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roberto.depietri:pub:einstein_toolkit [27/09/2011 04:41] – roberto.depietriroberto.depietri:pub:einstein_toolkit [03/10/2011 12:23] (versione attuale) – roberto.depietri
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 +====== EINSTEIN TOOLKIT ======
 +
 +We will first have a look at the various step we do have to do in order to
 +have a running executable on a local machine and that we look on how to
 +transpose the various steps on the TRAMONTANA grid cluster 
 +
 +
 +===== Basic downloads =====
 +
 +The web page of the project is [[http://einsteintoolkit.org/|einsteintoolkit.org]] and 
 +the tutorial for new user of the //Einstein Toolkit// is located at the following web page  [[http://docs.einsteintoolkit.org/et-docs/Tutorial_for_New_Users|TUTORIAL]].
 +
 +The main prerequisite for downloading the source code is that the revision control
 +software tools cvs, svn and git should be installed on the main node  
 +
 +The first step is indeed to have the source of our source code available on our 
 +machine. We should first create a directory where to save our compilation tree:
 +
 +  mkdir EinsteinToolkit
 +  cd EinsteinToolkit/
 +
 +We now get the download script and make it executable
 +
 +  wget --no-check-certificate https://github.com/gridaphobe/CRL/raw/ET_2011_05/GetComponents
 +  chmod 755 GetComponents
 +
 +and we proceed on getting all the components
 +
 +  ./GetComponents -a http://svn.einsteintoolkit.org/manifest/branches/ET_2011_05/einsteintoolkit.th
 +
 +At this point we have a complete source tree ready to be compiled. To appreciate the size of
 +the problem we have (to compile and run our program) we note that the size of the source tree
 +is 567MBytes and contains 55451 files.
 +
 +In fact we give the commands
 +
 +   tar czf Cactus_tree.tgz Cactus/ 
 +   du -hs Cactus* 
 +
 +we get the following output:
 +
 +   567M    Cactus
 +   145M    Cactus_tree.tgz
 +
 +
 +
 +
 +
 +===== COMPILING =====
 +
 +  make Einstein-config F77=gfortran F90=gfortran GSL=yes JPEG=yes SSL=yes  \
 +                       MPI=OpenMPI OPENMPI_DIR=/usr/lib64/openmpi/1.4-gcc/ \
 +                       OPENMP=yes
 +
 +
 +and it is required to answer "//yes//" to allow for a creation of a new executable configuration.
 +
 +The next step is to do an actual compilation to a running executable out of our source tree.
 +The way in which a Cactus executable is created of a source tree is selecting components
 +providing a "Thornlist" file. Another possibility is editing the list of all the components present
 +in the source tree or accepting the complete list of available components. The latter is achived
 +running the command:
 +
 +  make Einstein
 +
 +and answer "//no//". In this way a full compilation off all the available modules is obtained.
 +
 +At the end we obtain a file called "//''cactus_Einstein''//" in the exe subdirectory. Ready to be
 +lunched.
 +
 +We should note that the only real configuration needed on a Linux machine was to provide
 +the flavor of the MPI implementation available and directory where it is located. In the case of
 +the grid-ui user interface present here in Parma that is the same that it is available on TRAMONTANA.
