaps with some research interests at UWC Computer Science.

The workshop concluded with some agreements to collaborate between UCT and UWC on big data, but the perspectives delivered show that there is much more at play than the SKA. The fact that both UWC and UCT have established bioinformatics expertise and are located on the established SANReN backbone means that there's an immediate opportunity to share knowledge and experiments on projects that tackle all four V's of big data. Lots of ideas... the coming year will see how they can be put into practice.

An experimental Ceph storage cluster for the Computer Science Netlab

Ceph is an open source distributed object store and filesystem developed originally developed by Sage Weil for his PhD. Saying that again, but slower this time, Ceph is an object store where the objects are **distributed over a collection of drives and serves. And there's a filesystem component too. The basic blocks of Ceph are object storage daemons (OSDs) and monitoring daemons (MONs). Each OSD manages a block of storage into which are placed objects, aggregated into placement groups (PGs). A datastructure called a

CRUSH map, which is a distributed hash table used to look up where particular data objects are stored. Distributed hashtables underlie most distributed storage software (e.g. you also find one in GlusterFS). Keeping track of the state of everything are the MONs that use the PAXOS algorithm to maintain a consistent set of knowledge about the state of the cluster. There are always an odd number of MONs: typically 3 for a small cluster.

Once you put it all together you get RADOS, the Reliable Autonomic Distributed Object Store (see the 2007 paper if you want). Storage in RADOS is divided into pools where you set per-pool policy for object size and striping and replication. So a pool might have say 4096 PGs containing objects of maximum 4 MB each filled with 64 KB stripes of data, replicated to ensure that there are 3 copies of each PG available at all times.

Ceph provides 3 options for accessing RADOS: first there is the RADOS object gateway, a RESTful service allowing individual objects (e.g. VM images) to be stored and retrieved. Then there's the RADOS Block Device (RBD), a iSCSI like block device that can be mapped to a virtual drive on the client computer and finally there is CephFS, a POSIX-compliant filesystem running on top of storage pools in RADOS (the filesystem uses an extra daemon the metadata server (MDS), to map filesystem locations such as /home to objects).

The Ceph architecture allows heterogenous disks and servers to be aggregated into a storage pool in a way that is more flexible than traditional RAID and with substantially shorter rebuild times.

So to demo Ceph I set it up in the Computer Science Netlab at UWC, using a fair sprinkling of ansible scripting and the ceph-deploy tool. The architecture is three MONs, normandy, netlab2-ws and netlab6-ws and three OSDs, netlab2-ws, netlab6-ws and netlab17-ws. On the OSDs I've used the existing filesystem as the Ceph store - Ceph should have its own storage partitions, but I didn't want to go to the trouble of repartitioning machines for the demo. The release used is Giant, the latest and as-yet-unreleased Ceph release.

TODO: detail the initial installation

I'll hopefully getting around to documenting the initial steps, but let me show how I add a new OSD to the Ceph cluster.

First, create the /dfs directory on the new OSD (in this case netlab10-ws). The "-s -k -K" arguments for ansible mean ask for SSH password, ask for sudo password and use sudo. Since the commands I'm running need to be run as root on the remote machine, I need all that.

ansible -s -k -K -m file -a "name=/dfs owner=root state=directory" netlab10-ws

Then add a user to the remote machine. The password set is never actually used, since we'll be using SSH public keys to do the log in and passwordless sudo.

ansible  -u pvh -k -K -m user -a 'name=netlab-ceph home=/dfs/netlab-ceph createhome=yes password="SOMEENCRYPTEDSTUFF" shell=/bin/bash comment="Ceph User" state=present' netlab10-ws

ansible -k -s -K -m authorized_key -a 'user=netlab-ceph key="SSH PUBLIC KEY GOES HERE"' netlab10-ws

ansible -k -K -s -m copy -a 'content="netlab-ceph ALL = (root) NOPASSWD:ALL\n" dest=/etc/sudoers.d/050_ceph mode=0444 owner=root' netlab10-ws 

Next we need to install a NTP daemon and synchronise time (we should actually run an in-lab NTP server, but for now we're using a public one to set the time). Ceph relies on everything being in close time synchronisation to operate.

