An upgrade-friendly Slurm Installation

At SANBI we have a small HPC (see our Annual report) that uses Slurm as a scheduler. Its always a good idea to keep this up to date and unfortunately the version available in the Ubuntu package repository tends to be quite old (e.g. 17.11 for Ubuntu 18.04 and 19.05 for Slurm 20.04).

The Slurm upgrade procedure is mentioned in their Quick Start Administrator Guide. In short, the daemons need to be upgraded in a specific order, starting with slurmdbd, followed by a nested upgrade of slurmctld and the slurmd on each compute node. To facilitate this process our install is on shared storage (CephFS, but could also be NFS) and looks as follows:

    /tools/admin/slurm
    ├── 18.08.9
    ├── 19.05.7
    ├── 20.02.5
    ├── ctld -> /tools/admin/slurm/20.02.5
    ├── current -> /tools/admin/slurm/20.02.5
    ├── d -> /tools/admin/slurm/20.02.5
    ├── dbd -> /tools/admin/slurm/20.02.5
    ├── etc

To install slurm, the slurm source is unpacked and compiled with slurm, with the configure options like:

    ./configure --prefix=/tools/admin/slurm/20.02.5 --sysconfdir=/tools/admin/slurm/etc

As can be seen from the above listing, the d, ctld, dbd and current links link to the current version of Slurm in use.
Each daemon is managed by systemd and configured with a file in /etc/systemd/system. For example here is the configuration of slurmctld (i.e. /etc/systemd/system/slurmctld):

[Unit]
Description=Slurm controller daemon
After=network.target munge.service
ConditionPathExists=/tools/admin/slurm/etc/slurm.conf

[Service]
Type=oneshot
EnvironmentFile=-/etc/sysconfig/slurmctld
ExecStartPre=-/usr/bin/pkill -KILL slurmctld
ExecStart=/tools/admin/slurm/ctld/sbin/slurmctld $SLURMCTLD_OPTIONS
ExecReload=-/bin/kill -HUP $MAINPID
ExecStop=-/usr/bin/pkill -KILL slurmctld
PIDFile=/var/run/slurm/slurmctld.pid
KillMode=process
LimitNOFILE=51200
LimitMEMLOCK=infinity
LimitSTACK=infinity
RemainAfterExit=true

[Install]
WantedBy=multi-user.target

After installing this file, you need to run sudo systemctl daemon-reload.

Note the line in bold in the above config file. The executable is run via the /tools/admin/slurm/ctld/sbin folder. Because this /tools/admin/slurm/ctld path is a symlink, upgrading the slurmctld involves simply changing the symlink to point to the new slurm version.

The upgrade process for slurmdbd and slurmctld is quite straightforward, just follow the procedure for database backup and upgrade as mentioned in the docs. For slurmd, the upgrade procedure (backup of StateSaveLocation and restart of slurmd) needs to happen on each worker node. This can best be automated using ansible. As noted in the Slurm admin documentation, you can at most upgrade between two major releases. Due to a security issue older Slurm versions are not available from the main download page but you can still get them from Github (e.g. version 19.05).

A final note – this procedure, with per-version symlinks etc, was based on something I read online before executing at SANBI. I can’t recall where I read this but if you were the source and would like credit, please look me up and let me know.

Galaxy 21.05 upgrade and cluster_venv

As part of my (rather prolonged) work towards a M.Sc. in bioinformatics, I maintain a Galaxy server at SANBI. I’ve recently upgraded to Galaxy 21.05, at the time of this writing the latest Galaxy release. You can read more about that release here.

My Galaxy server is deployed using Ansible with a combination of the standard Galaxy roles and ones developed at SANBI to match our infrastructure. Specifically, we have roles for integrating with our infrastructure’s authentication, monitoring and CephFS filesystem. I also wrote a workaround for deploying letsencrypt based SSL. You can find this configuration in this repository.

