Merge branch 'with_java'

[simgrid.git] / doc / doxygen / bindings.doc

/*! \page bindings Bindings

\section bindings_binding_Ruby Ruby Binding
Check online for our specific [Simgrid-Ruby documentation](http://simgrid.gforge.inria.fr/documentation.html).

\section bindings_binding_Java Java Binding
Simgrid-java is a java API that let you use [Simgrid](http://simgrid.gforge.inria.fr/)
MSG API in your favorite language (java). Without it, you would be forced to
use C or one of the other bindings provided.

MSG was the first distributed programming environment provided within SimGrid.
While almost realistic, it remains quite simple. This describes the Java
bindings to this interface.

The javadoc is accessible [here](javadoc/index.html)

\subsection bindings_binding_Java_jMSG_who Who should use this (and who shouldn't)
You should use MSG if you want to study some heuristics for a given problem you
don't really want to implement. SimGrid-java let you use MSG while coding in
Java. So if your need is MSG + Java, you're in the right section!

\subsection SimGrid-java Usage overview 

To make a long story short, it's a JNI binding, so it implies that:
- Most of the MSG and SimGrid documentation about behavioral aspects applies
  directly to what you are programming. 
- MSG data structures are mapped to Java objects. So it means that from the
  syntax point of view, you have to know how those objects are. Fortunately,
  we have generated the Javadoc for those objects. So take a look at it

Finally, it implies also that your program can crash for 3 main reasons: 
- Your Java part is not good: you'll have a good old java exception thrown,
  and hence you should be able to correct it by yourself.
- Our java part is not good: you'll also have a java exception thrown, but
  we have real doubts this can happen, since the java part is only a JNI
  binding. The other option is that it crashed because you used incorrectly
  the MSG API, so this means also you should have an MSGException. It means
  you should read carefully MSG samples and/or documentation.
- Something has crashed in the C part. Okay, here comes the tricky thing.

C crashes mainly for 2 reasons: 
- When something goes wrong in your simulation, sometimes the C part stops
  because you used SimGrid incorrectly, and JNI bindings are not fond of that.
  It means that you'll have something that looks ugly, but you should be able
  to identify what's going wrong in your code by carefully reading the whole
  error message
- It may happen that the problem comes directly from SimGrid: in this case,
  the error should be uglier. In that case, you may submit a bug directly to
  SimGrid.

\subsection bindings_binding_java_install How to install Simgrid-java

To use java with Simgrid you have to install some dependencies:
- Simgrid (see [install Simgrid](http://simgrid.gforge.inria.fr/simgrid/latest/doc/install.html).
  You should set the `SIMGRID_ROOT` environment variable to the path where you installed SimGrid.
- Java JDK packages, such as `openjdk7` or `sun-java6-jdk` (with `libgcj10-dev` or another
  version of gcj). For maximal performance and scalability, use a coroutine-enabled JVM (see
  \ref bindings_binding_java_coroutines).
 
Then Download and install package Simgrid-java:
~~~~{.sh}
git clone git://scm.gforge.inria.fr/simgrid/simgrid-java.git
cd simgrid-java
cmake -DCMAKE_INSTALL_PREFIX=$HOME/Install/simgrid-java/ .
make install
~~~~
 
Cmake output
~~~~{.sh}
-- SITE        : Linux_2.6.38-8-generic_x86_64
-- BUILDNAME   : Simgrid-Java
-- Looking for lib SimGrid
-- Looking for lib SimGrid - found
-- Simgrid version : 3.8.1
-- Looking for gras.h
-- Looking for gras.h - found
-- Found Tesh: /home/user/Bureau/simgrid/git/bin/tesh
-- Found gras_stub_generator: /home/user/Bureau/simgrid/git/bin/gras_stub_generator
-- Java version 1.6.0.22 configured successfully!
-- Looking for jni.h
-- Looking for jni.h - found
-- Add flags -I/usr/lib/jvm/java-6-openjdk/include
-- Looking for jni_md.h
-- Looking for jni_md.h - found
-- Found javac: /usr/bin/javac
-- Found jar: /usr/bin/jar
-- Configuring done
-- Generating done
-- Build files have been written to: /home/user/workspace/simgrid-java/build
~~~~

If cmake complains that **jni could not be found**, you need to tell it where
JNI header files are located. the following command should tell you:

~~~~{.sh}
$ locate jni.h
/usr/lib/jvm/java-6-openjdk-amd64/include/jni.h
/usr/lib/jvm/java-7-openjdk-amd64/include/jni.h
~~~~

