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== Parallel GRASS jobs ==
== Parallel GRASS jobs ==


NOTE: GRASS 6 libraries are NOT thread safe (except for GPDE, see below).
The idea of parallel GRASS GIS jobs is to speed up the computation.
 
=== Background ===
 
This presentation from 2022 is a "must see":
 
'''[https://htmlpreview.github.io/?https://github.com/petrasovaa/FUTURES-CONUS-talk/blob/main/foss4g2022.html Tips for parallelization in GRASS GIS]'''
 
This you should know about GRASS' behaviour concerning multiple jobs:
* You can run '''multiple processes''' in '''multiple locations''' ([https://grass.osgeo.org/grass-stable/manuals/helptext.html what's that?]). ''Peaceful coexistence.''
* You can run multiple processes in the same mapset, but only if the region is untouched. If you are unsure, it's recommended to  launch each job in its own mapset within the location.
* You can run '''multiple processes''' in the '''same location''', but in '''different mapsets'''. ''Peaceful coexistence.''
 
=== Approaches ===
 
See also the [[Parallelizing Scripts]] wiki page
 
== File locking ==


GRASS doesn't perform any locking on the files within a GRASS
GRASS doesn't perform any locking on the files within a GRASS
Line 26: Line 43:
See below for ways around these limitations.
See below for ways around these limitations.


=== Background ===
== Working with tiles ==
 
This you should know about GRASS' behaviour concerning multiple jobs:
* You can run '''multiple processes''' in '''multiple locations''' ([http://grass.osgeo.org/grass64/manuals/html64_user/helptext.html what's that?]). ''Peaceful coexistence.''
* You can run multiple processes in the same mapset, but only if the region is untouched (but it's really not recommended). Better launch each job in its own mapset within the location.
* You can run '''multiple processes''' in the '''same location''', but in '''different mapsets'''. ''Peaceful coexistence.''
 
=== Approach ===
 
Essentially there are at least two approaches of "poor man" parallelization without modifying GRASS source code:
* split map into spatial chunks (possibly with overlap to gain smooth results)
* time series: run each map elaboration on a different node.
 
== Parallelized code ==
=== GPDE using OpenMP ===
 
The only parallelized library in GRASS >=6.3 is GRASS Partial Differential Equations Library (GPDE). Read more in [[OpenMP]].
 
=== GPU Programming ===


* See [[GPU]]
Huge map reprojection example:


== Cluster and Grid computing ==
'''Q:''' I'd like to try splitting a large raster into small chunks and then projecting each one separately, sending the project command to the background. The problem is that, if the GRASS command changes the region settings, things might not work.


=== Grid Engine ===
'''A:''' {{cmd|r.proj}} doesn't change the region.


* URL: <strike>[http://waybackmachine.org/*/gridengine.sunsource.net http://gridengine.sunsource.net/]</strike> (new site at http://sourceforge.net/projects/gridscheduler/)
Processing the map in chunks requires setting a different region for
* Lauching jobs: qsub
each command. That can be done by creating named regions and using the
* Navigating the Grid Engine System with GUI: qmon
WIND_OVERRIDE environment variable, e.g.:
* Job statstics: qstat -f
* User statstics: qacct -o


