Task: Implement util/mergeCarpetIOScalar.pl for Carpet/CarpetIOScalar thorn

thorn_name: Carpet/CarpetIOScalar
src_filename: util/mergeCarpetIOScalar.pl
interface: # Interface definition for thorn CarpetIOScalar

IMPLEMENTS: IOScalar

CCTK_INT last_output_iteration TYPE=scalar
CCTK_REAL last_output_time TYPE=scalar
CCTK_INT this_iteration TYPE=scalar

USES INCLUDE HEADER: Timer.hh

USES INCLUDE HEADER: carpet.hh
USES INCLUDE HEADER: typecase.hh
USES INCLUDE HEADER: typeprops.hh

# function to check whether existing output files should be truncated or not
CCTK_INT FUNCTION IO_TruncateOutputFiles \
  (CCTK_POINTER_TO_CONST IN GH)

REQUIRES FUNCTION IO_TruncateOutputFiles



# Return a pointer to an unmodifiable C string
# which contains a unique ID for this build
CCTK_POINTER_TO_CONST \
FUNCTION UniqueBuildID (CCTK_POINTER_TO_CONST IN  cctkGH)
USES FUNCTION UniqueBuildID

# Return a pointer to an unmodifiable C string
# which contains a unique ID for this simulation
CCTK_POINTER_TO_CONST \
FUNCTION UniqueSimulationID (CCTK_POINTER_TO_CONST IN  cctkGH)
USES FUNCTION UniqueSimulationID

# Return a pointer to an unmodifiable C string
# which contains a unique ID for this run
CCTK_POINTER_TO_CONST \
FUNCTION UniqueRunID (CCTK_POINTER_TO_CONST IN  cctkGH)
USES FUNCTION UniqueRunID

schedule: # Schedule definitions for thorn CarpetIOScalar

storage: last_output_iteration last_output_time this_iteration

schedule CarpetIOScalarStartup at STARTUP after IOUtil_Startup
{
  LANG: C
  OPTIONS: global
} "Startup routine"

schedule CarpetIOScalarInit at INITIAL
{
  LANG: C
  OPTIONS: global
} "Initialisation routine"

param: # Parameter definitions for thorn CarpetIOScalar



shares: IO

USES STRING out_dir

USES KEYWORD out_criterion
USES CCTK_INT out_every
USES CCTK_REAL out_dt

USES BOOLEAN strict_io_parameter_check
USES KEYWORD verbose
USES KEYWORD out_fileinfo
USES STRING out_group_separator



private:



BOOLEAN one_file_per_group "Write one file per group instead of per variable"
{
} "no"

BOOLEAN all_reductions_in_one_file "Write all requested reductions in one file instead of per reduction"
{
} "no"



INT out_precision "How many digits to output floating-point numbers with" STEERABLE = ALWAYS
{
  0:* :: "Number of precision digits"
} 15



CCTK_STRING outScalar_dir "Name of scalar output directory, overrides out_dir" STEERABLE = ALWAYS
{
  "^$" :: "Empty: use IO::out_dir"
  ".+" :: "Not empty: directory name"
} ""

CCTK_STRING outScalar_vars "Variables to output in scalar form" STEERABLE = ALWAYS
{
  "" :: "A regex which matches everything"
} ""

CCTK_STRING outScalar_reductions "List of reductions to output in scalar form" STEERABLE = ALWAYS
{
  "" :: "A regex which matches everything"
} "count minimum maximum sum average norm1 norm2 norm_inf icount iaverage inorm1 inorm2"



KEYWORD outScalar_criterion "Criterion to select scalar output intervals, overrides out_every" STEERABLE = ALWAYS
{
  "never"     :: "Never output"
  "iteration" :: "Output every so many iterations"
  "divisor"   :: "Output if iteration mod divisor == 0."
  "time"      :: "Output every that much coordinate time"
} "iteration"

CCTK_INT outScalar_every "How often to do scalar output, overrides IO::out_every" STEERABLE = ALWAYS
{
   1:* :: "Output every so many time steps"
  -1:0 :: "No output"
  -2   :: "Default to IO::out_every"
} -2

REAL outScalar_dt "How often to do scalar output, overrides out_dt" STEERABLE = ALWAYS
{
  (0:* :: "In intervals of that much coordinate time"
   0   :: "As often as possible"
  -1   :: "Disable output"
  -2   :: "Default to IO::out_dt"
} -2

configuration: # Configuration definitions for thorn CarpetIOScalar

REQUIRES Carpet CarpetLib IOUtil

context: make.code.defn:
```
# Main make.code.defn file for thorn CarpetIOScalar

# Source files in this directory
SRCS = ioscalar.cc

# Subdirectories containing source files
SUBDIRS = 

