Work around bug in netcdf-cxx4. See: Unidata/netcdf-cxx4#30

citibeth · Mar 28, 2016 · 9b1212b · 9b1212b
1 parent ba5e800
commit 9b1212b
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Showing 6 changed files with 32 additions and 9 deletions.
diff --git a/slib/ibmisc/ConstantSet.cpp b/slib/ibmisc/ConstantSet.cpp
@@ -86,7 +86,7 @@ double ConstantSet::get_as(std::string const &name,
 // =======================================================
 void ConstantSet::ncio(NcIO &ncio, std::string const &vname)
 {
-    auto constants_v = get_or_add_var(ncio, vname, netCDF::ncInt64, {});
+    auto constants_v = get_or_add_var(ncio, vname, "int64", {});
 
     // Get a list of the names of our constants
     if (ncio.rw == 'w') {

diff --git a/slib/ibmisc/indexing.hpp b/slib/ibmisc/indexing.hpp
@@ -111,7 +111,7 @@ void Indexing<TupleT, IndexT>::ncio(
     netCDF::NcType ncTupleT,
     std::string const &vname)
 {
-    auto info_v = get_or_add_var(ncio, vname, netCDF::ncInt64, {});
+    auto info_v = get_or_add_var(ncio, vname, "int64", {});
     get_or_put_att(info_v, ncio.rw, "base", ncTupleT, base);
     get_or_put_att(info_v, ncio.rw, "extent", ncTupleT, extent);
     get_or_put_att(info_v, ncio.rw, "indices", ncTupleT, indices);
@@ -153,7 +153,7 @@ void Domain<TupleT>::ncio(
     netCDF::NcType ncTupleT,
     std::string const &vname)
 {
-    auto info_v = get_or_add_var(ncio, vname, netCDF::ncInt64, {});
+    auto info_v = get_or_add_var(ncio, vname, "int64", {});
     get_or_put_att(info_v, ncio.rw, "low", ncTupleT, low);
     get_or_put_att(info_v, ncio.rw, "high", ncTupleT, high);
 }

diff --git a/slib/ibmisc/netcdf.cpp b/slib/ibmisc/netcdf.cpp
@@ -130,17 +130,34 @@ std::vector<netCDF::NcDim> get_or_add_dims(
     return ret;
 }
 // ====================================================
+/** This works only for NetCDF-3 types.  See:
+   https://github.com/Unidata/netcdf-cxx4/issues/30 */
 netCDF::NcVar get_or_add_var(
     NcIO &ncio,
     std::string const &vname,
     netCDF::NcType const &nc_type,
     std::vector<netCDF::NcDim> const &dims)
+{
+    std::string snc_type(nc_type.getName());
+    return get_or_add_var(ncio, vname, snc_type, dims);
+}
+
+/** This works for all valid NetCDF types. */
+netCDF::NcVar get_or_add_var(
+    NcIO &ncio,
+    std::string const &vname,
+    std::string const &snc_type,
+    std::vector<netCDF::NcDim> const &dims)
 {
     netCDF::NcVar ncvar;
     if (ncio.define) {
         ncvar = ncio.nc->getVar(vname);
+        std::vector<std::string> sdims;
+        for (auto dim=dims.begin(); dim != dims.end(); ++dim)
+            sdims.push_back(dim->getName());
+
         if (ncvar.isNull()) {
-            ncvar = ncio.nc->addVar(vname, nc_type, dims);
+            ncvar = ncio.nc->addVar(vname, snc_type, sdims);
         } else {
             // Check dimensions match
             if (ncvar.getDimCount() != dims.size()) {

diff --git a/slib/ibmisc/netcdf.hpp b/slib/ibmisc/netcdf.hpp
@@ -70,7 +70,7 @@ class NcIO {
         define(_mode == 'd') {}
 
     NcIO(std::string const &filePath, netCDF::NcFile::FileMode fMode = netCDF::NcFile::FileMode::read) :
-        _mync(filePath, fMode),
+        _mync(filePath, fMode, netCDF::NcFile::FileFormat::nc4),
         own_nc(true),
         nc(&_mync),
         rw(fMode == netCDF::NcFile::FileMode::read ? 'r' : 'w'),
@@ -155,6 +155,12 @@ netCDF::NcVar get_or_add_var(
     netCDF::NcType const &nc_type,
     std::vector<netCDF::NcDim> const &dims);
 
+netCDF::NcVar get_or_add_var(
+    NcIO &ncio,
+    std::string const &vname,
+    std::string const &snc_type,
+    std::vector<netCDF::NcDim> const &dims);
+
 template<class TypeT>
 void get_or_put_var(netCDF::NcVar &ncvar, char rw,
     std::vector<size_t> const &startp,

diff --git a/slib/spsparse/netcdf.hpp b/slib/spsparse/netcdf.hpp
@@ -117,10 +117,10 @@ void ncio_spsparse(
     if (ncio.rw == 'w') {
         dims = ibmisc::get_or_add_dims(ncio, dim_names, {A.size(), A.rank});
 
-        auto info_v = get_or_add_var(ncio, vname + ".info", netCDF::ncInt64, {});
+        auto info_v = get_or_add_var(ncio, vname + ".info", "int64", {});
         info_v.putAtt("shape", netCDF::ncUint64, A.rank, &A.shape[0]);
 
-        get_or_add_var(ncio, vname + ".indices", netCDF::ncInt64, dims);
+        get_or_add_var(ncio, vname + ".indices", "int64", dims);
         get_or_add_var(ncio, vname + ".vals", netCDF::ncDouble, {dims[0]});
         ncio += std::bind(&nc_write_spsparse<ArrayT>, ncio.nc, &A, vname);
     } else {

diff --git a/tests/ibmisc/test_netcdf.cpp b/tests/ibmisc/test_netcdf.cpp
@@ -123,7 +123,7 @@ TEST_F(NetcdfTest, blitz)
     ibmisc::ncio_blitz(ncio, A, true, "A", netCDF::ncDouble, dims);
     ibmisc::ncio_blitz(ncio, B, true, "B", netCDF::ncDouble, dims);
 
-    auto info_v = get_or_add_var(ncio, "info", netCDF::ncInt64, {});
+    auto info_v = get_or_add_var(ncio, "info", "int64", {});
     get_or_put_att(info_v, ncio.rw, "strings", strings);
 
     ncio.close();
@@ -139,7 +139,7 @@ TEST_F(NetcdfTest, blitz)
     ibmisc::ncio_blitz(ncio, A2, true, "A", netCDF::ncDouble, dims);
     ibmisc::ncio_blitz(ncio, B2, true, "B", netCDF::ncDouble, dims);
 
-    auto info_v = get_or_add_var(ncio, "info", netCDF::ncInt64, {});
+    auto info_v = get_or_add_var(ncio, "info", "int64", {});
     get_or_put_att(info_v, ncio.rw, "strings", strings2);
 
     ncio.close();