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MPD_SECRETWORD=secret

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Debugging

Debugging a parallel version of XBeach using multiple processes is possible, but not as convenient as debugging in, for example, Visual Studio. This section describes a way to truly debug a parallel program like XBeach.

Compile the program without optimization

In order to prevent the debugger to randomly skip through the code, optimizations should be prevented. This can be done to alter the above mentions call to the configuration script as follows:

 FC=gfortran44 FCFLAGS="-g -O0" ./configure --with-mpi 

The -g option makes sure debugging symbols are included in the result. The -O0 sets the optimizations to a minimum. By default these are set to -O2. Now create a binary file:

make distclean
make

Have an X Window system available

On Microsoft Windows, make sure an X Window emulator is running. For example, start Exceed: START -> Program -> Exceed -> Exceed

Run the model

Start the just compiled XBeach binary in your model directory in a bit peculiar way:

 mpirun -n <nr_of_processes> xterm -e gdb <path_to_binary>/xbeach 

This will start a number of command windows (xterm) equal to the number of processes you defined after the -n option. In each command window, a instance of the debugger (gdb) will be started. Each instance of the debugger will debug a specific subprocess of the XBeach program stored in the <path_to_binary> path.

Start debugging

The debugger provides at least the following commands, which can be used in each command window separately:

Especially the commands n or p might complain about a lack of line numbers or variables. This can be due to you are still using optimizations or you use an inferior type of debugging symbols. You might want to consider using another type, like DWARF-2. How? I don't know! If you do, please provide the info here...

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Compile XBeach parallel version for use on Linux/cluster

1. On your Windows PC, start Exceed > Exceed XDMCP Broadcast (or the icon on your desktop).
2. Choose 'devux.wldelft.nl'.
3. Under Sessions, choose 'GNOME'.
4. Use your Deltares user name and password to log in.
5. Start a Terminal session (Applications > System Tools > Terminal).
6. Make a directory "checkouts":

   Code Block
   mkdir ~/checkouts

7. Checkout the latest and greatest version of XBeach (enter your Deltares password if asked for):

   Code Block
   svn co https://repos.deltares.nl/repos/XBeach/trunk ~/checkouts/XBeach

   If you already have the local repository, but want to update it, use:

   Code Block
   svn update

8. Go to the XBeach directory:

   Code Block
   cd ~/checkouts/XBeach

9. Run

   Code Block
   FC=ifort ./configure

10. Run

    Code Block
    make

11. Make sure version 10 of the Intel Fortran compiler is used (instead of version 8):

    Code Block
    . /opt/intel/fc/10/bin/ifortvars.sh

12. Delete all files not needed for compiling to get rid of files that could mess it up:

    Code Block
    make clean

13. Compile the parallel version:

    Code Block
    PATH=/opt/mpich2-1.0.7/bin:$PATH USEMPI=yes ./configure && make

14. (optional) Copy the executable to your personal bin-folder:

    Code Block
    cd ~/bin cp ~/checkouts/bin/xbeach.mpi .

Compiled version

Compiled Linux versions of XBeach (both the MPI and serial version) can be found in Arend's bulletin box:

/BULLETIN/pool_ad/xbeach_linux/   # or
/u/pool_ad/BULLETIN/xbeach_linux/

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Run XBeach parallel version on h3 cluster

To run a parallel XBeach job on the h3 cluster (from now on 'h3'), you need 3 things:

1. A parallel version of XBeach somewhere on the u-drive (preferably in /u/username/bin)
2. A job (shell) file you feed to the cluster
3. A directory on your part of the u-drive with the simulation-data (params.txt, bathy.dep, etc)

Logging on to cluster

Windows
The easiest way to log on to h3, is using the program PuTTY, which can be found on the Desktop of your Deltares PC. The first time you connect to h3, you need to supply some basic parameters, which you can save for later use (with 'Save'). In the Dialog Box, under Host Name, fill in: h3.wldelft.nl; you don't need to touch the other options (leave the Protocol to SSH). Optionally, save the information as e.g. 'h3'. The first time you connect to h3, you'll probably see a message about the server's host key. Click Yes to accept. Log in with your Deltares user name and password.

Linux
If you want to connect from e.g. the development server (devux) to h3, you can connect from a terminal session. Type

ssh h3

to connect to h3. Your user name has already been sent for you, so you only need to submit your password.

Obtain latest version of XBeach executable

There are 2 ways to obtain the latest (or any) version of the parallel XBeach executable:

1. Compile it yourself (see the instructions in #compilexbeach)
2. Copy it from Arend Pool's BULLETIN:

   Code Block
   cd ~/bin cp /u/pool_ad/BULLETIN/xbeach_linux/current/xbeach.mpi .

Obtain the XBeach MPI job file

There are also 2 ways to obtain the job file to run xbeach.mpi on h3:

1. Copy it from Arend Pool's BULLETIN:

   Code Block
   mkdir ~/simulations # can be skipped if directory already exists cd ~/simulations cp /u/pool_ad/BULLETIN/xbeach_linux/xbeach.sh .

   In the above instructions, it is assumed you place the job file in the direction /simulations. If you want to place it somewhere else, feel free to do so and change the instructions accordingly.
2. Create the shell file yourself in a location you prefer. The file should contain the following code:

   Code Block
   #!/bin/sh . /opt/sge/InitSGE export PATH="/opt/mpich2/bin:$PATH" echo "numslots: $DELTAQ_NumSlots" echo "nodes: $DELTAQ_NodeList" echo $DELTAQ_NodeList | tr ' ' '\n' | sed 's/.wldelft.nl//' > machines echo "Machines file:" cat machines mpdboot -1 -n $DELTAQ_NumSlots -f machines mpirun -np $DELTAQ_NumSlots ~/bin/xbeach.mpi mpdallexit

   The second last line should contain the path to xbeach.mpi. Edit this if you have placed it somewhere else.

Run the parallel job

Make sure you have placed your simulation (directory) somewhere on a shared location (u-drive or p-drive) and go ('cd') there (for example):

cd /u/username/simulations/simulation1   # or
cd /p/project/simulations/simulation1

Finally, submit your job to the grid engine (h3) with the following command:

qsub -pe spread N /path-to-job-file/xbeach.sh

where N is the number of nodes you want to use and path-to-job-file the path to xbeach.sh.

More info

The SGE User Guide can be found at the ICT department space of this wiki.