 + 
 +
 +
 +
 +
 +===== EXECUTING =====
 +
 +
 +The executable is quite easy to use since it accept a parameter 
 +file and has MPI compiled and linked. To run the simulation
 +one typically gives the command
 +
 +  mpirun -np 4 -x OMP_NUM_THREADS=1 Einstein static_tov.par
 +
 +and an example of a parameter file is:
 +
 +  ## mclachlan tov_static
 +  ActiveThorns = "Time MoL"
 +  ActiveThorns = "Coordbase CartGrid3d Boundary StaticConformal"
 +  ActiveThorns = "SymBase ADMBase TmunuBase HydroBase InitBase ADMCoupling ADMMacros"
 +  ActiveThorns = "IOUtil Formaline"
 +  ActiveThorns = "SpaceMask CoordGauge Constants LocalReduce aeilocalinterp LoopControl"
 +  ActiveThorns = "Carpet CarpetLib CarpetReduce CarpetRegrid2 CarpetInterp"
 +  ActiveThorns = "CarpetIOASCII CarpetIOScalar CarpetIOHDF5 CarpetIOBasic"
 +  ActiveThorns = "ADMConstraints NaNChecker"
 +  ActiveThorns = "TerminationTrigger"
 +  # grid parameters
 +  CartGrid3D::type         = "coordbase"
 +  CartGrid3D::domain       = "full"
 +  CartGrid3D::avoid_origin = "no"
 +  CoordBase::xmin =   0.0
 +  CoordBase::ymin =   0.0
 +  CoordBase::zmin =   0.0
 +  CoordBase::xmax = 240.0
 +  CoordBase::ymax = 240.0
 +  CoordBase::zmax = 240.0
 +  CoordBase::dx   =   8
 +  CoordBase::dy   =   8
 +  CoordBase::dz   =   8
 +  CoordBase::boundary_size_x_lower        = 3
 +  CoordBase::boundary_size_y_lower        = 3
 +  CoordBase::boundary_size_z_lower        = 3
 +  CoordBase::boundary_size_x_upper        = 3
 +  CoordBase::boundary_size_y_upper        = 3
 +  CoordBase::boundary_size_z_upper        = 3
 +  CoordBase::boundary_shiftout_x_lower    = 1
 +  CoordBase::boundary_shiftout_y_lower    = 1
 +  CoordBase::boundary_shiftout_z_lower    = 1
 +  CoordBase::boundary_shiftout_x_upper    = 0
 +  CoordBase::boundary_shiftout_y_upper    = 0
 +  CoordBase::boundary_shiftout_z_upper    = 0
 +  ActiveThorns = "ReflectionSymmetry"
 +  ReflectionSymmetry::reflection_x = "yes"
 +  ReflectionSymmetry::reflection_y = "yes"
 +  ReflectionSymmetry::reflection_z = "yes"
 +  ReflectionSymmetry::avoid_origin_x = "no"
 +  ReflectionSymmetry::avoid_origin_y = "no"
 +  ReflectionSymmetry::avoid_origin_z = "no"
 +  TmunuBase::stress_energy_storage = yes
 +  TmunuBase::stress_energy_at_RHS  = yes
 +  TmunuBase::timelevels            =  1
 +  TmunuBase::prolongation_type     = none
 +  HydroBase::timelevels            = 3
 +  ADMMacros::spatial_order = 4
 +  ADMBase::metric_type     = "physical"
 +  ADMConstraints::bound            = "static"
 +  ADMConstraints::constraints_timelevels = 3
 +  ADMConstraints::constraints_persist    = yes
 +  SpaceMask::use_mask      = "yes"
 +  Cactus::terminate           = "time"
 +  Cactus::cctk_final_time     = 1000
 +  Carpet::domain_from_coordbase = "yes"
 +  Carpet::enable_all_storage       = no
 +  Carpet::use_buffer_zones         = "yes"
 +  Carpet::poison_new_timelevels    = "yes"
 +  Carpet::check_for_poison         = "no"
 +  Carpet::poison_value             = 113
 +  Carpet::init_3_timelevels        = no
 +  Carpet::init_fill_timelevels     = "yes"
 +  CarpetLib::poison_new_memory = "yes"
 +  CarpetLib::poison_value      = 114
 +  # system specific Carpet paramters
 +  Carpet::max_refinement_levels    = 10
 +  driver::ghost_size               = 3
 +  Carpet::prolongation_order_space = 3
 +  Carpet::prolongation_order_time  = 2
 +  CarpetRegrid2::regrid_every = 0
 +  CarpetRegrid2::num_centres  = 1
 +  CarpetRegrid2::num_levels_1 = 5
 +  CarpetRegrid2::radius_1[1]  =120.0
 +  CarpetRegrid2::radius_1[2]  = 60.0
 +  CarpetRegrid2::radius_1[3]  = 30.0
 +  CarpetRegrid2::radius_1[4]  = 15.0
 +  time::dtfac = 0.25
 +  MoL::ODE_Method             = "rk4"
 +  MoL::MoL_Intermediate_Steps = 4
 +  MoL::MoL_Num_Scratch_Levels = 1
