README-v1.9-Ubuntu.txt

adiosvm
=======

Packages and howtos for creating a linux system for ADIOS tutorials

Required steps to get plain ADIOS working: I.1,2,3,5 II.1,4 III.1

Steps:

I. Set up a Linux VM
====================

1. Install VirtualBox 

2. Get a debian linux ISO image
   We currently use Ubuntu 12.04 64bit and the descriptions below all refer to that system. 

3. Create a new VM
   Type=Linux, System=Ubuntu (64bit)
   Memory: at least 2048MB, we use 3072MB just for the sake of it
   Virtual hard drive: VMDK type, dynamically allocated, about 16GB
      - the more the better, but an exported images should fit on an USB stick...
   Video memory: 64MB - we don't really know how much is needed
      - do not enable 2D video or 3D acceleration
   Processor: 2 CPUs 
      - 1 is enough, 2 builds codes faster
   Storage: load the linux iso image into the DVD drive. 


   - Start the VM and install linux, preferably with updates. 
    Your name: ADIOS
    Your computer's nane: adiosVM
    Username: adios
    password: adios 
    Log in automatically: yes, because this is a tutorial vm

    Note: if you use a computer name other than adiosVM, make sure you substitute for the name
    everywhere in this document (e.g. Flexpath install)

   - Instead of restart, shut down and remove the linux DVD, start again
     - Click left-top icon (Dash Home) and search for Terminal
       - start it and immediately on the icon in the tray: right-click and "Lock to Launcher"
     - install updates (will come up automatically)

   - VirtualBox VM menu: Devices/Insert Guest Additions CD Image
     - will install kernel modules, need adios password to run
     - this allows for resizing the window and 
       for copy/paste between the VM and your host machine
        (set Devices/Shared Clipboard/Bidirectional)
     Note: This has to be repeated when updating or recompiling the kernel

   - You can remove the LibreOffice products to save some disk space.
     - Start Ubuntu Software Center
     - Click for Installed and search for "Libre", remove one by one
     - Ah well, df -h will reveal we did not save anything visible amount of space

   - Terminal setup (if you don't like the default one)
     - Start Terminal
     - Edit/Profile preferences
       General tab: unclick "Use the system fixed with font"
       Colors tab: Black on white
     - Scrolling tab: increase the scrollback to a few thousand lines (e.g. 5120)

   - Set HISTORY to longer: 
     $ vi ~/.bashrc
     increase HISTSIZE (to 5000) and HISTFILESIZE (to 10000)

   - Turn off screen saver and lock
     System Settings / Brightness and Lock
     Turn off screen when inactive for: Never
     Lock: off

4. Shared folder between your host machine and the VM (optional)
   This is not needed for tutorial, just if you want to share files between host and vm.

   - In VirtualBox, while the VM is shut down, set up a shared folder, with auto-mount.
   - Start VM. You can see a folder  /media/sf_<your folder name>
   - Need to set group rights for adios user to use the folder
     $ sudo vi /etc/group 
     add "adios" to the vboxfs entry so that it looks like this

     vboxsf:x:999:adios
   - log out and back, run 'groups' to check if you got the group rights.


5. Install some linux packages (apt-get install)
   $ sudo apt-get install  build-essential git-core libtool autoconf apt-file subversion cmake
   $ sudo apt-get autoremove 
     - this one to get rid of unnecessary packages after removing LibreOffice
   $ sudo apt-get install dkms
     - Dynamic Kernel Modules, to ensure rebuilding Guest Additions at future kernel updates
     - or just reinstall Guest Additions each time if you don't want dkms installed

6. Download this repository
   You can postpone step 6 and 7 after 8 if you have a github account
   and want to edit this repository content.