The Galaxy server integrates with our cluster, the worker nodes of which are running Ubuntu 18.04 (the Galaxy server is on Ubuntu 20.04). For a number of tasks, Galaxy requires tools to have some access to Python libraries that are not part of core Python for the business of “finishing” jobs (i.e. feeding results back into Galaxy) and so on. In the past I have found that using the single virtualenv that the Galaxy roles configure on the Galaxy server causes problems when running jobs on the cluster. Thus I have a specific venv for running on the cluster that is configured on the cluster. I.e. after the Galaxy server install was completed, I logged into one of the cluster worker nodes as root, deleted the old cluster_venv and ran:

cd /projects/galaxy/pvh_masters_galaxy1
export GALAXY_VIRTUAL_ENV=$(pwd)/cluster_venv
cd server
scripts/common_startup.sh --skip-client-build --skip-samples

Obviously it would be better to automate the above, but I have not go around to doing so yet. I’m not sure if this is the best approach but it works at least for our environment, so I’m writing this blog post in case it is useful to others (or to jog my own memory down the line!). This cluster_venv setup is exposed to the job runners in job_conf.xml – here is a snippet of my configuration:

<job_conf>
    <plugins workers="4">
        <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner"/>
        <plugin id="slurm" type="runner" load="galaxy.jobs.runners.slurm:SlurmJobRunner"/>
    </plugins>
    <destinations default="dynamic">
        <destination id="slurm" runner="slurm">
            <param id="tmp_dir">True</param>
            <env id="GALAXY_VIRTUAL_ENV">/projects/galaxy/pvh_masters_galaxy1/cluster_venv</env>
            <env id="GALAXY_CONFIG_FILE">/projects/galaxy/pvh_masters_galaxy1/config/galaxy.yml</env>
        </destination>
        <destination id="local" runner="local"/>
        <destination id="dynamic" runner="dynamic">
            <param id="tmp_dir">True</param>
            <param id="type">dtd</param>
        </destination>
        <destination id="cluster_default" runner="slurm">
            <param id="tmp_dir">True</param>
            <env id="SLURM_CONF">/tools/admin/slurm/etc/slurm.conf</env>
            <env id="GALAXY_VIRTUAL_ENV">/projects/galaxy/pvh_masters_galaxy1/cluster_venv</env>
            <env id="GALAXY_CONFIG_FILE">/projects/galaxy/pvh_masters_galaxy1/config/galaxy.yml</env>
            <param id="nativeSpecification">--mem=10000</param>
            <resubmit condition="memory_limit_reached" destination="cluster_20G" />
        </destination>

P.S. this was the only manual task I had to perform (on the Galaxy side of things). Mostly the update consisted of updating our SANBI ansible roles to support Ubuntu 20.04 (and Ceph octopus), switching to the latest roles (as described in the training material for Galaxy admins), flicking the version number from release_20.09 to release_21.05 and running the Ansible playbook.

Solving Bluetooth Audio Delay on Ubuntu 20.04

For quite some time I’ve been frustrated at the state of Ubuntu’s support for Bluetooth audio. As a result, I’ve always gone with wired headphones. Now maybe its something about me but I’ve not had the best of luck with this. Headphones last a few months before some plug or wire breaks. In the worst case scenario the headphone jack on my laptop starts giving issues… so wireless is great. If it works.

I had to replace my headset recently and bought a HAVIT H2590BT, a fairly entry-level thing, and it worked fine for listening to music but as soon as I wanted more “real time” audio there were problems. I first noticed this on Duolingo and a bit of debugging showed that the problem was a delay in the audio. This became rather embarasing when doing a call with colleagues.

Turns out that Bluetooth has audio profiles that affect the operation of the headset. A2DP focuses on giving best audio quality, whereas HFP and HSP are more focused on real-time responsiveness. Unfortunately with the standard PulseAudio (13.99.1) on my Ubuntu 20.04 I could only connect to the headphones using A2DP. I came across posts on askubuntu.com from 2015 onwards talking about this issue and some suggested switching profiles but I couldn’t seem to get that right.