'''General steps (for multiple serial jobs on many CPUs):'''
* Job definition
** Grid Engine setup (in the header): define calculation time, number of nodes, number of processors, amount of RAM for individual job;
** data are stored in centralized directory which is seen by all nodes, often mounted via NFS;
* Job execution (launch of jobs)
** user launches all jobs ("qsub"), they are submitted to the queue.
** the scheduler optimizes among all user the execution of the jobs according to available resources and requested resources;
** for the user this means that 0..max jobs are executed in parallel (unless the administrators didn't define either priority or limits). The user can then observe the job queue ("qstat") to see other jobs ahead and scheduling of own jobs. Once a job is running, the cluster possibly sends a notification email to the user, the same again when a job is terminating or is aborted.
** At the end of the worker script call a second batch job which only contains g.copy to copy the result into a common mapset.
* Job planning
** The challenging part for the user is to estimate the request for number of nodes and CPUs per node as well as the amount of needed RAM. Usually tests are needed to see the performance in order to impose the values correctly in the Grid Engine script (see below).
==== The Grid Engine script ====
Job launcher: 'launch_grassjob_on_GE.sh' to launch GRASS jobs with Grid Engine:
<source lang="bash">
<source lang="bash">
#!/bin/sh
      g.region ... save=region1
      g.region ... save=region2
# Serial job, MODIS LST elaboration
      ...
# Markus Neteler, 2008, 2011
      WIND_OVERRIDE=region1 r.proj ... &
      WIND_OVERRIDE=region2 r.proj ... &
## GE settings
      ...
# request Bourne shell as shell for job
</source>
#$ -S /bin/sh
# run in current working directory
#$ -cwd
# We want Grid Engine to send mail when the job begins and when it ends.
#$ -M neteler@somewhere.it
#$ -m abe
# uncomment next line for bash debug output
#set -x
############
# SUBMIT from home dir to node:
#  cd $HOME
#  qsub -cwd -l mem_free=3000M -v MYMODIS=aqua_lst1km20020706.LST_Night_1km.filt launch_grassjob_on_GE.sh
#
# WATCH
#  watch 'qstat | grep "$USER\|job-ID"'
#    Under the state column you can see the status of your job. Some of the codes are
#    * r: the job is running
#    * t: the job is being transferred to a cluster node
#    * qw: the job is queued (and not running yet)
#    * Eqw: an error occurred with the job
#
###########


# better say where to find libs and bins:
(for python see the grass.use_temp_region() function)
export PATH=$PATH:$HOME/binaries/bin:/usr/local/bin:$HOME/sge_batch_jobs
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/binaries/lib/


# generate machine (blade) unique TMP string
The main factor which is likely to affect parallelism is the fact that the processes won't share their caches, so there'll be some degree of inefficiency if there's substantial overlap between the source areas for the processes.
UNIQUE=`mktemp`
MYTMP=`basename $UNIQUE`


# path to GRASS binaries and libraries:
If you have more than one such map to project, processing entire maps in parallel might be a better choice (so that you get N maps projected in 10 hours rather than 1 map in 10/N hours).
export GISBASE=/usr/local/grass-6.4.1svn
export PATH=$PATH:$GISBASE/bin:$GISBASE/scripts
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GISBASE/lib


# use process ID (PID) as GRASS lock file number:
== Parallelized code ==
export GIS_LOCK=$$
export GRASS_MESSAGE_FORMAT=plain
export TERM=linux
 
# use Grid Engine jobid + unique string as MAPSET to avoid GRASS lock
MYMAPSET=sge.$JOB_ID.$MYTMP
MYLOC=patUTM32
MYUSER=$MYMAPSET
TARGETMAPSET=modisLSTinterpolation
 
# Note: remember to to use env vars for variable transfer
GRASS_BATCH_JOB=$HOME/binaries/bin/modis_interpolation_GRASS_RST.sh
 
# Note: remember to to use env vars for variable transfer
export MODISMAP="$MYMODIS"
 
# print nice percentages:
export GRASS_MESSAGE_FORMAT=plain


################ nothing to change below ############
=== OpenMP ===
#execute_your_command


echo "************ Starting job at `date` on blade `hostname` *************"
Good for a single system with a multi-core CPU.


# DEBUG turn on bash debugging, i.e. print all lines to
Configure GRASS 7 with:
# standard error before they are executed
./configure --with-openmp
# set -x


echo "SGE_ROOT $SGE_ROOT"
==== GPDE using OpenMP ====
echo "The cell in which the job runs $SGE_CELL. Got $NSLOTS slots on $NHOSTS hosts"


# temporarily store *locally* the stuff to avoid NFS overflow/locking problem
The only parallelized library in GRASS >=6.3 is GRASS Partial Differential Equations Library (GPDE) and the gmath library in GRASS 7. Read more in [[OpenMP]].
## Remove XXX to enable
grep XXX/storage/local /etc/mtab >/dev/null && (
if test "$MYMAPSET" = ""; then
  echo "You are crazy to not define \$MYMAPSET. Emergency exit."
  exit 1
else
  rm -rf /storage/local/$MYMAPSET
fi
        # (create new mapset on the fly)
mkdir /storage/local/$MYMAPSET
ln -s /storage/local/$MYMAPSET /grassdata/$MYLOC/$MYMAPSET
if [ $? -ne 0 ] ; then
  echo "ERROR: Something went wrong creating the local storage link..."
  exit 1
fi
) || ( # in case that /storage/local is unmounted:
        # (create new mapset on the fly)
        mkdir /grassdata/$MYLOC/$MYMAPSET
)