   $ cd
   $ git clone https://github.com/pnorbert/adiosvm.git

7. VIM setup
   $ sudo apt-get install vim
   copy from this repo: vimrc to ~/.vimrc
   $ cp ~/adiosvm/vimrc .vimrc

8. Github access setup
   This is only needed to get ADIOS master from github.

   We need an account to github and a config for ssh.
   A minimum .ssh/config is found in this repository:  
   $ cd 
   $ mkdir .ssh
   $ cp ~/adiosvm/ssh_config ~/.ssh/config

   If the shared folder has access to you .ssh:

   $ cp /media/sf_<yourfolder>/.ssh/config .ssh
   $ cp /media/sf_<yourfolder>/.ssh/id_dsa_github* .ssh

   If you have a github account and the config already, and postponed
   step 6, get the adiosvm repo now:

   $ sudo apt-get install corkscrew
   $ git clone github-cork:pnorbert/adiosvm.git

   Git settings:
   $ git config --global user.name "<your name>"
   $ git config --global user.email "<your email>"
   $ git config --global core.editor vim

   Of course, set an editor what you like.

II. Preparations to install ADIOS
=================================

1. Linux Packages
   $ sudo apt-get install gfortran mpich2
   $ sudo apt-get install python-cheetah python-yaml


2. Install DataSpaces
   Only if you want staging demos.

   Download dataspaces from www.dataspaces.org, or use 1.6 from adiosvm

   $ cd
   $ mkdir -p Software
   $ cd Software
   $ tar zxf ~/adiosvm/adiospackages/dataspaces-1.6.0.tar.gz 
   $ cd dataspaces-1.6.0
   $ ./autogen.sh
   $ ./configure --prefix=/opt/dataspaces --enable-dart-tcp CC=mpicc FC=mpif90 CFLAGS="-g -std=gnu99" LIBS="-lm"
   $ make
   $ sudo make install

   Test DataSpaces: follow the instructions in 
      ~/adiosvm/adiospackages/test_dataspaces.txt


3. Install MXML
   $ cd ~/Software
   $ tar zxf ~/adiosvm/adiospackages/mxml-2.9.tar.gz 
   $ cd mxml-2.9/
   $ ./configure --prefix=/opt/mxml
   $ make
   $ sudo make install

   In ~/.bashrc, add to LD_LIBRARY_PATH "/opt/mxml/lib"


4. Compression libraries
   Only if you want to demo the transform library.

   zlib and bzip2 are installed as linux packages:
   $ sudo apt-get install bzip2 libbz2-dev zlib1g zlib1g-dev

   SZIP and ISOBAR are provided in adiospackages/

   $ cd ~/Software
   $ tar zxf ~/adiosvm/adiospackages/szip-2.1.tar.gz 
   $ cd szip-2.1/
   $ ./configure --prefix=/opt/szip
   $ make
   $ sudo make install

   In ~/.bashrc, add to LD_LIBRARY_PATH "/opt/szip/lib"

   $ cd ~/Software
   $ tar zxf ~/adiosvm/adiospackages/isobar.0.3.0.tgz 
   $ cd isobar.0.3.0

   On 32bit systems, edit
      projs/ISOBAR_library/nbproject/Makefile-gcc-release-x64-static.mk
   and remove -m64 from CFLAGS

   $ make install

     This creates ./lib/libisobar.a
   
   Manually install it to /opt/isobar
   $ sudo mkdir /opt/isobar
   $ cd /opt/isobar
   $ sudo ln -s $HOME/Software/isobar.0.3.0/include 
   $ sudo ln -s $HOME/Software/isobar.0.3.0/lib 


5. Flexpath support
   Only if you want staging demos.
   We need to get CHAOS from Georgia Tech and build it. This will take a while...
   
   $ sudo apt-get install bison libbison-dev flex
   $ sudo mkdir -p /opt/chaos
   $ sudo chgrp adios /opt/chaos
   $ sudo chmod g+w /opt/chaos
   $ cd ~/Software
   $ svn --username anon --password anon co https://anon@svn.research.cc.gatech.edu/kaos/chaos_base/trunk chaos
   $ cd chaos
   $ cp build_config build_config.adiosVM
   Edit build_config.adiosVM
   - we only need to install: dill cercs_env atl ffs evpath
   - comment out the rest of packages
   - change the build area
     BUILD_AREA=/home/adios/Software/chaos
     RESULTS_FILES_DIR=$HOME/Software/chaos
   - change the install target
     INSTALL_DIRECTORY=/opt/chaos

   $ perl chaos_build.pl -c build_config.adiosVM 

   Enter 'anon' for both username and password if requested at svn checkout commands.
   Enter 'adios' for a question like "Password for 'default' GNOME keyring:"