 +  # check all physical variables for NaNs
 +  NaNChecker::check_every = 1
 +  NaNChecker::action_if_found = "just warn" #"terminate", "just warn", "abort"
 +  NaNChecker::check_vars = "ADMBase::metric ADMBase::lapse ADMBase::shift HydroBase::rho HydroBase::eps HydroBase::press HydroBase::vel"
 +  ## Lapse Condition:  \partial_t alpha = - alpha K
 +  ## Shift Condition:  \partial_t beta^i = 0
 +  # Hydro paramters
 +  ActiveThorns = "EOS_Omni"
 +  ActiveThorns = "GRHydro"
 +  HydroBase::evolution_method      = "GRHydro"
 +  GRHydro::riemann_solver            = "Marquina"
 +  GRHydro::GRHydro_eos_type           = "Polytype"
 +  GRHydro::GRHydro_eos_table          = "2D_Polytrope"
 +  GRHydro::recon_method              = "ppm"
 +  GRHydro::GRHydro_stencil            = 3
 +  GRHydro::bound                     = "none"
 +  GRHydro::rho_abs_min               = 1.e-10
 +  #GRHydro::GRHydro = 18 # Tmunu(10), rho,press,eps,w_lorentz,vel, tau
 +  #GRHydro::GRHydro    = 10    # gij(6), alpha, beta(3)
 +  ActiveThorns = "GenericFD NewRad"
 +  ActiveThorns = "ML_BSSN ML_BSSN_Helper"
 +  ADMBase::evolution_method        = "ML_BSSN"
 +  ADMBase::lapse_evolution_method  = "ML_BSSN"
 +  ADMBase::shift_evolution_method  = "ML_BSSN"
 +  ADMBase::dtlapse_evolution_method= "ML_BSSN"
 +  ADMBase::dtshift_evolution_method= "ML_BSSN"
 +  TmunuBase::support_old_CalcTmunu_mechanism = "no"
 +  ML_BSSN::timelevels = 3
 +  ML_BSSN::harmonicN           = 1      # 1+log
 +  ML_BSSN::harmonicF           = 1.0    # 1+log
 +  ML_BSSN::LapseACoeff         = 1.0
 +  ML_BSSN::ShiftBCoeff         = 1.0
 +  ML_BSSN::ShiftGammaCoeff     = 0.0
 +  ML_BSSN::AlphaDriver         = 0.0
 +  ML_BSSN::BetaDriver          = 0.0
 +  ML_BSSN::LapseAdvectionCoeff = 0.0
 +  ML_BSSN::ShiftAdvectionCoeff = 0.0
 +  ML_BSSN::MinimumLapse        = 1.0e-8
 +  ML_BSSN::my_initial_boundary_condition = "extrapolate-gammas"
 +  ML_BSSN::my_rhs_boundary_condition     = "NewRad"
 +  ML_BSSN::ML_log_confac_bound = "none"
 +  ML_BSSN::ML_metric_bound     = "none"
 +  ML_BSSN::ML_Gamma_bound      = "none"
 +  ML_BSSN::ML_trace_curv_bound = "none"
 +  ML_BSSN::ML_curv_bound       = "none"
 +  ML_BSSN::ML_lapse_bound      = "none"
 +  ML_BSSN::ML_dtlapse_bound    = "none"
 +  ML_BSSN::ML_shift_bound      = "none"
 +  ML_BSSN::ML_dtshift_bound    = "none"
 +  # init parameters
 +  InitBase::initial_data_setup_method = "init_some_levels"
 +  ActiveThorns = "TOVSolver"
 +  ADMBase::initial_data            = "tov"
 +  ADMBase::initial_lapse           = "tov"
 +  ADMBase::initial_shift           = "tov"
 +  ADMBase::initial_dtlapse         = "zero"
 +  ADMBase::initial_dtshift         = "zero"
 +  TOVSolver::TOV_Rho_Central[0] = 1.28e-3
 +  TOVSolver::TOV_Gamma[0]       = 2.0
 +  TOVSolver::TOV_K[0]           = 100.0
 +  IOBasic::outInfo_every              = 1
 +  IOBasic::outInfo_vars               = "HydroBase::rho ADMBase::lapse"
 +  IO::out_dir      = $parfile
 +  IOScalar::outScalar_every = 32
 +  IOScalar::one_file_per_group = yes
 +  IOScalar::outScalar_vars  = "
 +   HydroBase::rho
 +   HydroBase::press
 +   HydroBase::eps
 +   HydroBase::vel
 +   ADMBase::lapse
 +   ADMBase::metric
 +   ADMBase::curv
 +   ADMConstraints::ham
 +   ADMConstraints::momentum
 +  "
 +  IOASCII::out1D_every     = 128
 +  IOASCII::one_file_per_group = yes
 +  IOASCII::output_symmetry_points = no
 +  IOASCII::out3D_ghosts           = no
 +  IOASCII::out3D_outer_ghosts     = no
 +  IOASCII::out1D_vars      = "
 +   HydroBase::rho
 +   HydroBase::press
 +   HydroBase::eps
 +   HydroBase::vel
 +   ADMBase::lapse
 +   ADMBase::metric
 +   ADMBase::curv
 +   ADMConstraints::ham
 +   ADMConstraints::momentum
 +  "
 +  iohdf5::out_every    = 256
 +  iohdf5::out_vars     = "
 +      hydrobase::rho
