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    SNAP

    SNAP (Sentinel Application Platform) is a remote sensing toolbox architecture developed by the European Space Agency. It includes tools for all common remote sensing satellites.

    Available

    SNAP is available in Puhti with following versions:

    • 8.0 (Singularity container with snappy 8.0.3 and Python 3.6.9)
    • 7.0 (with snappy 6.0 and python 2.7.5)

    The 8.0 version has been installed as a singularity container. There are small differences in the commands between 7.0 and 8.0, see below

    Installed plugins

    • Sentinel toolboxes (1,2,3)
    • All Idepix processors (only in 7.0)
    • SMOS toolbox
    • SNAPHU (only in 7.0)
    • Radarsat toolbox
    • PROBA-V toolbox
    • Sen2Cor (external tool) (only in 7.0)

    You can install more plugins to your user directory from the SNAP Graphical user interface

    Usage

    SNAP is included in the snap module and can be loaded with

    module load snap

    This loads the newest available version. You can load an older version with

    module load snap/<VERSION>

    SNAP userdir and Java temp dir configuration

    SNAP uses significant amount of storage space for cache and temporary files. By default these are written to your HOME directory and may easily fill your HOME. For avoiding that configure your snap user directory and Java temporary folder. You should run this script every time you start using SNAP in Puhti or want to change the used folders.

    After loading the module run

    source snap_add_userdir <YOUR-PROJECTS-SCRATCH-FOLDER>

    You could also request a fast nvme disk in a batch job and run the command first in the batch job so that all the temp/cache files are written to a fast disk rather than the scratch. It might provide speed improvement in demanding calculations.

    source snap_add_userdir $LOCAL_SCRATCH with batch jobs

    source snap_add_userdir $TMPDIR with interactive jobs

    This scripts sets also Java temporary folder, it is set to be snap/temp subfolder in the folder you defined. If you want to set Java temporary folder to be somewhere else use: export _JAVA_OPTIONS=-Djava.io.tmpdir=<SOME-FOLDER>

    Note

    The graphical user interface does not follow snap.userdir setting, but it notices the Java setting. Using SNAP GUI will create a .snap folder inside your HOME directory and fill it. Empty it if you run out of space in your HOME directory.

    Using SNAP with graphical user interface

    If you have connected with NoMachine or have X11 enabled on your SSH connection, you can launch a graphical user interface on an interactive batch job session

    SNAP 8.0

    sinteractive -i
<set up snap.userdir>
singularity_wrapper exec snap

    SNAP 7.0

    sinteractive -i
<set up snap.userdir>
snap

    Note

    We recommend using NoMachine for launching graphical user interfaces on Puhti

    Using SNAP with Graph Processing Tool (gpt) command

    The Graph Processing Tool gpt is a command line tool used for bulk processing. It can be run for example with the following commands

    SNAP 8.0

    singularity_wrapper exec gpt <full_path_to_graph_xml_file> -Pfile=<inputfile> -t <outputfile>

    SNAP 7.0

    gpt <full_path_to_graph_xml_file> -Pfile=<inputfile> -t <outputfile>

    Some relevant gpt options include

    • -q Number of threads the gpt instance will use. Set it to the number of CPU cores requested or more
    • -c Cache size in bytes. Change this if storage space becomes an issue
    • -x Clear internal tile cache after writing a complete row of tiles to output file. Add this if memory becomes an issue

    More information on the SNAP command line tutorial

    There is a also a custom made gpt_array command that allows the usage of gpt with Puhti array jobs. It solves the problem of multiple jobs using the same cache folder. The command is otherwise the same as gpt but you include the cache-folder's path as first argument. In an array job you can define that cache folder dynamically with the iterating environment variable $SLURM_ARRAY_TASK_ID and make sure each job has an individual cache folder. SNAP 8.0

    singularity_wrapper exec gpt_array /scratch/<project>/snap/tmp_snap_userdir_"$SLURM_ARRAY_TASK_ID" <normal gpt arguments>

    SNAP 7.0

    gpt_array /scratch/<project>/snap/tmp_snap_userdir_"$SLURM_ARRAY_TASK_ID" <normal gpt arguments>

    Here is a full example of using gpt_array with Puhti array jobs

    Using SNAP with the Python library snappy

    It is also possible to access SNAP functionalities from Python with the snappy library.

    SNAP 8.0

    Running snappy scripts with batch jobs:

    singularity_wrapper exec python3 <YOUR-PYTHON-SCRIPT>

    See available packages:

    singularity_wrapper exec pip list

    Installing new packages to your HOME directory, see geoconda instructions how to change installation directory.

    singularity_wrapper exec pip <NEW-PACKAGE-NAME> --user

    SNAP 7.0

    The SNAP 7.0 has a conda environment that includes pandas, geopandas, rasterio, rasterstats, sentinelsat, spyder

    for retrieving the full list in Puhti use: list-packages

    License and citing

    All SNAP software is published under the GPL-3 license and its sources are available on GitHub.

    In your publications please acknowledge also oGIIR and CSC, for example “The authors wish to acknowledge for computational resources CSC – IT Center for Science, Finland (urn:nbn:fi:research-infras-2016072531) and the Open Geospatial Information Infrastructure for Research (oGIIR, urn:nbn:fi:research-infras-2016072513).”

    References

    Last edited Fri Mar 12 2021