   In ~/.bashrc, add to LD_LIBRARY_PATH "/opt/chaos/lib"


6. Sequential HDF5 support
   Only if you want bp2h5 conversion code.

   $ cd ~/Software
   $ tar jxf ~/adiosvm/adiospackages/hdf5-1.8.12.tar.bz2
   $ mv hdf5-1.8.12 hdf5-1.8.12-serial
   $ cd hdf5-1.8.12-serial
   $ ./configure --with-zlib=/usr --with-szlib=/opt/szip --prefix=/opt/hdf5-1.8.12 --enable-fortran
   $ make -j 4
   $ sudo make install

   In ~/.bashrc, add to PATH "/opt/hdf5-1.8.12/bin"


7. Parallel HDF5 support
   Only if you want PHDF5 transport method in ADIOS.

   $ cd ~/Software
   $ tar jxf ~/adiosvm/adiospackages/hdf5-1.8.12.tar.bz2
   $ mv hdf5-1.8.12 hdf5-1.8.12-parallel
   $ cd hdf5-1.8.12-parallel
   $ ./configure --with-zlib=/usr --with-szlib=/opt/szip --prefix=/opt/hdf5-1.8.12-parallel --enable-parallel --enable-fortran --with-pic  CC=mpicc FC=mpif90

   Verify that in the Features list:
        Parallel HDF5: yes

   Note: the -fPIC option is required for building parallel NetCDF4 later

   $ make -j 4
   $ sudo make install


8. Sequential NetCDF support
   Only if you want bp2ncd conversion code.

   $ cd ~/Software
   $ tar zxf ~/adiosvm/adiospackages/netcdf-4.3.0.tar.gz
   $ mv netcdf-4.3.0 netcdf-4.3.0-serial
   $ cd netcdf-4.3.0-serial
   $ ./configure --prefix=/opt/netcdf-4.3.0 --enable-netcdf4 CPPFLAGS="-I/opt/hdf5-1.8.12/include" LDFLAGS="-L/opt/hdf5-1.8.12/lib"
   $ make -j 4
   $ make check         
     This testing is optional
   $ sudo make install


9. Parallel NetCDF4 support (not PNetCDF!)
  ###   Just forget about this. It breaks the adios build  ###
   Only if you want NC4PAR transport method in ADIOS.

   $ cd ~/Software
   $ tar zxf ~/adiosvm/adiospackages/netcdf-4.3.0.tar.gz
   $ mv netcdf-4.3.0 netcdf-4.3.0-parallel
   $ cd netcdf-4.3.0-parallel
   $ ./configure --prefix=/opt/netcdf-4.3.0-parallel --enable-netcdf4 --with-pic CPPFLAGS="-I/opt/hdf5-1.8.12-parallel/include" LDFLAGS="-L/opt/hdf5-1.8.12-parallel/lib -L/opt/szip/lib" LIBS="-lsz" CC=mpicc FC=mpif90
   $ make -j 4
   $ sudo make install
   

10. Fastbit indexing support (needed for queries)
   $ cd ~/Software
   $ svn co https://codeforge.lbl.gov/anonscm/fastbit/trunk
   $ mv trunk fastbit
   $ cd fastbit/
   $ ./configure --with-pic -prefix=/opt/fastbit
   $ make
   -- this will be slooooow
   $ sudo make install

   In ~/.bashrc, add to LD_LIBRARY_PATH "/opt/fastbit/lib"

III. ADIOS Installation
=======================

1. Download ADIOS
   1. ADIOS 1.9 is in this repo: 
   $ cd ~/Software
   $ tar zxf ~/adiosvm/adiospackages/adios-1.9.0.tar.gz
   $ cd adios-1.9.0

   2. Download ADIOS master from repository
   $ cd ~/Software
   $ git clone github-cork:ornladios/ADIOS.git
     OR
   $ git clone https://github.com/ornladios/ADIOS.git
   $ cd ADIOS

2. Build ADIOS
   Then:
   $ cp ~/adiosvm/adiospackages/runconf.adiosvm .
   $ . ./runconf.adiosvm
   $ make -j 4; make -j 4 

3. Test ADIOS a bit
   $ make check

   $ cd tests/suite
   $ ./test.sh 01
     and so on up to 16 tests
     Some test fail because multiple processes write a text file which is 
     compared to a reference file, but some lines can get mixed up. Try 
     running the same test a couple of times. One 'OK' means the particular
     test is okay.

