PNCFile.cc

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// Copyright (C) 2012, 2013, 2014, 2015, 2016, 2017, 2019, 2020, 2021, 2023, 2024 PISM Authors
//
// This file is part of PISM.
//
// PISM is free software; you can redistribute it and/or modify it under the
// terms of the GNU General Public License as published by the Free Software
// Foundation; either version 3 of the License, or (at your option) any later
// version.
//
// PISM is distributed in the hope that it will be useful, but WITHOUT ANY
// WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
// FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
// details.
//
// You should have received a copy of the GNU General Public License
// along with PISM; if not, write to the Free Software
// Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 
#include <pnetcdf.h>
#include <sstream>
#include <cstring>              // memset
 
#include "pism/util/io/PNCFile.hh"
 
#include "pism/util/io/pism_type_conversion.hh" // has to go after pnetcdf.h
 
#include "pism/util/error_handling.hh"
#include "pism/util/pism_utilities.hh"
 
namespace pism {
namespace io {
 
PNCFile::PNCFile(MPI_Comm c)
  : NCFile(c) {
  MPI_Info_create(&m_mpi_info);
}
PNCFile::PNCFile(MPI_Comm c) {…}
 
 
PNCFile::~PNCFile() {
  MPI_Info_free(&m_mpi_info);
}
PNCFile::~PNCFile() {…}
 
static void check(const ErrorLocation &where, int return_code) {
  if (return_code != NC_NOERR) {
    throw RuntimeError(where, ncmpi_strerror(return_code));
  }
}
static void check(const ErrorLocation &where, int return_code) {…}
 
void PNCFile::open_impl(const std::string &fname, io::Mode mode) {
  int stat;
 
  init_hints();
 
  int open_mode = mode == io::PISM_READONLY ? NC_NOWRITE : NC_WRITE;
 
  stat = ncmpi_open(m_com, fname.c_str(), open_mode, m_mpi_info, &m_file_id);
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::open_impl(const std::string &fname, io::Mode mode) {…}
 
 
void PNCFile::create_impl(const std::string &fname) {
  int stat;
 
  init_hints();
 
  stat = ncmpi_create(m_com, fname.c_str(), NC_CLOBBER | NC_64BIT_DATA, m_mpi_info, &m_file_id);
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::create_impl(const std::string &fname) {…}
 
void PNCFile::sync_impl() const {
 
  int stat = ncmpi_sync(m_file_id);
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::sync_impl() const  {…}
 
 
void PNCFile::close_impl() {
  int stat = ncmpi_close(m_file_id);
  check(PISM_ERROR_LOCATION, stat);
 
  m_file_id = -1;
}
void PNCFile::close_impl() {…}
 
 
void PNCFile::enddef_impl() const {
 
  int stat = ncmpi_enddef(m_file_id);
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::enddef_impl() const  {…}
 
 
void PNCFile::redef_impl() const {
 
  int stat = ncmpi_redef(m_file_id);
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::redef_impl() const  {…}
 
 
void PNCFile::def_dim_impl(const std::string &name, size_t length) const {
  int dimid = 0, stat;
 
  stat = ncmpi_def_dim(m_file_id, name.c_str(), length, &dimid);
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::def_dim_impl(const std::string &name, size_t length) const  {…}
 
 
void PNCFile::inq_dimid_impl(const std::string &dimension_name, bool &exists) const {
  int tmp, stat;
 
  stat = ncmpi_inq_dimid(m_file_id, dimension_name.c_str(), &tmp);
 
  if (stat == NC_NOERR) {
    exists = true;
  } else {
    exists = false;
  }
}
void PNCFile::inq_dimid_impl(const std::string &dimension_name, bool &exists) const  {…}
 
 
void PNCFile::inq_dimlen_impl(const std::string &dimension_name, unsigned int &result) const {
  int stat, dimid = -1;
  MPI_Offset len;
 
  stat = ncmpi_inq_dimid(m_file_id, dimension_name.c_str(), &dimid);
  check(PISM_ERROR_LOCATION, stat);
 