ansible -s -k -K -m apt -a 'name=ntp state=present' netlab10-ws

ansible -s -k -K -m command -a 'ntpdate 0.pool.ntp.org' netlab10-ws
ansible -s -k -K -m service -a 'name=ntp state=started enabled=true' netlab10-ws

Then use the ceph-deploy tool to install the actual ceph packages, create a directory for the OSD to put its data in, initialize, activate and we're done!

ceph-deploy install --release=giant netlab10-ws

ansible -s -k -K -m file -a 'name=/dfs/osd3 state=directory' netlab10-ws

ceph-deploy osd prepare netlab10-ws:/dfs/osd3
ceph-deploy osd activate netlab10-ws:/dfs/osd3

You can check on the state of the cluster with sudo ceph status, where you'll see something like this:

netlab-ceph@normandy:~$ sudo ceph status
    cluster 915d5e83-2950-4860-ba97-2118c061036f
     health HEALTH_WARN 18 pgs degraded; 220 pgs peering; 93 pgs stuck inactive; 93 pgs stuck unclean; recovery 296/2880 objects degraded (10.278%)
     monmap e1: 3 mons at {netlab2-ws=10.0.0.16:6789/0,netlab6-ws=10.0.0.21:6789/0,normandy=10.0.0.1:6789/0}, election epoch 14, quorum 0,1,2 normandy,netlab2-ws,netlab6-ws
     mdsmap e5: 1/1/1 up {0=normandy=up:active}
     osdmap e64: 4 osds: 4 up, 4 in
      pgmap v4413: 320 pgs, 3 pools, 3723 MB data, 960 objects
            63303 MB used, 799 GB / 907 GB avail
            296/2880 objects degraded (10.278%)
                  18 active+degraded
                 220 peering
                  82 active+clean
recovery io 11307 kB/s, 2 objects/s
  client io 6596 kB/s wr, 4 op/s

Or you can watch it rebalancing itself with ceph -w:

netlab-ceph@normandy:~$ sudo ceph -w
    cluster 915d5e83-2950-4860-ba97-2118c061036f
     health HEALTH_WARN 121 pgs degraded; 8 pgs recovering; 28 pgs stuck unclean; recovery 1308/3864 objects degraded (33.851%)
     monmap e1: 3 mons at {netlab2-ws=10.0.0.16:6789/0,netlab6-ws=10.0.0.21:6789/0,normandy=10.0.0.1:6789/0}, election epoch 14, quorum 0,1,2 normandy,netlab2-ws,netlab6-ws
     mdsmap e5: 1/1/1 up {0=normandy=up:active}
     osdmap e64: 4 osds: 4 up, 4 in
      pgmap v4445: 320 pgs, 3 pools, 4991 MB data, 1288 objects
            63424 MB used, 799 GB / 907 GB avail
            1308/3864 objects degraded (33.851%)
                 113 active+degraded
                 199 active+clean
                   8 active+recovering+degraded
recovery io 14070 kB/s, 3 objects/s

2014-10-16 11:44:39.069514 mon.0 [INF] pgmap v4445: 320 pgs: 113 active+degraded, 199 active+clean, 8 active+recovering+degraded; 4991 MB data, 63424 MB used, 799 GB / 907 GB avail; 1308/3864 objects degraded (33.851%); 14070 kB/s, 3 objects/s recovering
2014-10-16 11:44:41.178062 mon.0 [INF] pgmap v4446: 320 pgs: 113 active+degraded, 199 active+clean, 8 active+recovering+degraded; 4991 MB data, 63473 MB used, 799 GB / 907 GB avail; 1306/3864 objects degraded (33.799%); 9782 kB/s, 2 objects/s recovering

To remove an OSD, you can use these commands (using out newly create osd.3 as an example) - they take the OSD out of the storage cluster, stop the daemon, remove it from the CRUSH map, delete authentication keys and finally remove the OSD from the cluster's list of OSDs.

netlab-ceph@normandy:~$ sudo ceph osd out 3
marked out osd.3. 
netlab-ceph@normandy:~$ ssh netlab10-ws sudo stop ceph-osd-all
ceph-osd-all stop/waiting
netlab-ceph@normandy:~$ sudo ceph osd crush remove osd.3
removed item id 3 name 'osd.3' from crush map
netlab-ceph@normandy:~$ sudo ceph auth del osd.3
updated
netlab-ceph@normandy:~$ sudo ceph osd rm 3
removed osd.3

Then, for good measure, you can remove the data:

netlab-ceph@normandy:~$ ssh netlab10-ws sudo rm -rf /dfs/osd3/\*

Also not covered in this blog is how I added a RBD device and how I created and mounted a CephFS filesystem. Well... bug me till I finish writing this thing.