4. Install 
   $ sudo make install
   In ~/.bashrc, add to LD_LIBRARY_PATH "/opt/adios/1.9/lib" and 
     add to PATH "/opt/adios/1.9/bin"

5. Build and install python wrapper

   To build Adios python wrapper, install following packages by:
   $ sudo apt-get install python python-dev
   $ sudo apt-get install python-numpy

   Note: To use a parallel version, we need mpi4py. However, the
   package installation from Ubuntu repository is not working here; it
   was out-dated and mal-configured. Instead, we can install by using
   pip:

   $ sudo apt-get install python-pip
   $ sudo pip install mpi4py
   
   Alternatively, we can install from a source code too:

   $ wget https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-2.0.0.tar.gz
   $ tar xvf mpi4py-2.0.0.tar.gz
   $ cd mpi4py-2.0.0
   $ python setup.py build
   $ sudo python setup.py install

   Then, we are ready to install adios and adios_mpi python module. An
   easy way is to use "pip".
   
   $ sudo "PATH=$PATH" pip install --upgrade \
     --global-option build_ext --global-option -lrt adios adios_mpi

   If there is any error, we can build from source. Go to the
   wrapper/numpy directory under the adios source directory:
   $ cd wrapper/numpy

   Type the following to build Adios python wrapper:
   $ python setup.py build_ext -lrt

   The following command is to install:
   $ sudo python setup.py install

   Same for adios_mpi module:
   $ python setup_mpi.py build_ext -lrt
   $ sudo python setup_mpi.py install

   Test:
   A quick test can be done:
   $ cd wrapper/numpy/tests
   $ python test_adios.py
   $ mpirun -n 4 python test_adios_mpi.py


IV. ADIOS Tutorial code
=======================

   For ADIOS 1.9, the tutorial is included in this repository
   ~/adiosvm/Tutorial

1. Linux Packages
   KSTAR demo requires gnuplot
   $ sudo apt-get install gnuplot
   


V. Build Visit from release
===========================

- Need to have many linux packages installed.
- Build a Visit release using it's build script that
  downloads/builds a lot of dependencies.


1. Linux packages
  $ sudo apt-get install dialog gcc-multilib subversion libx11-dev tcl tk
  $ sudo apt-get install libglu1-mesa-dev 
  $ sudo libxt-dev
  $ sudo apt-get install xutils-dev

  For Silo reader to believe in good Qt installation
  $ sudo apt-get install libxmu-dev libxi-dev

  Qt development packages (required or visit will build its own)
  $ sudo apt-get libqt4-dev 
  This will install all dependent packages

2. Build latest Visit release (with many dependencies)
   https://wci.llnl.gov/codes/visit/source.html

   Visit 2.7.2 release uses adios 1.6.0 but it downloads and builds its own
   version without compression or staging. 

   $ cd ~/Software
   $ mkdir -p visit
   $ cd visit
   $ wget http://portal.nersc.gov/svn/visit/trunk/releases/2.7.2/build_visit2_7_2
     Or download the latest build script from the website
     https://wci.llnl.gov/codes/visit/source.html

   $ chmod +x build_visit2_7_2
   $ ./build_visit2_7_2 --parallel --mesa --mxml --adios --hdf5 --xdmf --zlib --szip --silo
   $ ./build_visit --system-qt --parallel --mesa --mxml --adios --hdf5 --xdmf --zlib --szip --silo --console

    This script should be started again and again after fixing build problems.
    All log is founf in build_visit2_7_2_log, appended at each try.