If you have several version of jni installed (as in the example
above), you need to check the version of java that is used by default
on your machine (using javac -version), and pick the right one. Then
set the `JAVA_INCLUDE_PATH` environment variable to the right path (note
that we remove the filename `jni.h` from that path), and relaunch cmake.

~~~~{.sh}
$ export JAVA_INCLUDE_PATH=/usr/lib/jvm/java-6-openjdk-amd64/include/
$ cmake .
~~~~

\subsubsection bindings_binding_java_use How to use Simgrid-java

To execute the examples you need to add the path where you installed
the generated `libSG_java` library (`<build_dir>/lib`) and `libsimgrid`
(`$SIMGRID_ROOT/lib`) into the `LD_LIBRARY_PATH`.

Be careful on Mac, this variable is called `DYLD_LIBRARY_PATH` and not
`LD_LIBRARY_PATH`.

~~~~{.sh}
$ export SIMGRID_ROOT="$HOME/Install/simgrid/" # change it to the path where you installed the SimGrid library
$ export SIMGRID_JAVA_ROOT="$HOME/Install/simgrid-java" # change it to the path where you installed the java bindings of SimGrid 
$ export LD_LIBRARY_PATH=${LD_LIBRARY_PATH:+$LD_LIBRARY_PATH:}$SIMGRID_ROOT/lib:$SIMGRID_JAVA_ROOT/java
$ cd examples
$ java -cp .:../simgrid.jar basic/BasicTest platform.xml basic/basicDeployment.xml
~~~~

If you want to make these settings permanent even after a reboot, you
need to add the export lines into your `~/.bashrc` file, or equivalent.

\subsubsection bindings_binding_java_coroutines How to use the coroutines context factory

There is two main motivations to use the coroutine variant of SimGrid
Java bindings: it's about 5 times faster than the default thread-based
context factory, and the amount of runnable processes is then only
limited by the amount of RAM that you have. The drawbacks are that it
requires a specific and rather experimental JVM to run, and that this
context factory itself remains a bit experimental so far.

\subsubsection  bindings_java_coro_install Getting a mlvm JVM

You need to get a patched JVM from [here](http://ssw.jku.at/General/Staff/LS/coro/)
(many thanks to Lukas Stadler for this work!). 

You can either get a prebuilt binary, or recompile your own JVM. Make
sure to get a coro-simple version, as we don't need to serialize nor
migrate stacks in SimGrid. You should be able to follow the `README.txt`
that you'll get in the repository, but here is how we did it, just in
case. The instructions are given for a debian or Ubuntu box, but I
think you should manage to convert it to your system quite easily.
Finally, if you're really stuck, you can get the version compiled by
Jonathan Rouzaud-Cornabas from his web page. This version is known to
work with SimGrid for sure!
http://graal.ens-lyon.fr/~jrouzaud/files/corosimple-linux-amd64-20120914.tgz
 
 -# Install mercurial and some dependencies
~~~~{.sh}
sudo apt-get install mercurial ksh libfreetype6-dev libcups2-dev libasound2-dev gawk openjdk-7-jdk libxext-dev libxrender-dev libxtst-dev
# Grab the forest extension: we need to source-install it
hg clone https://bitbucket.org/gxti/hgforest hgforest \endverbatim
~~~~
 -# Configure the mercurial extensions: Edit ~/.hgrc and paste the
    following lines. Don't forget to change the /path/to/forest.py to
    point to where you just downloaded the source. 
    