```

ioscalar.cc:
```
#include <cassert>
#include <cctype>
#include <cstdlib>
#include <cstring>
#include <fstream>
#include <iomanip>
#include <list>
#include <sstream>
#include <string>
#include <vector>

#include <cctk.h>
#include <cctk_Arguments.h>
#include <cctk_Parameters.h>
#include <util_Network.h>

#include <Timer.hh>

#include "CactusBase/IOUtil/src/ioGH.h"
#include "CactusBase/IOUtil/src/ioutil_Utils.h"

#include "carpet.hh"

#include "typeprops.hh"

// That's a hack
namespace Carpet {
void UnsupportedVarType(const int vindex);
}

namespace CarpetIOScalar {

using namespace std;
using namespace Carpet;

// Definition of local types
struct info {
  string reduction;
  int handle;
};

// Begin a new line without flushing the output buffer
char const *const eol = "\n";

// Registered functions
static void *SetupGH(tFleshConfig *fc, int convLevel, cGH *cctkGH);
static int OutputGH(const cGH *cctkGH);
static int OutputVarAs(const cGH *cctkGH, const char *varname,
                       const char *alias);
static int OutputVarAs(const cGH *cctkGH, const char *varname,
                       const char *alias, const char *out_reductions);
static int TimeToOutput(const cGH *cctkGH, int vindex);
static int TriggerOutput(const cGH *cctkGH, int vindex);

// Internal functions
#if 0
  static void SetFlag (int index, const char* optstring, void* arg);
#endif
static void CheckSteerableParameters(const cGH *const cctkGH,
                                     bool first_time = false);

// Definition of static members
vector<bool> do_truncate;
vector<bool> reductions_changed;
vector<int> last_output;

/* CarpetScalar GH extension structure */
static struct {
  /* list of variables to output */
  char *out_vars;

  /* reductions to apply */
  char *out_reductions;
  char **var_reductions;

  /* stop on I/O parameter parsing errors ? */
  int stop_on_parse_errors;

  /* I/O request description list (for all variables) */
  ioRequest **requests;
} IOparameters;

extern "C" int CarpetIOScalarStartup() {
  CCTK_RegisterBanner("AMR scalar I/O provided by CarpetIOScalar");

  int GHExtension = CCTK_RegisterGHExtension("CarpetIOScalar");
  CCTK_RegisterGHExtensionSetupGH(GHExtension, SetupGH);

  int IOMethod = CCTK_RegisterIOMethod("CarpetIOScalar");
  CCTK_RegisterIOMethodOutputGH(IOMethod, OutputGH);
  CCTK_RegisterIOMethodOutputVarAs(IOMethod, OutputVarAs);
  CCTK_RegisterIOMethodTimeToOutput(IOMethod, TimeToOutput);
  CCTK_RegisterIOMethodTriggerOutput(IOMethod, TriggerOutput);

  return 0;
}

extern "C" void CarpetIOScalarInit(CCTK_ARGUMENTS) {
  DECLARE_CCTK_ARGUMENTS;

  *this_iteration = 0;
  *last_output_iteration = 0;
  *last_output_time = cctkGH->cctk_time;
}

void *SetupGH(tFleshConfig *const fc, int const convLevel, cGH *const cctkGH) {
  DECLARE_CCTK_PARAMETERS;
  const void *dummy;

  dummy = &fc;
  dummy = &convLevel;
  dummy = &cctkGH;
  dummy = &dummy;

  // Truncate all files if this is not a restart
  const int numvars = CCTK_NumVars();
  do_truncate.resize(numvars, true);
  reductions_changed.resize(numvars, false);

  // No iterations have yet been output
  last_output.resize(numvars, -1);

  IOparameters.requests = (ioRequest **)calloc(numvars, sizeof(ioRequest *));
  IOparameters.out_vars = strdup("");
  IOparameters.out_reductions = strdup("");
  IOparameters.var_reductions = (char **)calloc(numvars, sizeof(char *));

  // initial I/O parameter check
  IOparameters.stop_on_parse_errors = strict_io_parameter_check;
  CheckSteerableParameters(cctkGH, true);
  IOparameters.stop_on_parse_errors = 0;

  // We register only once, ergo we get only one handle.  We store
  // that statically, so there is no need to pass anything to
  // Cactus.
  return NULL;
}

int OutputGH(const cGH *const cctkGH) {
  static Timers::Timer timer("OutputGH");
  timer.start();
  CheckSteerableParameters(cctkGH);
  if (strcmp(IOparameters.out_vars, "")) {
    for (int vindex = 0; vindex < CCTK_NumVars(); ++vindex) {
      if (TimeToOutput(cctkGH, vindex)) {
        TriggerOutput(cctkGH, vindex);
      }
    }
  }
  timer.stop();
  return 0;
}

int OutputVarAs(const cGH *const cctkGH, const char *const varname,
                const char *const alias) {
  DECLARE_CCTK_PARAMETERS;

  int const retval = OutputVarAs(cctkGH, varname, alias, outScalar_reductions);

  return retval;
}

int OutputVarAs(const cGH *const cctkGH, const char *const varname,
                const char *const alias, const char *out_reductions) {
  DECLARE_CCTK_ARGUMENTS;
  DECLARE_CCTK_PARAMETERS;

  assert(is_level_mode() or (is_singlemap_mode() and maps == 1) or
         (is_local_mode() and maps == 1 and
          vhh.at(Carpet::map)->local_components(reflevel) == 1));
  BEGIN_LEVEL_MODE(cctkGH) {

    const int n = CCTK_VarIndex(varname);
    if (n < 0) {
      CCTK_VWarn(1, __LINE__, __FILE__, CCTK_THORNSTRING,
                 "Variable \"%s\" does not exist", varname);
      return -1;
    }
    assert(n >= 0 and n < CCTK_NumVars());
    const int group = CCTK_GroupIndexFromVarI(n);
    assert(group >= 0 and group < (int)Carpet::arrdata.size());
    const int n0 = CCTK_FirstVarIndexI(group);
    assert(n0 >= 0 and n0 < CCTK_NumVars());
    const int var = n - n0;
    assert(var >= 0 and var < CCTK_NumVarsInGroupI(group));
    const int num_tl = CCTK_MaxActiveTimeLevelsVI(cctkGH, n);
    assert(num_tl >= 1);

    // Check for storage
    if (not CCTK_QueryGroupStorageI(cctkGH, group)) {