    In the dialogs, just accept everything


                     |     You many now try to run VisIt by cd'ing into the     │  
                     │ visit2.7.2/src/bin directory and invoking "visit".       │  
                     │                                                          │  
                     │     To create a binary distribution tarball from this    │  
                     │ build, cd to                                             │  
                     │ /home/adios/Software/visit/visit2.7.2/src                │  
                     │     then enter: "make package"                           │  
                     │                                                          │  
                     │     This will produce a tarball called                   │  
                     │ visitVERSION.ARCH.tar.gz, where     VERSION is the       │  
                     │ version number, and ARCH is the OS architecure.          │  
                     │                                                          │  
                     │     To install the above tarball in a directory called   │  
                     │ "INSTALL_DIR_PATH",    enter: svn_bin/visit-install      │  
                     │ VERSION ARCH INSTALL_DIR_PATH                            |



3. Build Visit from svn trunk
- Get Visit trunk from repository and build against dependencies
  that has been built in the previous step
- You need to do step 2 (build visit from source release)

   $ cd ~/Software
   $ svn co http://portal.nersc.gov/svn/visit/trunk/src visit.src
   $ cd visit.src
   
   Get the local build cmake config created by build_visit2.7.2 and edit
   $ cp ~/Software/visit/adiosVM.cmake ./config-site
   
     - Add CMAKE_INSTALL_PREFIX to point to desired installation target (/opt/visit):

         VISIT_OPTION_DEFAULT(CMAKE_INSTALL_PREFIX /opt/visit)

     - Edit VISIT_ADIOS_DIR to point to desired ADIOS install (/opt/adios/1.9):

         VISIT_OPTION_DEFAULT(VISIT_ADIOS_DIR /opt/adios/1.9.0)


   Configure visit with cmake that was built by visit release
   $ rm CMakeCache.txt
   $ ~/Software/visit/cmake-2.8.10.2/bin/cmake .
   $ make -j 4
   $ make install


   If a dependency package's version is updated, you need to download and build a new one.
   E.g. with VTK 6.1

   $ cd ~/Software/visit
   $ wget http://www.vtk.org/files/release/6.1/VTK-6.1.0.tar.gz
   $ tar zxf VTK-6.1.0.tar.gz
   $ mkdir VTK-6.1.0-build
   $ cd VTK-6.1.0-build
   
   In ../build_visit2.7.1_log, search for "Configuring VTK . . ." and see how cmake was called (a long line).
   Replace the CMAKE_INSTALL_PREFIX:PATH and run that command

   $ "/home/adios/Software/visit/visit/cmake/2.8.10.2/linux-x86_64_gcc-4.6/bin/cmake" <whatever appears here> ../VTK-6.1.0




V. Build Plotter
=================

If you still want to use the our own plotter instead of / besides visit.

  $ sudo apt-get install grace

  If not installed Visit yet:
  $ sudo apt-get install libglu1-mesa-dev libxt-dev

  $ mkdir ~/Software/plotter
  $ cd ~/Software/plotter


  1. Build Mesa library
  $ cd ~/Software/plotter
  $ tar zxf ~/adiosvm/plotterpackages/Mesa-7.8.2.tar.gz
  $ cd Mesa-7.8.2
  $ ./configure CFLAGS="-I/usr/include/i386-linux-gnu -O2 -DUSE_MGL_NAMESPACE -fPIC -DGLX_USE_TLS" CXXFLAGS="-O2 -DUSE_MGL_NAMESPACE -fPIC -DGLX_USE_TLS" --prefix=/opt/plotter --with-driver=osmesa --disable-driglx-direct 
  $ make -j 4
  $ sudo make install


  2. Build vtk-5.8 (saved from old Visit config)
  
  $ tar zxf  ~/adiosvm/plotterpackages/visit-vtk-5.8.tar.gz
  $ mkdir vtk-5.8-build
  $ cd vtk-5.8-build
  $ export LD_LIBRARY_PATH=/opt/plotter/lib:$LD_LIBRARY_PATH
  $ cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/plotter ../visit-vtk-5.8

  Check if CMakeCache.txt has VTK_OPENGL_HAS_OSMESA:BOOL=ON, if not, turn on and rerun cmake. 
  It has to find the Mesa options and have this in CMakeCache.txt

    //Path to a file.
    OSMESA_INCLUDE_DIR:PATH=/opt/plotter/include

    //Path to a library.
    OSMESA_LIBRARY:FILEPATH=/opt/plotter/lib/libOSMesa.so
    ...
    //Use mangled Mesa with OpenGL.
    VTK_USE_MANGLED_MESA:BOOL=OFF  <-- This is OFF!!


