Category Archives: HPC

Markus Neteler joins the management of mundialis in Bonn

Press release

From March 2016 onwards, Dr. Markus Neteler, a prominent head of the Open Source GIS scene, will join the management board of mundialis GmbH & Co. KG in Bonn, Germany. Founded in 2015, mundialis combines remote sensing and satellite data analysis in the field of Big Data with Open Source WebGIS solutions.

Since 2008, Dr. Neteler was the head of the GIS and remote sensing unit at the Edmund Mach Foundation in Trento (Italy) and worked in this capacity on numerous projects related to biodiversity, environmental and agricultural research. He is also a founding member of the Open Source Geospatial Foundation (OSGeo), a nonprofit organization with headquarters in Delaware (USA), that promotes the development and use of free and open source geographic information systems (GIS). Since 1998 he coordinated the development of the well known GRASS GIS software project, a powerful Open Source GIS that supports processing of time series of several thousand raster, 3D raster or vector maps in a short time. Mongolia as seen by Sentinel-2A

Markus will keep his role as “Mr. GRASS” at mundialis, especially because the company also sees itself as a research and development enterprise that puts its focus on the open source interfaces between geoinformation and remote sensing. Although a new company, mundialis offers more than 50 years of experience in GIS, due to the background of its management. Besides Neteler, there are Till Adams and Hinrich Paulsen, both at the same time the founders and CEOs of terrestris in Bonn, a company that develops Open Source GIS solutions since 2002. These many years of experience in the construction of WebGIS and Geoportal architectures using free software as well as in the application of common OGC standards – are now combined with mundialis’ expertise in the processing of big data with spatial reference and remote sensing data.

Contact: http://www.mundialis.de/

Building a cluster for GRASS GIS and other software from the OSGeo stack

Lucky to have (access to) a cluster? Here some notes on how to do geospatial number crunching on it a.k.a. HPC (High Performance Computing).

Preparing the disks
We decided to use the ext3 file system. An initial problem was the formatting of the RAID5 disk set since it exceeded the file system specifications. Then, setting the ext3 block size to 4k instead of 1k we could format it.

Storage: a home for GIS data
The disks are available via NFS to all nodes (blades in our case). All raw/original data sets and the GRASS database are sitting in an NFS exported directory which I even link on my laptop to easily add/access/modify stuff.

Front-end machine and blades configuration
The cluster is a (currently) 56CPU blades system, we’ll expand to 128 CPUs later this year (16 blades with 2 procs a 4 core and 16GB RAM per blade). Additionally, we have a front-end machine to run the job manager and to link in further disks, all via NFS.
The blades are configured diskless, i.e. that once started, they receive their operating system from the front end machine via network (10GB/s ethernet). Like this, we have a single directory on the front end which contains all software, this is then propagated to all blades. Very convenient. We use Scientific Linux (the LiveDVD copied onto the disk, there is a special directory to store your modifications which are then merged in on the fly once you boot the blades, pretty cool concept). The job software is (SUN) Grid Engine, also free software. Job control with GRASS I have described here:

http://grass.osgeo.org/wiki/Parallel_GRASS_jobs
-> Grid Engine

GRASS: Avoiding replicated import of large data files through virtual linking
New in GRASS 6.4 is that you can just register a geodata file on the fly with r.external. Altogether I have 1.4TB of new GIS data from our province, naturally I didn’t want to by a new disk array just for my provincial GRASS location! Here r.external comes handy to minimize the “import” to a few bytes. As expected, it leverages GDAL to get data into GRASS, the overhead is minimal.

Power consumption
Power consumption is measured, too: The entire system consumes around 2000W (each blade less than 200W), so it’s going into the direction of “green” computing (there is no such thing!). If we had a solar panel at least…

Outcome
All in all a very nice solution. I made a stress test and removed all internal switches and shut down the blades while I was processing 8000 MODIS satellite maps. Everything survived and the Grid engine job manager collected the crashed jobs and restarted them without complaining. All resulting maps are collected in the target GRASS mapset and could be even exported to common GIS formats, if needed.
If you want to run Web Processing Services (e.g., pyWPS), you can likewise send each session to a node, giving you enormous possibilities for your customers.