Re: "_clamping" grid output
Steven Phillips
I was running a model on a large dataset with the new version of
Maxent (3.2.1), and the software ran out of hard disk space just
before completion (I've included the log file below).
You could write the output in .gri format to save space (or use .mxe,
which saves even more space, and was described in some posts on this
group a couple of months ago).
There are now
two .asc output files in my output directory--one has my species
abbreviation + ".asc," while the other has my species abbreviation +
"_clamping.asc." I don't understand what the difference is between
the two, and why both are now produced by the new version. I haven't
found anything in the documentation, but perhaps I'm just missing
it...?
The clamping output is used to make the clamping picture, which is
described in the .html output.
I'm wondering if one of these output files was a temporary file that
would have been deleted subsequent to successful completion of the
run, or whether there is an additional output layer now being
provided. If it's the latter, is there a way "shut off" this
additional output? I worry about the processing time and hard drive
space it will add to a large modeling project I'm working on, where
there will be thousands of runs of Maxent required.
Yes, click on the help button, and at the end of the help page you'll
see the "dontwriteclampgrid" flag, which turns off writing of that
output.
-- Steven
Sam Veloz
was going fine until writing the clamping png file. Maxent then barfed
and stopped running. All 3 asc files finished writing and the csv files
are fine but it quits before I get the complete html file which would be
nice to have. The other weird thing is that the projected asc file (in
raw format) has max values of ~ 9. I thought raw files shouldn't have
values>1??
Thanks,
Sam
Below is the log:
Mon Mar 10 20:55:21 PDT 2008
MaxEnt version 3.2.1
Checking header of C:\Mimulus\ascii2\alt.asc
Checking header of C:\Mimulus\ascii2\aspect.asc
Checking header of C:\Mimulus\ascii2\bare.asc
Checking header of C:\Mimulus\ascii2\bio1.asc
Checking header of C:\Mimulus\ascii2\bio10.asc
Checking header of C:\Mimulus\ascii2\bio11.asc
Checking header of C:\Mimulus\ascii2\bio12.asc
Checking header of C:\Mimulus\ascii2\bio13.asc
Checking header of C:\Mimulus\ascii2\bio14.asc
Checking header of C:\Mimulus\ascii2\bio15.asc
Checking header of C:\Mimulus\ascii2\bio16.asc
Checking header of C:\Mimulus\ascii2\bio17.asc
Checking header of C:\Mimulus\ascii2\bio18.asc
Checking header of C:\Mimulus\ascii2\bio19.asc
Checking header of C:\Mimulus\ascii2\bio2.asc
Checking header of C:\Mimulus\ascii2\bio3.asc
Checking header of C:\Mimulus\ascii2\bio4.asc
Checking header of C:\Mimulus\ascii2\bio5.asc
Checking header of C:\Mimulus\ascii2\bio6.asc
Checking header of C:\Mimulus\ascii2\bio7.asc
Checking header of C:\Mimulus\ascii2\bio8.asc
Checking header of C:\Mimulus\ascii2\bio9.asc
Checking header of C:\Mimulus\ascii2\cti.asc
Checking header of C:\Mimulus\ascii2\fa.asc
Checking header of C:\Mimulus\ascii2\herb.asc
Checking header of C:\Mimulus\ascii2\lcover.asc
Checking header of C:\Mimulus\ascii2\mask.asc
Checking header of C:\Mimulus\ascii2\slope.asc
Checking header of C:\Mimulus\ascii2\tree.asc
Reading samples from sublist.csv
Read samples: max memory 1065484288, total allocated 6590464, free
2194904, used 4395560, increment 4395560
Reading file alt.mxe
Extractor: max memory 1065484288, total allocated 40996864, free
10975960, used 30020904, increment 25625344
Time since start: 3.453
Extracting random background and sample data
Time since start: 107.188
Extracting random background and sample data
Warning: Sample at-1936007.22278, -97053.486621 in sublist.csv is
missing some environmental data
Warning: Skipping sample at -1936007.22278, -97053.486621
Warning: Sample at-1935996.68525, -97052.905955 in sublist.csv is
