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Running C# MPI.NET Applications with Mono and OpenMPI

Saliya Ekanayake 9:24 PM , , , , 9 comments
I wrote an earlier post on the same subject, but just realized it's not detailed enough even for me to retry, hence the reason for this post.
I've tested this in FutreGrid with Infiniband to run our C# based pairwise clustering program on real data up to 32 nodes (I didn't find any restriction to go above this many nodes - it was just the maximum I could reserve at that time)
What you'll need
  • Mono 3.4.0
  • MPI.NET source code revision 338.
      svn co https://svn.osl.iu.edu/svn/mpi_net/trunk -r 338 mpi.net
  • OpenMPI 1.4.3. Note this is a retired version of OpenMPI and we are using it only because that's the best that I could get MPI.NET to compile against. If in future MPI.NET team provides support for a newer version of OpenMPI, you may be able to use it as well.
  • Automake 1.9. Newer versions may work, but I encountered some errors in the past, which made me stick with version 1.9.
How to install
  1. I suggest installing everything to a user directory, which will avoid you requiring super user privileges. Let's create a directory called build_mono inside home directory.
     mkdir ~/build_mono
    The following lines added to your ~/.bashrc will help you follow the rest of the document.
     BUILD_MONO=~/build_mono
 PATH=$BUILD_MONO/bin:$PATH
 LD_LIBRARY_PATH=$BUILD_MONO/lib
 ac_cv_path_ILASM=$BUILD_MONO/bin/ilasm

 export BUILD_MONO PATH LD_LIBRARY_PATH ac_cv_path_ILASM
    Once these lines are added do,
     source ~/.bashrc
  2. Build automake by first going to the directory that containst automake-1.9.tar.gz and doing,
     tar -xzf automake-1.9.tar.gz
 cd automake-1.9
 ./configure --prefix=$BUILD_MONO
 make
 make install
    You can verify the installation by typing which automake, which should point to automake inside $BUILD_MONO/bin
  3. Build OpenMPI. Again, change directory to where you downloaded openmpi-1.4.3.tar.gz and do,
     tar -xzf openmpi-1.4.3.tar.gz
 cd openmpi-1.4.3
 ./configure --prefix=$BUILD_MONO
 make
 make install
    Optionally if Infiniband is available you can point to the verbs.h (usually this is in /usr/include/infiniband/) by specifying the folder /usr in the above configure command as,
     ./configure --prefix=$BUILD_MONO --with-openib=/usr
    If building OpenMPI is successfull, you'll see the following output for mpirun --version command,
     mpirun (Open MPI) 1.4.3

 Report bugs to http://www.open-mpi.org/community/help/
    Also, to make sure the Infiniband module is built correctly (if specified) you can do,
     ompi_info|grep openib
    which, should output the following.
     MCA btl: openib (MCA v2.0, API v2.0, Component v1.4.3)
  4. Build Mono. Go to directory containing mono-3.4.0.tar.bz2 and do,
     tar -xjf mono-3.4.0.tar.bz2
 cd mono-3.4.0
    Mono 3.4.0 release is missing a file, which you'll need to add by pasting the following content to a file called./mcs/tools/xbuild/targets/Microsoft.Portable.Common.targets
     <Project xmlns="http://schemas.microsoft.com/developer/msbuild/2003">
     <Import Project="..\Microsoft.Portable.Core.props" />
     <Import Project="..\Microsoft.Portable.Core.targets" />
 </Project>
    You can continue with the build by following,
     ./configure --prefix=$BUILD_MONO
 make
 make install
    There are several configuration parameters that you can play with and I suggest going through them either in README.md or in./configure --help. One parameter, in particular, that I'd like to test with is --with-tls=pthread
  5. Build MPI.NET. If you were wonder why we had that ac_cv_path_ILASM variable in ~/.bashrc then this is where it'll be used. MPI.NET by default tries to find the Intermediate Language Assembler (ILASM) at /usr/bin/ilasm2, which for 1. does not exist because we built Mono into $BUILD_MONO and not /usr 2. does not exist because newer versions of Mono calls this ilasm notilasm2. Therefore, after digging through the configure file I found that we can specify the path to the ILASM by exporting the above environment variable.
    Alright, back to building MPI.NET. First copy the downloaded Unsafe.pl.patch to the subversion checkout of MPI.NET. Then change directory there and do,
     patch MPI/Unsafe.pl < Unsafe.pl.patch
    This will say some hunks failed to apply, but that should be fine. It only means that those are already fixed in the checkout. Once patching is completed continue with the following.
     ./autogen.sh
 ./configure --prefix=$BUILD_MONO
 make
 make install
    At this point you should be able to find MPI.dll and MPI.dll.config inside MPI directory, which you can use to bind against your C# MPI application.
How to run
  • Here's a sample MPI program written in C# using MPI.NET.
      using System;
  using MPI;
  namespace MPINETinMono
  {
      class Program
      {
          static void Main(string[] args)
          {
              using (new MPI.Environment(ref args))
              {
                  Console.Write("Rank {0} of {1} running on {2}\n",
                                  Communicator.world.Rank,
                                  Communicator.world.Size,
                                  MPI.Environment.ProcessorName);
              }
          }
      }
  }
  • There are two ways that you can compile this program.
    1. Use Visual Studio referring to MPI.dll built on Windows
    2. Use mcs from Linux referring to MPI.dll built on Linux
      mcs Program.cs -reference:$MPI.NET_DIR/tools/mpi_net/MPI/MPI.dll
      where $MPI.NET_DIR refers to the subversion checkout directory of MPI.NET
      Either way you should be able to get Program.exe in the end.
  • Once you have the executable you can use mono with mpirun to run this in Linux. For example you can do the following within the directory of the executable,
      mpirun -np 4 mono ./Program.exe
    which will produce,
      Rank 0 of 4 running on i81
  Rank 2 of 4 running on i81
  Rank 1 of 4 running on i81
  Rank 3 of 4 running on i81
    where i81 is one of the compute nodes in FutureGrid cluster.
    You may also use other advance options with mpirun to determine process mapping and binding. Note. the syntax for such controlling is different from latest versions of OpenMPI. Therefore, it's a good idea to look at different options from mpirun --help. For example you may be interested in specifying the following options,
      hostfile=<path-to-hostfile-listing-available-computing-nodes>
  ppn=<number-of-processes-per-node>
  cpp=<number-of-cpus-to-allocate-for-a-process>