 +      hydrobase::press
 +      hydrobase::eps
 +      hydrobase::vel
 +      ADMBase::lapse
 +      ADMBase::shift
 +      ADMBase::curv
 +      ADMBase::metric
 +  "
 +  IO::out_mode         = "proc"
 +  IO::out_unchunked    = "no"
 +  #==================================
 +  # Checkpoint parameters
 +  #==================================
 +    IO::checkpoint_dir   = "CHECKPOINT"
 +  IO::recover_dir      = "CHECKPOINT"
 +  IO::checkpoint_every = 512
 +  IO::checkpoint_keep  = 2
 +  IO::recover          = "autoprobe"
 +  IO::checkpoint_on_terminate                = "yes"
 +  IO::recover_file                          = "checkpoint.chkpt"
 +  IOHDF5::checkpoint                        = "yes"
 +  IOHDF5::use_reflevels_from_checkpoint     = "yes"
 +  #--------------------------------------------------
 +  TerminationTrigger::on_remaining_walltime = 5
 +  TerminationTrigger::max_walltime = 1
 +  TerminationTrigger::create_termination_file = yes
 +  TerminationTrigger::termination_file = "cactus_terminate"
 +  TerminationTrigger::check_file_every = 1
 +  TerminationTrigger::termination_from_file = yes
 +
 +One of the nice features of this program it is automatically
 +produce CheckPoint every so iteration. Moreover if it finds
 +a CheckPoint automatically restart from it. Also check for walltime
 +and stop accordingly.
 +
 +
 +====== EINSTEIN TOOLKIT on the GRID ======
 +
 +
 +This is a very different application with respect to the "CHROMA" lattice qcd one. 
 +The main difference is that this is a very data-intense application and parallelism
 +is not used to speed up execution but to allow to simulate bigger problem. Where bigger
 +should be indented using increased resolution. This is also an application that would 
 +require an huge amount of data do be saved and transfer once the run is finished.
 +Moreover we will need to restart the simulation more than once in order to overcome
 +the queue wall time limits. That means that we need to save checkpoints !
 +
 +For the above reason the creation of "tar" file with all the data to be moved out
 +the storage elements is not an effective approach.  
 +
 +
 +===== Compiling EINSTEIN TOOLKIT on the GRID =====
 +
 +The compilation procedure can be performed with this simple
 +shell script
 +
 +  #!/bin/bash
 +  ###################################################################
 +  ##  We can compile on a directory that would not be automatically
 +  ##  DELETED once the Jobs end
 +  ###################################################################
 +  umask 007
 +  echo "pwd $(pwd)"
 +  export BaseDir="$(cd ../../../thogea10 ; pwd)/CompileET"
 +  echo "BaseDir= $BaseDir"
 +  mkdir -p ${BaseDir}
 +  cd ${BaseDir}
 +  ## ----------------------------------------
 +  ## First we get the tra file we previously
 +  ## saved on the GRID storage 
 +  ## But we can also use direct FS access
 +  ## ----------------------------------------
 +  export BASESRM=/gpfs/gpfshds/srm/theophys/IS_OG51/Parma/CorsoGrid
 +  tar xzvf ${BASESRM}/Cactus_tree.tgz  
 +  cd Cactus
 +  echo "yes" | \
 +  make Einstein-config F77=gfortran F90=gfortran GSL=yes JPEG=yes SSL=yes  \
 +                     MPI=OpenMPI OPENMPI_DIR=/usr/lib64/openmpi/1.4-gcc/ \
 +                     OPENMP=yes
 +  echo "no" | \
 +  make -j 8 Einstein
 +  lcg-cr -v --vo theophys -d srm://gridsrm.pi.infn.it/theophys/IS_OG51/Parma/CorsoGrid/Einstein.v2  \
 +    -l lfn:/grid/theophys/IS_OG51/Parma/CorsoGrid/Einstein.v2 file://$(pwd)/exe/cactus_Einstein
 + 
 +
 +where should be noted the "make -j 8 Einstein" that would allow us to use all the 8 core we allocated 
 +to compile. A lot of caution should used using this trick because "self made" make sometimes do
 +not always explicitly encode in a proper way all the dependencies.