  $ make -j 4
  $ sudo make install


  3. Build plotter
  $ cd ~/Software
  $ svn co https://svn.ccs.ornl.gov/svn-ewok/wf.src/trunk/plotter 
    ...OR...
  $ tar zxf ~/adiosvm/plotterpackages/plotter.tar.gz
  $ cd plotter
  
  Edit Makefile.adiosVM to point to the correct ADIOS, HDF5 (sequential), NetCDF (sequential), Grace and VTK libraries. 

  $ make
  $ sudo INSTALL_DIR=/opt/plotter INSTALL_CMD=install make install
  
  In ~/.bashrc, add to PATH "/opt/plotter/bin"




VI. Clean-up a bit
==================
Not much space left after building visit and plotter. You can remove this big offenders

1.9GB  ~/Software/plotter/vtk-5.8-build
1.3GB  ~/Software/visit/qt-everywhere-opensource-src-4.8.3
       ~/Software/visit/qt-everywhere-opensource-src-4.8.3.tar.gz
       ~/Software/visit/VTK*-build




VII. Installing R and pbdR 
===========================

This is for the pbdR tutorial. Not required for an ADIOS-only tutorial. 

Packages that will be needed: 
$ sudo apt-get install libcurl4-gnutls-dev

Install R
---------
See instructions on http://cran.r-project.org/bin/linux/ubuntu/

$ sudo vi /etc/apt/sources.list
add a line to the end:
deb http://mirrors.nics.utk.edu/cran/bin/linux/ubuntu precise/

Add the key for this mirror
$ sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9

$ sudo apt-get install r-base r-base-dev

If these above don't work, you need to resort building from source.
from http://cran.r-project.org/sources.html
e.g. http://cran.r-project.org/src/base/R-3/R-3.1.2.tar.gz

--- SUDO version below, non-SUDO after ---

Install 'rlecuyer' 
------------------
from http://cran.r-project.org/web/packages/rlecuyer/index.html

$ sudo R
> install.packages("rlecuyer", repos="http://mirrors.nics.utk.edu/cran/")
should get messages ending with:
* DONE (rlecuyer)
> q()
quit R (or ctrl+D)

Test if it is installed correctly:
$ R
> library(help=rlecuyer)
> q()

> install.packages("raster", repos="http://mirrors.nics.utk.edu/cran/")

Install pbdR
-------------

$ sudo R
install.packages("devtools", repos="http://mirrors.nics.utk.edu/cran/")
library(devtools)
install_github("RBigData/pbdMPI")
install_github("RBigData/pbdSLAP")
install_github("wrathematics/RNACI")
install_github("RBigData/pbdBASE") 
install_github("RBigData/pbdDMAT") 
install_github("RBigData/pbdDEMO") 
install_github("RBigData/pbdPAPI") 
install.packages("pbdPROF", repos="http://mirrors.nics.utk.edu/cran/")
> q()


Install pbdADIOS
----------------
$ cd ~/Software
$ git clone https://github.com/sgn11/pbdADIOS.git
$ sudo R CMD INSTALL pbdADIOS --configure-args="--with-adios-home=/opt/adios/1.9" --no-test-load
-- quick test
$ R
> library(pbdADIOS)
Loading required package: pbdMPI
Loading required package: rlecuyer
> quit()


--- non-SUDO version below, SUDO above ---

$ sudo mkdir -p /opt/R/library
$ sudo chgrp -R adios /opt/R
$ sudo chmod -R g+w /opt/R

$ export R_LIBS_USER=/opt/R/library
$ R
> install.packages("rlecuyer", repos="http://mirrors.nics.utk.edu/cran/", lib="/opt/R/library")
> install.packages("raster", repos="http://mirrors.nics.utk.edu/cran/", lib="/opt/R/library")

install_github("RBigData/pbdMPI")
install_github("RBigData/pbdSLAP")
install_github("wrathematics/RNACI")
install_github("RBigData/pbdBASE")
install_github("RBigData/pbdDMAT")
install_github("RBigData/pbdDEMO")
install_github("RBigData/pbdPAPI")
install.packages("pbdPROF", repos="http://mirrors.nics.utk.edu/cran/")
quit()