    Forest extension is needed to download the openjdk source code and
    patches while the mq line is needed to apply the patches. The
    username is needed at the step "preparing the sources", not sure why.
~~~~
[ui]
username = YouUserameWithoutSpaces
[extensions]
forest=/path/to/forest.py
mq=
~~~~
 -# Prepare the source code
~~~~{.sh}
# create a working directory, and enter it
mkdir davinci; cd davinci

# Grab the sources
hg fclone http://hg.openjdk.java.net/hsx/hotspot-comp sources
# Grab the patches
hg fclone http://hg.openjdk.java.net/mlvm/mlvm patches

# Link the patch directories into the sources
bash patches/make/link-patch-dirs.sh sources patches
# Test wether the previous command worked with
ls -i patches/hotspot/series sources/hotspot/.hg/patches/series
# It should display something like the following.
# (note that both file share the same inode number)
#  9707849 patches/hotspot/series  
#  9707849 sources/hotspot/.hg/patches/series


# Specify what to compile. 
export davinci=$(pwd) guards="buildable testable coro-simple"
# Apply the patches
sh patches/make/each-patch-repo.sh hg qselect --reapply $guards '$(sh $davinci/patches/make/current-release.sh)'
# Check that it understood that you want the patch applied:
grep GLOBAL_GUARDS patches/make/* -r
# this should display something like the following (maybe amonst other unrelated lines)
# GLOBAL_GUARDS=buildable testable coro-simple
# If this does not work, edit patches/make/Makefile,
#   manually coro-simple to GLOBAL_GUARDS and then 
#   rerun the patches/make/each-patch-repo.sh script as earlier


# Finish the setup
(cd patches/make; make setup && make force && make && make FORCE_VERSIONS=1 && echo "Sources are properly setup")
# If this last command failed, check your mercurial config within ~/.hgrc (see above)
~~~~       
 -# Compile it all
~~~~{.sh}
unset LD_LIBRARY_PATH
export ALT_BOOTDIR=/usr/lib/jvm/java-7-openjdk-amd64/
cd sources
# Check that everything is fine
make sanity
# Go for it (it takes about half an hour on my machine)
make all

# Check that the coroutine library got compiled in
ls sources/build/linux-amd64/classes/java/dyn/
# This should display a bunch of class files. If not, something went wrong, you need to investigate further
~~~~

\subsubsection  bindings_java_coro_use Using coroutine contexts

SimGrid Java will automatically switch to the coroutine context
factory if your JVM support it, so you will just need to execute your
simulation with the correct JVM. The selected context factory gets
displayed automatically.
~~~~{.sh}
export LD_LIBRARY_PATH=/path/to/simgrid.so:/path/to/libSG_java.so
cd examples
$PATH_TO_COROUTINE_JVM/java -cp .:../simgrid.jar masterslave.Masterslave masterslave/ masterslaveDeployment.xml platform.xml
~~~~

Note that you may have to adjust the "coro.stacksPerThread"
configuration option to run large simulations. The default is 100 and
you want to increase it to run more processes.
~~~~{.sh}
$ $PATH_TO_COROUTINE_JVM/java -Dcoro.stacksPerThread=$STACKS_NUMBER -cp .:../simgrid.jar basic/BasicTest platform.xml basic/basicDeployment.xml
~~~~

If you reach the point where the creation of new simulated processes
fail with the message "Can't create coroutine object", you may need to
increase the relevant system limit with the following command.
~~~~{.sh}
sysctl -w vm.max_map_count = 131072
~~~~

The full story is that each coroutine requires two memory maps, and
that Linux puts a limit on the total amount of memory maps that each
process can manage (by default, this limit is often at 65535). Since
the JVM needs a few dozen of such maps on its own (three maps per
dynamic library -- check `/proc/the_pid/maps` if you don't believe it),
this is enough to create over 30,000 simulated processes. But to go
futher, that limit must be modified. 

If you want to make this change permanent on your machine, edit your
`/etc/sysctl.conf` file. Otherwise, you have to redo it by calling
sysctl after each reboot.

\section bindings_binding_lua Lua Binding

Most of Simgrid modules require a  good level in C programming, since simgrid is used to be as standard C library.
 Sometime users prefer using some kind of “easy scripts” or a language easier to code with, for their works,
 which avoid dealing with C errors, and sometime an important  gain of time.
Besides Java Binding, Lua  and Ruby bindings are available since version 3.4 of Simgrid
for MSG Module, and we are currenlty working on bindings for other modules.

\subsection bindings_binding_lua_about What is lua ?
Lua is a lightweight, reflective, imperative and functional programming language,
 designed as a scripting language with extensible semantics as a primary goal (see official web site <a href="http://www.lua.org">here</a>).
\subsubsection bindings_binding_lua_why Why lua ?
Lua is a fast, portable and powerful script language, quite simple to use for developpers.
it combines procedural features with powerful data description facilities,
 by using a simple, yet powerful, mechanism of tables.
Lua has a relatively simple C API compared to other scripting languages,
and accordingly it provides a robust, easy to use it.
\subsubsection bindings_binding_lua_simgrid How to use lua in Simgrid ?
Actually, the use of lua in Simgrid is quite simple, you have just to follow the same steps as coding with C in Simgird :
  - Coding functions coresponding to each process
  - loading the platforme/deployment XML file that describe the environment of simulation
  - and … Running the Simulation.

