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Merged
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Dec 12, 2017
Merged

Change to mask directory instead of individual mask files #289

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20d577c
Change to mask directory instead of MOC mask file
xylar Aug 25, 2017
b7adb36
Update example config files with mask directories
xylar Sep 18, 2017
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12 changes: 5 additions & 7 deletions configs/anvil/config.20170926.FCT2.A_WCYCL1850S.ne30_oECv3.anvil
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Expand Up @@ -55,7 +55,7 @@ htmlSubdirectory = html
# option:
# ./run_mpas_analysis config.analysis --generate \
# all,no_ocean,all_timeSeries
# The climatologyMapAntarcticMelt task is disabled because this run did not
# The climatologyMapAntarcticMelt task is disabled because this run did not
# include ice-shelf cavities.`
generate = ['all', 'no_climatologyMapAntarcticMelt']

Expand Down Expand Up @@ -127,10 +127,8 @@ baseDirectory = /lcrc/group/acme/mpas_analysis/ACMEv0_lowres/B1850C5_ne30_v0.4/i
# plot on polar plot
polarPlot = False

[streamfunctionMOC]
## options related to plotting the streamfunction of the meridional overturning
## circulation (MOC)
maxChunkSize = 1000
[regions]
## options related to ocean regions used in several analysis modules

# Mask file for ocean basin regional computation
regionMaskFiles = /lcrc/group/acme/mpas_analysis/region_masks/oEC60to30v3_Atlantic_region_and_southern_transect.nc
# Directory for region mask files
regionMaskDirectory = /global/project/projectdirs/acme/mapping/grids/
2 changes: 1 addition & 1 deletion configs/anvil/job_script.anvil.bash
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Expand Up @@ -54,7 +54,7 @@ ncclimoParallelMode = $ncclimo_mode
EOF

# first, perform setup only without mpirun to create the mapping files
$mpas_analysis_dir/run_mpas_analysis --purge --setup_only $run_config_file \
$mpas_analysis_dir/run_mpas_analysis --setup_only $run_config_file \
$job_config_file
# next, do the full run now tht we have mapping files, but this time launching
# with mpirun
Expand Down
12 changes: 5 additions & 7 deletions configs/edison/config.20170807.beta1.G_oQU240.edison
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Expand Up @@ -56,7 +56,7 @@ htmlSubdirectory = html
# option:
# ./run_mpas_analysis config.analysis --generate \
# all,no_ocean,all_timeSeries
# The climatologyMapAntarcticMelt task is disabled because this run did not
# The climatologyMapAntarcticMelt task is disabled because this run did not
# include ice-shelf cavities.`
generate = ['all', 'no_climatologyMapAntarcticMelt']

Expand Down Expand Up @@ -128,10 +128,8 @@ baseDirectory = /global/project/projectdirs/acme/ACMEv0_lowres/B1850C5_ne30_v0.
# plot on polar plot
polarPlot = False

[streamfunctionMOC]
## options related to plotting the streamfunction of the meridional overturning
## circulation (MOC)
maxChunkSize = 1000
[regions]
## options related to ocean regions used in several analysis modules

# Mask file for ocean basin regional computation
regionMaskFiles = /global/project/projectdirs/acme/mpas_analysis/region_masks/oQU240v3_SingleRegionAtlanticWTransportTransects_masks.nc
# Directory for region mask files
regionMaskDirectory = /global/project/projectdirs/acme/mpas_analysis/region_masks
10 changes: 6 additions & 4 deletions configs/edison/config.20170915.beta2.A_WCYCL1850S.ne30_oECv3_ICG.edison
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Expand Up @@ -71,7 +71,7 @@ htmlSubdirectory = html
# option:
# ./run_mpas_analysis config.analysis --generate \
# all,no_ocean,all_timeSeries
# The climatologyMapAntarcticMelt task is disabled because this run did not
# The climatologyMapAntarcticMelt task is disabled because this run did not
# include ice-shelf cavities.`
generate = ['all', 'no_climatologyMapAntarcticMelt']

Expand Down Expand Up @@ -143,6 +143,8 @@ baseDirectory = /global/project/projectdirs/acme/ACMEv0_lowres/B1850C5_ne30_v0.
# plot on polar plot
polarPlot = False

[streamfunctionMOC]
# Mask file for ocean basin regional computation
regionMaskFiles = /global/project/projectdirs/acme/mapping/grids/oEC60to30v3_SingleRegionAtlanticWTransportTransects_masks.nc
[regions]
## options related to ocean regions used in several analysis modules