$ cd source
$ git clone https://github.com/sgn11/pbdADIOS.git
$ R CMD INSTALL pbdADIOS --configure-args="--with-adios-home=/opt/adios/1.9" --no-test-load

Add to ~/.bashrc
    export R_LIBS_USER=/opt/R/library



Quick test of pbdR
------------------
$ cd ~/adiosvm
$ mpirun -np 2 Rscript test_pbdR.r 
COMM.RANK = 0
[1] 0
COMM.RANK = 1
[1] 1


Download pbdR tutorial examples
-------------------------------
$ cd 
$ wget https://github.com/RBigData/RBigData.github.io/blob/master/tutorial/scripts.zip?raw=true
$ unzip  scripts.zip?raw=true

or get it using a browser from http://r-pbd.org/tutorial

Quick test of scripts:
----------------------
$ scripts/pbdMPI/quick_examples
$ mpirun -np 4 Rscript 1_rank.r
COMM.RANK = 0
[1] 0
COMM.RANK = 1
[1] 1
COMM.RANK = 2
[1] 2
COMM.RANK = 3
[1] 3


Install R Studio
----------------
$ sudo apt-get install libjpeg62
$ cd adiosvm/Rpackages
 if not there, get it from the web
$ wget http://download1.rstudio.org/rstudio-0.98.1091-i386.deb

$ sudo dpkg -i rstudio-0.98.1091-i386.deb


VII. Others
===========
Ubuntu Metacity's Ambiance theme
--------------------------------
  The window border is a single pixel, it's hard to resize window. 
  http://askubuntu.com/questions/8498/how-can-i-make-the-draggable-window-border-thicker-without-changing-the-appeara

  Change the following parameters in the appropriate Metacity XML file.  
  $ sudo vi /usr/share/themes/Ambiance/metacity-1/metacity-theme-1.xml

  The folowing parameters change the width of the borders and consequently the width of the re-size area:

  "<distance name="left_width" value="1"/>"
  "<distance name="right_width" value="1"/>"
  "<distance name="bottom_height" value="1"/>"

  By default they are set to "1", but I found that changing them to 4 to 6 doesn't change the appearance very drastically, but makes it very much easier to re-size using the mouse.
    
  To reload the theme without logging out you can run the command: 
  $ metacity-message reload-theme  
  

Enable GDB debugging
--------------------
See http://askubuntu.com/questions/146160/what-is-the-ptrace-scope-workaround-for-wine-programs-and-are-there-any-risks
Ubuntu prohibits ptrace to see other processes so gdb will fail with permissions. 
Enable GDB binary to see your processes:

  $ sudo apt-get install libcap2-bin 
  $ sudo setcap cap_sys_ptrace=eip /usr/bin/gdb


GLOBAL/GTAGS
-------------
   GTAGS is useful for quickly finding definitions of functions in source codes in VIM
   It needs to be installed from source to make it work in VIM
   $ cd ~/Software
   $ tar zxf ~/adiosvm/linuxpackages/global-6.3.4.tar.gz
   $ cd global-6.3.4
   $ ./configure
   $ make
   $ sudo make install

   $ mkdir -p ~/.vim/plugin
   $ cp ~/adiosvm/linuxpackages/gtags.vim ~/.vim/plugin/
   NOTE: .vimrc already contains the flag to turn it on

   Generate the tags for a source
   $ cd ~/Software/ADIOS/src
   $ gtags
   $ ls G*
   GPATH  GRTAGS  GSYMS  GTAGS

   $ vi write/adios_posix.c
   /adios_posix_read_version
   Hit Ctrl-\ Ctrl-\
   Vi should open new file core/adios_bp_v1.c and jump to the definition of adios_posix_read_version
   :b#    -- to go back to the previous file

   If there are multiple finds, you can move among them with Ctrl-\ Ctrl-[   and  Ctrl-\ Ctrl-] 
   The commands can be modified at the bottom of ~/.vim/plugin/gtags.vim


   Add a path of any software so that gtags will search the GTAGS file there to find external references. 
   In .bashrc, add
   export GTAGSLIBPATH=/home/adios/Software/ADIOS/src
 
   You also need to run gtags in your application (top) source directory too, to get global/gtag working.