  mpirun --display-map --mca btl ^tcp --hostfile $hostfile --bind-to-core --bysocket --npernode $ppn --cpus-per-proc $cpp -np $(($nodes*$ppn)) ...
    where, --display-map will print how processes are bind to processing units and --mca btl ^tcp forces to turn off tcp
That's all you'll need to run C# based MPI.NET applications in Linux with Mono and OpenMPI. Hope this helps!

9 comments :

  1. nomen6:24 AM

    Hello Saliya,

    very nice post, but unfortunately the link to Unsafe.pl.patch appears to be broken. Do you still have a copy of the file?

    Regards,

    ReplyDelete
    Replies
    1. Saliya Ekanayake5:54 AM

      Hi,

      It's unfortunate that this file is being removed from everywhere. Here's something that'll work http://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/sys-cluster/mpi-dotnet/files/Unsafe.pl.patch

      Thanks

      Delete
  2. nomen3:06 PM

    Thanks for the link to the patch.

    I made MPI.NET work with OpenMpi 1.6 (I did not try the latest [1.8.x]) by:
    - configuring, compiling and installing OpenMpi 1.4.3
    - configuring MPI.NET against OpenMpi 1.4.3 (so MPI.NET can import OpenMpi's data types)
    - uninstalling OpenMpi 1.4.3
    - loading module OpenMpi 1.6
    - compiling and installing MPI.NET

    Works fine! Thanks again for this valuable post

    ReplyDelete
    Replies
    1. Saliya Ekanayake6:03 PM

      Great to hear that you got it working!

      Delete
  3. Tun Tun Lin12:47 AM

    Hello Saliya

    am using CentOS 7 with openMPI.
    I have some error to install mpi.net.

    I apply the patches with the following three commands:

    patch MPI/Unsafe.pl < Unsafe.pl.patch

    Downloaded this patch from --->
    https://sources.gentoo.org/cgi-bin/viewvc.cgi/gentoo-x86/sys-cluster/mpi-dotnet/files/?hideattic=0

    I used the make command.

    In this section we have error :

    CustomUnsafe.cs
    CustomUnsafe.cs(112,41): error CS1525: Unexpected symbol `;'
    CustomUnsafe.cs(3238,12): error CS1525: Unexpected symbol `switch'
    CustomUnsafe.cs(3240,16): error CS1525: Unexpected symbol `case'
    CustomUnsafe.cs(3287,1): error CS8025: Parsing error
    Compilation failed: 4 error(s), 0 warnings

    Please help me, how to fix it.


    ReplyDelete
    Replies
    1. Saliya Ekanayake5:21 AM

      It seems like something is wrong with your Mono installation. Can you check if a simple HelloWorld C# program can be compiled and run successfully with Mono?

      Delete
    2. Tun Tun Lin2:40 AM

      Can we get your email address?

      Thank..

      Delete
    3. Saliya Ekanayake7:17 AM

      esaliya.shared@gmail.com

      Delete
    4. Tun Tun Lin8:57 PM

      Thank Saliya..

      Delete

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