Data Submission

Submission of Data Procedure

Any submission of data to the AeroCom database requires to follow the following steps:

format data to agreed netCDF htap standards, cf compliant
adjust filenames
check format with cf compliance checker, correct and check again
obtain account on htap server to access aerocom-users server
transfer data to the aerocom-users.met.no at the Norwegian Meteorological Institute
notify metno that data have been submitted
update errors on submission log on htap wiki page

1) format data

Note: these commands cover the elder phase 3 naming scheme, but should nevertheless still usefull

The AeroCom standard is described in the section “submitting to the AeroCom database”.
https://wiki.met.no/aerocom/data_submission

Below simple nco commands are listed which can be of help to reformat.

A public set of format correction tools is under development and can be accessed here:
https://github.com/metno/aerocom-data-correction-tools

How to remind me of nco commands

Just type the command without arguments on a command line

How to rename variables

ncrename -v oldvar,newvar in.nc

How to add an attribute

ncatted -a experiment,newvar,a,c,"BASE" in.nc

Split files per variable

cdo splitname in.nc

rename dimension

ncrename -O -d LATITUDE,y temp.nc

sums

ncap2 -O -s "LOAD_BCPOM[time,x,y]=LOAD_BC+LOAD_POM" ${file} ${file}

compute vertical integrals

rm dummy.nc ncwa -O -v AERH2O3D_AER -a z -y ttl ${file} dummy.nc ncrename -O -v AERH2O3D_AER,AERH2O_AER dummy.nc ncks -F -A -v AERH2O_AER dummy.nc ${file}

add variable to file

ncks -F -A -v AIRE temp.nc ${file}

make the time dimension unlimited

ncecat -O $file $file ncpdq -O -a time,record $file $file ncwa -O -a record $file $file ncpdq -O -a time,y,x $file $file

turn z

ncpdq -O -a -z $file $file

create yearly mean file

from 12 months in one file

orgfile=MM_${model}.an${an}.mALLYEAR_an.nc ncwa -F -O -a time ${file} ${orgfile}

calculate yearly average

fom 12 files each containing 1 month

ncra -F -O modis_2000??.nc ${yearfile}

create record dimension

ncecat -O $file $file

delete useless record dimension

ncwa -O -a record $file $file

turn lat to have right order

with interpolated files

ncpdq -O -a "-y" $file $file

Shift left and right hemispheres

file1=aire_1.nc ncks -h -F -O -d x,1,180 $file $file1 file2=aire_2.nc ncks -h -F -O -d x,181,360 $file $file2 ncap -O -s "x[x]=x-360" $file2 $file2ncrcat -O $file2 $file1 $file \rm $file1 $file2

Similar reorder of longitude

ncecat -O $file $file ncpdq -O -a x,record $file $file ncwa -O -a record $file $filefile1=DD_${model}.an${AN}.mALLYEAR_1.nc ncks -F -O -d x,1,180 $file $file1file2=DD_${model}.an${AN}.mALLYEAR_2.nc ncks -F -O -d x,181,360 $file $file2 ncap -O -s "x[x]=x-360" $file2 $file2 ncrcat -O $file2 $file1 $file \rm $file1 $file2ncpdq -O -a time,y,x $file $file

missing values

ncatted -O -a missing_value,$var,o,f,0 ${file} ncatted -O -a missing_value,$var,o,f,-9999 ${file}

actually better use attribute _FillValue (see http://nco.sourceforge.net)

compute monthly mean files

for IMTH in ${MTH[*]} ; do file=DD_${model}.an${AN}.m${IMTH}.nc filemean=DD_${model}.an${AN}.m${IMTH}_m.nc ncra -F -O ${file} ${filemean} done

delete attributes

ncatted -O -a ,,d,, interdummy.nc ncatted -h -a ,global,d,, interdummy.nc ncatted -h -a missing_value,,d,, interdummy.nc

2) adjust filenames

The obligatory filename for using the cf checker and the submission of data is:
aerocom3_<ModelName>-<MeteoConfigSpecifier>_<ExperimentName>-<PerturbationName>_<VariableName>_<VerticalCoordinateType>_<Period>_<Frequency>.nc

Details about new file naming can be found here: AeroCom experiments diagnostics sheets 28.2.2019

Be aware of updates !

versions will have a date attached.