\dontinclude lua/masterslave/master.lua
\subsection bindings_binding_lua_example_master_slave Master/Slave Example

 \li Master Code
 \until end_of_master
we mainly  use   simgrid.Task.new(task_name,computation_size,communication_size) to create our MSG Task,
         then simgrid.Task.send(task,alias) to send it.
we use also simgrid.Task.name(task), to get the task's name.

\dontinclude lua/masterslave/slave.lua
\li Slave Code
\until end_of_slave
Here, we see the use of simgrid.Task.recv(alias) to receive a task with a specific alias,
this function return directly the task recevied.

\dontinclude lua/masterslave/master_slave.lua
\li Set Environmenet and run application
\until end-of-master-slave

\subsection bindings_binding_lua_example_data Exchanging Data
You can also exchange data between Process using lua. for that, you have to deal with lua task as a table,
since lua is based itself on a mechanism of tables,
so you can exchange any kind of data (tables, matrix, strings,…) between process via tasks.

\li Sender process
\verbatim
  task = simgrid.Task.new("data_task",task_comp,task_comm);
  task['matrix'] = my_matrix;
  task['table'] = my_table;
  task['message'] = "Hello from (Lua || Simgrid ) !! "
  …
  simgrid.Task.send(task,alias)
\endverbatim
        After creating task, we associate to it various kind of data with a specific key (string in this case)
        to distinguish between data variables. The receiver will use this key to access easily to datas.


\li Receiver processe
\verbatim
  task = simgrid.Task.recv(alias);
  sender_matrix = task['matrix'];
  sender_table = task['table'];
  sender_message = task['message']
  ...
\endverbatim
        Note that in lua, both sender and receiver share the same lua task.
        So that the receiver could joint data directly on the received task without sending it back.
        You can find  a complet example (matrix multiplication case) in the file example/lua/mult_matrix.lua.


\subsection bindings_binding_lua_example_bypass Bypass XML
        maybe you wonder if there is a way to bypass the XML files,
         and describe your platform directly from the code, with lua bindings it's Possible !! how ?
        We provide some additional (tricky?) functions in lua that allows you to set up your own platform without using the XML files
     ( this can be useful for large platforms, so a simple for loop will avoid you to deal with an annoying XML File ;) )


\li set Routing mode
\verbatim
   simgrid.AS.new{id="AS0",mode="Full"};
\endverbatim

\li set Hosts
\verbatim
  simgrid.Host.new{id="Tremblay",power=98095000};
  simgrid.Host.new{id="Jupiter",power=76296000};
  simgrid.Host.new{id="Fafard",power=76296000};
  simgrid.Host.new{id="Ginette",power=48492000};
  simgrid.Host.new{id="Bourassa",power=48492000};
\endverbatim
  we use simgrid.Host.new{id=id_host,power=power_host} to instanciate our hosts.

\li set Links
\verbatim
  for i=0,11 do
    simgrid.Link.new{id=i,bandwidth=252750+ i*768,latency=0.000270544+i*0.087};    --  some crazy values ;)
  end
\endverbatim
  we used simgrid.Link.new{id=link_id,bandwidth=bw,latency=lat} with a simple for loop to create all links we need (much easier than XML hein ?)

\li set Routes
\verbatim
-- simgrid.Route.new(src_id,des_id,links_nb,links_list)
   simgrid.Route.new("Tremblay","Jupiter",1,{"1"});
   simgrid.Route.new("Tremblay","Fafard",6,{"0","1","2","3","4","8"});
   simgrid.Route.new("Tremblay","Ginette",3,{"3","4","5"});
   simgrid.Route.new("Tremblay","Bourassa",7,{"0","1","3","2","4","6","7"});

   simgrid.Route.new("Jupiter","Tremblay",1,{"1"});
   simgrid.Route.new("Jupiter","Fafard",7,{"0","1","2","3","4","8","9"});
   simgrid.Route.new("Jupiter","Ginette",4,{"3","4","5","9"});
   simgrid.Route.new("Jupiter","Bourassa",8,{"0","1","2","3","4","6","7","9"});
   ...
\endverbatim
  for each host you have to specify which route to choose to access to the rest of hosts connected in the grid.