# Directory for region mask files
regionMaskDirectory = /global/project/projectdirs/acme/mpas_analysis/region_masks
10 changes: 6 additions & 4 deletions configs/edison/config.20171102.beta3rc02_1850.ne30_oECv3_ICG.edison
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Expand Up @@ -57,7 +57,7 @@ htmlSubdirectory = html
# option:
# ./run_mpas_analysis config.analysis --generate \
# all,no_ocean,all_timeSeries
# The climatologyMapAntarcticMelt task is disabled because this run did not
# The climatologyMapAntarcticMelt task is disabled because this run did not
# include ice-shelf cavities.`
generate = ['all', 'no_climatologyMapAntarcticMelt']

Expand Down Expand Up @@ -129,6 +129,8 @@ baseDirectory = /global/project/projectdirs/acme/ACMEv0_lowres/B1850C5_ne30_v0.
# plot on polar plot
polarPlot = False

[streamfunctionMOC]
# Mask file for ocean basin regional computation
regionMaskFiles = /global/project/projectdirs/acme/mapping/grids/oEC60to30v3_SingleRegionAtlanticWTransportTransects_masks.nc
[regions]
## options related to ocean regions used in several analysis modules

# Directory for region mask files
regionMaskDirectory = /global/project/projectdirs/acme/mpas_analysis/region_masks
16 changes: 9 additions & 7 deletions configs/edison/config.B_low_res_ice_shelves_1696_JWolfe_layout_Edison
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Expand Up @@ -43,6 +43,11 @@ mappingDirectory = /global/project/projectdirs/acme/mpas_analysis/mapping
# directory where analysis should be written
baseDirectory = /dir/to/analysis/output

# provide an absolute path to put HTML in an alternative location (e.g. a web
# portal)
# htmlSubdirectory = /global/project/projectdirs/acme/www/USERNAME/RUNNAME
htmlSubdirectory = html

# a list of analyses to generate. Valid names can be seen by running:
# ./run_mpas_analysis --list
# This command also lists tags for each analysis.
Expand Down Expand Up @@ -133,11 +138,8 @@ baseDirectory = /global/project/projectdirs/acme/ACMEv0_lowres/B1850C5_ne30_v0.
# plot on polar plot
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@milenaveneziani milenaveneziani Dec 11, 2017 •
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Could you add these lines in this file, right before line 46:

# provide an absolute path to put HTML in an alternative location (e.g. a web
# portal)
# htmlSubdirectory = /global/project/projectdirs/acme/www/USERNAME/RUNNAME
htmlSubdirectory = html

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@xylar xylar Dec 12, 2017

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done

polarPlot = False

[streamfunctionMOC]
## options related to plotting the streamfunction of the meridional overturning
## circulation (MOC)
maxChunkSize = 1000

# Mask file for ocean basin regional computation
regionMaskFiles = /global/project/projectdirs/acme/mpas_analysis/region_masks/oEC60to30v3wLI_SingleRegionAtlanticWTransportTransects_masks.nc
[regions]
## options related to ocean regions used in several analysis modules

# Directory for region mask files
regionMaskDirectory = /global/project/projectdirs/acme/mpas_analysis/region_masks
11 changes: 5 additions & 6 deletions configs/lanl/config.MatchBoth_orig
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Expand Up @@ -51,7 +51,7 @@ baseDirectory = /dir/to/analysis/output
# option:
# ./run_mpas_analysis config.analysis --generate \
# all,no_ocean,all_timeSeries
# The climatologyMapAntarcticMelt task is disabled because this run did not
# The climatologyMapAntarcticMelt task is disabled because this run did not
# include ice-shelf cavities.`
generate = ['all', 'no_climatologyMapAntarcticMelt']

Expand Down Expand Up @@ -111,9 +111,8 @@ baseDirectory = /usr/projects/climate/SHARED_CLIMATE/observations/SeaIce
# directory where ocean reference simulation results are stored
baseDirectory = /usr/projects/climate/SHARED_CLIMATE/ACMEv0_lowres/B1850C5_ne30_v0.4/ice/postprocessing

[streamfunctionMOC]
## options related to plotting the streamfunction of the meridional overturning
## circulation (MOC)
[regions]
## options related to ocean regions used in several analysis modules