 +
 +===== Executing the EINSTEIN TOOLKIT on the GRID =====
 +
 +===== A typical script for General Relativistic Hydro Jobs =====
 +
 +But first we may want to have a look to our typical 
 +script ....
 +
 +  !/bin/bash
 +  ### -----------------------------------------------------------------
 +  ###
 +  ###  These are the settings on Tramontana
 +  ###
 +  ### -----------------------------------------------------------------
 +  export LOCALSRM=/gpfs/gpfshds/srm/theophys/IS_OG51/Parma
 +  export CATALOG=lfn:/grid/theophys/IS_OG51/Parma
 +  export SRM=srm://gridsrm.pi.infn.it/theophys/IS_OG51/Parma
 +  export EXECUTABLE=Whisky.exe
 +  ### -----------------------------------------------------------------
 +  ###
 +  ###  Setting to Run Whisky:
 +  ###
 +  ###  We assume that the precompiled exe are already stored on 
 +  ###  Tramonta. The same is assumed for the parameters files
 +  ###
 +  ###  We also needs an area where JOBS are executed and results saved
 +  ### -----------------------------------------------------------------
 +  export DIRpar=${LOCALSRM}/CACTUS/par
 +  export EXEcommand="${EXECUTABLE} $2.par" #${DIRpar}/$2.par"
 +  export DIRcheckpoint=CHECKPOINT/$2
 +  echo "pwd $(pwd)"
 +  export EXPmar11="$(cd ../../../thogea10 ; pwd)/EXPmar11"
 +  echo "EXPmar11= $EXPmar11"
 +  export CACTUSexe="${EXPmar11}/build/Cactus/exe/cactus_EXPmar11"
 +  export CACTUSexe=${LOCALSRM}/CACTUS/exe/WHISKYexp
 +  export LOCALexe=${CACTUSexe}
 +  export executionDIR="${EXPmar11}/run/$2/$1";
 +  umask 007
 +  echo "======================================"
 +  echo "** mkdir -p ${executionDIR}"
 +  echo "** cd ${executionDIR}"
 +  mkdir -p ${executionDIR}
 +  cd ${executionDIR}
 +  echo "======================================"
 +  echo "========= JOB executions ==============="
 +  echo "We will run the exe file: ${EXECUTABLE}"
 +  echo "Copied from: ${LOCALexe}" 
 +  echo "Running command is: ${EXEcommand}"
 +  echo "Recover DIR: ${LOCALSRM}/${DIRcheckpoint} "
 +  echo "========================================"
 +  ln -s /gpfs/gpfshds/csn4home/thogea10/EXPmar11/run/$2/output-0000/CHECKPOINT CHECKPOINT_RECOVER
 +  echo "========================================"
 +  echo "===================================="
 +  sed "s/IO::recover_dir      = \"CHECKPOINT\"/IO::recover_dir      = \"CHECKPOINT_RECOVER\"/" ${DIRpar}/$2.par > $2.par 
 +  cat $2.par
 +  echo "===================================="
 +  ## ------------------------------------
 +  ##  GET and create The MPI nodelist
 +  ## ------------------------------------
 +  NODEFILE1=/tmp/hf1.$(date +"%m%d%y%H%M%S")
 +  NODEFILE2=/tmp/hf2.$(date +"%m%d%y%H%M%S")
 +  RANKFILE=/tmp/hf3.$(date +"%m%d%y%H%M%S")
 +  AWKcommand=/tmp/hf4.$(date +"%m%d%y%H%M%S")
 +  touch $NODEFILE1
 +  touch $NODEFILE2
 +  touch $AWKcommand
 +  # echo "{print \"rank \" i++ \"=\" \$1 \" slot=0-3\"}"   >> $AWKcommand
 +  # echo "{print \"rank \" i++ \"=\" \$1 \" slot=4-7\"}"   >> $AWKcommand
 +  ### -----------------------------------------------------------------
 +  ###  The following setting is for a run with one thread for processor 
 +  ###  Nt is the numer of threads for processor
 +  ### -----------------------------------------------------------------
 +  NT=1
 +  echo "{print \"rank \" i++ \"=\" \$1 \" slot=0\"}"   >> $AWKcommand
 +  echo "{print \"rank \" i++ \"=\" \$1 \" slot=1\"}"   >> $AWKcommand
 +  echo "{print \"rank \" i++ \"=\" \$1 \" slot=2\"}"   >> $AWKcommand
