calcuations for 330k data

2013-09-06

++ calcuations for 330k data

Now that I see that the program works for one gpr
(see [test of one 330k gpr for cv and entropy normalized and non-normalized])
, I would like to run the program for many gprs on the saguaro supercomputer to run them quickly.

First I need to make sure that I can run a java program from the command line.

I also want to run the java program with more RAM.  I ran the program with 6 GB of ram and this worked before.
So I think the command would be something like this
java "classname" -Xmx6144
so
java Test_Immunosignature_Data_030413d0955.class -Xmx6144
-"F:\kurt\storage\CIM Research Folder\DR\2013\9-4-13\330k gpr test\EntropyOfArray090213\src\Test_Immunosignature_Data_030413d0955.class"

I'll try this out.

I'll copy the gpr to a new location, copy the source code to the same location, and modify the Test_Immunosignature_Data_030413d0955 class so that it refers to the correct file location.

I ended up making a jar file of the project in eclipse, and I specified the main class with the main method.  Then I ran the command

java -jar "F:\kurt\storage\CIM Research Folder\DR\2013\9-4-13\cmd test\EntropyOfArray090413.jar" "F:\kurt\storage\CIM Research Folder\DR\2013\9-4-13\cmd test" "4-22 S4 A1 Hi P60 092612 #8-15 5um K" -Xmx6144

No I can get everything setup to run on Saguaro.
I'll just make a bunch of commands to run all 251 gpr files

I copied the jar file here
"S:\Research\Cancer_Eradication\Discovering tumor specific antigens\entropy\9-4-13\EntropyOfArray090413.jar"

Commands for dealing with data and files on saguaro super computer
"F:\kurt\storage\CIM Research Folder\DR\2013\9-4-13\commands for copying gprs 9-4-13.xlsx"

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