Examples:

aerocom3_GOCARTv7.2_AP3-CTRL_od550aer_Column_2010_monthly.nc
aerocom3_GISS-MATRIX-met2010_AP3-ACRI-AFRICA_od550aer_Column_2010_daily.nc
aerocom3_GOCARTv7.2-met2010_AP3-CTRL-od550aer_Column_1850_monthly.nc
aerocom3_GISS-MATRIX-fSST_AP3-CTRL-od550aer_Column_1850_monthly.nc

OLD (aerocom phase3)
aerocom3_<ModelName>_<ExperimentName>_<VariableName>_<VerticalCoordinateType>_<Period>_<Frequency>.nc

OLD (aerocom phase 2) aerocom naming convention is also fine for now:
aerocom_<ModelName>_<ExperimentName>_<VariableName>_<Period>_<Frequency>.nc

<ModelName> ⇒ can be chosen such that Model Name, Model version and possibly the institution can be identified. No underscores (_) are allowed in <!ModelName>, use (-) instead. Restrict <ModelName> to max 20 characters.
<MeteoConfigSpecifiers> ⇒ “met2010” (default, nudged to 2010 meteo) / “fSST” (fixed 2010 SST monthly fields, not nudged) / “CPL” (coupled AOGCM model, not nudged) A MeteoSpecifier has to be present
<ExperimentName> ⇒ see Experiment Specifications
<PerturbationName> see experiment descriptions on aerocom wiki, if required for the experiment, use exact case sensitive name from description
<VariableName> ⇒ see output variable names in excel sheet
<VerticalCoordinateType> ⇒ “Surface”, “Column”, “ModelLevel”, “SurfaceAtStations”, “ModelLevelAtStations”
<Period> ⇒ eg “2008”, “2010”
<Frequency> ⇒ “timeinvariant”, “hourly”, “3hourly”, “daily”, “monthly”, “sat1000”, “sat1330”, “sat2200”, “sat0130”

3) check format

Typical files must be checked prior to submission via a cf-compliance-checker. cfconventions.org maintains a list of working and frequently updated CF checkers. Some come as a script, and to others one can upload a file.

For the upload checker you want to check a typical but small file. To achieve this, you can cut out the first time steps with the nco command: ncks -O -d time,0,10 sourcefile.nc filetest.nc

Per default, a check shall comprise at least one file of each VerticalCoordinateType and each Frequency and each experiment, best varying the variables!

4) obtain account

An account at met.no is needed to submit data and give users access via ssh to the aerocom-users.met.no server. Please contact anna.benedictow@met.no (and in case of missing response also michaels at met.no) for password and user name. You will then be notified further about the procedure. A public ssh-key has to be sent to Anna to activate the account.

5) transfer data

After obtaining an account, data can then be uploaded to the aerocom user server aerocom-users.met.no:

Create a directory with an understandable, unique name under /media/scratch/incoming/
Use the model name as used for file names.
Put files in that directory. Overall size limit of ca 10 TB (limit for all users)
Inform Anna and Michael on upload, purpose and experiment by email !

Large submissions (> 500 GB) may require extra attention (use rsync, sftp). They might require prior coordination with Met.No, please send an e-mail to anna.benedictow@met.no and michael.schulz@met.no, in particular in times of simultaneous heavy upload activity.

If correct in format and with correct file names, results uploaded here will be processed over night and appear after a day as image catalogue on https://aerocom-classic.met.no/cgi-bin/aerocom/surfobs_annualrs.pl?PROJECT=AEROCOM&MODELLIST=AEROCOM-Phase-III

6) notify met.no

When files are uploaded send email to anna.benedictow@met.no and jan.griesfeller@met.no and michael.schulz@met.no (AND coordinator of project), so that the files can be transferred from aerocom-users to the database. When the data are included in the database the files appear on aerocom-users.met.no under /metno/aerocom-users-database/PROJECT(AEROCOM-PHASE-III)/<ModelName>_<exp>/.

After the data has been transferred to the database, it will be deleted form the aerocom-users' scratch area.

7) updates

In case of updates of files, the model version identifier should also contain information on the resubmission of model results. Additional files which do not change an earlier submission may contain the same version number as an older submission. Corrections and a model rerun should be accompanied by a new model version identifier. Old still valid files may be merged upon request with new data. Old versions of model submissions will be temporally moved to a separate directory by Met.No, and where possible, deleted after some time. An exception will be made for versions that have been used in publications. Modellers are responsible for communication of major updates to their models (e-mail and log-files, see below). Model analysers are responsible for frequently verifying changes in model submissions (e.g. before submitting a paper).