 +  echo "{print \"rank \" i++ \"=\" \$1 \" slot=3\"}"   >> $AWKcommand
 +  echo "{print \"rank \" i++ \"=\" \$1 \" slot=4\"}"   >> $AWKcommand
 +  echo "{print \"rank \" i++ \"=\" \$1 \" slot=5\"}"   >> $AWKcommand
 +  echo "{print \"rank \" i++ \"=\" \$1 \" slot=6\"}"   >> $AWKcommand
 +  echo "{print \"rank \" i++ \"=\" \$1 \" slot=7\"}"   >> $AWKcommand
 +  for host in $LSB_HOSTS; do echo $host >> $NODEFILE1; done;
 +  sort -u  ${NODEFILE1} > ${NODEFILE2}
 +  awk -f $AWKcommand  ${NODEFILE2} > ${RANKFILE}
 +  NCPU=$[`cat ${NODEFILE1} | wc --lines`]
 +  NNODES=$[`cat ${NODEFILE2} | wc --lines`]
 +  NP=$[`cat ${RANKFILE} | wc --lines`]
 +  MPIRUN="mpirun -np $NP -x OMP_NUM_THREADS=$NT -hostfile $NODEFILE2 --rankfile ${RANKFILE}"
 +  echo "========= MPI PARAMETER ================"
 +  echo "N cpus    = ${NCPU}"
 +  echo "N nodes   = ${NNODES}"
 +  echo "Np  = ${NP}"
 +  echo "Nt  = ${NT}"
 +  echo "mpirun = " $(which mpirun)
 +  echo "MPI --> ${MPIRUN}"
 +  echo "========================================"
 +  echo "** cat  $RANKFILE"
 +  cat   $RANKFILE
 +  echo "========================================"
 +  # echo "** cat  $NODEFILE1"
 +  # cat   $NODEFILE1
 +  # echo "========================================"
 +  echo "** cat  $NODEFILE2"
 +  cat   $NODEFILE2
 +  echo "========================================"
 +  # echo "** cat  $AWKcommand"
 +  # cat   $AWKcommand
 +  # echo "========================================"
 +  echo "** cleaning previous open-mpi leftover"
 +  echo "** mpirun --pernode  --hostfile $NODEFILE2 orte-clean --verbose"
 +  mpirun --pernode  --hostfile $NODEFILE2 orte-clean --verbose
 +  echo "========================================"
 +  echo "======================================"
 +  echo "I'm running here [$(pwd)]" | tee OUTPUT
 +  echo "======================================"
 +  ls -l
 +  pwd
 +  ### -----------------------------------------------------------------
 +  ### First I copy the executable to be run on the working directory
 +  ### and change attribute in such a way that I can execute it
 +  ### -----------------------------------------------------------------
 +  cp ${LOCALexe} ${EXECUTABLE}
 +  chmod +x ${EXECUTABLE}
 +  echo "**************************************************"
 +  echo "**(TIME)  START: " $(date)
 +  echo "**************************************************"
 +  ### -----------------------------------------------------------------
 +  ### HERE GOES THE ACTUAL EXECUTIONS COMMAND 
 +  ### -----------------------------------------------------------------
 +  runCMD="${MPIRUN} ${EXEcommand} 2>&1 | tee -a RunTrace.out"
 +  echo "----------------------------- Command ----------------"
 +  echo "-- executing: ${runCMD}"
 +  eval ${runCMD}
 +  echo "$runCMD = ${runCMD}"
 +  echo "----------------------------- Command END ------------"
 +  chmod -R g+rwX data
 +  chmod -R g+rwX CHECKPOINT
 +  echo "**************************************************"
 +  echo "**(TIME)   STOP: " $(date)
 +  echo "**************************************************"
 +  ## ------------------------------------
 +  # Save the result file from the WN  to the SE
 +  ## ------------------------------------
 +  rm  ${EXECUTABLE}
 +  rm  ${RANKFILE}
 +  rm  ${NODEFILE1}
 +  rm  ${NODEFILE2}
 +  rm  ${AWKcommand}
 +
 +And you may find it particularly involved. But that is becouse we like
 +to share acces to more that one member of the group to the data and
 +the ability to run various step of the simulation.