Installing Slurm on CentOS using Ansible

Helping the UWC Student Cluster Challenge team prepare for the final round (at the CHPC National Meeting) has given me an excuse to play with some new toys: I've got a mini-cluster of three VMs running on my laptop (using KVM and libvirt), and I've been looking into Slurm as a cluster scheduler. At SANBI we run SGE, lots of other people use Torque, but I've been interested in Slurm for a while, because its a fully open source scheduler with some big name users and seemingly a bright future. Then, I'm big into systems administration task automation: at SANBI we use puppet (and I personally use fabric), but Bruce Becker introduced me to Ansible, and so I took the opportunity to build an Ansible playbook to install Slurm on my mini-cluster.

Ansible playbooks are written in YAML and describe a set of tasks that need to be applied to a set of servers. These tasks are defined in terms of a set of modules and executed using ssh  (optionally using ZeroMQ to speed up data transfer) so you need to have ssh access to the machines you want to administer. I did this by adding my ssh key to the authorized_keys file for the root users on my mini-cluster. Like puppet recipes, ansible playbooks are (largely) declarative: you specify what you want, not how to achieve it. Unlike puppet recipes, ansible playbooks run tasks in order, first to last.

So my cluster has three nodes: head (the head node), and two workers: worker1 and worker2. These are on a private (virtual) LAN with DNS being provided by the head node (so the DNS names are head.cluster, etc). My laptop is the VM host and the IP addresses of all nodes are in /etc/hosts on the machine. The laptop has Ansible 1.4 installed from Rodney Quillo's PPA. This is crucial: I use a bunch of features that are only available in 1.4.

The Slurm Quick Start Administrator Guide outlines the steps needed to install Slurm in a general way. First, I downloaded Slurm 2.6.4 and then installed the dependencies I needed to compile it:

openmpi-devel pam-devel hwloc-devel rrdtool-devel ncurses-devel munge-devel

This is not an exhaustive list: I had previously installed software on the nodes, so there might be stuff I left off this list. To identify missing dependencies, look at the config.log after the configure stage and search for WARNING messages. I unpacked Slurm and did:

./configure --prefix=/opt/slurm
make
sudo make install

This installed Slurm in /opt/slurm. I then created an archive of the slurm install:

cd /opt
tar jcf /var/tmp/slurm-bin.tar.bz2 slurm/*

I deployed this with Ansible to the nodes in the cluster. My Ansible setup uses a hostfile (/etc/ansible/hosts) that defines the hosts and host groups:

[workers]
worker1.cluster
worker2.cluster
[head]
head.cluster
[cluster:children]
head
workers

(You don't need to use a system-wide hosts file like I did, you can specify an alternative hostfile with the -i flag on the ansible-playbook command line.) This was my initial ansible playbook (slurm.yml):

---
- hosts: cluster
 remote_user: root
 tasks:
 - name: create slurm user
 user: name=slurm createhome=no home=/opt/slurm 
 shell=/sbin/nologin state=present
 - name: install slurm dependencies
 yum: name={{item}} 
 with_items:
 - pam 
 - hwloc 
 - rrdtool 
 - ncurses 
 - munge
 - name: create slurm directories
 file: path=/var/spool/slurmd owner=slurm mode=0755 state=directory
 - name: copy slurm binaries to /tmp
 copy: src=slurm-bin.tar.bz2 dest=/tmp/slurm-bin.tar.bz2
 - name: unpack slurm binary distribution
 command: /bin/tar jxf /tmp/slurm-bin.tar.bz2 chdir=/opt 
 creates=/opt/slurm
 - name: install slurm configuration file
 copy: src=slurm.conf dest=/opt/slurm/etc/slurm.conf
 notify: restart slurm
 - name: install slurm path file in /etc/profile.d
 copy: src=slurm.sh dest=/etc/profile.d/slurm.sh mode=0755 owner=root
 - name: install slurm started script in /etc/init.d
 copy: src=init.d.slurm dest=/etc/init.d/slurm mode=0755 owner=root
 - name: enable munge service
 service: name=munge state=started enabled=yes
 - name: enable slurm service startup
 service: name=slurm state=started enabled=yes
 handlers:
 - name: restart slurm
 service: name=slurm state=restarted