  stat = ncmpi_inq_dimlen(m_file_id, dimid, &len);
  check(PISM_ERROR_LOCATION, stat);
 
  result = static_cast<unsigned int>(len);
}
void PNCFile::inq_dimlen_impl(const std::string &dimension_name, unsigned int &result) const  {…}
 
 
void PNCFile::inq_unlimdim_impl(std::string &result) const {
  int stat = NC_NOERR, dimid = -1;
  char dimname[NC_MAX_NAME];
 
  stat = ncmpi_inq_unlimdim(m_file_id, &dimid);
  check(PISM_ERROR_LOCATION, stat);
 
  if (dimid == -1) {
    result.clear();
  } else {
    stat = ncmpi_inq_dimname(m_file_id, dimid, dimname);
    check(PISM_ERROR_LOCATION, stat);
 
    result = dimname;
  }
}
void PNCFile::inq_unlimdim_impl(std::string &result) const  {…}
 
void PNCFile::def_var_impl(const std::string &name, io::Type nctype,
                           const std::vector<std::string> &dims) const {
  std::vector<int> dimids;
  int stat, varid;
 
  for (auto d : dims) {
    int dimid = -1;
    stat      = ncmpi_inq_dimid(m_file_id, d.c_str(), &dimid);
    check(PISM_ERROR_LOCATION, stat);
    dimids.push_back(dimid);
  }
 
  stat = ncmpi_def_var(m_file_id, name.c_str(), pism_type_to_nc_type(nctype),
                       static_cast<int>(dims.size()), dimids.data(), &varid);
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::def_var_impl(const std::string &name, io::Type nctype, {…}
 
 
void PNCFile::get_vara_double_impl(const std::string &variable_name,
                                   const std::vector<unsigned int> &start,
                                   const std::vector<unsigned int> &count, double *ip) const {
  return this->get_var_double(variable_name, start, count, ip);
}
void PNCFile::get_vara_double_impl(const std::string &variable_name, {…}
 
 
void PNCFile::put_vara_double_impl(const std::string &variable_name,
                                   const std::vector<unsigned int> &start,
                                   const std::vector<unsigned int> &count, const double *op) const {
  int stat, varid, ndims = static_cast<int>(start.size());
 
  std::vector<MPI_Offset> nc_start(ndims), nc_count(ndims);
 
  stat = ncmpi_inq_varid(m_file_id, variable_name.c_str(), &varid);
  check(PISM_ERROR_LOCATION, stat);
 
  for (int j = 0; j < ndims; ++j) {
    nc_start[j]  = start[j];
    nc_count[j]  = count[j];
  }
 
  stat = ncmpi_put_vara_double_all(m_file_id, varid, nc_start.data(), nc_count.data(), op);
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::put_vara_double_impl(const std::string &variable_name, {…}
 
void PNCFile::inq_nvars_impl(int &result) const {
  int stat;
 
  stat = ncmpi_inq_nvars(m_file_id, &result);
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::inq_nvars_impl(int &result) const  {…}
 
 
void PNCFile::inq_vardimid_impl(const std::string &variable_name,
                                std::vector<std::string> &result) const {
  int stat, ndims, varid = -1;
  std::vector<int> dimids;
 
  stat = ncmpi_inq_varid(m_file_id, variable_name.c_str(), &varid);
  check(PISM_ERROR_LOCATION, stat);
 
  stat = ncmpi_inq_varndims(m_file_id, varid, &ndims);
  check(PISM_ERROR_LOCATION, stat);
 
  if (ndims == 0) {
    result.clear();
    return;
  }
 
  result.resize(ndims);
  dimids.resize(ndims);
 
  stat = ncmpi_inq_vardimid(m_file_id, varid, dimids.data());
  check(PISM_ERROR_LOCATION, stat);
 
  for (int k = 0; k < ndims; ++k) {
    char name[NC_MAX_NAME];
    memset(name, 0, NC_MAX_NAME);
 
    stat = ncmpi_inq_dimname(m_file_id, dimids[k], name);
    check(PISM_ERROR_LOCATION, stat);
 
    result[k] = name;
  }
}
void PNCFile::inq_vardimid_impl(const std::string &variable_name, {…}
 