Then I found this post from @normankev141. Unfortunately the plugin that he suggested has been deprecated by the author, who suggested moving to PipeWire. I switched to PipeWire using the instructions from this askubuntu post, rebooted and now I’ve got a much richer selection of profiles:

$ pactl list cards
[...]
Card #54
Name: bluez_card.C5_78_21_3A_9F_DB
Driver: module-bluez5-device.c
Owner Module: n/a
[...]
Profiles:
    off: Off (sinks: 0, sources: 0, priority: 0, available: yes)
    a2dp-sink: High Fidelity Playback (A2DP Sink) (sinks: 1, sources: 0, priority: 0, available: yes)
    headset-head-unit: Headset Head Unit (HSP/HFP) (sinks: 1, sources: 1, priority: 0, available: yes)
    a2dp-sink-sbc: High Fidelity Playback (A2DP Sink, codec SBC) (sinks: 1, sources: 0, priority: 0, available: yes)
    headset-head-unit-cvsd: Headset Head Unit (HSP/HFP, codec CVSD) (sinks: 1, sources: 1, priority: 0,    available: yes)
Active Profile: a2dp-sink-sbc

I can now switch profiles with pactl set-card-profile bluez_card.C5_78_21_3A_9F_DB a2dp-sink or pactl set-card-profile bluez_card.C5_78_21_3A_9F_DB headset-head-unit. I’ve made these two aliases for my shell:

alias goodaudio="pactl set-card-profile $(pactl list cards |grep 'Name: bluez' |awk '{print $2}') a2dp-sink"
alias headset="pactl set-card-profile $(pactl list cards |grep 'Name: bluez' |awk '{print $2}') headset-head-unit"

I haven’t yet got around to linking these to some kind of Gnome utility so that I can toggle the profiles yet. Its on the TODO list.

Galaxy and the notorious rfind() error: HistoryDatasetAssociation objects aren’t strings

I have repeatedly triggered this error when writing Galaxy tool wrappers:

2018-03-26 13:36:58,408 ERROR [galaxy.jobs.runners] (2) Failure preparing job
Traceback (most recent call last):
File "/tmp/tmp9OzX0h/galaxy-dev/lib/galaxy/jobs/runners/init.py", line 170, in prepare_job
job_wrapper.prepare()
File "/tmp/tmp9OzX0h/galaxy-dev/lib/galaxy/jobs/init.py", line 909, in prepare
self.command_line, self.extra_filenames, self.environment_variables = tool_evaluator.build()
File "/tmp/tmp9OzX0h/galaxy-dev/lib/galaxy/tools/evaluation.py", line 445, in build
raise e
AttributeError: 'HistoryDatasetAssociation' object has no attribute 'rfind'
FAIL

The command in the tool wrapper at the time included:

#import os.path
#set report_name os.path.splitext(os.path.basename($input_vcf))[0] + '.html'
tbvcfreport generate '$input_vcf' &&
mv '$report_name' $output

In the main part of the template, $input_vcf, which is a reference to an input dataset, effectively behaves like a string, as
it is substituted with the filename of the input dataset. In the #set part, however, it is a Python variable that refers
to the underlying HistoryDatasetAssociation. Thus the obscure looking error message, because a HDA is indeed not a string
and has no .rfind() method.

The error can be fixed by wrapping $input_vcf in a str() call to convert it into its string representation, i.e.
the filename I am interested in:

#import os.path
#set report_name os.path.splitext(os.path.basename(str($input_vcf)))[0] + '.html'
tbvcfreport generate '$input_vcf' &&
mv '$report_name' $output

Thanks to Marius van den Beek (@mvdbeek) for catching this for me.

A Galaxy 18.01 install

We are preparing for Galaxy Africa in a few weeks’ time, which will feature some Galaxy training. In preparation for that I installed a new Ubuntu 16.04 virtual machine to host a 18.01 Galaxy server. The aim is to set up a production Galaxy server. To that end, the server is being hosted on a 1 TB Ceph RBD partition mounted on /galaxy. A user called galaxyuser was created on our FreeIPA authentication environment, and /galaxy/galaxysrv was created to host Galaxy files.

The first step of setup was to clone Galaxy 18.01 release and configure it for production use. The postgresql database server was installed and a user created for galaxyuser and then that user used to create the galaxy database. I configured the database and added myself (pvh@sanbi.ac.za) as an admin user.

The next step was to install nginx. As far as possible I tried to not alter the “out of the box” nginx configuration, to make it easier to do upgrades later. To that end, firstly, a SSL certificate was added using certbot and Let’s Encrypt by installing the certbot and python-certbot-nginx packages, and running certbox --nginx certonly. This yielded /etc/letsencrypt/live/galaxy.sanbi.ac.za and associated files. The /etc/nginx/ssl directory as created and a /etc/nginx/ssl/dhparam.pem file was created with openssl dhparam -out /etc/nginx/ssl/dhparam.pem 4096. This was in order to create a more secure configuration than default as explained here.