# Mask file for ocean basin regional computation
regionMaskFiles = /turquoise/usr/projects/climate/SHARED_CLIMATE/mpas_analysis/region_masks/oEC60to30v3_Atlantic_region_and_southern_transect.nc
# Directory for region mask files
regionMaskDirectory = /turquoise/usr/projects/climate/SHARED_CLIMATE/mpas_analysis/region_masks
14 changes: 11 additions & 3 deletions configs/olcf/config.20170313.beta1.A_WCYCL1850S.ne30_oECv3_ICG.edison
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Expand Up @@ -32,6 +32,11 @@ mappingDirectory = /lustre/atlas/proj-shared/cli115/mpas_analysis/mapping/
# directory where analysis should be written
baseDirectory = /dir/to/analysis/output

# provide an absolute path to put HTML in an alternative location (e.g. a web
# portal)
# htmlSubdirectory = /ccs/proj/cli115/www/USERNAME/RUNNAME
htmlSubdirectory = html

# a list of analyses to generate. Valid names can be seen by running:
# ./run_mpas_analysis --list
# This command also lists tags for each analysis.
Expand All @@ -51,7 +56,7 @@ baseDirectory = /dir/to/analysis/output
# option:
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@milenaveneziani milenaveneziani Dec 11, 2017 •
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Could you add these, right before line 35:

# provide an absolute path to put HTML in an alternative location (e.g. a web
# portal)
# htmlSubdirectory = /ccs/proj/cli115/www/USERNAME/RUNNAME
htmlSubdirectory = html

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@xylar xylar Dec 12, 2017

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done

# ./run_mpas_analysis config.analysis --generate \
# all,no_ocean,all_timeSeries
# The climatologyMapAntarcticMelt task is disabled because this run did not
# The climatologyMapAntarcticMelt task is disabled because this run did not
# include ice-shelf cavities.`
generate = ['all', 'no_climatologyMapAntarcticMelt']

Expand Down Expand Up @@ -122,5 +127,8 @@ baseDirectory = /lustre/atlas/proj-shared/cli115/milena/ACMEv0_lowres/B1850C5_n
# Supported options are Atlantic and IndoPacific
regionNames = ['Atlantic']

# Mask file for ocean basin regional computation
regionMaskFiles = /lustre/atlas/proj-shared/cli115/mpas_analysis/region_masks/oEC60to30v3_SingleRegionAtlanticWTransportTransects_masks.nc
[regions]
## options related to ocean regions used in several analysis modules

# Directory for region mask files
regionMaskDirectory = /lustre/atlas/proj-shared/cli115/mpas_analysis/region_masks/
14 changes: 11 additions & 3 deletions configs/olcf/config.20170915.beta2.A_WCYCL1850S.ne30_oECv3_ICG.edison
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Expand Up @@ -37,7 +37,7 @@ seaIceNamelistFileName = run/mpas-cice_in
seaIceStreamsFileName = run/streams.cice

# names of ocean and sea ice meshes (e.g. EC60to30, QU240, RRS30to10, etc.)
mpasMeshName = EC60to30v3
mpasMeshName = oEC60to30v3

# Directory for mapping files (if they have been generated already). If mapping
# files needed by the analysis are not found here, they will be generated and
Expand All @@ -51,6 +51,11 @@ mappingDirectory = /lustre/atlas/proj-shared/cli115/mpas_analysis/mapping/
# directory where analysis should be written
baseDirectory = /dir/to/analysis/output

# provide an absolute path to put HTML in an alternative location (e.g. a web
# portal)
# htmlSubdirectory = /ccs/proj/cli115/www/USERNAME/RUNNAME
htmlSubdirectory = html

# a list of analyses to generate. Valid names can be seen by running:
# ./run_mpas_analysis --list
# This command also lists tags for each analysis.
Expand Down Expand Up @@ -139,5 +144,8 @@ baseDirectory = /lustre/atlas/proj-shared/cli115/milena/ACMEv0_lowres/B1850C5_n
# Supported options are Atlantic and IndoPacific
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Could you change mpasMeshName to oEC60to30v3?

And then add, before line 54:

# provide an absolute path to put HTML in an alternative location (e.g. a web
# portal)
# htmlSubdirectory = /ccs/proj/cli115/www/USERNAME/RUNNAME
htmlSubdirectory = html

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@xylar xylar Dec 12, 2017

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done

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@milenaveneziani milenaveneziani Dec 12, 2017

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I think you forgot to adjust the mpasMeshName.