      CCTK_VWarn(1, __LINE__, __FILE__, CCTK_THORNSTRING,
                 "Cannot output variable \"%s\" because it has no storage",
                 varname);
      return 0;
    }

    assert(do_global_mode);

    const int vartype = CCTK_VarTypeI(n);
    assert(vartype >= 0);

    // Get grid hierarchy extentsion from IOUtil
    const ioGH *const iogh = (const ioGH *)CCTK_GHExtension(cctkGH, "IO");
    assert(iogh);

    // Create the output directory
    const char *myoutdir = outScalar_dir;
    if (CCTK_EQUALS(myoutdir, "")) {
      myoutdir = out_dir;
    }
    int const iret = IOUtil_CreateDirectory(cctkGH, myoutdir, 0, 0);
    if (iret < 0) {
      CCTK_VWarn(1, __LINE__, __FILE__, CCTK_THORNSTRING,
                 "Could not create output directory \"%s\"", myoutdir);
    } else if (CCTK_Equals(verbose, "full")) {
      static bool firsttime = true;
      if (firsttime and iret > 0) {
        CCTK_VInfo(CCTK_THORNSTRING, "Output directory \"%s\" exists already",
                   myoutdir);
      } else if (not firsttime and iret == 0) {
        CCTK_VInfo(CCTK_THORNSTRING, "Created output directory \"%s\"",
                   myoutdir);
      }
      firsttime = false;
    }

    // Find the set of desired reductions
    list<info> reductions;
    string const redlist(out_reductions);
    string::const_iterator p = redlist.begin();
    while (p != redlist.end()) {
      while (p != redlist.end() and isspace(*p))
        ++p;
      if (p == redlist.end())
        break;
      string::const_iterator const start = p;
      while (p != redlist.end() and not isspace(*p))
        ++p;
      string::const_iterator const end = p;
      string const reduction(start, end);
      int const handle = CCTK_ReductionHandle(reduction.c_str());
      if (handle < 0) {
        CCTK_VWarn(1, __LINE__, __FILE__, CCTK_THORNSTRING,
                   "Reduction operator \"%s\" does not exist (maybe there is "
                   "no reduction thorn active?)",
                   reduction.c_str());
      } else {
        info i;
        i.reduction = reduction;
        i.handle = handle;
        reductions.push_back(i);
      }
    }

    // Output in global mode
    BEGIN_GLOBAL_MODE(cctkGH) {

      // single fstreams object used for all output files.
      // This violates resource-allocation-is-initialization but is required
      // when outputting all reductions into a single file (in which case there
      // is only a single stream)
      fstream file;
      CCTK_REAL io_files = 0;
      CCTK_REAL io_bytes_begin = 0, io_bytes_end = 0;
      if (all_reductions_in_one_file) {
        BeginTimingIO(cctkGH);
      }

      for (list<info>::const_iterator ireduction = reductions.begin();
           ireduction != reductions.end(); ++ireduction) {
        string const reduction = ireduction->reduction;

        if (not all_reductions_in_one_file) {
          BeginTimingIO(cctkGH);
          io_files = 0;
          io_bytes_begin = 0;
          io_bytes_end = 0;
        }
        if (CCTK_MyProc(cctkGH) == 0) {

          bool created_file = false;

          if (not all_reductions_in_one_file || not file.is_open()) {
            // Invent a file name
            ostringstream filenamebuf;
            filenamebuf << myoutdir << "/" << alias;
            if (not all_reductions_in_one_file)
              filenamebuf << "." << reduction;
            else
              filenamebuf << ".scalars";
            filenamebuf << ".asc";
            // we need a persistent temporary here
            string filenamestr = filenamebuf.str();
            const char *const filename = filenamestr.c_str();

            if (do_truncate.at(n) and IO_TruncateOutputFiles(cctkGH)) {
              file.open(filename, ios::out | ios::trunc);
            } else {
              file.open(filename, ios::out | ios::app);
            }
            if (not file.good()) {
              CCTK_VWarn(
                  0, __LINE__, __FILE__, CCTK_THORNSTRING,
                  "Could not open output file \"%s\" for variable \"%s\"",
                  filename, varname);
            }
            assert(file.is_open());

            // first time we open this file if do_truncate is true
            // TODO: add the logic of DidOoutput from IOASCII
            created_file = do_truncate.at(n);

            io_files += 1;
          }
          io_bytes_begin = file.tellg();

          // write header if reductions changed or we create a new file
          if (created_file or reductions_changed.at(n)) {
            bool want_labels = false;
            bool want_date = false;
            bool want_parfilename = false;
            bool want_other = false;
            if (CCTK_EQUALS(out_fileinfo, "none")) {
              // do nothing
            } else if (CCTK_EQUALS(out_fileinfo, "axis labels")) {
              want_labels = true;
            } else if (CCTK_EQUALS(out_fileinfo, "creation date")) {
              want_date = true;
            } else if (CCTK_EQUALS(out_fileinfo, "parameter filename")) {
              want_parfilename = true;
            } else if (CCTK_EQUALS(out_fileinfo, "all")) {
              want_labels = true;
              want_date = true;
              want_parfilename = true;
              want_other = true;
            } else {
              CCTK_WARN(0, "internal error");
            }
            file << "# Scalar ASCII output created by CarpetIOScalar" << eol;
