Re: JLink Java exception reading netcdf file via input
- To: mathgroup at smc.vnet.net
- Subject: [mg113946] Re: JLink Java exception reading netcdf file via input
- From: Herman Kuun <oomkoos1 at gmail.com>
- Date: Fri, 19 Nov 2010 05:07:38 -0500 (EST)
Looking at the error message;
"OutOfMemoryError: Java heap "
Try increasing the Java Virtual Machine's heapsize by editing;
$UserBaseDirectory/Kernel/init.m
and add the following two lines;
Needs["JLink`"];
ReinstallJava[JVMArguments -> "-Xmx800m"];
Best
Herman
On Thu, Nov 18, 2010 at 2:05 PM, m. r. <schaferk at bellsouth.net> wrote:
> greetings:
> Mathematica version 7.0.1 Mac OSX x86
>
>
> i use the (below) code to read a netcdf file successfully with 50M
> file
>
> nx=600;ny=300;
>
> eta = Partition[
> Partition[
> Import[ "Eta.NCOM.ARPS.input.nc", {"Datasets", "Eta"}
> ] // Flatten, nx
> ], ny
> ];
>
> [PBG5:LZS64/expt_104/run] me% ls -l Eta.NCOM.ARPS.input.nc
> -rw-r--r-- 1 me me 59768432 Sep 28 2009 /Users/me/Papers/
> 4paperMindoro/nc/Eta.NCOM.ARPS.input.nc
>
> when i try the same technique on another file of approximately 200M,
> i get a JLink exception.
>
> nx=348;ny0;
>
> eta = Partition[
> Partition[
> Import[ "Eta.MITgcm.LZS64.02.1.4.8.input.nc", {"Datasets", "Eta"}
> ] // Flatten, nx
> ], ny
> ];
>
> [PBG5:LZS64/expt_104/run] schaferk% ls -l *.nc
> -rw-r--r-- 1 me me 200761728 Oct 15 19:34
> Eta.MITgcm.LZS64.02.1.4.8.input.nc
>
> here is the error message:
>
> JLink`Java::"excptn" : "
> StyleBox[\"\\\"\<A Java exception occurred: \>\\\"\", \"MT\"] \
> [NoBreak]
> StyleBox[\"\\\"\<java.lang.OutOfMemoryError: Java heap \
> space\\\\\\\\n\\\\\\\\tat \
> ucar.ma2.ArrayFloat.<init>(ArrayFloat.java:86)\\\\\\\\n\\\\\\\\tat \
> ucar.ma2.ArrayFloat$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
>
>