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@xylar xylar Dec 12, 2017

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Yes, I missed that. I'll fix it now.

regionNames = ['Atlantic']

# Mask file for ocean basin regional computation
regionMaskFiles = /lustre/atlas/proj-shared/cli115/mpas_analysis/region_masks/oEC60to30v3_SingleRegionAtlanticWTransportTransects_masks.nc
[regions]
## options related to ocean regions used in several analysis modules

# Directory for region mask files
regionMaskDirectory = /lustre/atlas/proj-shared/cli115/mpas_analysis/region_masks
35 changes: 15 additions & 20 deletions configs/olcf/config.GMPAS-IAF_oRRS18to6v3.titan
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Expand Up @@ -19,12 +19,14 @@ preprocessedReferenceRunName = None
## options related to reading in the results to be analyzed

# directory containing model results
baseDirectory = /lustre/atlas1/cli115/scratch/vanroek/GMPAS-IAF_oRRS18to6v3/run
baseDirectory = /lustre/atlas1/cli115/proj-shared/vanroek/run

mpasMeshName = oRRS18to6v3

# Directory for mapping files (if they have been generated already). If mapping
# files needed by the analysis are not found here, they will be generated and
# placed in the output mappingSubdirectory
# mappingDirectory = /dir/for/mapping/files
mappingDirectory = /lustre/atlas/proj-shared/cli115/mpas_analysis/mapping

[output]
## options related to writing out plots, intermediate cached data sets, logs,
Expand All @@ -34,6 +36,11 @@ baseDirectory = /lustre/atlas1/cli115/scratch/vanroek/GMPAS-IAF_oRRS18to6v3/run
# NOTE: This directory path must be specific to each test case.
baseDirectory = /dir/to/analysis/output

# provide an absolute path to put HTML in an alternative location (e.g. a web
# portal)
# htmlSubdirectory = /ccs/proj/cli115/www/USERNAME/RUNNAME
htmlSubdirectory = html

# a list of analyses to generate. Valid names can be seen by running:
# ./run_mpas_analysis --list
# This command also lists tags for each analysis.
Expand All @@ -53,7 +60,7 @@ baseDirectory = /dir/to/analysis/output
# option:
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@milenaveneziani milenaveneziani Dec 11, 2017 •
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This one is missing a few things (mind you, I haven't had a chance to test this yet, because of the nco problems with large files, which I mentioned in the email):

  • as noted by @vanroekel, the input baseDirectory should be changed to /lustre/atlas1/cli115/proj-shared/vanroek/run
  • mpasMeshName
  • there is the piece with Directory with mapping files, but not this newer part:
# Directory for region mask files
regionMaskDirectory =
  • these lines before line 37:
# provide an absolute path to put HTML in an alternative location (e.g. a web
# portal)
# htmlSubdirectory = /ccs/proj/cli115/www/USERNAME/RUNNAME
htmlSubdirectory = html

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@xylar xylar Dec 12, 2017

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I do see the regionMaskDirectory part in my version at the bottom. I have changed the rest as you suggested.

# ./run_mpas_analysis config.analysis --generate \
# all,no_ocean,all_timeSeries
# The climatologyMapAntarcticMelt task is disabled because this run did not
# The climatologyMapAntarcticMelt task is disabled because this run did not
# include ice-shelf cavities.`
generate = ['all', 'no_climatologyMapAntarcticMelt']

Expand Down Expand Up @@ -148,20 +155,8 @@ baseDirectory = /dir/to/seaice/reference
# directory where ocean reference simulation results are stored
baseDirectory = /dir/to/seaice/reference

[streamfunctionMOC]
## options related to plotting the streamfunction of the meridional overturning
## circulation (MOC)

# Mask file for post-processing regional MOC computation
regionMaskFiles = /lustre/atlas1/cli115/proj-shared/mpas_analysis/region_masks/oRRS18to6v3.170111.SingleRegionAtlanticWTransportTransects_masks.nc

# xarray (with dask) divides data sets into "chunks", allowing computations
# to be made on data that is larger than the available memory. MPAS-Analysis
# supports setting a maximum chunk size for data sets generally, and a
# separate option specific to loading the 3D velocity field in the MOC
# specifically. By default, maxChunkSize is left undefined, so that chunking
# is handled automatically. If the MOC calculation encounters memory problems,
# consider setting maxChunkSize to a number significantly lower than nEdges
# in your MPAS mesh so that the calculation will be divided into smaller
# pieces.
maxChunkSize = 500
[regions]
## options related to ocean regions used in several analysis modules