=== Python ===


# Set the global grassrc file to individual file name
[http://grass.osgeo.org/grass73/manuals/libpython/pygrass.modules.interface.html?highlight=parallelmodulequeue#pygrass.modules.interface.module.ParallelModuleQueue PyGRASS ParallelModuleQueue]
MYGISRC="$HOME/.grassrc6.$MYUSER.`uname -n`.$MYTMP"


#generate GISRCRC
=== pthreads ===
echo "GISDBASE: /grassdata" > "$MYGISRC"
echo "LOCATION_NAME: $MYLOC" >> "$MYGISRC"
echo "MAPSET: $MYMAPSET" >> "$MYGISRC"
echo "GRASS_GUI: text" >> "$MYGISRC"


# path to GRASS settings file
Note: only used in the r.mapcalc ''parser''!
export GISRC=$MYGISRC


# fix WIND in the newly created mapset
Good for a single system with a multi-core CPU.
cp "/grassdata/$MYLOC/PERMANENT/DEFAULT_WIND" "/grassdata/$MYLOC/$MYMAPSET/WIND"
db.connect -c --quiet


# run the GRASS job:
Configure GRASS 7 with:
. $GRASS_BATCH_JOB
./configure --with-pthread


# cleaning up temporary files
The ''parser'' of {{cmd|r.mapcalc}} in GRASS 7 has been parallelized using GNU {{wikipedia|pthreads}}. The computation itself is executed serially.
$GISBASE/etc/clean_temp > /dev/null
rm -f ${MYGISRC}
rm -rf /tmp/grass6-$USER-$GIS_LOCK
# leave breadcrumb to find related mapsets back when moving results
# into final mapset:
touch /storage/local/$MYMAPSET/$JOB_NAME
# move data back from local disk to NFS
## Remove XXX to enable
grep XXX/storage/local /etc/mtab >/dev/null && (
if test "$MYMAPSET" = ""; then
  echo "You are crazy to not define \$MYMAPSET. Emergency exit."
  exit 1
else
  # rm temporary link:
  rm -fr /grassdata/$MYLOC/$MYMAPSET/.tmp
  rm -f /grassdata/$MYLOC/$MYMAPSET
  # copy stuff
  cp -rp /storage/local/$MYMAPSET /grassdata/$MYLOC/$MYMAPSET
  if [ $? -ne 0 ] ; then
    echo "ERROR: Something went wrong copying back from local storage to NFS directory..."
    exit 1
  fi
  rm -rf /storage/local/$MYMAPSET
fi
)


echo "************ Finished at `date` *************"
=== Bourne and Python Scripts ===
exit 0
</source>


==== The GRASS worker script ====
Good for a single system with a multi-core CPU.


The '''real GRASS job''' is just the bare script (no #!/bin/sh nor exit 0 must be included) containing the commands to be executed. As defined in 'launch_grassjob_on_GE.sh', it must be stored as '$HOME/binaries/bin/modis_interpolation_GRASS_RST.sh':
Often very easy & can be done without modification to the main source code.


<source lang="bash">
* See the [[Parallelizing Scripts]] wiki page
# GRASS job for usage in Grid Engine
###################################
# MN 2008, 2011


# $MYMODIS is passed on via qsub job submission (-v variable)
=== OpenMPI ===
r.info $MYMODIS
# do something
</source>


Good for a multi-system cluster connected by a fast network.


==== Collecting the results ====
The {{AddonCmd|GIPE}} ''i.vi.mpi'' addon module has been created as a MPI ({{wikipedia|Message Passing Interface}}) implementation of the {{AddonCmd|GIPE}} ''i.vi'' addon module.
* See also the [[Agriculture and HPC]] wiki page.