            if (want_date) {
              char run_host[1000];
              Util_GetHostName(run_host, sizeof run_host);
              char const *run_user = getenv("USER");
              if (not run_user) {
                run_user = "";
              }
              char run_date[1000];
              Util_CurrentDate(sizeof run_date, run_date);
              char run_time[1000];
              Util_CurrentTime(sizeof run_time, run_time);
              file << "# created on " << run_host << " by " << run_user
                   << " on " << run_date << " at " << run_time << eol;
            }
            if (want_parfilename) {
              char parameter_filename[10000];
              CCTK_ParameterFilename(sizeof parameter_filename,
                                     parameter_filename);
              file << "# parameter filename: \"" << parameter_filename << "\""
                   << eol;
            }
            if (want_other) {
              if (CCTK_IsFunctionAliased("UniqueBuildID")) {
                char const *const build_id =
                    (char const *)UniqueBuildID(cctkGH);
                file << "# Build ID: " << build_id << eol;
              }
              if (CCTK_IsFunctionAliased("UniqueSimulationID")) {
                char const *const job_id =
                    static_cast<char const *>(UniqueSimulationID(cctkGH));
                file << "# Simulation ID: " << job_id << eol;
              }
              if (CCTK_IsFunctionAliased("UniqueRunID")) {
                char const *const job_id =
                    static_cast<char const *>(UniqueRunID(cctkGH));
                file << "# Run ID: " << job_id << eol;
              }
            }
            file << "#" << eol;
            if (want_labels) {
              file << "# " << varname << " (" << alias << ")" << eol;
              file << "# 1:iteration 2:time 3:data" << eol;
              int col = 3;
              if (one_file_per_group or all_reductions_in_one_file) {
                file << "# data columns:";
                int const firstvar =
                    one_file_per_group ? CCTK_FirstVarIndexI(group) : n;
                int const numvars =
                    one_file_per_group ? CCTK_NumVarsInGroupI(group) : 1;
                list<info>::const_iterator first_reduction =
                    all_reductions_in_one_file ? reductions.begin()
                                               : ireduction;
                list<info>::const_iterator end_reduction =
                    all_reductions_in_one_file
                        ? reductions.end()
                        : ++list<info>::const_iterator(ireduction);
                for (list<info>::const_iterator jreduction = first_reduction;
                     jreduction != end_reduction; ++jreduction) {
                  for (int n = firstvar; n < firstvar + numvars; ++n) {
                    file << " " << col << ":" << CCTK_VarName(n);
                    if (all_reductions_in_one_file)
                      file << "(" << jreduction->reduction << ")";
                    col += CarpetSimpleMPIDatatypeLength(vartype);
                  }
                }
                file << eol;
              }
            }

            // Don't write header again (unless the reductions change)
            reductions_changed.at(n) = false;
          }

          file << setprecision(out_precision);
          assert(file.good());

        } // if on the root processor

        if (CCTK_MyProc(cctkGH) == 0) {
          if (not all_reductions_in_one_file or
              ireduction == reductions.begin()) {
            file << cctk_iteration << " " << cctk_time;
          }
        }

        int const handle = ireduction->handle;

        char result[100]; // assuming no type is larger

        int const firstvar =
            one_file_per_group ? CCTK_FirstVarIndexI(group) : n;
        int const numvars =
            one_file_per_group ? CCTK_NumVarsInGroupI(group) : 1;

        for (int n = firstvar; n < firstvar + numvars; ++n) {

          int const ierr =
              CCTK_Reduce(cctkGH, 0, handle, 1, vartype, result, 1, n);
          if (ierr) {
            char *const fullname = CCTK_FullName(n);
            CCTK_VWarn(1, __LINE__, __FILE__, CCTK_THORNSTRING,
                       "Error during reduction for variable \"%s\"", fullname);
            free(fullname);
            memset(result, 0, sizeof result);
          }

          if (CCTK_MyProc(cctkGH) == 0) {
            file << " ";

            switch (specific_cactus_type(vartype)) {
#define CARPET_NO_COMPLEX
#define TYPECASE(N, T)                                                         \
  case N:                                                                      \
    file << *(T const *)result;                                                \
    break;
#include "typecase.hh"
#undef TYPECASE
#undef CARPET_NO_COMPLEX
#define CARPET_COMPLEX
#define TYPECASE(N, T)                                                         \
  case N:                                                                      \
    file << real(*(T const *)result) << " " << imag(*(T const *)result);       \
    break;
#include "typecase.hh"
#undef TYPECASE
#undef CARPET_COMPLEX
            default:
              UnsupportedVarType(n);
            }
          }

        } // for n

        if (not all_reductions_in_one_file) {
          if (CCTK_MyProc(cctkGH) == 0) {