# Directory for region mask files
regionMaskDirectory = /lustre/atlas1/cli115/proj-shared/mpas_analysis/region_masks
10 changes: 1 addition & 9 deletions configs/theta/config.20171031.tenYearTest.GMPAS-IAF.T62_oEC60to30v3wLI.60layer.theta
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Expand Up @@ -135,17 +135,9 @@ baseDirectory = /projects/OceanClimate/mpas-analysis_data/ACMEv0_lowres/B1850C5
# plot on polar plot
polarPlot = False

[streamfunctionMOC]
## options related to plotting the streamfunction of the meridional overturning
## circulation (MOC)
maxChunkSize = 1000

# Mask file for ocean basin regional computation
regionMaskFiles = /projects/OceanClimate/mpas-analysis_data/mpas_analysis/region_masks/oEC60to30v3wLI_Atlantic_region_masks_and_southern_transect.nc

[regions]
# Directory containing mask files for ocean basins and ice shelves
regionMaskDirectory = /projects/OceanClimate/mpas-analysis_data/mpas_analysis/region_masks/
regionMaskDirectory = /projects/OceanClimate/mpas-analysis_data/mpas_analysis/region_masks

[climatologyMapSoseTemperature]
# Times for comparison times (Jan, Feb, Mar, Apr, May, Jun, Jul, Aug, Sep, Oct,
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do we have a htmlSubdirectory on theta?

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@xylar xylar Dec 12, 2017

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No, as far as I'm aware, there's no web portal on theta.

Expand Down
2 changes: 1 addition & 1 deletion configs/theta/job_script.theta.bash
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Expand Up @@ -61,7 +61,7 @@ module unload python
module use /projects/OceanClimate/modulefiles/all
module load python/anaconda-2.7-acme

$mpas_analysis_dir/run_mpas_analysis --purge \
$mpas_analysis_dir/run_mpas_analysis \
$run_config_file $job_config_file
EOF

Expand Down
6 changes: 3 additions & 3 deletions mpas_analysis/config.default
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Expand Up @@ -430,9 +430,6 @@ movingAveragePoints = 1
# Supported options are Atlantic and IndoPacific
regionNames = ['Atlantic']

# Mask file for post-processing regional MOC computation
regionMaskFiles = /path/to/MOCregional/mask/file

# xarray (with dask) divides data sets into "chunks", allowing computations
# to be made on data that is larger than the available memory. MPAS-Analysis
# supports setting a maximum chunk size for data sets generally, and a
Expand Down Expand Up @@ -758,6 +755,9 @@ regions = ['arctic', 'equatorial', 'so', 'nino3', 'nino4', 'nino3.4', 'global']
plotTitles = ['Arctic', 'Equatorial (15S-15N)', 'Southern Ocean', 'Nino 3',
'Nino 4', 'Nino 3.4', 'Global Ocean']

# Directory for region mask files
regionMaskDirectory = /path/to/masks/

[plot]
## options related to plotting that are the defaults across all analysis
## modules
Expand Down
16 changes: 10 additions & 6 deletions mpas_analysis/ocean/streamfunction_moc.py
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Expand Up @@ -293,17 +293,21 @@ def _compute_moc_climo_postprocess(self): # {{{
'regionNames')

# Load basin region related variables and save them to dictionary
# NB: The following will need to change with new regional mapping files
regionMaskFiles = config.get(self.sectionName, 'regionMaskFiles')
if not os.path.exists(regionMaskFiles):
raise IOError('Regional masking file for MOC calculation '
'does not exist')
mpasMeshName = config.get('input', 'mpasMeshName')
regionMaskDirectory = config.get('regions', 'regionMaskDirectory')

regionMaskFile = '{}/{}_SingleRegionAtlanticWTransportTransects_' \
'masks.nc'.format(regionMaskDirectory, mpasMeshName)

if not os.path.exists(regionMaskFile):
raise IOError('Regional masking file {} for MOC calculation '
'does not exist'.format(regionMaskFile))
iRegion = 0
self.dictRegion = {}
for region in self.regionNames:
self.logger.info('\n Reading region and transect mask for '
'{}...'.format(region))
ncFileRegional = netCDF4.Dataset(regionMaskFiles, mode='r')
ncFileRegional = netCDF4.Dataset(regionMaskFile, mode='r')
maxEdgesInTransect = \
ncFileRegional.dimensions['maxEdgesInTransect'].size
transectEdgeMaskSigns = \
Expand Down