int PNCFile::get_varid(const std::string &variable_name) const {
  if (variable_name == "PISM_GLOBAL") {
    return NC_GLOBAL;
  }
 
  int varid = -1;
  int stat  = ncmpi_inq_varid(m_file_id, variable_name.c_str(), &varid);
  check(PISM_ERROR_LOCATION, stat);
 
  return varid;
}
int PNCFile::get_varid(const std::string &variable_name) const  {…}
 
void PNCFile::inq_varnatts_impl(const std::string &variable_name, int &result) const {
 
  int stat = ncmpi_inq_varnatts(m_file_id, get_varid(variable_name), &result);
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::inq_varnatts_impl(const std::string &variable_name, int &result) const  {…}
 
 
void PNCFile::inq_varid_impl(const std::string &variable_name, bool &exists) const {
  int stat, flag = -1;
 
  stat = ncmpi_inq_varid(m_file_id, variable_name.c_str(), &flag);
 
  exists = (stat == NC_NOERR);
}
void PNCFile::inq_varid_impl(const std::string &variable_name, bool &exists) const  {…}
 
 
void PNCFile::inq_varname_impl(unsigned int j, std::string &result) const {
  int stat;
  char varname[NC_MAX_NAME];
  memset(varname, 0, NC_MAX_NAME);
 
  stat = ncmpi_inq_varname(m_file_id, j, varname);
  check(PISM_ERROR_LOCATION, stat);
 
  result = varname;
}
void PNCFile::inq_varname_impl(unsigned int j, std::string &result) const  {…}
 
void PNCFile::get_att_double_impl(const std::string &variable_name, const std::string &att_name,
                                  std::vector<double> &result) const {
  int len, varid = get_varid(variable_name);
  MPI_Offset attlen = 0;
 
  // Read the attribute length:
  int stat = ncmpi_inq_attlen(m_file_id, varid, att_name.c_str(), &attlen);
 
  if (stat == NC_NOERR) {
    len = static_cast<int>(attlen);
  } else if (stat == NC_ENOTATT) {
    len = 0;
  } else {
    check(PISM_ERROR_LOCATION, stat);
    len = 0;
  }
 
  if (len == 0) {
    result.clear();
    return;
  }
 
  result.resize(len);
 
  // Now read data and broadcast stat to see if we succeeded:
  stat = ncmpi_get_att_double(m_file_id, varid, att_name.c_str(), result.data());
  check(PISM_ERROR_LOCATION, stat);
 
  // On error, print a message and stop.
  if (stat != NC_NOERR) {
    fprintf(stderr, "Error reading the %s attribute; (varid %d, NetCDF error %s)", att_name.c_str(),
            varid, ncmpi_strerror(stat));
  }
}
void PNCFile::get_att_double_impl(const std::string &variable_name, const std::string &att_name, {…}
 
 
void PNCFile::get_att_text_impl(const std::string &variable_name, const std::string &att_name,
                                std::string &result) const {
  int varid = get_varid(variable_name);
 
  // Read the attribute length:
  MPI_Offset attlen = 0;
 
  int stat = ncmpi_inq_attlen(m_file_id, varid, att_name.c_str(), &attlen);
  int len  = (stat == NC_NOERR) ? static_cast<int>(attlen) : 0;
 
  // Allocate some memory or set result to NULL and return:
  if (len == 0) {
    result.clear();
    return;
  }
 
  std::vector<char> str(len + 1, 0);
 
  // Now read the string and see if we succeeded:
  stat = ncmpi_get_att_text(m_file_id, varid, att_name.c_str(), str.data());
  check(PISM_ERROR_LOCATION, stat);
 
  result = str.data();
}
void PNCFile::get_att_text_impl(const std::string &variable_name, const std::string &att_name, {…}
 
void PNCFile::del_att_impl(const std::string &variable_name, const std::string &att_name) const {
  int stat = ncmpi_del_att(m_file_id, get_varid(variable_name), att_name.c_str());
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::del_att_impl(const std::string &variable_name, const std::string &att_name) const  {…}
 