As mentioned previously, ansible playbooks are read top down. So the steps taken are:

  1. Create slurm user.
  2. Install slurm dependencies (the non-devel versions of the previously mentioned packages).
  3. Create slurm spool directory (/var/spool/slurmd) and make it owned by the slurm user.
  4. Upload and unpack the slurm-bin.tar.bz2 that was previously created.
  5. Install the slurm configuration file to /opt/slurm/etc/slurm.conf. The first draft of this was created with the Slurm 2.6 configuration tool and the final version is here.
  6. Install the slurm.sh script to /etc/profile.d that sets the PATH to include slurm binaries. This file contains:

    PATH=$PATH:/opt/slurm/bin:/opt/slurm/sbin

    if [ -z "$MANPATH" ] ; then
    MANPATH=/opt/slurm/share/man
    else
    MANPATH=$MANPATH:/opt/slurm/share/man
    fi
    export PATH MANPATH 

  7. Install init.d.slurm from slurm distribution's etc/ directory to /etc/init.d/slurm. This handles start/stop of both slurmctld (on head) and slurmd (on worker nodes).
  8. Ensure that the munge daemon is started. I have previously generated a munge key using the instructions on the munge website and distributed this to /etc/munge/munge.key on each of the nodes in the cluster. This was done with another ansible playbook (not shown).

  9. Once the file is installed the service is enabled (with something like chkconfig slurm on) and the slurm daemons are started (service slurm start).
  10. The playbook was then split up into Ansible roles and roles were added to create a NFS server on the head node and share /home from the head node and mount it over /home on the worker nodes.

Once this was all up and running, the system was tested by using sbatch to run a simple script. Here's the script, hello.sh:

#!/bin/sh

echo Hello World

This was submitted with the command:

sbatch hello.sh

After that worked the AMG benchmark was run using MPI. Here's the test_amg.sh script:

#!/bin/sh
echo NTASKS $SLURM_NTASKS
LD_LIBRARY_PATH=/usr/lib64/openmpi/lib
export LD_LIBRARY_PATH
mpirun src/test/amg2013 -laplace -P 1 1 $SLURM_NTASKS -n 64 64 64 -solver 2

and run using:

sbatch -n 2 test_amg.sh

Compared to my experience with SGE, Slurm seems to run jobs really fast and compared to Torque+Maui it seems pretty easy to set up.

As mentioned above I switched over my playbook to using Ansible roles. Roles allow you to split out the components of configured into a particular directory structure and then mix these into your final playbook. So the roles structures I currently have is:

roles
├── munge
│   ├── files
│   │   └── munge.key
│   ├── handlers
│   │   └── main.yml
│   └── tasks
│       └── main.yml
├── nfs-client
│   └── tasks
│       └── main.yml
├── nfs-common
│   └── tasks
│       └── main.yml
├── nfs-server
│   ├── files
│   │   └── exports
│   ├── handlers
│   │   └── main.yml
│   └── tasks
│       └── main.yml
└── slurm
    ├── files
    │   ├── init.d.slurm
    │   ├── slurm-bin.tar.bz2
    │   ├── slurm.conf
    │   └── slurm.sh
    ├── handlers
    │   └── main.yml
    └── tasks
        └── main.yml

Effectively what Ansible roles do is to split the sections of your playbook out into a directory structure. This is then used in the final playbook (slurm.yml):

---
- hosts: cluster
 remote_user: root
 roles:
 - munge
 - slurm
 - nfs-common
 tasks:
 - name: disable firewall
 service: name=iptables enabled=no state=stopped
- hosts: head
 remote_user: root
 roles:
 - nfs-server
- hosts: workers
 remote_user: root
 roles:
 - nfs-client

And finally I'm at a stage where I can run:

ansible-playbook slurm.yml

And have the complete infrastructure required for a Slurm install set up on my virtual cluster.
[edited to add whitespace to Ansible playbooks as per suggestion from Michael de Haan @laserllama]