wiki:Public/User_Guide/OpenCHK

What is OpenCHK?

The OpenCHK model is a pragma-based checkpointing model developed by the Programming Models group at the Barcelona Supercomputing Center.

The aim of this model is to provide a generic and portable way to checkpoint and recover data in C/C++ and Fortran High Performance Computing applications.

The prototype implementation of the model is based on two software components:

Mercurium source-to-source compiler Transparent Checkpoint Library

Loading the OpenCHK module

Firstly, it is required to append some paths to your "MODULEPATH" environment variable:

modulepath="/usr/local/software/skylake/Stages/2018b/modules/all/Core:$modulepath"
modulepath="/usr/local/software/skylake/Stages/2018b/modules/all/Compiler/mpi/intel/2019.0.117-GCC-7.3.0:$modulepath"
modulepath="/usr/local/software/skylake/Stages/2018b/modules/all/MPI/intel/2019.0.117-GCC-7.3.0/psmpi/5.2.1-1-mt:$modulepath"
export MODULEPATH="$modulepath:$MODULEPATH"

Once this is done, simply load the following modules:

module load Intel/2019.0.117-GCC-7.3.0
module load ParaStationMPI/5.2.1-1-mt
module load OpenCHK/1.0

Documentation and User guide

Manual: https://github.com/bsc-pm/OpenCHK-model

Quick Start Guide

Before the Execution

TCL provides support for three different backends: FTI, SCR and VeloC. The backend library must be chosen using the environment variable "TCL_BACKEND".
NOTE: In the current installation, the only enabled backend is FTI.

export TCL_BACKEND=FTI

When using FTI as backend library, the user needs to provide an FTI configuration file using the environment variable "FTI_CONF_FILE". (see attachments: config.fti)

export FTI_CONF_FILE=config.fti

OpenCHK syntax

  • The init construct defines the initialization of a checkpoint context. None of the other constructs must be used without initializing a checkpoint context.
  • The shutdown construct defines the finalization of a checkpoint context.
  • The 'store' construct specifies that some variables and memory regions are going to be saved in a new checkpoint.
  • The 'load' construct specifies that some variables and memory regions are goind to be updated with the stored values that we have previously checkpointed (if any).

Example C/C++

Compile the example:

mpicxx -cxx=mcxx  --checkpoint -o test_scalar-cpp test_scalar.cpp

Run the example:
NOTE: Remember that you should have set TCL_BACKEND=FTI and a valid FTI_CONF_FILE.

mpirun -np 8 ./test_scalar-cpp [step_to_inject_error]
#include <iostream>
#include <cassert>
#include <stdlib.h>

void error_handler(int err_code)
{
    std::cout << "Error inside CheckpointLib. Error code: " << err_code << "." << std::endl;
    exit(-1);
}

int main(int argc, char **argv)
{
    int err = MPI_Init(&argc, &argv);
    assert(err == MPI_SUCCESS);
    MPI_Comm comm = MPI_COMM_WORLD;

    int inject_error = -1;
    if(argc == 2) {
        inject_error = std::atoi(argv[1]);
        std::cout << "Inject error at step " << inject_error << "." << std::endl;
    }

    #pragma chk init comm(comm)
    {
        int data, i = 0;
        bool restored = false;

        #pragma chk load(i, data)
        if(i != 0) {
            std::cout << "Restored data from iteration " << i << ". data = " << data << "." << std::endl;
            restored = true;
        }
        for(i; i < 10; i++) {
            data = i;
            #pragma chk store(i, data) kind(CHK_FULL) id(i) level((i%4)+1) if(1) handler(error_handler)
            if(i == inject_error && !restored) {
                std::cout << "Injected error." << std::endl;
                exit(-1);
            }
            std::cout << "Completed step " << i << std::endl;
        }
    }
    #pragma chk shutdown

    MPI_Finalize();
}

Example Fortran

Compile the example:

mpif90 -fc=ifort-mfc  --checkpoint -o test_scalar-fortran test_scalar.f90

Run the example:
NOTE: Remember that you should have set TCL_BACKEND=FTI and a valid FTI_CONF_FILE.

mpirun -np 8 ./test_scalar-fortran [step_to_inject_error]
PROGRAM T1
   include 'mpif.h'
   integer rank, size, ierror, tag, comm, status(MPI_STATUS_SIZE)
   integer actual_data = 0, restored_i = 0, restored = 0, inject_error = -1, i
    CHARACTER(len=32) :: arg

   call MPI_INIT(ierror)
   comm = MPI_COMM_WORLD

   if (iargc() == 1) then
       call getarg(1, arg)
       read (arg,'(I10)') inject_error
       print *, 'Inject error at step ', inject_error, '.'
   endif

!$chk init comm(comm)
!$chk load(restored_i, actual_data)
   if (restored_i .ne. 0) then
       print *, 'Restored data from iteration ', restored_i , '. data = ', actual_data, '.'
       restored = 1
   end if

   do i = restored_i, 10
       actual_data = i
!$chk store(i, actual_data) kind(0) id(i) level(mod(i,4)+1) if(i .ge. 0)
       if (i .eq. inject_error .AND. restored .eq. 0) then
           print *, 'Injected error'
           call EXIT(-1)
       end if
       print *, 'Completed step ', i
   end do
!$chk shutdown

   call MPI_FINALIZE(ierror)
END PROGRAM

More Examples

More examples can be found in: https://github.com/bsc-pm/OpenCHK-model/tree/master/examples

Last modified 3 years ago Last modified on Jun 18, 2019, 11:26:01 AM