Following the instructions from the Galaxy Receiving Files with nginx documentation and advice from Marius van den Beek, nginx-extras was installed from the recommended PPA, yielding nginx, nginx-common and nginx-extras packages for version 1.10.3-0ubuntu0.16.04.2ppa1. Then a file /etc/nginx/conf.d/custom.conf was created with content as per this gist. This is effectively a combination of the options suggested by the Galaxy admin docs with those in /etc/letsencrypt/options-ssl-nginx.conf. The server configuration directives from the recommended Galaxy configuration were adapted and put in /etc/nginx/sites-available/galaxy. The resulting configuration is in this gist. Once added, the configuration was activated by removing the /etc/nginx/sites-enabled/default file and linking the galaxy configuration fie in its place. Finally, /etc/nginx/nginx.conf was altered by changing the user used to run the server to galaxyuser (i.e. “user galaxyuser”). To connect Galaxy to nginx, the socket: option in the Galaxy config/galaxy.yml and the configuration in the nginx site configuration were harmonised as per the relevant documentation. Since the unix socket was not created on startup, a http connection and thus TCP socket on localhost was used.

The third step was configuring Galaxy to start using supervisord. This was based on the [program:web] configuration from the Galaxy starting and stopping configuration guide. And this is where things started going wrong. Using this configuration, the data upload tool didn’t work as it used the system Python, not Python from the Galaxy virtualenv configured in /galaxy/galaxysrv/galaxy/.venv. To ensure that the Galaxy virtualenv was activated before running the upload tool, the VIRTUAL_ENV config was added to the /etc/supervisor/conf.d/galaxy configuration, resulting in the config shown in this gist.

The fourth step was to configure CVMFS to allow access to the reference data collection used on usegalaxy.org. I installed the cvmfs package by following the instructions to install the apt repository and then apt-get install cvmfs. The correct configuration was learned from Björn Grüning (@bgruening)’s bgruening/galaxy-stable Docker container with some help from @scholtalbers on gitter:

a. In /etc/cvmfs/domain.d/galaxyproject.org.conf put the line as per this gist.

b. In /etc/cvmfs/default.local put:

CVMFS_REPOSITORIES="data.galaxyproject.org"
CVMFS_HTTP_PROXY="DIRECT"
CVMFS_QUOTA_LIMIT="4000"
CVMFS_USE_GEOAPI="yes"

c. In /etc/cvmfs/keys/data.galaxyproject.org.pub put:

-----BEGIN PUBLIC KEY-----
MIIBIjANBgkqhkiG9w0BAQEFAAOCAQ8AMIIBCgKCAQEA5LHQuKWzcX5iBbCGsXGt
6CRi9+a9cKZG4UlX/lJukEJ+3dSxVDWJs88PSdLk+E25494oU56hB8YeVq+W8AQE
3LWx2K2ruRjEAI2o8sRgs/IbafjZ7cBuERzqj3Tn5qUIBFoKUMWMSIiWTQe2Sfnj
GzfDoswr5TTk7aH/FIXUjLnLGGCOzPtUC244IhHARzu86bWYxQJUw0/kZl5wVGcH
maSgr39h1xPst0Vx1keJ95AH0wqxPbCcyBGtF1L6HQlLidmoIDqcCQpLsGJJEoOs
NVNhhcb66OJHah5ppI1N3cZehdaKyr1XcF9eedwLFTvuiwTn6qMmttT/tHX7rcxT
owIDAQAB
-----END PUBLIC KEY-----

d. Add the line /cvmfs /etc/auto.cvmfs to /etc/auto.master yielding a file looking like this gist.

e. A /cvmfs directory was created to be a mount point (mkdir /cvmfs).

f. The autofs service was restarted (systemctl restart autofs) and then a ls /cvmfs/data.galaxyproject.org/byhand shows a pretty collection of reference data.

g. updated The config/galaxy.yml file was updated so that the tool_data_table_config_path key contains references to the files that are stored in CVMFS. The final value of this key was:

tool_data_table_config_path: /cvmfs/data.galaxyproject.org/byhand/location/tool_data_table_conf.xml,/cvmfs/data.galaxyproject.org/managed/location/tool_data_table_conf.xml,config/tool_data_table_conf.xml

This might not fit on your screen, so see the config fragment here. After the update to the Galaxy config all service were restarted (with sudo supervisorctl restart all).