            file << eol;
            assert(file.good());

            io_bytes_end = file.tellg();
            file.close();
            assert(file.good());
          }

          assert(not file.is_open());

          CCTK_REAL const io_bytes = io_bytes_end - io_bytes_begin;
          EndTimingIO(cctkGH, io_files, io_bytes, false);
        }

      } // for reductions

      if (all_reductions_in_one_file) {
        if (CCTK_MyProc(cctkGH) == 0) {
          file << eol;
          assert(file.good());

          io_bytes_end = file.tellg();
          file.close();
          assert(file.good());
        }

        assert(not file.is_open());

        CCTK_REAL const io_bytes = io_bytes_end - io_bytes_begin;
        EndTimingIO(cctkGH, io_files, io_bytes, false);
      }

      assert(not file.is_open());
    }
    END_GLOBAL_MODE;

    // Don't truncate again, this is a per-variable setting, not a
    // per-file setting so it cannot be moved inside of the loop over
    // reductions
    do_truncate.at(n) = false;
  }
  END_LEVEL_MODE;

  return 0;
}

int TimeToOutput(const cGH *const cctkGH, int const vindex) {
  DECLARE_CCTK_ARGUMENTS;
  DECLARE_CCTK_PARAMETERS;

  assert(vindex >= 0 and vindex < CCTK_NumVars());

  if (not do_global_mode)
    return 0;

  // check if output for this variable was requested
  if (not IOparameters.requests[vindex]) {
    return (0);
  }

  // check whether to output at this iteration
  bool output_this_iteration;

  const char *myoutcriterion = outScalar_criterion;
  if (CCTK_EQUALS(myoutcriterion, "default")) {
    myoutcriterion = out_criterion;
  }

  if (CCTK_EQUALS(myoutcriterion, "never")) {

    // Never output
    output_this_iteration = false;

  } else if (CCTK_EQUALS(myoutcriterion, "iteration")) {

    int myoutevery = outScalar_every;
    if (myoutevery == -2) {
      myoutevery = out_every;
    }
    if (myoutevery <= 0) {
      // output is disabled
      output_this_iteration = false;
    } else if (cctk_iteration == *this_iteration) {
      // we already decided to output this iteration
      output_this_iteration = true;
    } else if (cctk_iteration >= *last_output_iteration + myoutevery) {
      // it is time for the next output
      output_this_iteration = true;
      *last_output_iteration = cctk_iteration;
      *this_iteration = cctk_iteration;
    } else {
      // we want no output at this iteration
      output_this_iteration = false;
    }

  } else if (CCTK_EQUALS(myoutcriterion, "divisor")) {

    int myoutevery = outScalar_every;
    if (myoutevery == -2) {
      myoutevery = out_every;
    }
    if (myoutevery <= 0) {
      // output is disabled
      output_this_iteration = false;
    } else if ((cctk_iteration % myoutevery) == 0) {
      // we already decided to output this iteration
      output_this_iteration = true;
    } else {
      // we want no output at this iteration
      output_this_iteration = false;
    }

  } else if (CCTK_EQUALS(myoutcriterion, "time")) {

    CCTK_REAL myoutdt = outScalar_dt;
    if (myoutdt == -2) {
      myoutdt = out_dt;
    }
    if (myoutdt < 0) {
      // output is disabled
      output_this_iteration = false;
    } else if (myoutdt == 0) {
      // output all iterations
      output_this_iteration = true;
    } else if (cctk_iteration == *this_iteration) {
      // we already decided to output this iteration
      output_this_iteration = true;
    } else {
      int do_output =
          (cctk_time / cctk_delta_time >=
           (*last_output_time + myoutdt) / cctk_delta_time - 1.0e-12);
      MPI_Bcast(&do_output, 1, MPI_INT, 0, dist::comm());
      if (do_output) {
        // it is time for the next output
        output_this_iteration = true;
        *last_output_time = cctk_time;
        *this_iteration = cctk_iteration;
      } else {
        // we want no output at this iteration
        output_this_iteration = false;
      }
    }

  } else {

    assert(0);

  } // select output criterion

  if (not output_this_iteration)
    return 0;

#if 0
    // check which variables to output
    static vector<bool> output_variables;
    static int output_variables_iteration = -1;

    if (cctk_iteration > output_variables_iteration) {
      output_variables.resize (CCTK_NumVars());

      const char* const varlist = outScalar_vars;
      if (CCTK_TraverseString (varlist, SetFlag, &output_variables,
                               CCTK_GROUP_OR_VAR) < 0)
      {
        CCTK_WARN (output_variables_iteration < 0 and strict_io_parameter_check ?
                   0 : 1,
                   "error while parsing parameter 'IOScalar::outScalar_vars'");
      }

      output_variables_iteration = cctk_iteration;
    }

    if (not output_variables.at(vindex)) return 0;
#endif

  if (last_output.at(vindex) == cctk_iteration) {
    // Has already been output during this iteration
    char *const varname = CCTK_FullName(vindex);
    CCTK_VWarn(5, __LINE__, __FILE__, CCTK_THORNSTRING,
               "Skipping output for variable \"%s\", because this variable "
               "has already been output during the current iteration -- "
               "probably via a trigger during the analysis stage",
               varname);
    free(varname);
    return 0;
  }

  assert(last_output.at(vindex) < cctk_iteration);

  // Should be output during this iteration
  return 1;
}

int TriggerOutput(const cGH *const cctkGH, int const vindex) {