Finally, since we leave the temporary mapsets as is in the Grid Engine processing, we have to '''collect all results''' and store them into the target mapset. We do this by checking all mapsets which contain the breadcrumb left therein (launch job script name as emtpy file, see above). This scripts 'gcollector_job.sh' checks and transfers the map(s):
=== MPI Programming ===
<source lang="bash">
#!/bin/sh


# Markus Neteler, 2011
There is a sample implementation at module level in [https://github.com/OSGeo/grass-addons/tree/grass8/src/imagery/i.vi.mpi i.vi.mpi]
# Copy all raster maps from the temporaneous Grid Engine mapsets into target mapset


if [ $# -ne 3 ] ; then
=== GPU Programming ===
  echo "Script to move Grid Engine job results to GRASS target mapset"
  echo ""
  echo "Usage: $0 targetlocation targetmapset name_of_launch_script"
  echo "Example:"
  echo "  $0 patUTM32  modis_final launch_grassjob_on_GE.sh"
  exit 0
fi


# define location to work in
Good for certain kinds of calculations (e.g. ray-tracing) on a single system with a fast graphics card.
GRASSDBROOT=/grassdata
MYLOC=$1
MYMAPSET=$2
BREADCRUMBFILE=$3


# path to GRASS binaries and libraries:
There is a version of the {{cmd|r.sun}} module which has been modified to use {{wikipedia|OpenCL}}. (works; still experimental)
export GISBASE=/usr/local/grass-6.4.1svn
export PATH=$PATH:$GISBASE/bin:$GISBASE/scripts
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GISBASE/lib


# use process ID (PID) as GRASS lock file number:
* See [[GPU]]
export GIS_LOCK=$$
export GRASS_MESSAGE_FORMAT=plain


# path to GRASS settings file
Configure GRASS GIS with:
export GISRC=$HOME/.grassrc6
  ./configure --with-opencl
GISDBASE=`cat $GISRC | grep GISDBASE | cut -d' ' -f2`


TOCOLLECTFILE=to_be_collected_$JOB_NAME.csv
== Cluster and Grid computing ==
find $GRASSDBROOT/$MYLOC/sge* -type f -name "$BREADCRUMBFILE" > $GRASSDBROOT/$MYLOC/$TOCOLLECTFILE
 
rm -f $GRASSDBROOT/$MYLOC/clean_$TOCOLLECTFILE
for myname in `cat $GRASSDBROOT/$MYLOC/$TOCOLLECTFILE` ; do
    basename `dirname $myname` >> $GRASSDBROOT/$MYLOC/clean_$TOCOLLECTFILE
done
 
LIST=`cat $GRASSDBROOT/$MYLOC/clean_$TOCOLLECTFILE`
rm -f $GRASSDBROOT/$MYLOC/clean_$TOCOLLECTFILE
 
countmapsets=0
countmaps=0
for mapset in $LIST ; do
    countmapsets=`expr $countmapsets + 1`
    MAPS=`g.mlist rast mapset=$mapset`
    for map in $MAPS ; do
        countmaps=`expr $countmaps + 1`
g.copy rast=$map@$mapset,$map --o
    done
done
 
rm -f $GRASSDBROOT/$MYLOC/$MYMAPSET/.gislock
unset $GISBASE $GIS_LOCK $GRASS_MESSAGE_FORMAT $GISRC
 
echo "----------------------------------------------------"
echo "In total $countmaps maps transferred from $countmapsets mapsets into $MYMAPSET"
echo "Now you can remove all maps with:
  cd $GISDBASE/$MYLOC/
  rm -rf \`cat $GRASSDBROOT/$MYLOC/$TOCOLLECTFILE | sed \"s+$BREADCRUMBFILE++g\"\`
  rm -f $GRASSDBROOT/$MYLOC/$TOCOLLECTFILE
"
exit 0
</source>
 
 
==== Launching a single job ====
 
To submit a '''single''' job from home directory to cluster node, enter:
<source lang="bash">
cd $HOME
qsub -cwd -l mem_free=3000M -v MYMODIS=aqua_lst1km20020706.LST_Night_1km.filt launch_grassjob_on_GE.sh
sh gcollector_job.sh patUTM32 modis_final launch_grassjob_on_GE.sh
</source>


A cluster or grid computing system  consists of a number of computers that are tightly coupled together. The manager or master controls the utilization of compute nodes.