My fifth and final step was to test the Galaxy server by installing bowtie2 from the toolshed and working through the first steps of the mapping tutorial. Both human (hg19) and fruitfly (dm3) reference genomes were downloaded (and apparently stored in /var/lib/cvmfs/shared) using CVMFS and the bowtie2 mapping was run against them successfully, yielding the results expected from the tutorial.

Future work? There is lots – I have to connect the server to a cluster, using Slurm, and enable Interactive Environments… I’ll blog about that when I get there.

MegaRAID write cache policy with lsmcli

A couple of weeks ago I had a near disaster when some of our servers lost power while their RAID was set to “write-through” caching with non-working batteries. The result was filesystem corruption and failure on 2 out of 3 Ceph monitor servers. In the past I have written about using MegaCLI for RAID admin. MegaCLI has been replaced by StorCLI, which I found here on the Broadcom web pages. I unpacked the various zip files until I got the storcli-007.0309.0000.0000-1.noarch.rpm RPM and installed that to get the MegaRAID storcli64 tool. Instead of using that directly I’m using the libstoragemgmt tools with the lsmcli tool. On CentOS 7 this required installing libstoragemgmt and libstoragemgmt-megaraid-plugin and starting the lsmd daemon systemctl start libstoragemgmt.

This all set up, I found the volume with lsmcli -u megaraid:// list --type VOLUMES:

[root@ceph-mon2 ~]# lsmcli -u megaraid:// list --type VOLUMES
ID                               | Name | SCSI VPD 0x83                    | Size         | Disabled | Pool ID | System ID | Disk Paths
---------------------------------------------------------------------------------------------------------------------------------------
6003048016dfd2001cf1d19f0af655a3 | VD 0 | 6003048016dfd2001cf1d19f0af655a3 | 597998698496 | No       | :DG0    |           | /dev/sda  

then the volume-cache-info command:

[root@ceph-mon2 ~]# lsmcli -u megaraid:// volume-cache-info --vol  6003048016dfd2001cf1d19f0af655a3
Volume ID                        | Write Cache Policy | Write Cache | Read Cache Policy | Read Cache | Physical Disk Cache
--------------------------------------------------------------------------------------------------------------------------
6003048016dfd2001cf1d19f0af655a3 | Write Back         | Write Back  | Enabled           | Enabled    | Use Disk Setting   

and set the policy to AUTO (which means write-back when the battery is ok, write-through otherwise):

[root@ceph-mon2 ~]# lsmcli -u megaraid:// volume-write-cache-policy-update --vol  6003048016dfd2001cf1d19f0af655a3 --policy AUTO
Volume ID                        | Write Cache Policy | Write Cache   | Read Cache Policy | Read Cache | Physical Disk Cache
----------------------------------------------------------------------------------------------------------------------------
6003048016dfd2001cf1d19f0af655a3 | Write Through      | Write Through | Enabled           | Enabled    | Use Disk Setting   

There doesn’t seem to be a direct way to query the battery backup unit (BBU) with lsmcli but /opt/MegaRAID/storcli/storcli64 show will show you what the status is.

MaterializeCSS vs ReactJS: the case of the select

For historical reasons, the COMBAT TB web interface uses materialize for its styling. So far so good. That is, until I tried to deploy my code, written with React.JS. See, as I understand it, materialize has in some cases decided to replace some HTML elements with its own version of them. Notably the <select> element. And ReactJS relies on these elements for its own operation.

The first problem I had was that <select> elements vanished. Turns out you need a bit of Javascript to make them work:

$(document).ready(function() {
    $('select').material_select();
});

The next problem, however, was that the onChange handlers that ReactJS uses don’t trigger events. Luckily that has been discussed before.

