Containers¶
There are two most commonly used container formats available:
- Docker/Podman
- Singularity/Apptainer
with FLEXPART and recipes can be found in containers folder.
Since version 11, FLEXPART is also available as a container. There is a Dockerfile and some instructions on how to build the container from scratch using for example podman/docker or singularity/apptainer:
Specifications:
- compiled using march=core-avx2, compatible with CPUs above AVX2 (since Haswell or Zen)
- ecCodes
# build container using podman (adjust for docker)
$ ./containers/build.sh
Building flexpart v11 branch: master : 2464aef
Press any key to continue or Ctrl+C to exit...
STEP 1/16: FROM rockylinux:9-minimal
...
STEP 16/16: CMD ["FLEXPART_ETA"]
--> Using cache 200844128a6919007417f3fa905221c8dbdea4bb285895ef80e89d3df80274b6
COMMIT flexpartv11-master:2464aef
--> 200844128a69
Successfully tagged localhost/flexpartv11-master:2464aef
200844128a6919007417f3fa905221c8dbdea4bb285895ef80e89d3df80274b6
# finished
# using singularity/apptainer for running FLEXPART
# there might be some warnings about EPERM (can be ignored)
$ ./containers/build.sh apptainer
Building flexpart v11 branch: master : 2464aef
Press any key to continue or Ctrl+C to exit...
INFO: Starting build...
INFO: Adding environment to container
INFO: Adding startscript
INFO: Adding runscript
INFO: Creating SIF file...
INFO: Build complete: flexpartv11-master-2464aef.sif
# finished
running it using podman/docker or singularity/apptainer:
# simple run the container with default settings
podman run localhost/flexpartv11-master:2464aef
# running the container requires a writable output directory
# mounting the local directory to /output inside the container
apptainer run -B .:/output flexpartv11-master-2464aef.sif
podman/docker flexpart run log
Welcome, running FLEXPART
Using defaults (/pathnames)
/options/
/output/
/inputs/
/inputs/AVAILABLE
Mount volumes to change inputs
Git: c5bdd94 HEAD -> master, origin/master, origin/HEAD Tue Nov 21 16:15:27 2023 +0100
EXECUTING FLEXPART
trying to execute: /src/FLEXPART_ETA
Executing: /src/FLEXPART_ETA
Welcome to FLEXPART Version 11
Git: undefined
FLEXPART is free software released under the GNU General Public License.
FLEXPART is running with ETA coordinates.
----------------
INFORMATION: SUBGRIDSCALE TERRAIN EFFECT IS
NOT PARAMETERIZED DURING THIS SIMULATION.
----------------
*********** WARNING **********************************
* FLEXPART running in parallel mode *
* Number of uncertainty classes in *
* set to number of threads: 1 *
* All other computations are done with 8 threads. *
*******************************************************
FLEXPART WARNING: TIME DIFFERENCE BETWEEN TWO
WIND FIELDS IS BIG. THIS MAY CAUSE A DEGRADATION
OF SIMULATION QUALITY.
ECMWF metdata detected
NXSHIFT is set to 0
grid dim: 181 91 92 92 91 92
Vertical levels in ECMWF data: 92 92
Mother domain:
Longitude range: -178.00000 to 182.00000 Grid distance: 2.00000
Latitude range : -90.00000 to 90.00000 Grid distance: 2.00000
Number of receptors: 2
Releasepoints : 1
reading SPECIES 24
Particle shape SPHERE for particle 24
SPECIES: 24 AIRTRACER (GAS)
Wet removal for gases is turned: OFF
Dry deposition for gases is turned: OFF
Below-cloud scavenging: OFF
In-cloud scavenging: OFF
Particles released (numpartmax): 10000
Total mass released: 1.0000000E+00
Allocating fields for global output (x,y): 85 65
Concentrations are calculated using kernel
WARNING: turbulence switched off.
Simulated 0.0 hours ( 0 s), 0 particles
Time: 0 seconds. Total spawned: 0 alive: 0 terminated: 0
Allocating 10000 particles 0 0 0
Finished allocation
Time: 900 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 1800 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 2700 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 3600 seconds. Total spawned: 10000 alive: 10000 terminated: 0
3600 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
Time: 4500 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 5400 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 6300 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 7200 seconds. Total spawned: 10000 alive: 10000 terminated: 0
7200 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
Time: 8100 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 9000 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 9900 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 10800 seconds. Total spawned: 10000 alive: 10000 terminated: 0
10800 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
Read wind fields: 0.609375000 seconds
Timemanager: 1.17187500 seconds,first timestep: 1.09375000 seconds
Write particle files: 4.68750000E-02 seconds
Total running time: 1.81250000 seconds
tps,io,tot: 1.95312500E-02 0.131249994 1.81250000
CONGRATULATIONS: YOU HAVE SUCCESSFULLY COMPLETED A FLEXPART MODEL RUN!