 +
 +
 +
 +
 +
 +====== EINSTEIN TOOLKIT on the GRID (mpi-start)======
 +
 +The mpi-start automatically takes care of mixed OMP/MPI parallelism
 +and will greatly simplify MPI job submission.    
 +
 +
 +
 +
 +===== Execution on the PARMA cluster (no INFINIBAND) =====
 +
 +RunET_PR.jdl
 +
 +  # RunET_PR.jdl
 +  JobType = "Normal";
 +  CPUNumber = 1;
 +  Executable    = "RunET_PR.sh";
 +  Arguments     = "static_tov NODE";
 +  StdOutput     = "std.out";
 +  StdError      = "std.err";
 +  PerusalFileEnable = true;
 +  PerusalTimeInterval = 10;
 +  InputSandbox  = {"RunET_PR.sh"}; 
 +  OutputSandbox = {"std.out", "std.err"};
 +  MyProxyServer = "myproxy.cnaf.infn.it";
 +  Requirements=(other.GlueCEUniqueID=="cream-ce.pr.infn.it:8443/cream-pbs-parallel");
 +  CeRequirements = "hostsmpsize==8 &&  wholenodes==\"true\"  && hostnumber==1";
 +
 +RunET_PR.sh
 +
 +  #!/bin/bash
 +  ###################################################################
 +  ##  We can compile on a directory that would not be automatically
 +  ##  DELETED once the Jobs end
 +  ###################################################################
 +  umask 007
 +  echo "pwd $(pwd)"
 +  export BaseDir="$(cd ../../../theophys/IS_OG51 ; pwd)/RunET/$1/$2"
 +  echo "BaseDir= $BaseDir"
 +  mkdir -p ${BaseDir}
 +  cd ${BaseDir}
 +  ## ----------------------------------------
 +  ## First we get the tra file we previously
 +  ## saved on the GRID storage 
 +  ## But we can also use direct FS access
 +  ## ----------------------------------------
 +  export LFN=lfn:/grid/theophys/IS_OG51/Parma/CorsoGrid
 +  lcg-cp -v --vo theophys ${LFN}/Einstein.v2.PR file://$(pwd)/Einstein
 +  lcg-cp -v --vo theophys ${LFN}/$1.par file://$(pwd)/$1.par
 +  chmod +x Einstein
 +  if [  "x${2}" = "xCORE" ] ;then 
 +    echo CORE  
 +    mpi-start -t openmpi -pcore -d MPI_USE_AFFINITY=1 -d MPI_USE_OMP=1  -vv -- ./Einstein $1.par 
 +  else if [ "x${2}" = "xNODE" ]; then  
 +    echo NODE
 +    mpi-start -t openmpi -pnode -d MPI_USE_AFFINITY=1 -d MPI_USE_OMP=1  -vv -- ./Einstein $1.par 
 +  else if [ "x${2}" = "xSOCKET" ]; then  
 +    echo SOCKET
 +    mpi-start -t openmpi -psocket -d MPI_USE_AFFINITY=1 -d MPI_USE_OMP=1  -vv -- ./Einstein $1.par 
 +  else
 +    echo NONE
 +    ./Einstein $1.par 
 +  fi
 +  fi
 +  fi
 +
 +This allow to check which kind of parallelization should
 +be preferred.
 +
 +  Np 1 Nt 8 N. iterations in 1 hour 11776
 +  Np 2 Nt 4 N. iterations in 1 hour 16256
 +  Np 8 Nt 1 N. iterations in 1 hour 10464
 +
 +Doing the same at double resolution (the size of the problem is
 +8 times bigger since we are doing a 3D simulation) 
 +
 +  8xSIZE Np 1 Nt 8 N. iterations in 1 hour 2624
 +  8xSIZE Np 2 Nt 4 N. iterations in 1 hour 3072
 +  8xSIZE Np 8 Nt 1 N. iterations in 1 hour 3072
 +
 +The scaling is never perfect !
 +
  
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