entropy on saguaro 9-5-13

2013-09-10

++ entropy on saguaro 9-5-13

Tried to get entropy program running in Saguaro
see Saguaro Supercomputer portal 9-5-13

Note that the previous time I tried to run the program with Saguaro there was an error. This seems to have been caused by the fact that when my program calls directories the delimiters need to be forward slashes to work with Linux. I did this part correctly. However, when my program deals with escaping a character in a regular expression, then these still characters still need to be backslashes, and I had them as forward slashes. I made the necessary change, recompiled the jar file, copied the new jar file to saguaro, and tried running the program.


Tried running this command
java -jar "/home/lwang138/entropy/input/EntropyOfArray090413_2.jar" home/lwang138/entropy/input/46/110 "4-22 S4 A1 Hi P60 092612 #8-15 5um K" -Xmx6144


Tried this
java -jar "/home/lwang138/entropy/input/EntropyOfArray090413_2.jar" /home/lwang138/entropy/input/46/110 "4-22 S4 A1 Hi P60 092612 #8-15 5um K" -Xmx6144



The pbs file Lu has me working with is located here
/home/lwang138/sas/jar.pbs



Obtained results from program here:
/home/lwang138/jar.pbs.o6107643
and
/home/lwang138/entropy/input/46/110

entropy: 8.28
cv: 1.74
normalized entropy: 6.09
normalized cv: 1.75

^All of these values are exactly what they should be, and the program finished in this time:
2013/09/05 11:20:17
2013/09/05 17:52:19
from 2013/09/05 11:20:17 to 2013/09/05 17:52:19
6hr32m2s

time and space required to calculate entropy of one gpr on saguaro

Since there are 251 gprs the total time should be about 251*6.5=1,632hr


Next we got the program running on saguaro
Josh made some scripts and files to do this. . found here
"F:\kurt\storage\CIM Research Folder\DR\2013\9-10-13\scripts and files from Josh"