==== Launching many jobs ====
=== Job scheduler ===


To submit a '''series of jobs''', use a "for" loop as described in the PBS section above.
Common job schedulers are [https://slurm.schedmd.com/ SLURM], [http://www.adaptivecomputing.com/products/open-source/torque/ TORQUE], [http://www.pbspro.org/ PBS], [https://arc.liv.ac.uk/trac/SGE Son of Grid Engine], and [https://kubernetes.io/ kubernetes]
In the HOME directory stdout and stderr logs will be stored for each job.


We do this by simply looping over all map names to elaborate:
See also [https://slurm.schedmd.com/rosetta.html Rosetta Stone of Workload Managers]
<source lang="bash">
      cd $HOME
      # loop and launch (we just pick the names from the GRASS DB itself; here: do all maps)
      # instead of launching immediately, we create a launch script:
      for i in `find /grassdata/myloc/modis_originals/cell/ -name '*'` ; do
          NAME=`basename $i`
          echo qsub -v MYMODIS=$NAME ./launch_grassjob_on_GE.sh
      done | sort > launch1.sh


      # now really launch the jobs:
A job consists of tasks, e.g. processing of a single raster map in a time series of many raster maps. Jobs are assigned to a queue and started as soon as a slot in the queue is free. Jobs are removed from the queue once they finished.
      sh launch1.sh
</source>


That's it! Emails will arrive to notify upon begin, abort (hopefully not!) and end of job execution.
=== GRASS on a cluster ===


After '''all jobs are completed''', run the 'gcollector_job.sh' script from above
If you want to launch several GRASS jobs in parallel, you might consider to launch each job in its own mapset.


=== PBS Scheduler ===
* set up chunks of data to be processed (temporal or spatial, temporal chunks are usually easier to handle)
* write a script with the actual processing of one chunk
* write a script that initializes GRASS, creates a unique mapset, executes the script with the actual processing, and copies the results to a common mapset
* add that script as a task to a job, create one job for each data chunk


It works similar to Grid Engine, see above.
The general concept is to create a script that


=== OpenMosix ===
# creates a unique temporary mapset
# creates a unique temporary GISRC file for this mapset
# does the processing in this mapset
# changes to the target mapset by updating the GISRC file, verify with g.gisenv
# copies results from the temporary mapset to the target mapset
# deletes the temporary mapset and GISRC file


''NOTE: The openMosix Project has officially closed as of March 1, 2008.''
Such a script should not call grassXY and must be executable outside GRASS, because it is establishing a GRASS session, performing some processing, and closing the GRASS session, all by itself. See also [[GRASS_and_Shell|GRASS and Shell]].


If you want to launch several GRASS jobs in parallel, you have to launch each job in its own mapset. Be sure to indicate the mapset correctly in the GISRC file (see above). You can use the process ID (PID, get with $$ or use PBS jobname) to generate a almost unique number which you can add to the mapset name.
Such a script will take arguments to specify the particular data to be processed.


A job specification for an HPC job scheduler would then contain this script with specific arguments.


Now you could launch the jobs on an [http://openmosix.sourceforge.net/ openMosix cluster] (just install openMosix on your colleague's computers...).
The common bottleneck when using GRASS on a cluster is often disk I/O. Try to start the jobs with nice/ionice to reduce strain on the storage devices.


== Cloud computing ==
== Cloud computing ==


GRASS GIS 7 is running in the cloud as web processing service backend. Have a look at:
GRASS GIS is running in the cloud as web processing service backend. Have a look at:


{{YouTube|jg2pb_Xjq8Y&vq|desc=GRASS 7 in the cloud (by Sören Gebbert)}}
{{YouTube|jg2pb_Xjq8Y|desc=GRASS 7 in the cloud (by Sören Gebbert)}}


This Open Cloud GIS has been set up in a private Amazon compatible cloud environment using:
This Open Cloud GIS has been set up in a private Amazon compatible cloud environment using:
Line 373: Line 179:
* wps-grass-bridge latest svn
* wps-grass-bridge latest svn
* QGIS 1.7 with a modified QWPS plugin
* QGIS 1.7 with a modified QWPS plugin
For latest development, visit: https://github.com/actinia-org/actinia-core
== GRASS GIS on VPS ==
Instructions to run GRASS GIS on a commercial VPS to do some memory-intensive operations:
https://plantarum.ca/2014/08/19/medium-performance-cluster-computing/