void PNCFile::put_att_double_impl(const std::string &variable_name, const std::string &att_name,
                                  io::Type nctype, const std::vector<double> &data) const {
 
  int stat = ncmpi_put_att_double(m_file_id, get_varid(variable_name), att_name.c_str(),
                                  pism_type_to_nc_type(nctype), data.size(), data.data());
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::put_att_double_impl(const std::string &variable_name, const std::string &att_name, {…}
 
 
void PNCFile::put_att_text_impl(const std::string &variable_name, const std::string &att_name,
                                const std::string &value) const {
  int stat = ncmpi_put_att_text(m_file_id, get_varid(variable_name), att_name.c_str(), value.size(),
                                value.c_str());
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::put_att_text_impl(const std::string &variable_name, const std::string &att_name, {…}
 
 
void PNCFile::inq_attname_impl(const std::string &variable_name, unsigned int n,
                               std::string &result) const {
  int stat;
  char name[NC_MAX_NAME];
  memset(name, 0, NC_MAX_NAME);
 
  int varid = get_varid(variable_name);
 
  stat = ncmpi_inq_attname(m_file_id, varid, n, name);
  check(PISM_ERROR_LOCATION, stat);
 
  result = name;
}
void PNCFile::inq_attname_impl(const std::string &variable_name, unsigned int n, {…}
 
 
void PNCFile::inq_atttype_impl(const std::string &variable_name, const std::string &att_name,
                               io::Type &result) const {
  int varid = get_varid(variable_name);
 
  nc_type tmp = NC_NAT;
  int stat    = ncmpi_inq_atttype(m_file_id, varid, att_name.c_str(), &tmp);
  if (stat == NC_ENOTATT) {
    tmp = NC_NAT;
  } else {
    check(PISM_ERROR_LOCATION, stat);
  }
 
  result = nc_type_to_pism_type(tmp);
}
void PNCFile::inq_atttype_impl(const std::string &variable_name, const std::string &att_name, {…}
 
 
void PNCFile::set_fill_impl(int fillmode, int &old_modep) const {
  int stat = ncmpi_set_fill(m_file_id, fillmode, &old_modep);
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::set_fill_impl(int fillmode, int &old_modep) const  {…}
 
 
void PNCFile::get_var_double(const std::string &variable_name,
                             const std::vector<unsigned int> &start,
                             const std::vector<unsigned int> &count, double *ip) const {
  int stat, varid, ndims = static_cast<int>(start.size());
 
  std::vector<MPI_Offset> nc_start(ndims), nc_count(ndims);
 
  stat = ncmpi_inq_varid(m_file_id, variable_name.c_str(), &varid);
  check(PISM_ERROR_LOCATION, stat);
 
  for (int j = 0; j < ndims; ++j) {
    nc_start[j] = start[j];
    nc_count[j] = count[j];
  }
 
  stat = ncmpi_get_vara_double_all(m_file_id, varid, nc_start.data(), nc_count.data(), ip);
  check(PISM_ERROR_LOCATION, stat);
}
void PNCFile::get_var_double(const std::string &variable_name, {…}
 
void PNCFile::init_hints() {
 
  for (auto hint : m_mpi_io_hints) {
    auto words = split(hint, ':');
 
    if (words.size() == 2) {
      // printf("Setting MPI I/O hint \"%s\" to \"%s\"...\n",
      //        words[0].c_str(), words[1].c_str());
 
      MPI_Info_set(m_mpi_info,
                   const_cast<char*>(words[0].c_str()),
                   const_cast<char*>(words[1].c_str()));
    } else {
      int rank = 0;
      MPI_Comm_rank(m_com, &rank);
      if (rank == 0) {
        printf("PISM WARNING: invalid MPI I/O hint: %s. Ignoring it...\n",
               hint.c_str());
      }
    }
  }
}
void PNCFile::init_hints() {…}
 
void PNCFile::set_compression_level_impl(int level) const {
  (void) level;
  // NetCDF-3 does not support compression.
}
void PNCFile::set_compression_level_impl(int level) const  {…}
 
} // end of namespace io
} // end of namespace pism