NullAndVoid

From AIMSWiki

Table of contents
1 Members
2 Notes

2.1 FORTRAN
2.2 Making malaria application
2.3 Exercise 3

3 Thursday Exercise 1


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Members

  1. User:Andyr Andy Rabagliati (AIMS, South Africa)
  2. User:Rudolf Jim Rudolf (ICV, Switzerland)
  3. User:Jan Jan Groenewald (AIMS, South Africa)
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Notes

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FORTRAN

Serial number for Intel Professional Fortran: V6XF-RJW75F9J... Ubuntu 6.06 is not supported, but we'll give it a shot anyway...

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Making malaria application

BOINC has its own libraries which are linked to the client. These need to be compiled, and, for convenience, installed.

So...

  • make & install boinc 
cd ~/mcdn/boinc
./configure --disable-client
make
make install
  • set up environment variables for fortran compiler: 
sh /opt/intel/fc/10.0.025/bin/ifortvars.sh
  • make malaria model 
cd ~/mcdn/malariaModel
./configure
make test

Which on success will answer with boinc initialized.

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Exercise 3

Don't forget to add --db_passwd=XXXXXX to tools/make_project.

This is how to modify Apache config file & restart with Apache2, which is slightly different than the instructions given after successful project creation: 

sudo cp /malaria/malaria/malariacontrol.httpd.conf /etc/apache2/conf.d/malaria.conf
sudo apache2ctl restart
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Thursday Exercise 1

We tried using gcj to compile the java down to a single executable, removing the requirement to find and run an interpreter.

Having downloaded a Work Unit, we found these jar files in the directory :- 

jaxp.jar        ## javax/xml/parsers/
parser.jar      ## org/xml/sax/, org/w3c/dom/, com/sun/xml/parser/, com/sun/xml/util/, com/sun/xml/tree/
stdsim2.jar     ## Main STDSIM java program

We compiled the libraries, which generated object files, and the main stdsim2.jar was compiled and linked, like this :- 

gcj -c jaxp.jar
gcj -c parser.jar
gcj --main=stdsim2 -o stdsim2 stdsim2.jar jaxp.o parser.o

This left us with stdsim2 executable. We benchmarked this and the two different java interpreters, like this :- 

time /usr/lib/jvm/java-6-sun-1.6.0.00/bin/java -Xmx512m -jar stdsim2.jar -run -iscenario -s1 -n1
          inputfile scenario 13315323 events processed in 122790 msec                   ## user    1m51.227s
time ./stdsim2 -run -iscenario -s1 -n1
          inputfile scenario 15133294 events processed in 297429 msec                   ## user    3m49.918s
# with -O2 optimisation on compilation :-
time ./stdsim2 -run -iscenario -s1 -n1
          inputfile scenario 13315323 events processed in 176097 msec                   ## user    2m33.070s
time java -Xmx512m -jar stdsim2.jar -run -iscenario -s1 -n1
          inputfile scenario 13315323 events processed in 1928192 msec                  ## user    29m20.522s

Optimisation of the compilation also reduced memory usage from 150Meg to 130Meg (Virtual).

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