== Hints for NFS users ==
== Hints for NFS users ==
Line 378: Line 192:
* be careful with concurrent file writing (use "lockfile" locking, the lockfile command is provided by [http://www.procmail.org/ procmail]);
* be careful with concurrent file writing (use "lockfile" locking, the lockfile command is provided by [http://www.procmail.org/ procmail]);
* store as much temporary data as possible (even the final maps) on the local blade disks if you have.
* store as much temporary data as possible (even the final maps) on the local blade disks if you have.
* finally collect all results from local blade disks *after* the parallel job execution in a sequential collector jog (I am writing that now) to not kill NFS. For example, Grid Engine offers a "hold" function to only execute the collector job after having done the rest.
* finally collect all results from local blade disks *after* the parallel job execution in a sequential collector job (I am writing that now) to not kill NFS. For example, Grid Engine offers a "hold" function to only execute the collector job after having done the rest.
* If all else fails, and the I/O load is not too great, consider using {{wikipedia|sshfs}} with ssh passkeys instead of NFS.
* In some situations it is necessary to preserve the same directory structure on all nodes, and symlinks are a nice way to do that, but some (closed source 3rd party which will remain nameless) software insists on expanding symlinks. In this situation the [http://code.google.com/p/bindfs/ bindfs] FUSE extension can help. It is safer to use than "mount" binds, and you don't have to be root to set them up. As with ''sshfs'' there is a performance penalty so it may not be appropriate in high I/O situations.
 
== Error: Too many open files ==
 
When working with long time series and {{cmd|r.series}} starts to complain that files are missing/not readable or the message
Too many open files
 
For a solution, see [[Large_raster_data_processing#Number_of_open_files_limitation]]


== Misc Tips & Tricks ==
== Misc Tips & Tricks ==
See the poor-man's multi-processing script on the [[Parallelizing Scripts]] wiki page. This approach has been used in the {{cmd|r3.in.xyz}} script.
== Workshop on Parallelization ==
Haedrich, C., Petrasova, A. Parallelization for big EO data processing, OpenGeoHub Summer School 2023
* https://doi.org/10.5446/63123


* When working with long time series and {{cmd|r.series}} starts to complain that files are missing/not readable, check if you opened more than 1024 files in this process. this is the typical limit (check with ulimit -n). To overcome this problem, the admin has to add in /etc/security/limits.conf something like this:
'''Schedule'''


  # Limit user nofile - max number of open files
Session 1
  * soft  nofile 1500
* [Slides] Introduction to Parallelization, GRASS GIS and Python
  * hard  nofile 1800
* [Lab] Introduction to Parallelization with GRASS GIS and Python Notebook


For less invasive solution which still requires root access, see [http://lists.osgeo.org/pipermail/grass-dev/2008-November/040886.html here].
Session 2
* [Lab] Parallelization Case Study: Urban Growth Modeling


* See the poor-man's multi-processing script on the [[OpenMP]] wiki page. This approach has been used in the {{AddonCmd|r3.in.xyz}} addon script.
Jupyter Notebook:
* https://github.com/ncsu-geoforall-lab/opengeohub-2023
** https://github.com/ncsu-geoforall-lab/opengeohub-2023/blob/main/01_intro_to_GRASS_parallelization.ipynb


== See also ==
== See also ==


This Wiki:
* [[GRASS_and_Shell#Automated_batch_jobs:_Setting_the_GRASS_environmental_variables|GRASS batch jobs]] (by settings env. variables)
* [[GRASS_and_Shell#Automated_batch_jobs:_Setting_the_GRASS_environmental_variables|GRASS batch jobs]] (by settings env. variables)
* The [[OpenMP]] wiki page.
* The [[OpenMP]] wiki page.
* [http://gfoss.blogspot.com/2008/11/building-cluster-for-grass-gis-and.html Building a cluster for GRASS GIS and other software from the OSGeo stack]
* The [[Parallelizing Scripts]] wiki page.
* [[GPU]]
* [[GPU]] computing


Elsewhere:
* [https://neteler.org/blog/building-a-cluster-for-grass-gis-and-other-software-from-the-osgeo-stack/ Building a cluster for GRASS GIS and other software from the OSGeo stack]
* [https://research.csc.fi/geocomputing Using supercomputers for spatial analysis]
* [https://github.com/csc-training/geocomputing/tree/master/grass GRASS batch job and parallelization examples for a supercomputer with SLURM]


[[Category:Parallelization]]
[[Category:Parallelization]]
[[Category: massive data analysis]]

Latest revision as of 19:43, 27 December 2023

Parallel GRASS jobs

The idea of parallel GRASS GIS jobs is to speed up the computation.

