A seemingly OK variable will completely break DV3D #1155
Description
We have found a variable that will completely break DV3D: we get the following message and core dump
Warning, can't open data file 'None'
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Abort (core dumped)
The variable can be downloaded with
wget http://dods.ipsl.jussieu.fr/brocksce/tmp/temp.nc
The variable seems OK and vcs will not complain when plotting 2D slices of the variable. DV3D will work again if we create the axes of the variable from scratch, to create a new variable, so there must be some metadata in the original variable that DV3D is not happy with
You can use the following script to reproduce the crash, or try to plot the corrected variable
#!/usr/bin/env python
import numpy as np
import cdms2, vcs, sys
# A variable that dv3d is happy with
f = cdms2.open( sys.prefix+"/sample_data/geos5-sample.nc" )
v_ok = f('uwnd')
f.close()
print '=== Some information about a variable that works in dv3d:'
v_ok.info()
# A variable that will break dv3d
# wget http://dods.ipsl.jussieu.fr/brocksce/tmp/temp.nc
f = cdms2.open("./temp.nc" )
v_pb = f('TEMP', longitude=(0, 360, 'co'))
f.close()
print '\n=== Some information about the variable that breaks dv3d:\n'
v_pb.info()
# Replacing the axes of the 'buggy' variable will make dv3d happy again
new_lon = cdms2.createUniformLongitudeAxis(0.5, 360, 1.)
new_lat = cdms2.createUniformLatitudeAxis(-89.5, 180, 1.)
new_lev = cdms2.createAxis(v_pb.getLevel()[:], id='level')
new_lev.designateLevel()
new_lev.units = 'meters'
v_corrected = cdms2.createVariable(v_pb, axes=(new_lev, new_lat, new_lon), id='TEMP')
print '\n=== Some information about the corrected variable:'
v_corrected.info()
dv3d = vcs.get3d_scalar()
x = vcs.init()
raw_input('\n\nPress return to try to plot the buggy variable, or CTRL-C')
x.plot(v_pb, dv3d)
x.interact()
# The end
Running the script will produce the following output (including the variables v.info() output):
>python -i pb_dv3d_crash.py
=== Some information about a variable that works in dv3d:
*** Description of Slab uwnd ***
id: uwnd
shape: (1, 14, 181, 360)
filename:
missing_value: 1e+15
comments:
grid_name: <None>
grid_type: generic
time_statistic:
long_name: Zonal Wind
units: m/s
_FillValue: [ 9.99999987e+14]
autoApiInfo: <AutoAPI.AutoAPI.Info instance at 0x7fb2fd263998>
vmin: [ 9.99999987e+14]
tileIndex: None
vmax: [ 9.99999987e+14]
fmissing_value: [ 9.99999987e+14]
Grid has Python id 0x7fb2fde84e10.
Gridtype: generic
Grid shape: (181, 360)
Order: yx
** Dimension 1 **
id: time
Designated a time axis.
units: minutes since 2011-05-01 00:00:00
Length: 1
First: 0
Last: 0
Other axis attributes:
begin_date: [20110501]
begin_time: [0]
long_name: time
time_increment: [60000]
calendar: gregorian
axis: T
Python id: 0x7fb2da908490
** Dimension 2 **
id: lev
Designated a level axis.
units: mb
Length: 14
First: 10.0
Last: 1000.0
Other axis attributes:
positive: down
axis: Z
long_name: vertical level
Python id: 0x7fb2da908e90
** Dimension 3 **
id: lat
Designated a latitude axis.
units: degrees_north
Length: 181
First: -90.0
Last: 90.0
Other axis attributes:
long_name: latitude
axis: Y
Python id: 0x7fb2da908f50
** Dimension 4 **
id: lon
Designated a longitude axis.
units: degrees_east
Length: 360
First: 0.0
Last: 359.0
Other axis attributes:
long_name: longitude
axis: X
modulo: 360.0
topology: circular
Python id: 0x7fb2da908850
*** End of description for uwnd ***
=== Some information about the variable that breaks dv3d:
*** Description of Slab TEMP ***
id: TEMP
shape: (20, 180, 360)
filename:
missing_value: [ -1.00000000e+10]
comments:
grid_name: <None>
grid_type: generic
time_statistic:
long_name: TEMPERATURE
units: DEG C
_FillValue: [ -1.00000000e+10]
autoApiInfo: <AutoAPI.AutoAPI.Info instance at 0x7fb2da979248>
tileIndex: None
history: From /usr/local/install/ferret-6.9/data/levitus_climatology.cdf
Grid has Python id 0x7fb2da916c90.
Gridtype: generic
Grid shape: (180, 360)
Order: yx
** Dimension 1 **
id: ZAXLEVITR
Designated a level axis.
units: meters
Length: 20
First: 0.0
Last: 5000.0
Other axis attributes:
positive: down
point_spacing: uneven
standard_name: depth
axis: Z
Python id: 0x7fb2fde84dd0
** Dimension 2 **
id: YAXLEVITR
Designated a latitude axis.
units: degrees_north
Length: 180
First: -89.5
Last: 89.5
Other axis attributes:
standard_name: latitude
point_spacing: even
axis: Y
Python id: 0x7fb2da908090
** Dimension 3 **
id: XAXLEVITR
Designated a longitude axis.
units: degrees_east
Length: 360
First: 0.5
Last: 359.5
Other axis attributes:
modulo: 360.0
point_spacing: even
standard_name: longitude
axis: X
topology: circular
Python id: 0x7fb2da908310
*** End of description for TEMP ***
=== Some information about the corrected variable:
*** Description of Slab TEMP ***
id: TEMP
shape: (20, 180, 360)
filename:
missing_value: [ -1.00000000e+10]
comments:
grid_name: <None>
grid_type: generic
time_statistic:
long_name: TEMPERATURE
units: DEG C
autoApiInfo: <AutoAPI.AutoAPI.Info instance at 0x7fb2da979638>
tileIndex: None
history: From /usr/local/install/ferret-6.9/data/levitus_climatology.cdf
Grid has Python id 0x7fb2da916c90.
Gridtype: generic
Grid shape: (180, 360)
Order: yx
** Dimension 1 **
id: level
Designated a level axis.
units: meters
Length: 20
First: 0.0
Last: 5000.0
Other axis attributes:
axis: Z
Python id: 0x7fb2da916090
** Dimension 2 **
id: latitude
Designated a latitude axis.
units: degrees_north
Length: 180
First: -89.5
Last: 89.5
Other axis attributes:
axis: Y
Python id: 0x7fb2da916210
** Dimension 3 **
id: longitude
Designated a longitude axis.
units: degrees_east
Length: 360
First: 0.5
Last: 359.5
Other axis attributes:
axis: X
modulo: 360.0
topology: circular
Python id: 0x7fb2fde84d90
*** End of description for TEMP ***