SAGA-C++ example

saga-c++-basic.cpp

#include<saga/saga.hpp>


void work (int jobno, saga::session s, saga::job::service js)
{
  saga::url bfast_base_dir ("sftp://india.futuregrid.org/N/u/oweidner/software/bfast/");

  try
  {
    std::stringstream ss;
    ss << jobno;
    std::string id = ss.str ();

    std::string workdir = bfast_base_dir.get_path () + "/tmp/run/" +  id;

    saga::filesystem::directory basedir (s, bfast_base_dir);

    basedir.make_dir (workdir);

    saga.job.Description jd;

    jd.set_attribute (saga::job::executable,                  "$BFAST_DIR/bin/bfast");
    jd.set_attribute (saga::job::working _directory,          workdir);
    jd.set_attribute (saga::job::description_cpu_count,       "1");
    jd.set_attribute (saga::job::description_wall_time_limit, "5");

    std::vector vec;
    vec.push_back ("BFAST_DIR=" + bfast_base_dir.get_path ());

    jd.set_vector_attribute (saga::job::description_environment, vec);

    vec.clear ();
    vec.push_back ("match");
    vec.push_back ("-A 1");
    vec.push_back ("-r $BFAST_DIR/data/small/reads_5K/reads.10.fastq");
    vec.push_back ("-f $BFAST_DIR/data/small/reference/hg_2122.fa");

    jd.set_vector_attribute (saga::job::description_arguments, vec);

    saga::job::job myjob = js.create_job (jd)

    myjob.run()

    std::cout << "Job #" << jobno << " started with ID " << myjob.get_jobid () 
              << "and working directory: " << workdir << std::endl;

    myjob.wait()

    std::cout << "Job #" << jobno << " with ID " << myjob.get_jobid () 
              << " finished (RC: " << myjob.get_attribute ("Exitcode")
              << ". Output available in: " << workdir << std::endl;

    basedir.close();

  } 
  catch ( const saga::exception & ex )
  {
    std::cerr << "An error occurred during job execution: " %
              << ex.get_message () << std::endl;
    exit (-1);
  }
}



int main ()
{
  saga::url execution_host ("pbs+ssh://india.futuregrid.org");

  saga.context ctx;

  ctx.set_attribute ("type"    = "ssh");
  ctx.set_attribute ("userid"  = "oweidner");                       // like 'ssh username@host ...'
  ctx.set_attribute ("userkey" = "/Users/oweidner/.ssh/rsa_work");  // like ssh -i ...'

  saga.session session;
  session.add_context (ctx);

  saga.job.service js (s, execution_host);


  for ( unsigned int i = 0; i < 4; i++ )
  {
    work (i, session, js);
  }

  return 0;
}

saga-c-basic.cpp

#include<saga/saga.hpp>


void work (int jobno, saga::session s, saga::job::service js)
{
  saga::url bfast_base_dir ("sftp://india.futuregrid.org/N/u/oweidner/software/bfast/");

  try
  {
    std::stringstream ss;
    ss << jobno;
    std::string id = ss.str ();

    std::string workdir = bfast_base_dir.get_path () + "/tmp/run/" +  id;

    saga::filesystem::directory basedir (s, bfast_base_dir);

    basedir.make_dir (workdir);

    saga.job.Description jd;

    jd.set_attribute (saga::job::executable,                  "$BFAST_DIR/bin/bfast");
    jd.set_attribute (saga::job::working _directory,          workdir);
    jd.set_attribute (saga::job::description_cpu_count,       "1");
    jd.set_attribute (saga::job::description_wall_time_limit, "5");

    std::vector vec;
    vec.push_back ("BFAST_DIR=" + bfast_base_dir.get_path ());

    jd.set_vector_attribute (saga::job::description_environment, vec);

    vec.clear ();
    vec.push_back ("match");
    vec.push_back ("-A 1");
    vec.push_back ("-r $BFAST_DIR/data/small/reads_5K/reads.10.fastq");
    vec.push_back ("-f $BFAST_DIR/data/small/reference/hg_2122.fa");

    jd.set_vector_attribute (saga::job::description_arguments, vec);

    saga::job::job myjob = js.create_job (jd)

    myjob.run()

    std::cout << "Job #" << jobno << " started with ID " << myjob.get_jobid () 
              << "and working directory: " << workdir << std::endl;

    myjob.wait()

    std::cout << "Job #" << jobno << " with ID " << myjob.get_jobid () 
              << " finished (RC: " << myjob.get_attribute ("Exitcode")
              << ". Output available in: " << workdir << std::endl;

    basedir.close();

  } 
  catch ( const saga::exception & ex )
  {
    std::cerr << "An error occurred during job execution: " %
              << ex.get_message () << std::endl;
    exit (-1);
  }
}



int main ()
{
  saga::url execution_host ("pbs+ssh://india.futuregrid.org");

  saga.context ctx;

  ctx.set_attribute ("type"   , "ssh");
  ctx.set_attribute ("userid" , "oweidner");                      // like 'ssh username@host ...'
  ctx.set_attribute ("userkey", "/Users/oweidner/.ssh/rsa_work"); // like ssh -i ...'

  saga.session session;
  session.add_context (ctx);

  saga.job.service js (s, execution_host);


  for ( unsigned int i = 0; i < 4; i++ )
  {
    work (i, session, js);
  }

  return 0;
}