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  • Message Passing Interface (MPI)

    So you have installed your cluster and you are done with introductory material on Windows HPC. Now you want to develop an application with the most common programming model: Message Passing Interface.The MPI programming model is a standard with implementations from many vendors. For newbies (like myself!), I have aggregated below links for getting started.Non-Microsoft MPI resources (useful even if you are not on the Windows platform)1. Message Passing Interface on wikipedia. 2. The MPI standard.3. MPICH2 - an MPI implementation.4. Tutorial on MPI by William Gropp.5. MPI patterns presented as a tutorial with sample code. 6. THE official MPI Forum (maintains the standard) including the wiki discussing the MPI future.7. Great MPI tutorial including at the end the MPI Exercise.8. C++ MPI Exercises by John Burkardt.9. Book online: MPI The Complete Reference.MS-MPI10. Windows HPC Server 2008 - Using MS-MPI whitepaper (15 page doc).11. Tracing MPI applications (27 page doc).12. Using Microsoft MPI (TechNet section).13. Windows HPC Server MPI forum (for posting questions). MPI.NET14. MPI.NET Home Page (not owned by Microsoft).15. MPI.NET Tutorial.16. HPC Development using F# using MPI.NET (38 page doc).Next time I'll post resources for the Microsoft Cluster SOA programming model - happy coding... Comments about this post welcome at the original blog.

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  • Autoconf macro for Boost MPI?

    - by baol
    I'm searching an autoconf macro to use in my configure.ac that checks for Boost MPI. It's not hard to find a couple of them on the Internet but none of the one I tried worked as expected. What ax_boost_mpi.m4 do you use?

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  • MPI Cluster Debugger launch integration in VS2010

    Let's assume that you have all the HPC bits installed and that you have existing MPI code (or you created a "Hello World" project using the MPI project template). Of course, you create a single MPI application and at runtime it will correspond to multiple processes (of the same app) launched on multiple nodes (i.e. machines) on the cluster. So how do you debug such a situation by simply hitting the familiar "F5" keystroke (i.e. Debug - Start Debugging)?WATCH IT INSTEAD OF READING ABOUT ITIf you can't bear to read through all the details below, just watch this 19-minute screencast explaining this VS2010 feature. Alternatively, or even additionally, keep on reading.REQUIREMENTWhen you debug an MPI application, you would want the copying of resources from your client machine (where Visual Studio is installed) to each compute node (where Windows HPC Server is installed) to take place automatically for you. 'Resources' in the previous sentence includes your application binary, plus any binary or data dependencies it may have, plus PDBs if needed, plus the debug CRT of the correct bitness, plus msvsmon for remote debugging to work. You would also want, after copying is complete, to have your app and msvsmon launched and attached so that you can hit breakpoints back in Visual Studio on your client machine. All these thing that you would want are delivered in VS2010.STEPS TO F51. In your MPI project where you have placed a breakpoint go to Project Properties - Configuration Properties - Debugging. Ensure the "Debugger to launch" combo box value is set to MPI Cluster Debugger.2. There are a whole bunch of properties here and typically you can ignore all of them except one: Run Environment. By default it is set to run 1 process on your local machine and if you change the number after that to, for example, 4 it will launch 4 processes of your app on your local machine.You want this to run on your cluster though, so go to the dropdown arrow at the end of the Run Environment cell and open it to expose the "Edit Hpc node" menu which opens the Node Selector dialog:In this dialog you can enter (or pick from a list) the cluster head node name and then the number of processes you want to execute on the cluster and then hit OK and… you are done.3. Press F5 and watch your breakpoint get hit (after giving it some time for copying, remote execution, attachment and symbol resolution to take place).GOING DEEPERIn the MPI Cluster Debugger project properties above, you can see many additional properties to the Run Environment. They are all optional, but you may want to understand them in order to fine tune your cluster debugging. Read all about each one of these on the MSDN page Configuration Properties for the MPI Cluster Debugger.In the Node Selector dialog above you can see more options than just the Head Node name and Number of Process to run. They should be self-explanatory but I also cover them in depth in my screencast showing you an example of why you would choose to schedule processes per core versus per node. You can also read about these options on MSDN as part of the page How to: Configure and Launch the MPI Cluster Debugger.To read through an example that touches on MPI project creation, project properties, node selector, and also usage of MPI with OpenMP plus MPI with PPL, read the MSDN page Walkthrough: Launching the MPI Cluster Debugger in Visual Studio 2010.Happy MPI debugging! Comments about this post welcome at the original blog.