  DECLARE_CCTK_ARGUMENTS;
  DECLARE_CCTK_PARAMETERS;

  assert(vindex >= 0 and vindex < CCTK_NumVars());

  // use individual reductions list for this variable when given
  // otherwise IOScalar::outScalar_reductions
  const char *out_reductions = IOparameters.requests[vindex]->reductions;
  if (not out_reductions)
    out_reductions = outScalar_reductions;

  int retval;

  if (one_file_per_group) {

    char *const fullname = CCTK_FullName(vindex);
    int const gindex = CCTK_GroupIndexFromVarI(vindex);
    char *const groupname_c = CCTK_GroupName(gindex);
    string groupname(groupname_c);
    transform(groupname.begin(), groupname.end(), groupname.begin(), ::tolower);
    string const oldsep("::");
    size_t const oldseppos = groupname.find(oldsep);
    assert(oldseppos != string::npos);
    groupname.replace(oldseppos, oldsep.size(), out_group_separator);
    retval = OutputVarAs(cctkGH, fullname, groupname.c_str(), out_reductions);
    free(fullname);

    int const firstvar = CCTK_FirstVarIndexI(gindex);
    int const numvars = CCTK_NumVarsInGroupI(gindex);
    for (int n = firstvar; n < firstvar + numvars; ++n) {
      last_output.at(n) = cctk_iteration;
    }

  } else {

    char *const fullname = CCTK_FullName(vindex);
    char const *const varname = CCTK_VarName(vindex);
    retval = OutputVarAs(cctkGH, fullname, varname, out_reductions);
    free(fullname);

    last_output.at(vindex) = cctk_iteration;
  }

  return retval;
}

static void CheckSteerableParameters(const cGH *const cctkGH, bool first_time) {
  DECLARE_CCTK_PARAMETERS;

  const int numvars = CCTK_NumVars();

  // re-parse the 'IOScalar::outScalar_vars' parameter if it has changed
  if (strcmp(outScalar_vars, IOparameters.out_vars)) {
#ifdef IOUTIL_PARSER_HAS_OUT_DT
    IOUtil_ParseVarsForOutput(cctkGH, CCTK_THORNSTRING,
                              "IOScalar::outScalar_vars",
                              IOparameters.stop_on_parse_errors, outScalar_vars,
                              -1, -1.0, IOparameters.requests);
#else
    IOUtil_ParseVarsForOutput(cctkGH, CCTK_THORNSTRING,
                              "IOScalar::outScalar_vars",
                              IOparameters.stop_on_parse_errors, outScalar_vars,
                              -1, IOparameters.requests);
#endif

    // notify the user about the new setting
    if (not CCTK_Equals(verbose, "none")) {
      int count = 0;
      ostringstream msg;
      msg << "Periodic scalar output requested for:";
      for (int vi = 0; vi < CCTK_NumVars(); ++vi) {
        if (IOparameters.requests[vi]) {
          ++count;
          char *const fullname = CCTK_FullName(vi);
          msg << eol << "   " << fullname;
          free(fullname);
        }
      }
      if (count > 0) {
        CCTK_INFO(msg.str().c_str());
      }
    }

    // save the last setting of 'IOScalar::outScalar_vars' parameter
    free(IOparameters.out_vars);
    IOparameters.out_vars = strdup(outScalar_vars);

    for (int vi = 0; vi < numvars; ++vi) {
      if (not IOparameters.requests[vi])
        continue;

      // if the setting differ copy the setting (NULL or string) into
      // IOparameters
      if ((IOparameters.requests[vi]->reductions and
           not IOparameters.var_reductions[vi]) or
          (not IOparameters.requests[vi]->reductions and
           IOparameters.var_reductions[vi]) or
          (IOparameters.requests[vi]->reductions and
           IOparameters.var_reductions[vi] and
           strcmp(IOparameters.requests[vi]->reductions,
                  IOparameters.var_reductions[vi]))) {
        if (not IOparameters.var_reductions[vi]) {
          free(IOparameters.var_reductions[vi]);
        }
        IOparameters.var_reductions[vi] =
            IOparameters.requests[vi]->reductions
                ? strdup(IOparameters.requests[vi]->reductions)
                : NULL;
        // only all_reductions_in_one_file actually mentions the reduction in
        // the header
        // we must ignore the initial change when we first learn of
        // requested reductions. This means no header is generated if
        // a checkpoint-recovery changes the reductions.
        // TODO: re-write header in one_file_per_group mode if variables change
        reductions_changed[vi] = all_reductions_in_one_file and not first_time;
      }
    }
  }

  if (strcmp(outScalar_reductions, IOparameters.out_reductions)) {
    // save the last seeting of 'IOScalar::outScalar_reductions' parameter
    free(IOparameters.out_reductions);
    IOparameters.out_reductions = strdup(outScalar_reductions);
    // bit of an overkill. We ask for new headers for all variables, even though
    // the ones using per-variable reductions will not have differing headers
    for (int vi = 0; vi < numvars; ++vi) {
      // only all_reductions_in_one_file actually mentions the reduction in the
      // header
      // we must ignore the initial change when we first learn of
      // requested reductions. This means no header is generated if
      // a checkpoint-recovery changes the reductions.
      reductions_changed[vi] = all_reductions_in_one_file and not first_time;
    }
  }
}

#if 0
  void
  SetFlag (int const index, const char * const optstring, void * const arg)
  {
    const void *dummy;

    dummy = &optstring;
    dummy = &dummy;

    vector<bool>& flags = *(vector<bool>*)arg;
    flags.at(index) = true;
  }
#endif

} // namespace CarpetIOScalar

