Implement NC4_Serial

This class uses rank 0 to write NetCDF-4 files.

src/util/CMakeLists.txt

@@ -31,6 +31,7 @@ set(PISMUTIL_SRC
   io/LocalInterpCtx.cc
   io/File.cc
   io/NC_Serial.cc
+  io/NC4_Serial.cc
   io/NC4File.cc
   io/NCFile.cc
   io/io_helpers.cc

src/util/io/NC4_Serial.cc

@@ -1,4 +1,4 @@
-// Copyright (C) 2012, 2013, 2014, 2015, 2019 PISM Authors
+// Copyright (C) 2012, 2013, 2014, 2015, 2019, 2020 PISM Authors
 //
 // This file is part of PISM.
 //
@@ -16,7 +16,7 @@
 // along with PISM; if not, write to the Free Software
 // Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
 
-#include "PISMNC4_Serial.hh"
+#include "NC4_Serial.hh"
 
 // The following is a stupid kludge necessary to make NetCDF 4.x work in
 // serial mode in an MPI program:
@@ -25,18 +25,66 @@
 #endif
 #include <netcdf.h>
 
+#include "pism/util/error_handling.hh"
+
 namespace pism {
 namespace io {
 
-int NC4_Serial::open_impl(const std::string &fname, IO_Mode mode) {
-  int open_mode = mode == PISM_READONLY ? NC_NOWRITE : NC_WRITE;
+//! \brief Prints an error message; for debugging.
+static void check(const ErrorLocation &where, int return_code) {
+  if (return_code != NC_NOERR) {
+    throw RuntimeError(where, nc_strerror(return_code));
+  }
+}
+
+NC4_Serial::NC4_Serial(MPI_Comm c)
+  : NC_Serial(c), m_compression_level(0) {
+  // empty
+}
+
+NC4_Serial::~NC4_Serial() {
+  // empty
+}
+
+void NC4_Serial::create_impl(const std::string &fname) {
+  int stat = NC_NOERR;
+
+  if (m_rank == 0) {
+    stat = nc_create(fname.c_str(), NC_CLOBBER | NC_NETCDF4, &m_file_id);
+  }
+
+  MPI_Barrier(m_com);
+  MPI_Bcast(&m_file_id, 1, MPI_INT, 0, m_com);
+  MPI_Bcast(&stat, 1, MPI_INT, 0, m_com);
 
-  int stat = nc_open(fname.c_str(), open_mode, &m_file_id);
   check(PISM_ERROR_LOCATION, stat);
 }
 
-int NC4_Serial::create_impl(const std::string &fname) {
-  int stat = nc_create(fname.c_str(), NC_NETCDF4, &m_file_id);
+void NC4_Serial::set_compression_level_impl(int level) const {
+  m_compression_level = level;
+}
+
+void NC4_Serial::def_var_impl(const std::string &name,
+                              IO_Type nctype,
+                              const std::vector<std::string> &dims) const {
+
+  // use the parent class to define the variable
+  NC_Serial::def_var_impl(name, nctype, dims);
+
+  int stat = NC_NOERR;
+
+  // set compression level (except for scalars and time-series)
+  if (m_compression_level > 0 and dims.size() > 1) {
+    if (m_rank == 0) {
+      int varid = get_varid(name);
+
+      stat = nc_def_var_deflate(m_file_id, varid, 0, 1, m_compression_level);
+    }
+  }
+
+  MPI_Barrier(m_com);
+  MPI_Bcast(&stat, 1, MPI_INT, 0, m_com);
+
   check(PISM_ERROR_LOCATION, stat);
 }
 

src/util/io/NC4_Serial.hh

@@ -1,4 +1,4 @@
-// Copyright (C) 2012, 2013, 2014, 2015, 2019 PISM Authors
+// Copyright (C) 2012, 2013, 2014, 2015, 2019, 2020 PISM Authors
 //
 // This file is part of PISM.
 //
@@ -19,24 +19,27 @@
 #ifndef _NC4_Serial_H_
 #define _NC4_Serial_H_
 
-#include "PISMNC4File.hh"
+#include "NC_Serial.hh"
 
 namespace pism {
 namespace io {
 
-class NC4_Serial : public NC4File
+class NC4_Serial : public NC_Serial
 {
 public:
-  NC4_Serial(MPI_Comm c, unsigned int compression_level)
-    : NC4File(c, compression_level) {}
-  virtual ~NC4_Serial() {}
+  NC4_Serial(MPI_Comm c);
+  virtual ~NC4_Serial();
+
 protected:
-  // open/create/close
-  void open_impl(const std::string &filename, IO_Mode mode);
+  void set_compression_level_impl(int level) const;
 
   void create_impl(const std::string &filename);
-};
 
+  void def_var_impl(const std::string &name, IO_Type nctype,
+                    const std::vector<std::string> &dims) const;
+
+  mutable int m_compression_level;
+};
 
 } // end of namespace io
 } // end of namespace pism

src/util/io/NC_Serial.hh

@@ -37,7 +37,7 @@ protected:
   // open/create/close
   void open_impl(const std::string &filename, IO_Mode mode);
 
-  void create_impl(const std::string &filename);
+  virtual void create_impl(const std::string &filename);
 
   void sync_impl() const;
 
@@ -58,7 +58,7 @@ protected:
   void inq_unlimdim_impl(std::string &result) const;
 
   // var
-  void def_var_impl(const std::string &name, IO_Type nctype, const std::vector<std::string> &dims) const;
+  virtual void def_var_impl(const std::string &name, IO_Type nctype, const std::vector<std::string> &dims) const;
 
   void get_vara_double_impl(const std::string &variable_name,
                       const std::vector<unsigned int> &start,
@@ -86,7 +86,7 @@ protected:
 
   void inq_varname_impl(unsigned int j, std::string &result) const;
 
-  void set_compression_level_impl(int level) const;
+  virtual void set_compression_level_impl(int level) const;
 
   // att
   void get_att_double_impl(const std::string &variable_name, const std::string &att_name, std::vector<double> &result) const;
@@ -105,16 +105,18 @@ protected:
   void set_fill_impl(int fillmode, int &old_modep) const;
 
   void del_att_impl(const std::string &variable_name, const std::string &att_name) const;
-private:
+
   int m_rank;
 
+  int get_varid(const std::string &variable_name) const;
+
+private:
+
   void get_var_double(const std::string &variable_name,
                      const std::vector<unsigned int> &start,
                      const std::vector<unsigned int> &count,
                      const std::vector<unsigned int> &imap, double *ip,
                      bool transposed) const;
-
-  int get_varid(const std::string &variable_name) const;
   };
 
 } // end of namespace io