FINISHED
singularity/apptainer flexpart run log
INFO: gocryptfs not found, will not be able to use gocryptfs
Welcome, running FLEXPART
Using defaults (/pathnames)
/options/
/output/
/inputs/
/inputs/AVAILABLE
Mount volumes to change inputs
Git: c5bdd94 HEAD -> master, origin/master, origin/HEAD Tue Nov 21 16:15:27 2023 +0100
EXECUTING FLEXPART
trying to execute: /src/FLEXPART_ETA
Executing: /src/FLEXPART_ETA
Welcome to FLEXPART Version 11
Git: undefined
FLEXPART is free software released under the GNU General Public License.
FLEXPART is running with ETA coordinates.
----------------
INFORMATION: SUBGRIDSCALE TERRAIN EFFECT IS
NOT PARAMETERIZED DURING THIS SIMULATION.
----------------
*********** WARNING **********************************
* FLEXPART running in parallel mode *
* Number of uncertainty classes in *
* set to number of threads: 1 *
* All other computations are done with 8 threads. *
*******************************************************
FLEXPART WARNING: TIME DIFFERENCE BETWEEN TWO
WIND FIELDS IS BIG. THIS MAY CAUSE A DEGRADATION
OF SIMULATION QUALITY.
ECMWF metdata detected
NXSHIFT is set to 0
grid dim: 181 91 92 92 91 92
Vertical levels in ECMWF data: 92 92
Mother domain:
Longitude range: -178.00000 to 182.00000 Grid distance: 2.00000
Latitude range : -90.00000 to 90.00000 Grid distance: 2.00000
Number of receptors: 2
Releasepoints : 1
reading SPECIES 24
Particle shape SPHERE for particle 24
SPECIES: 24 AIRTRACER (GAS)
Wet removal for gases is turned: OFF
Dry deposition for gases is turned: OFF
Below-cloud scavenging: OFF
In-cloud scavenging: OFF
Particles released (numpartmax): 10000
Total mass released: 1.0000000E+00
Allocating fields for global output (x,y): 85 65
Concentrations are calculated using kernel
WARNING: turbulence switched off.
Simulated 0.0 hours ( 0 s), 0 particles
Time: 0 seconds. Total spawned: 0 alive: 0 terminated: 0
Allocating 10000 particles 0 0 0
Finished allocation
Time: 900 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 1800 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 2700 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 3600 seconds. Total spawned: 10000 alive: 10000 terminated: 0
3600 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
Time: 4500 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 5400 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 6300 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 7200 seconds. Total spawned: 10000 alive: 10000 terminated: 0
7200 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
Time: 8100 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 9000 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 9900 seconds. Total spawned: 10000 alive: 10000 terminated: 0
Time: 10800 seconds. Total spawned: 10000 alive: 10000 terminated: 0
10800 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
Read wind fields: 0.703125000 seconds
Timemanager: 1.25000000 seconds,first timestep: 1.15625000 seconds
Write particle files: 1.56250000E-02 seconds
Total running time: 2.00000000 seconds
tps,io,tot: 2.34375000E-02 0.143749997 2.00000000
CONGRATULATIONS: YOU HAVE SUCCESSFULLY COMPLETED A FLEXPART MODEL RUN!