```


combined_doc_context: ## README (README):
```
Cactus Code Thorn CarpetIOScalar
Author(s)    : Erik Schnetter <schnetter@cct.lsu.edu>
Maintainer(s): Erik Schnetter <schnetter@cct.lsu.edu>
Licence      : GPLv2+
--------------------------------------------------------------------------

1. Purpose

This thorn provides scalar output for Carpet.

```

## Documentation (.tex files):
Files: documentation.tex

```tex
=== documentation.tex ===
% *======================================================================*
%  Cactus Thorn template for ThornGuide documentation
%  Author: Ian Kelley
%  Date: Sun Jun 02, 2002
%
%  Thorn documentation in the latex file doc/documentation.tex
%  will be included in ThornGuides built with the Cactus make system.
%  The scripts employed by the make system automatically include
%  pages about variables, parameters and scheduling parsed from the
%  relevant thorn CCL files.
%
%  This template contains guidelines which help to assure that your
%  documentation will be correctly added to ThornGuides. More
%  information is available in the Cactus UsersGuide.
%
%  Guidelines:
%   - Do not change anything before the line
%       % START CACTUS THORNGUIDE",
%     except for filling in the title, author, date, etc. fields.
%        - Each of these fields should only be on ONE line.
%        - Author names should be separated with a \\ or a comma.
%   - You can define your own macros, but they must appear after
%     the START CACTUS THORNGUIDE line, and must not redefine standard
%     latex commands.
%   - To avoid name clashes with other thorns, 'labels', 'citations',
%     'references', and 'image' names should conform to the following
%     convention:
%       ARRANGEMENT_THORN_LABEL
%     For example, an image wave.eps in the arrangement CactusWave and
%     thorn WaveToyC should be renamed to CactusWave_WaveToyC_wave.eps
%   - Graphics should only be included using the graphicx package.
%     More specifically, with the "\includegraphics" command.  Do
%     not specify any graphic file extensions in your .tex file. This
%     will allow us to create a PDF version of the ThornGuide
%     via pdflatex.
%   - References should be included with the latex "\bibitem" command.
%   - Use \begin{abstract}...\end{abstract} instead of \abstract{...}
%   - Do not use \appendix, instead include any appendices you need as
%     standard sections.
%   - For the benefit of our Perl scripts, and for future extensions,
%     please use simple latex.
%
% *======================================================================*
%
% Example of including a graphic image:
%    \begin{figure}[ht]
% 	\begin{center}
%    	   \includegraphics[width=6cm]{MyArrangement_MyThorn_MyFigure}
% 	\end{center}
% 	\caption{Illustration of this and that}
% 	\label{MyArrangement_MyThorn_MyLabel}
%    \end{figure}
%
% Example of using a label:
%   \label{MyArrangement_MyThorn_MyLabel}
%
% Example of a citation:
%    \cite{MyArrangement_MyThorn_Author99}
%
% Example of including a reference
%   \bibitem{MyArrangement_MyThorn_Author99}
%   {J. Author, {\em The Title of the Book, Journal, or periodical}, 1 (1999),
%   1--16. {\tt http://www.nowhere.com/}}
%
% *======================================================================*

\documentclass{article}

% Use the Cactus ThornGuide style file
% (Automatically used from Cactus distribution, if you have a
%  thorn without the Cactus Flesh download this from the Cactus
%  homepage at www.cactuscode.org)
\usepackage{../../../../doc/latex/cactus}

\begin{document}

% The author of the documentation
\author{Erik Schnetter \textless schnetter@aei.mpg.de\textgreater}