Background

This presentation from 2022 is a "must see":

Tips for parallelization in GRASS GIS

This you should know about GRASS' behaviour concerning multiple jobs:

  • You can run multiple processes in multiple locations (what's that?). Peaceful coexistence.
  • You can run multiple processes in the same mapset, but only if the region is untouched. If you are unsure, it's recommended to launch each job in its own mapset within the location.
  • You can run multiple processes in the same location, but in different mapsets. Peaceful coexistence.

Approaches

See also the Parallelizing Scripts wiki page

File locking

GRASS doesn't perform any locking on the files within a GRASS database, so the user may end up with one process reading a file while another process is in the middle of writing it. The most problematic case is the WIND file, which contains the current region, although there are others.

If a user wants to run multiple commands concurrently, steps need to be taken to ensure that this type of conflict doesn't happen. For the current region, the user can use the WIND_OVERRIDE environment variable to specify a named region which should be used instead of the WIND file.

Or the user can use the GRASS_REGION environment variable to specify the region parameters (the syntax is the same as the WIND file, but with newlines replaced with semicolons). With this approach, the region can only be read, not modified.

Problems can also arise if the user reads files from another mapset while another session is modifying those files. The WIND file isn't an issue here, nor are the files containing raster data (which are updated atomically), but the various support files may be.

See below for ways around these limitations.

Working with tiles

Huge map reprojection example:

Q: I'd like to try splitting a large raster into small chunks and then projecting each one separately, sending the project command to the background. The problem is that, if the GRASS command changes the region settings, things might not work.

A: r.proj doesn't change the region.

Processing the map in chunks requires setting a different region for each command. That can be done by creating named regions and using the WIND_OVERRIDE environment variable, e.g.: 

       g.region ... save=region1
       g.region ... save=region2
       ...
       WIND_OVERRIDE=region1 r.proj ... &
       WIND_OVERRIDE=region2 r.proj ... &
       ...

(for python see the grass.use_temp_region() function)

The main factor which is likely to affect parallelism is the fact that the processes won't share their caches, so there'll be some degree of inefficiency if there's substantial overlap between the source areas for the processes.

If you have more than one such map to project, processing entire maps in parallel might be a better choice (so that you get N maps projected in 10 hours rather than 1 map in 10/N hours).

Parallelized code

OpenMP

Good for a single system with a multi-core CPU.

Configure GRASS 7 with: 

./configure --with-openmp

GPDE using OpenMP

The only parallelized library in GRASS >=6.3 is GRASS Partial Differential Equations Library (GPDE) and the gmath library in GRASS 7. Read more in OpenMP.

Python

PyGRASS ParallelModuleQueue

pthreads

Note: only used in the r.mapcalc parser!

Good for a single system with a multi-core CPU.

Configure GRASS 7 with: 

./configure --with-pthread

The parser of r.mapcalc in GRASS 7 has been parallelized using GNU pthreads. The computation itself is executed serially.

Bourne and Python Scripts

Good for a single system with a multi-core CPU.

Often very easy & can be done without modification to the main source code.

OpenMPI

Good for a multi-system cluster connected by a fast network.

The GIPE i.vi.mpi addon module has been created as a MPI (Message Passing Interface) implementation of the GIPE i.vi addon module.

MPI Programming

There is a sample implementation at module level in i.vi.mpi

GPU Programming

Good for certain kinds of calculations (e.g. ray-tracing) on a single system with a fast graphics card.

There is a version of the r.sun module which has been modified to use OpenCL. (works; still experimental)

Configure GRASS GIS with: 

 ./configure --with-opencl

Cluster and Grid computing

A cluster or grid computing system consists of a number of computers that are tightly coupled together. The manager or master controls the utilization of compute nodes.