I’ve got two types of <select> element in the code I was writing for the COMBAT TB Explorer web application: static ones (there from the birth of the page) and dynamically generated ones. For the static ones I added some code to link up the events in the componentDidMount handler:

componentDidMount: function() {
    $(document).ready(function() {
        $('select').material_select();
    });
    $('#modeselectdiv').on('change', 'select', null, this.handleModeChange);
    $('#multicompselectdiv').on('change', 'select', null, this.handleMultiCompChange);

},

but this didn’t work for the dynamically generated elements, I think because they are only rendered after an AJAX call returns. For since I know a state change triggers the render event, I added the handler hook-up after the data was return and deployed (to the application’s state), for example:

success: function(datasets) {
    var dataset_list = [];
    var dataset_list_length = datasets.length
    for (var i = 0; i < dataset_list_length; i++) {
        dataset_list.push({'name': datasets[i]['name'], id: datasets[i]['id']});
    }
    this.setState({datasets: dataset_list, dataset_id: dataset_list[0].id});
    $('select').material_select();
    $('#datasetselectdiv').on('change', 'select', null, this.handleDatasetChange);
}.bind(this),

Turns out this works. The state change handlers are now linked in, they keep the state up to date with what the user is doing on the form, and the whole thing (that links the application to a Galaxy instance) works. Yay!

Making Ubuntu 14.04 and CentOS 7 NFS work together

I just spent a frustrating morning configuring our servers to talk NFS to each other properly. So we have:

1) NFS servers (ceph-mon1 and so on) running CentOS 7.
2) NFS clients (gridj1 and so on) running Ubuntu 14.04.

The first problem: RBD mounting and NFS startup were not configured on the servers. I fixed that by adding entries in /etc/ceph/rbdmap and enabling the rbdmap and nfs-server services using systemctl enable. I also used e2label to label the ext4 filesystems in the RBDs and then used these labels in /etc/fstab instead of device names. And used the _netdev option in the mount options because these devices are network devices.

The second problem: I had to add the insecure option to the exports in /etc/exports. This is because the mount request comes from a port higher than 1024, a so-called insecure port. And then exportfs -r to resync everything.

And the third problem: Ubuntu autofs makes a NFS4 mount request by default (even though I had specified nfsvers=3 in the mount options), and I haven’t configured NFS4’s authenticated mounts, so I was getting authenticated mount request from 192.168.6.71:862 messages in /var/log.messages on the NFS server. I switched the NFS server to not do NFS4 by adding --no-nfs-version 4 to the RPCNFSDARGS variable in /etc/sysconfig/nfs on the server, restarted the NFS server (systemctl restart nfs-server) and the mounts finally worked.

Finally, documented this here for posterity…

Faster Galaxy with uWSGI

I recently switched out local Galaxy server to be run using uWSGI and supervisord instead of the standard run.sh (which uses Paste under the hood). I followed the Galaxy scaling guide and it was pretty accurate except for a few details. I won’t be showing the changes to Galaxy config files, they are exactly as related on that page.

I installed supervisord by doing pip install supervisor in the virtualenv that Galaxy uses. Then I put a supervisord.conf in the config/ directory of our Galaxy install and it starts like this:

[inet_http_server]
port=127.0.0.1:9001

[supervisord]

[supervisorctl]

The [inet_http_server] section directs supervisord to listen on localhost port 9001. The following two sections, [supervisord] and [supervisorctl] need to be present but can be empty. The rest of the configuration is as per that on the Scaling page with a few changes I’ll explain below:

[program:galaxy_uwsgi]
command         = /opt/galaxy/.venv/bin/uwsgi --plugin python --ini-paste /opt/galaxy/config/galaxy.ini --die-on-term
directory       = /opt/galaxy
umask           = 022
autostart       = true
autorestart     = true
startsecs       = 10
user            = galaxy
environment     = PATH=/opt/galaxy/.venv:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin,PYTHON_EGG_CACHE=/opt/galaxy/.python-eggs,PYTHONPATH=/opt/galaxy/eggs/PasteDeploy-1.5.0-    py2.7.egg,SGE_ROOT=/var/lib/gridengine
numprocs        = 1
stopsignal      = TERM