missing some environmental data
Warning: Skipping sample at -1935996.68525, -97052.905955
Time since start: 138.875
Adding samples to background in feature space
Command line:
Species: MIBI
Layers: alt aspect bare bio1 bio10 bio11 bio12 bio13 bio14 bio15 bio16
bio17 bio18 bio19 bio2 bio3 bio4 bio5 bio6 bio7 bio8 bio9 cti fa herb
lcover mask slope tree
Layertypes: Continuous Continuous Continuous Continuous Continuous
Continuous Continuous Continuous Continuous Continuous Continuous
Continuous Continuous Continuous Continuous Continuous Continuous
Continuous Continuous Continuous Continuous Continuous Continuous
Continuous Continuous Categorical Continuous Continuous Continuous
Linear: true, Quadratic: true, Product: true, Threshold: true, Hinge:
true, Auto: true
Species file: C:\Mimulus\sp_proj\sublist.csv
Environmental variables directory: C:\Mimulus\ascii2
Output directory: E:\Max_out\mcp_test
Projection layers directory: C:\Mimulus\EnvLayers\asciis
Output format: Raw
Output file type: .asc
Maximum iterations: 500
Convergence threshold: 1.0E-5
Remove duplicates: true
Number of background points: 10000
Bias file:
Random test percentage: 0
Test sample file:
getSamples: max memory 1065484288, total allocated 71299072, free
25041728, used 46257344, increment 16236440
Time since start: 151.688
Making features
Time since start: 153.063
makeFeatures: max memory 1065484288, total allocated 106250240, free
35582744, used 70667496, increment 24410152
MIBI:
beta_cat = 0.25,beta_thr = 1.13,beta_hge = 0.5,beta_lqp = 0.1428571428571429
Beta multiplier: 1.0
Time since start: 154.25
87 samples
Density: max memory 1065484288, total allocated 106250240, free
16673696, used 89576544, increment 18909048
linearPredictor: max memory 1065484288, total allocated 106250240, free
16593000, used 89657240, increment 80696
Deactivating (lcover=7.0)
Deactivating (lcover=9.0)
Deactivating (lcover=11.0)
Deactivating (lcover=14.0)
Deactivating (lcover=18.0)
Deactivating (lcover=21.0)
Deactivating (lcover=22.0)
Deactivating (lcover=23.0)
Deactivating (lcover=24.0)
Deactivating (lcover=26.0)
Deactivating (lcover=28.0)
FeaturedSpace: max memory 1065484288, total allocated 106250240, free
16593000, used 89657240, increment 0
Sequential: max memory 1065484288, total allocated 106250240, free
16581848, used 89668392, increment 11152
Initial loss: 9.218804450388312
Time since start: 195.563
500: time = 40.860000 loss = 7.809634
Time since start: 204.313
Projecting...
Writing file E:\Max_out\mcp_test\MIBI.asc
Time since start: 245.985
Reading file MIBI.asc
Time since start: 261.453
FLOAT, 11550 pixels with data
readGrid: max memory 1065484288, total allocated 174936064, free
68632840, used 106303224, increment 16634832
Writing E:\Max_out\mcp_test\plots\MIBI.png
Projecting...
Time since start: 264.36
Writing file E:\Max_out\mcp_test\MIBI_asciis_clamping.asc
Time since start: 618.672
Writing file E:\Max_out\mcp_test\MIBI_asciis.asc
Time since start: 918.235
Reading file MIBI_asciis.asc
Time since start: 940.969
FLOAT, 1429373 pixels with data
readGrid: max memory 1065484288, total allocated 174936064, free
44710624, used 130225440, increment 23922216
Writing E:\Max_out\mcp_test\plots\MIBI_asciis.png
Time since start: 945.016
Reading file MIBI_asciis_clamping.asc
Time since start: 948.813
Fatal Error: java.lang.NumberFormatException: For input string: "?"
java.lang.NumberFormatException: For input string: "?"
at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source)
at java.lang.Float.parseFloat(Unknown Source)
at density.GridIO.readASC(GridIO.java:288)
at density.GridIO.readGrid(GridIO.java:36)
at density.Runner.makePicture(Runner.java:657)
at density.Runner.start(Runner.java:497)
at density.GUI$7.construct(GUI.java:392)
at density.SwingWorker$2.run(SwingWorker.java:108)
at java.lang.Thread.run(Unknown Source)