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  • MPI Cluster Debugger launch integration in VS2010

    Let's assume that you have all the HPC bits installed and that you have existing MPI code (or you created a "Hello World" project using the MPI project template). Of course, you create a single MPI application and at runtime it will correspond to multiple processes (of the same app) launched on multiple nodes (i.e. machines) on the cluster. So how do you debug such a situation by simply hitting the familiar "F5" keystroke (i.e. Debug - Start Debugging)?WATCH IT INSTEAD OF READING ABOUT ITIf you can't bear to read through all the details below, just watch this 19-minute screencast explaining this VS2010 feature. Alternatively, or even additionally, keep on reading.REQUIREMENTWhen you debug an MPI application, you would want the copying of resources from your client machine (where Visual Studio is installed) to each compute node (where Windows HPC Server is installed) to take place automatically for you. 'Resources' in the previous sentence includes your application binary, plus any binary or data dependencies it may have, plus PDBs if needed, plus the debug CRT of the correct bitness, plus msvsmon for remote debugging to work. You would also want, after copying is complete, to have your app and msvsmon launched and attached so that you can hit breakpoints back in Visual Studio on your client machine. All these thing that you would want are delivered in VS2010.STEPS TO F51. In your MPI project where you have placed a breakpoint go to Project Properties - Configuration Properties - Debugging. Ensure the "Debugger to launch" combo box value is set to MPI Cluster Debugger.2. There are a whole bunch of properties here and typically you can ignore all of them except one: Run Environment. By default it is set to run 1 process on your local machine and if you change the number after that to, for example, 4 it will launch 4 processes of your app on your local machine.You want this to run on your cluster though, so go to the dropdown arrow at the end of the Run Environment cell and open it to expose the "Edit Hpc node" menu which opens the Node Selector dialog:In this dialog you can enter (or pick from a list) the cluster head node name and then the number of processes you want to execute on the cluster and then hit OK and… you are done.3. Press F5 and watch your breakpoint get hit (after giving it some time for copying, remote execution, attachment and symbol resolution to take place).GOING DEEPERIn the MPI Cluster Debugger project properties above, you can see many additional properties to the Run Environment. They are all optional, but you may want to understand them in order to fine tune your cluster debugging. Read all about each one of these on the MSDN page Configuration Properties for the MPI Cluster Debugger.In the Node Selector dialog above you can see more options than just the Head Node name and Number of Process to run. They should be self-explanatory but I also cover them in depth in my screencast showing you an example of why you would choose to schedule processes per core versus per node. You can also read about these options on MSDN as part of the page How to: Configure and Launch the MPI Cluster Debugger.To read through an example that touches on MPI project creation, project properties, node selector, and also usage of MPI with OpenMP plus MPI with PPL, read the MSDN page Walkthrough: Launching the MPI Cluster Debugger in Visual Studio 2010.Happy MPI debugging! Comments about this post welcome at the original blog.

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  • MPI: is there mpi libraries capable of message compression?

    - by osgx
    Sometimes MPI is used to send low-entropy data in messages. So it can be useful to try to compress messages before sending it. I know that MPI can work on very fast networks (10 Gbit/s and more), but many MPI programs are used with cheap network like 0,1G or 1Gbit/s Ethernet and with cheap (slow, low bisection) network switch. There is a very fast Snappy (wikipedia) compression algorithm, which has Compression speed is 250 MB/s and decompression speed is 500 MB/s so on compressible data and slow network it will give some speedup. Is there any MPI library which can compress MPI messages (at layer of MPI; not the compression of ip packets like in PPP). MPI messages are also structured, so there can be some special method, like compression of exponent part in array of double.

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  • MPI Project Template for VS2010

    If you are developing MS MPI applications with Visual Studio 2010, you are probably tired of following some tedious steps for every new C++ project that you create, similar to the following:1. In Solution Explorer, right-click YourProjectName, then click Properties to open the Property Pages dialog box.2. Expand Configuration Properties and then under VC++ Directories place the cursor at the beginning of the list that appears in the Include Directories text box and then specify the location of the MS MPI C header files, followed by a semicolon, e.g.C:\Program Files\Microsoft HPC Pack 2008 SDK\Include;3. Still under Configuration Properties and under VC++ Directories place the cursor at the beginning of the list that appears in the Library Directories text box and then specify the location of the Microsoft HPC Pack 2008 SDK library file, followed by a semicolon, e.g.if you want to build/debug 32bit application:C:\Program Files\Microsoft HPC Pack 2008 SDK\Lib\i386;if you want to build/debug 64bit application:C:\Program Files\Microsoft HPC Pack 2008 SDK\Lib\amd64;4. Under Configuration Properties and then under Linker, select Input and place the cursor at the beginning of the list that appears in the Additional Dependencies text box and then type the name of the MS MPI library, i.e.msmpi.lib;5. In the code file#include "mpi.h"6. To debug the MPI project you have just setup, under Configuration Properties select Debugging and then switch the Debugger to launch combo value from Local Windows Debugger to MPI Cluster Debugger.Wouldn't it be great if at C++ project creation time you could choose an MPI Project Template that included the steps/configurations above? If you answered "yes", I have good news for you courtesy of a developer on our team (Qing). Feel free to download from Visual Studio gallery the MPI Project Template. Comments about this post welcome at the original blog.

