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JLink Java exception reading netcdf file via input

  • To: mathgroup at smc.vnet.net
  • Subject: [mg113926] JLink Java exception reading netcdf file via input
  • From: "m. r." <schaferk at bellsouth.net>
  • Date: Thu, 18 Nov 2010 07:05:38 -0500 (EST)

greetings:
Mathematica version 7.0.1 Mac OSX x86


i use the (below) code to read a netcdf file successfully with 50M
file

nx=600;ny=300;

eta = Partition[
 Partition[
  Import[ "Eta.NCOM.ARPS.input.nc", {"Datasets", "Eta"}
    ] // Flatten, nx
  ], ny
 ];

[PBG5:LZS64/expt_104/run] me% ls -l Eta.NCOM.ARPS.input.nc
-rw-r--r--  1 me  me  59768432 Sep 28  2009 /Users/me/Papers/
4paperMindoro/nc/Eta.NCOM.ARPS.input.nc

when i try the same technique on another file of approximately  200M,
i get a JLink exception.

nx=348;ny0;

eta = Partition[
 Partition[
  Import[ "Eta.MITgcm.LZS64.02.1.4.8.input.nc", {"Datasets", "Eta"}
    ] // Flatten, nx
  ], ny
 ];

[PBG5:LZS64/expt_104/run] schaferk% ls -l *.nc
-rw-r--r--  1 me  me  200761728 Oct 15 19:34
Eta.MITgcm.LZS64.02.1.4.8.input.nc

here is the error message:

JLink`Java::"excptn" :  "
StyleBox[\"\\\"\<A Java exception occurred: \>\\\"\", \"MT\"] \
[NoBreak]
StyleBox[\"\\\"\<java.lang.OutOfMemoryError: Java heap \
space\\\\\\\\n\\\\\\\\tat \
ucar.ma2.ArrayFloat.<init>(ArrayFloat.java:86)\\\\\\\\n\\\\\\\\tat \
ucar.ma2.ArrayFloat$D4.<init>(ArrayFloat.java:313)\\\\\\\\n\\\\\\\
\tat \
ucar.ma2.ArrayFloat$D4.<init>(ArrayFloat.java:305)\\\\\\\\n\\\\\\\
\tat \
ucar.ma2.ArrayFloat.factory(ArrayFloat.java:51)\\\\\\\\n\\\\\\\\tat \
ucar.ma2.ArrayFloat.factory(ArrayFloat.java:36)\\\\\\\\n\\\\\\\\tat \
ucar.ma2.Array.factory(Array.java:130)\\\\\\\\n\\\\\\\\tat \
ucar.ma2.Array.factory(Array.java:90)\\\\\\\\n\\\\\\\\tat \
ucar.ma2.Array.copy(Array.java:449)\\\\\\\\n\\\\\\\\tat \
ucar.ma2.Array.copyTo1DJavaArray(Array.java:478)\>\\\"\", \"MT\"] \
[NoBreak]
StyleBox[\"\\\"\<.\>\\\"\", \"MT\"] "

the tech support fellow said that the 50 million entry array Eta is
running into a
bottle neck in the Import process and that there is no workaround.

another popular math software system was able to read the file in a
few seconds.

any ideas of a workaround in Mathematica?

michael schaferkotter


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