[program:handler]
command         = /opt/galaxy/.venv/bin/python ./scripts/paster.py serve config/galaxy.ini --server-name=handler%(process_num)s --pid-file=/opt/galaxy/handler%(process_num)s.pid --log-    file=/opt/galaxy/handler%(process_num)s.log
directory       = /opt/galaxy
process_name    = handler%(process_num)s
numprocs        = 2
umask           = 022
autostart       = true
autorestart     = true
startsecs       = 15
user            = galaxy
environment     = PYTHON_EGG_CACHE=/opt/galaxy/.python-eggs,SGE_ROOT=/var/lib/gridengine

The SGE_ROOT is necessary because our cluster uses Sun Grid Engine and the SGE DRMAA library requires this environment variable. Otherwise this config uses uWSGI installed (using pip) in the virtualenv that Galaxy uses.

This snipped of nginx configuration shows what was commented out and what was added to link nginx to uWSGI:

#proxy_set_header REMOTE_USER $remote_user;
#proxy_set_header X-Forwarded-Host $host;
#proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
#proxy_set_header X-URL-SCHEME https;
#proxy_pass http://galaxy_app;
uwsgi_pass 127.0.0.1:4001;
uwsgi_param UWSGI_SCHEME $scheme;
include uwsgi_params;

Then, how to start and stop it all? Firstly, the supervisord config. The basis for this was the debian-norrgard script from the supervisord initscripts repository. The final script is in this gist. Note these lines:

NAME=supervisord
GALAXY_USER=galaxy
GALAXY_HOME=/opt/galaxy
GALAXY_VENV=$GALAXY_HOME/.venv
DAEMON=$GALAXY_VENV/bin/$NAME
SUPERVISORCTL=$GALAXY_VENV/bin/supervisorctl

They link supervisord to Galaxy settings. Then /etc/init.d/galaxy is in this gist. It depends on the supervisord startup script and starts and stops Galaxy using supervisorctl.

Two things remain unsatisfactory:

  1. The shutdown of Galaxy doesn’t work reliably. The use of uWSGI’s --die-on-term and stopsignal = TERM in the supervisord.conf is an attempt to remedy this.

  2. The uWSGI config relies on the PasteDeploy egg. This exists on our Galaxy server because it was downloaded by the historical Galaxy startup script. With the switch towards wheel based (instead of egg based) packages, this script is no longer part of a Galaxy install. The uWSGI settings might need to be changed because of this, however, the PasteDeploy package is installed in the virtualenv that Galaxy uses, so perhaps no change is necessary. I haven’t tested this.

With these limitations, however, our Galaxy server is working and much more responsive than before.

Automatically commit and push IPython notebook

I’m currently teaching Python at a Software Carpentry workshop at North West University in Potchefstroom. As always there are concerns about pace and about how people can catch up if they fall behind. In a recent discussion on this topic on the Software Carpentry mailing list, David Dotson mentioned that he commits his IPython notebooks by pressing a custom keyboard shortcut which triggers an automatic git add/commit/push. No code was available, but I poked around a bit and found this StackOverflow question and answer which showed how to add a post-save hook to an IPython notebook (with details on doing the same for the newer Project Jupyter notebooks).

So here’s my code:

import os
from subprocess import check_call
from shlex import split

def post_save(model, os_path, contents_manager):
    """post-save hook for doing a git commit / push"""
    if model['type'] != 'notebook':
        return # only do this for notebooks
    workdir, filename = os.path.split(os_path)
    if filename.startswith('Scratch') or filename.startswith('Untitled'):
        return # skip scratch and untitled notebooks
    # now do git add / git commit / git push
    check_call(split('git add {}'.format(filename)), cwd=workdir)
    check_call(split('git commit -m "notebook save" {}'.format(filename)), cwd=workdir)
    check_call(split('git push'), cwd=workdir)

c.FileContentsManager.post_save_hook = post_save

This code obviously assumes that your working directory is a git repository and it has been configured with a remote to push to. For this workshop my notebooks are in this git repo on GitHub.

I created a new IPython profile (ipython profile create swcteaching) for use while teaching and added that code to the ipython_notebook_config.py file. You can find this file’s location with ipython profile locate swcteaching.

The one little niggle is that the commit message is always the same. I don’t know IPython’s front-end code well enough, but perhaps there is a way to pop up a window and request a commit message (going towards something more like David Dotson’s solution and less like mine).