Re: [Boost-users] [mpi] - why this code hangs on gather?

Subject: Re: [Boost-users] [mpi] - why this code hangs on gather?
From: Matthieu Brucher (matthieu.brucher_at_[hidden])
Date: 2009-10-27 08:49:47

Hi,

If I understood your code correctly, you are sending every piece of
data through rank 0 and then it waits for the completion of the
operations. Then, every rank receives data, as well as the first rank.
But the first rank is waiting for ots own receive to finish, which can
never happen. You should put the wait all after the receptions.

Matthieu

2009/10/27 tomasz jankowski <tomasz_jacek_at_[hidden]>:
> hello boost users
>
> please look (if you find few minutes) code bellow
> first i'm declaring molecule class (with needed serialization)
> in main() first I'm building vector of data (which are molecules)
> then vector is divided to chunks and send in point to point nonblocking
> communication model to rest of mpi processes.
> after that some calculation on molecules are done.
> at the end I want gather all data but the program hangs on gather in
> proces with rank 0
>
> does anyone has idea what is wrong in this code?
>
> tom
>
>
> #include <vector>
> #include <algorithm>
> #include <boost/mpi.hpp>
> #include <boost/serialization/string.hpp>
> #include <boost/serialization/vector.hpp>
> #include <boost/lexical_cast.hpp>
> #include <iostream>
> #include <cstdlib>
> #include <string>
> #include <boost/random/linear_congruential.hpp>
> #include <boost/random/uniform_real.hpp>
> #include <boost/random/variate_generator.hpp>
> #include <boost/format.hpp>
>
> namespace mpi = boost::mpi;
>
> class molecule
> {
>
>    friend std::ostream & operator<<(std::ostream &os, const molecule &prot);
>    friend class boost::serialization::access;
>
>    template<class Archive>
>    void serialize(Archive & ar, const unsigned int){
>        ar & x_ & y_ & z_ & number_ & message_;
>    }
>
>
> public:
>    // constructor
>    molecule(){x_=0; y_=0; z_=0; number_= 0; message_ = "";};
>    molecule(double x, double y, double z, unsigned int n, std::string m) :
>        x_(x), y_(y), z_(z), number_(n), message_(m)
>    {}
>    void print(){
>        std::cout << (boost::format("%.6f") % x_) << " | "<<
> (boost::format("%.6f") % y_) << " | " << (boost::format("%.6f") % z_) <<
> " | " << number_ << "\t| " << message_ << std::endl;
>
>    }
>    double x_;
>    double y_;
>    double z_;
>    unsigned int number_;
>    std::string message_;
>
> };
>
>
> int main(int argc, char* argv[])
> {
>
>
>  //generator
>  boost::minstd_rand generator_real(42u);
>  //distribution
>  boost::uniform_real<> uni_dist_real(0,1);
>  //functor
>  boost::variate_generator<boost::minstd_rand, boost::uniform_real<> >
> uni_real(generator_real, uni_dist_real);
>
>
>
>
>
>  mpi::environment env(argc, argv);
>  mpi::communicator world;
>
>  // data construction
>  std::vector<molecule> data;
>  if (world.rank() == 0) {
>    for(unsigned int i=0;i<8020;++i){
>      std::string txt("see you later aligator");
>      molecule tmp(1,1,1,i,txt);
>      data.push_back(tmp);
>    }
>  }
>
>
>  //broadcast(world,data,0);
>  //we could do it by broadcast (line above) - but lets do it by point to
> point with only amount of data we need
>
>
>  //work vectors
>  std::vector<molecule> res;
>  std::vector<std::vector<molecule> > allRes;
>  // we need to divide our data between processes
>  unsigned int nProcs=world.size();
>  unsigned int chunkSize=data.size() / nProcs;
>  unsigned int extraBits=data.size() % nProcs;
>
>  // extra bits we will do in root process
>  if( world.rank() == 0 ){
>
>    mpi::request reqs[nProcs-1];
>
>    for(unsigned int i=1;i<nProcs;++i){
>      std::vector<molecule> sendmol;
>        unsigned int pos=extraBits+i*chunkSize;
>
>      for(unsigned int j=0;j<chunkSize;++j){
>        sendmol.push_back(data[pos]);
>        pos++;
>      }
>
>     reqs[i-1] = world.isend(i, 0, sendmol);
>      std::cout<<"msg sended to "<< i <<std::endl;std::cout.flush();
>    }
>
>    for(unsigned int i=0;i<chunkSize + extraBits;++i){
>      molecule tmp = data[i];
>      tmp.x_ *= uni_real();
>      tmp.y_ *= uni_real();
>      tmp.z_ *= uni_real();
>      tmp.message_ = "from process: " +
> boost::lexical_cast<std::string>(world.rank());
>      res.push_back(tmp);
>    }
>
>    mpi::wait_all(reqs, reqs + nProcs - 1);
>    std::cout<<"calculation finished in 0 "<<std::endl;std::cout.flush();
>
>  }
>
>
>
>
>   std::vector<molecule> recvmol;
>   mpi::request recv;
>   recv = world.irecv(0, 0, recvmol);
>   recv.wait();
>   std::cout<<"receiving finished
> "<<world.rank()<<std::endl;std::cout.flush();
>
>
>  for(unsigned int i=0;i<recvmol.size();++i){
>    molecule tmp = recvmol[i];
>    tmp.x_ *= uni_real();
>    tmp.y_ *= uni_real();
>    tmp.z_ *= uni_real();
>    tmp.print();
>    tmp.message_ =  "from process: " +
> boost::lexical_cast<std::string>(world.rank());
>    res.push_back(tmp);
>  }
>      std::cout<<"calculation finished in
> "<<world.rank()<<std::endl;std::cout.flush();
>
>  //wysylanie wynikow ze wszystkich procesow mpi do procesu 0
>  if( world.rank() == 0 ){
>    gather(world,res,allRes,0);
>  std::cout<<"gather finished "<<world.rank()<<std::endl;std::cout.flush();
>
>  } else {
>    gather(world,res,0);
>  std::cout<<"gather finished"<<world.rank()<<std::endl;std::cout.flush();
>
>  }
>
>  // output
>  if(world.rank()==0){
>    for(unsigned int i=0;i<static_cast<unsigned int>(world.size());++i){
>      std::cout<<"results from process "<<i<<": "<<std::endl;
>
>      for(int k=0; k<allRes[i].size();k++){
>        allRes[i][k].print();
>      }
>      std::cout<<std::endl;
>
>    }
>  std::cout<<"making output finished
> "<<world.rank()<<std::endl;std::cout.flush();
>
>  }
>
>  return 0;
> }
>
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-- 
Information System Engineer, Ph.D.
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