\li Save platform
\verbatim
  simgrid.register_platform();
\endverbatim
Don't forget to register your platform, that SURF callbacks starts their work ;)

\li set application
\verbatim
   simgrid.Host.setFunction("Tremblay","Master",4,{"20","550000000","1000000","4"});
   simgrid.Host.setFunction("Bourassa","Slave",1,{"0"});
   simgrid.Host.setFunction("Jupiter","Slave",1,{"1"});
   simgrid.Host.setFunction("Fafard","Slave",1,{"2"});
   simgrid.Host.setFunction("Ginette","Slave",1,{"3"});
\endverbatim
  you don't  need to use a deployment XML file, thanks to  simgrid.Host.setFunction(host_id,function,args_number,args_list)
  you can associate functions for each host with arguments if needed .

\li
\verbatim
   simgrid.register_application();
\endverbatim
Yes, Here too you have to register your application before running the simulation.

the full example is distributed in the file examples/lua/master_slave_bypass.lua

\subsection MSG_ex_master_slave_lua Master/slave Lua application

Simulation of a master-slave application using lua bindings    
- \ref MSG_ext_ms_master_lua
- \ref MSG_ext_ms_slave_lua
- \ref MSG_ext_ms_core_lua
- \ref MSG_ext_ms_helping
- \ref MSG_ext_ms_application
- \ref MSG_ext_ms_platform


     
\subsubsection MSG_ext_ms_master_lua Master code

as described in the C native master/Slave example, this function has to be assigned to a msg_process_t that will behave as the master.

Lua style arguments (...) in for the master are interpreted as:
- the number of tasks to distribute
- the computation size of each task
- the size of the files associated to each task
- a list of host that will accept those tasks.

Tasks are dumbly sent in a round-robin style.
\dontinclude lua/masterslave/master.lua
\skip Dispatch the tasks
\until Done sending
\until end


\subsubsection MSG_ext_ms_slave_lua Slave code

This function has to be assigned to a #msg_process_t that has to behave as a slave.
This function keeps waiting for tasks and executes them as it receives them.
\dontinclude lua/masterslave/slave.lua
\until end_of_slave
\subsubsection MSG_ext_ms_core_lua Simulation core

in this section the core of the simulation which start by including the simgrid lib for bindings
: <i>require "simgrid" </i>

-# Simulation settings : <i>simgrid.platform</i> creates a realistic
   environment
-# Application deployment : create the processes on the right locations with
    <i>simgrid.application</i>
-# The simulation is run with <i>simgrid.run</i>

Its arguments are:
- <i>platform_file</i>: the name of a file containing an valid surfxml platform description.( first command line argument)
- <i>application_file</i>: the name of a file containing a valid surfxml application description ( second commande line argument )
\dontinclude lua/masterslave/master_slave.lua
\skip platform
\until run


\subsection MSG_ex_master_slave_lua_bypass Master/slave Bypass Lua application

Simulation of a master-slave application using lua bindings, Bypassing the XML parser
- \ref MSG_ext_ms_bp_master_lua
- \ref MSG_ext_ms_bp_slave_lua
- \ref MSG_ext_ms_bp_core_lua

      

\subsubsection MSG_ext_ms_bp_master_lua Master code

as described in the C native master/Slave example, this function has to be assigned to a msg_process_t that will behave as the master.

Lua style arguments (...) in for the master are interpreted as:
- the number of tasks to distribute
- the computation size of each task
- the size of the files associated to each task
- a list of host that will accept those tasks.

Tasks are dumbly sent in a round-robin style.

\dontinclude lua/console/master.lua
\until end_of_master

\subsubsection MSG_ext_ms_bp_slave_lua Slave code

This function has to be assigned to a #msg_process_t that has to behave as a slave.
This function keeps waiting for tasks and executes them as it receives them.

\dontinclude lua/console/slave.lua
\until end_of_slave

\subsubsection MSG_ext_ms_bp_core_lua Simulation core

in this section the core of the simulation which start by including the simgrid lib for bindings, then create the resources we need to set up our environment bypassing the XML parser.
: <i>require "simgrid" </i>

-# Hosts : <i>simgrid.Host.new</i> instanciate a new host with an id, and power.
-# Links : <i>simgrid.Link.new</i> instanictae a new link that will require an id, bandwith and latency values.
-# Route : <i>simgrid.Route.new</i> define a route between two hosts specifying the links to use.
-# Simulation settings : <i>simgrid.register_platform();</i> register own platform without using the XML SURF parser.

we can also bypass the XML deployment file, and associate functions for each of defined hosts.
- <i>simgrid.Host.setFunction</i>: associate a function to a host, specifying arguments if needed.
- <i>simgrid.register_application()</i>: saving the deployment settings before running the simualtion.

\include lua/console/master_slave_bypass.lua


 */