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  • trying to build Boost MPI, but the lib files are not created. What's going on?

    - by unknownthreat
    I am trying to run a program with Boost MPI, but the thing is I don't have the .lib. So I try to create one by following the instruction at http://www.boost.org/doc/libs/1_43_0/doc/html/mpi/getting_started.html#mpi.config The instruction says "For many users using LAM/MPI, MPICH, or OpenMPI, configuration is almost automatic", I got myself OpenMPI in C:\, but I didn't do anything more with it. Do we need to do anything with it? Beside that, another statement from the instruction: "If you don't already have a file user-config.jam in your home directory, copy tools/build/v2/user-config.jam there." Well, I simply do what it says. I got myself "user-config.jam" in C:\boost_1_43_0 along with "using mpi ;" into the file. Next, this is what I've done: bjam --with-mpi C:\boost_1_43_0>bjam --with-mpi WARNING: No python installation configured and autoconfiguration failed. See http://www.boost.org/libs/python/doc/building.html for configuration instructions or pass --without-python to suppress this message and silently skip all Boost.Python targets Building the Boost C++ Libraries. warning: skipping optional Message Passing Interface (MPI) library. note: to enable MPI support, add "using mpi ;" to user-config.jam. note: to suppress this message, pass "--without-mpi" to bjam. note: otherwise, you can safely ignore this message. warning: Unable to construct ./stage-unversioned warning: Unable to construct ./stage-unversioned Component configuration: - date_time : not building - filesystem : not building - graph : not building - graph_parallel : not building - iostreams : not building - math : not building - mpi : building - program_options : not building - python : not building - random : not building - regex : not building - serialization : not building - signals : not building - system : not building - test : not building - thread : not building - wave : not building ...found 1 target... The Boost C++ Libraries were successfully built! The following directory should be added to compiler include paths: C:\boost_1_43_0 The following directory should be added to linker library paths: C:\boost_1_43_0\stage\lib C:\boost_1_43_0> I see that there are many libs in C:\boost_1_43_0\stage\lib, but I see no trace of libboost_mpi-vc100-mt-1_43.lib or libboost_mpi-vc100-mt-gd-1_43.lib at all. These are the libraries required for linking in mpi applications. What could possibly gone wrong when libraries are not being built?

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  • How do I debug an MPI program?

    - by Jay Conrod
    I have an MPI program which compiles and runs, but I would like to step through it to make sure nothing bizarre is happening. Ideally, I would like a simple way to attach GDB to any particular process, but I'm not really sure whether that's possible or how to do it. An alternative would be having each process write debug output to a separate log file, but this doesn't really give the same freedom as a debugger. Are there better approaches? How do you debug MPI programs?

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  • Which python mpi library to use?

    - by Dana the Sane
    I'm starting work on some simulations using MPI and want to do the programming in Python/scipy. The scipy site lists a number of mpi libraries, but I was hoping to get feedback on quality, ease of use, etc from anyone who has used one.

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  • Boost::Serialization Mpi Sending array of user defined types

    - by Noman Javed
    I want to send my Array class using boost Mpi template class Array { private: int size; T* data; public: // constructors + other stuff }; Here T can be any built in type or user defined type. Suppose I have a class complex struct complex { std::vector real_imag; // contain two elements }; So the question is how can I send Array using Boost::Mpi + serialization. Thanks in anticipation Regards Noman

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  • MPI datatype for 2 d array

    - by dks
    I need to pass an array of integer arrays (basically a 2 d array )to all the processors from root.I am using MPI in C programs. How to declare MPI datatype for 2 d array.and how to send the message (should i use broadcast or scatter)

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  • Using MPI under VC++ MFC project?

    - by Mike
    Does any body know how can I use MS_MPI in my VC++ MFC project? I already have a big MFC project and I only want to use parallel processing in a part of it with MPI. (I know how to use MPI in a separate code, but I don't know how to integrate it with my VC++ MFC project)

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  • Communicate between separate MPI-Programs

    - by Fyg
    I have the following problem: Program 1 has a huge amount of data, say 10GB. The data in question consists of large integer- and double-arrays. Program 2 has 1..n MPI processes that use tiles of this data to compute results. How can I send the data from program 1 to the MPI Processes? Using File I/O is out of question. The compute node has sufficient RAM.