Job scheduler

Common job schedulers are SLURM, TORQUE, PBS, Son of Grid Engine, and kubernetes

See also Rosetta Stone of Workload Managers

A job consists of tasks, e.g. processing of a single raster map in a time series of many raster maps. Jobs are assigned to a queue and started as soon as a slot in the queue is free. Jobs are removed from the queue once they finished.

GRASS on a cluster

If you want to launch several GRASS jobs in parallel, you might consider to launch each job in its own mapset.

  • set up chunks of data to be processed (temporal or spatial, temporal chunks are usually easier to handle)
  • write a script with the actual processing of one chunk
  • write a script that initializes GRASS, creates a unique mapset, executes the script with the actual processing, and copies the results to a common mapset
  • add that script as a task to a job, create one job for each data chunk

The general concept is to create a script that

  1. creates a unique temporary mapset
  2. creates a unique temporary GISRC file for this mapset
  3. does the processing in this mapset
  4. changes to the target mapset by updating the GISRC file, verify with g.gisenv
  5. copies results from the temporary mapset to the target mapset
  6. deletes the temporary mapset and GISRC file

Such a script should not call grassXY and must be executable outside GRASS, because it is establishing a GRASS session, performing some processing, and closing the GRASS session, all by itself. See also GRASS and Shell.

Such a script will take arguments to specify the particular data to be processed.

A job specification for an HPC job scheduler would then contain this script with specific arguments.

The common bottleneck when using GRASS on a cluster is often disk I/O. Try to start the jobs with nice/ionice to reduce strain on the storage devices.

Cloud computing

GRASS GIS is running in the cloud as web processing service backend. Have a look at:


Load video
YouTube
GRASS 7 in the cloud (by Sören Gebbert)

This Open Cloud GIS has been set up in a private Amazon compatible cloud environment using:

  • Ubuntu 10.04 LTS and 10.10 cloud server edition
  • Eucalyptus Cloud
  • GRASS GIS 7 latest svn
  • PyWPS latest svn
  • wps-grass-bridge latest svn
  • QGIS 1.7 with a modified QWPS plugin

For latest development, visit: https://github.com/actinia-org/actinia-core

GRASS GIS on VPS

Instructions to run GRASS GIS on a commercial VPS to do some memory-intensive operations:

https://plantarum.ca/2014/08/19/medium-performance-cluster-computing/

Hints for NFS users

  • AVOID script forking on the cluster (but inclusion via ". script.sh" works ok). This means that the GRASS_BATCH_JOB approach is prone to fail. It is highly recommended to simply set a series of environmental variables to define the GRASS session, see here how to do that.
  • be careful with concurrent file writing (use "lockfile" locking, the lockfile command is provided by procmail);
  • store as much temporary data as possible (even the final maps) on the local blade disks if you have.
  • finally collect all results from local blade disks *after* the parallel job execution in a sequential collector job (I am writing that now) to not kill NFS. For example, Grid Engine offers a "hold" function to only execute the collector job after having done the rest.
  • If all else fails, and the I/O load is not too great, consider using sshfs with ssh passkeys instead of NFS.
  • In some situations it is necessary to preserve the same directory structure on all nodes, and symlinks are a nice way to do that, but some (closed source 3rd party which will remain nameless) software insists on expanding symlinks. In this situation the bindfs FUSE extension can help. It is safer to use than "mount" binds, and you don't have to be root to set them up. As with sshfs there is a performance penalty so it may not be appropriate in high I/O situations.

Error: Too many open files

When working with long time series and r.series starts to complain that files are missing/not readable or the message 

Too many open files

For a solution, see Large_raster_data_processing#Number_of_open_files_limitation

Misc Tips & Tricks

See the poor-man's multi-processing script on the Parallelizing Scripts wiki page. This approach has been used in the r3.in.xyz script.

Workshop on Parallelization

Haedrich, C., Petrasova, A. Parallelization for big EO data processing, OpenGeoHub Summer School 2023

Schedule

Session 1

  • [Slides] Introduction to Parallelization, GRASS GIS and Python
  • [Lab] Introduction to Parallelization with GRASS GIS and Python Notebook

Session 2

  • [Lab] Parallelization Case Study: Urban Growth Modeling

Jupyter Notebook:

See also

This Wiki:

Elsewhere:

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