FINISHED
ncdump of default run output
# check the output
ncdump -h grid_conc_20090101000000.nc
netcdf grid_conc_20090101000000 {
dimensions:
time = UNLIMITED ; // (3 currently)
longitude = 85 ;
latitude = 65 ;
height = 4 ;
numspec = 1 ;
pointspec = 1 ;
nageclass = 1 ;
nchar = 45 ;
ncharrec = 16 ;
numpoint = 1 ;
receptor = UNLIMITED ; // (2 currently)
variables:
int time(time) ;
time:units = "seconds since 2009-01-01 00:00" ;
time:calendar = "proleptic_gregorian" ;
float longitude(longitude) ;
longitude:long_name = "longitude in degree east" ;
longitude:axis = "Lon" ;
longitude:units = "degrees_east" ;
longitude:standard_name = "grid_longitude" ;
longitude:description = "grid cell centers" ;
float latitude(latitude) ;
latitude:long_name = "latitude in degree north" ;
latitude:axis = "Lat" ;
latitude:units = "degrees_north" ;
latitude:standard_name = "grid_latitude" ;
latitude:description = "grid cell centers" ;
float height(height) ;
height:units = "meters" ;
height:positive = "up" ;
height:standard_name = "height" ;
height:long_name = "height above ground" ;
char RELCOM(numpoint, nchar) ;
RELCOM:long_name = "release point name" ;
float RELLNG1(numpoint) ;
RELLNG1:units = "degrees_east" ;
RELLNG1:long_name = "release longitude lower left corner" ;
float RELLNG2(numpoint) ;
RELLNG2:units = "degrees_east" ;
RELLNG2:long_name = "release longitude upper right corner" ;
float RELLAT1(numpoint) ;
RELLAT1:units = "degrees_north" ;
RELLAT1:long_name = "release latitude lower left corner" ;
float RELLAT2(numpoint) ;
RELLAT2:units = "degrees_north" ;
RELLAT2:long_name = "release latitude upper right corner" ;
float RELZZ1(numpoint) ;
RELZZ1:units = "meters" ;
RELZZ1:long_name = "release height bottom" ;
float RELZZ2(numpoint) ;
RELZZ2:units = "meters" ;
RELZZ2:long_name = "release height top" ;
int RELKINDZ(numpoint) ;
RELKINDZ:long_name = "release kind" ;
int RELSTART(numpoint) ;
RELSTART:units = "seconds" ;
RELSTART:long_name = "release start relative to simulation start" ;
int RELEND(numpoint) ;
RELEND:units = "seconds" ;
RELEND:long_name = "release end relative to simulation start" ;
int RELPART(numpoint) ;
RELPART:long_name = "number of release particles" ;
float RELXMASS(numspec, numpoint) ;
RELXMASS:long_name = "total release particle mass" ;
int LAGE(nageclass) ;
LAGE:units = "seconds" ;
LAGE:long_name = "age class" ;
int ORO(latitude, longitude) ;
ORO:standard_name = "surface altitude" ;
ORO:long_name = "outgrid surface altitude" ;
ORO:units = "m" ;
char receptor(receptor, ncharrec) ;
receptor:long_name = "receptor name" ;
float spec001_mr(nageclass, pointspec, time, height, latitude, longitude) ;
spec001_mr:units = "ng m-3" ;
spec001_mr:long_name = "AIRTRACER" ;
spec001_mr:decay = -0.07001485f ;
spec001_mr:weightmolar = 29.f ;
spec001_mr:ohcconst = -9.e-10f ;
spec001_mr:ohdconst = -9.9f ;
spec001_mr:vsetaver = 0.f ;
float receptor_conc001(receptor, time) ;
receptor_conc001:units = "ng m-3" ;
receptor_conc001:_FillValue = -1.f ;
receptor_conc001:positive = "up" ;
receptor_conc001:standard_name = "receptor_conc" ;
receptor_conc001:long_name = "receptor_concentration" ;
// global attributes:
:Conventions = "CF-1.6" ;
:title = "FLEXPART model output" ;
:git = "undefined" ;
:source = "Version 11 model output" ;
:history = "2023-11-21 16:22 +0100 created by mblaschek on NB513" ;
:references = "Stohl et al., Atmos. Chem. Phys., 2005, doi:10.5194/acp-5-2461-200" ;
:outlon0 = -25.f ;
:outlat0 = 10.f ;
:dxout = 1.f ;
:dyout = 1.f ;
:ldirect = 1 ;
:ibdate = "20090101" ;
:ibtime = "000000" ;
:iedate = "20090101" ;
:ietime = "030000" ;
:loutstep = 3600 ;
:loutaver = 3600 ;
:loutsample = 900 ;
:loutrestart = -1 ;
:lsynctime = 900 ;
:ctl = -0.2f ;
:ifine = 1 ;
:iout = 1 ;
:ipout = 0 ;
:lsubgrid = 0 ;
:lconvection = 0 ;
:lagespectra = 0 ;
:ipin = 0 ;
:ioutputforeachrelease = 0 ;
:iflux = 0 ;
:mdomainfill = 0 ;
:ind_source = 1 ;
:ind_receptor = 1 ;
:mquasilag = 0 ;
:nested_output = 0 ;
:sfc_only = 0 ;
:linit_cond = 0 ;
}
Interactive shells can be launched into containers, to have a look at configurations and to better understand what might go wrong. Podman/Docker allows to alter files inside of the container and save these changes. Singularity/Apptainer containers are not writeable, but acts like a normal executable with access to host files.
# using podman
$ podman run -it localhost/flexpartv11-master:2464aef /bin/bash
Welcome, running FLEXPART
Using defaults (/pathnames) [ OK]
/options/
/output/
/inputs/
/inputs/AVAILABLE
Mount volumes to change inputs
Git: 2464aef
EXECUTING FLEXPART
Executing: /src//bin/bash [ FAILED]
Executing: /bin/bash [ OK]
bash-5.1#
# now you are inside the container
bash-5.1# pwd
/src
# important directories are /input, /output, /src, /options
#
# using singularity/apptainer
$ apptainer run