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  • Mpi function define

    - by Simone
    I wrote a program in c using MPI (Message Passing Inteface) that compute recursively the inverse of a lower triangular matrix. Every cpu sends 2 submatrices to other two cpus, they compute them and they give them back to the cpu caller. When the cpu caller has its submatrices it has to perform a matrix multiplication. In the recurrence equation the bottle neck is matrix multiplication. I implemented parallel multiplication with mpi in c but i'm not able to embed it into a function. Is it possible? thanks, Simone

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  • Why isn't Hadoop implemented using MPI?

    - by artif
    Correct me if I'm wrong, but my understanding is that Hadoop does not use MPI for communication between different nodes. What are the technical reasons for this? I could hazard a few guesses, but I do not know enough of how MPI is implemented "under the hood" to know whether or not I'm right. Come to think of it, I'm not entirely familiar with Hadoop's internals either. I understand the framework at a conceptual level (map/combine/shuffle/reduce and how that works at a high level) but I don't know the nitty gritty implementation details. I've always assumed Hadoop was transmitting serialized data structures (perhaps GPBs) over a TCP connection, eg during the shuffle phase. Let me know if that's not true.

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  • MPI Large Data all to all transfer

    - by csslayer
    My application of MPI has some process that generate some large data. Say we have N+1 process (one for master control, others are workers), each of worker processes generate large data, which is now simply write to normal file, named file1, file2, ..., fileN. The size of each file may be quite different. Now I need to send all fileM to rank M process to do the next job, So it's just like all to all data transfer. My problem is how should I use MPI API to send these files efficiently? I used to use windows share folder to transfer these before, but I think it's not a good idea. I have think about MPI_file and MPI_All_to_all, but these functions seems not to be so suitable for my case. Simple MPI_Send and MPI_Recv seems hard to be used because every process need to transfer large data, and I don't want to use distributed file system for now.

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  • How to pass user-defined structs using boost mpi

    - by lava
    I am trying to send a user-defined structure named ABC using boost::mpi::send () call. The given struct contains a vector "data" whose size is determined at runtime. Objects of struct ABC are sent by master to slaves. But the slaves need to know the size of vector "data" so that the sufficient buffer is available on the slave to receive this data. I can work around it by sending the size first and initialize sufficient buffer on the slave before receiving the objects of struct ABC. But that defeats the whole purpose of using STL containers. Does anyone know of a better way to do handle this ? Any suggestions are greatly appreciated. Here is a sample code that describes the intent of my program. This code fails at runtime due to above mentioned reason. struct ABC { double cur_stock_price; double strike_price; double risk_free_rate; double option_price; std::vector <char> data; }; namespace boost { namespace serialization { template<class Archive> void serialize (Archive &ar, struct ABC &abc, unsigned int version) { ar & abc.cur_stock_price; ar & abc.strike_price; ar & abc.risk_free_rate; ar & abc.option_price; ar & bopr.data; } } } BOOST_IS_MPI_DATATYPE (ABC); int main(int argc, char* argv[]) { mpi::environment env (argc, argv); mpi::communicator world; if (world.rank () == 0) { ABC abc_obj; abc.cur_stock_price = 1.0; abc.strike_price = 5.0; abc.risk_free_rate = 2.5; abc.option_price = 3.0; abc_obj.data.push_back ('a'); abc_obj.data.push_back ('b'); world.send ( 1, ANY_TAG, abc_obj;); std::cout << "Rank 0 OK!" << std::endl; } else if (world.rank () == 1) { ABC abc_obj; // Fails here because abc_obj is not big enough world.recv (0,ANY_TAG, abc_obj;); std::cout << "Rank 1 OK!" << std::endl; for (int i = 0; i < abc_obj;.data.size(); i++) std::cout << i << "=" << abc_obj.data[i] << std::endl; } MPI_Finalize(); return 0; }

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  • MPI and C structs

    - by hanno
    I have to admit, I was quite shocked to see how many lines of code are required to transfer one C struct with MPI. Under what circumstances will it work to simply transmit a struct using the predefined dataype MPI_CHAR? Consider the following example: struct particle { double x; double y; long i; }; struct particle p; MPI_Isend(&p, sizeof(particle), MPI_CHAR, tag, MPI_COMM_WORLD, &sendr); In my case, all processes run on the same architecture. Is padding the only issue?

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