% The title of the document (not necessarily the name of the Thorn)
\title{}

% the date your document was last changed, if your document is in CVS,
% please use:
\date{June 11, 2004}

\maketitle

% Do not delete next line
% START CACTUS THORNGUIDE

% Add all definitions used in this documentation here
%   \def\mydef etc

% Add an abstract for this thorn's documentation
\begin{abstract}

\end{abstract}

% The following sections are suggestive only.
% Remove them or add your own.

\section{Introduction}



%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Utilities}
\label{sec:utils}

These scripts may be useful handling CarpetIOASCII data:
\begin{itemize}
\item {\bf Carpet2ygraph.pl} A perl script to convert to a format
  suitable for the {\it xgraph} or {\it ygraph} packages of P. Walker
  and D. Pollney.
\item {\bf mergeCarpetIOScalar.pl} A perl script to remove duplicate datasets from file(s).
\end{itemize}

The first script resides in CarpetIOASCII/src/utils and was meant primarily to convert 1D data,
since the CarpetIOScalar data format is easily readable also by ygraph. Anyway, this script converts
also scalar data files to the original 2-column ygraph format.
Usage: {\tt Carpet2ygraphCat.pl Inputfile}.

The second script can be used to merge CarpetIOScalar output written before and after recovery. It
reads one or more files in CarpetIOScalar format and writes their contents to STDOUT, eliminating
duplicate datasets (all but the last occurance are discarded), which may be created when a run died
abruptly without checkpointing at the last output itaration and is recovered from a previous
checkpoint.  
Usage: {\tt mergeCarpetIOScalar.pl list of files}. \\
Example 1: {\tt mergeCarpetIOScalar.pl alp.norm1.asc > alp.norm1.asc.merged}.\\ 
Example 2: {\tt mergeCarpetIOScalar.pl alp.norm1.asc.firstCHKPT alp.norm1.asc.secondCHKPT > alp.norm1.asc.merged}.\\
This script was written by Thomas Radke.


\begin{thebibliography}{9}

\end{thebibliography}

% Do not delete next line
% END CACTUS THORNGUIDE

\end{document}

```



Reference answer:
src_code: #! /usr/bin/perl -w
#/*@@
#  @file      mergeCarpetIOScalar.pl
#  @date      Tue 15 August 2006
#  @author    Thomas Radke
#  @desc
#             Perl script to merge CarpetIOScalar output files,
#             eliminating duplicate timesteps.
#
#             Source code comments also by Thomas Radke :-)
#  @enddesc
#@@*/


my $help = $#ARGV < 0;
for (my $arg = 0; $arg <= $#ARGV; $arg++) {
  $help |= ($ARGV[$arg] eq '-h'    or
            $ARGV[$arg] eq '-help' or
            $ARGV[$arg] eq '--help');
}
if ($help) {
  print << "EOF";

  Usage: $0 [-h | -help | --help] <list of files>

  This script can be used to merge  CarpetIOScalar output  written before
  and after recovery. It reads one or more files in CarpetIOScalar format
  and  writes their contents  to STDOUT,  eliminating duplicate timesteps
  (all but the last occurance are discarded).

    Example: $0 alp.norm1.asc > alp.norm1.asc.merged

EOF
  exit;
}

# Rauten-Feld zum Merken der Anzahl und Haeufigkeit vorhandener Datensaetze
my %timesteps = ();

# Liste aller Eingabe-Dateien
my @filelist = @ARGV;

# lies zeilenweise alle Eingabe-Dateien
while (<>) {

  # falls diese Zeile eine Datenzeile ist:
  # merke den Datensatz mit seinem Zeitschritt
  $timesteps{$1} = $_ if (/^(\d+(\.\d+)?)\s+/);
}

# stelle die Liste aller Eingabe-Dateien wieder her
@ARGV = @filelist;

# lies zeilenweise alle Eingabe-Dateien
while (<>) {
  # gib alle Zeilen bis zur ersten Datenzeile aus
  last if (/^\d+(\.\d+)?\s+/);
  print;
}

# gib alle Datenzeilen aus, sortiert nach Zeitschritten
foreach my $timestep (sort {$a <=> $b} keys %timesteps) {
  print $timesteps{$timestep};
}