update minimum cmake version, based on the oldest I can access

.github/workflows/cmake.yml

@@ -56,7 +56,7 @@ jobs:
         cd build
         cmake -Wno-dev -DNetCDF_C_LIBRARY=/usr/lib/x86_64-linux-gnu/libnetcdf.so \
         -DNetCDF_C_INCLUDE_DIR=/usr/include -DPnetCDF_PATH='/home/runner/pnetcdf' \
-        -DPIO_ENABLE_FORTRAN=Off -DPIO_HDF5_LOGGING=On -DPIO_USE_MALLOC=On \
+        -DPIO_ENABLE_FORTRAN=Off \
         -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off  -DMPIEXEC_PREFLAGS="--oversubscribe" ..
         make VERBOSE=1
         make tests VERBOSE=1

.github/workflows/cmake_ncint.yml

@@ -60,7 +60,7 @@ jobs:
           cmake -Wno-dev -DPIO_ENABLE_NETCDF_INTEGRATION=OFF \
           -DNetCDF_C_LIBRARY=/usr/lib/x86_64-linux-gnu/libnetcdf.so \
           -DNetCDF_C_INCLUDE_DIR=/usr/include -DPnetCDF_PATH='/home/runner/pnetcdf' \
-          -DPIO_HDF5_LOGGING=On -DPIO_ENABLE_FORTRAN=OFF -DPIO_USE_MALLOC=On \
+          -DPIO_ENABLE_FORTRAN=OFF \
           -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off -DMPIEXEC_PREFLAGS="--oversubscribe" ..
           make VERBOSE=1
           make tests VERBOSE=1

CMakeLists.txt

@@ -4,9 +4,8 @@
 
 # Jim Edwards
 
-cmake_minimum_required (VERSION 2.8.12)
+cmake_minimum_required (VERSION 3.9.1)
 project (PIO C)
-#cmake_policy(VERSION 3.5.2)
 
 # The project version number.
 set(VERSION_MAJOR   2   CACHE STRING "Project major version number.")
@@ -107,9 +106,6 @@ else()
   set(USE_VARD 0)
 endif()
 
-# Set a variable that appears in the config.h.in file.
-set(USE_MALLOC 1)
-
 # Set a variable that appears in the config.h.in file.
 if(PIO_ENABLE_LOGGING)
   set(ENABLE_LOGGING 1)
@@ -281,7 +277,11 @@ add_subdirectory (src)
 
 # Custom "piotests" target (builds the test executables)
 add_custom_target (tests)
-add_dependencies (tests pioc piof)
+if (PIO_ENABLE_FORTRAN)
+  add_dependencies (tests pioc piof)
+else()
+  add_dependencies (tests pioc)
+endif()
 
 # Custom "check" target that depends upon "tests"
 add_custom_target (check COMMAND ${CMAKE_CTEST_COMMAND})

cmake_config.h.in

@@ -15,10 +15,6 @@
 /** The patch part of the version number. */
 #define PIO_VERSION_PATCH @VERSION_PATCH@
 
-/** Set to non-zero to use native malloc. By defauly the PIO library
- * will use the included bget() package for memory management. */
-#define PIO_USE_MALLOC @USE_MALLOC@
-
 /** Set to non-zero to turn on logging. Output may be large. */
 #define PIO_ENABLE_LOGGING @ENABLE_LOGGING@
 

configure.ac

@@ -92,9 +92,6 @@ if test -n "$fc_version_info"; then
   FC_VERSION="$FC_VERSION ( $fc_version_info)"
 fi
 
-# Always use malloc in autotools builds.
-AC_DEFINE([PIO_USE_MALLOC], [1], [use malloc for memory])
-
 AC_MSG_CHECKING([whether a PIO_BUFFER_SIZE was specified])
 AC_ARG_WITH([piobuffersize],
               [AS_HELP_STRING([--with-piobuffersize=<integer>],

ctest/CTestEnvironment-anlworkstation.cmake

@@ -24,7 +24,3 @@ if (DEFINED ENV{VALGRIND_CHECK})
     set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DPIO_VALGRIND_CHECK=ON")
 endif ()
 
-# If USE_MALLOC environment variable is set, then use native malloc (instead of bget package)
-if (DEFINED ENV{USE_MALLOC})
-    set (CTEST_CONFIGURE_OPTIONS "${CTEST_CONFIGURE_OPTIONS} -DPIO_USE_MALLOC=ON")
-endif ()

src/clib/pio_rearrange.c

@@ -2174,8 +2174,9 @@ subset_rearrange_create(iosystem_desc_t *ios, int maplen, PIO_Offset *compmap,
     }
 //    PLOG((2,"At line %d rdispls[%d]=%d rcount=%d",__LINE__,1,rdispls[0], iodesc->rcount[0]));
     /* Determine whether fill values will be needed. */
-    if ((ret = determine_fill(ios, iodesc, gdimlen, compmap)))
-        return pio_err(ios, NULL, ret, __FILE__, __LINE__);
+    if(! iodesc->readonly)
+        if ((ret = determine_fill(ios, iodesc, gdimlen, compmap)))
+            return pio_err(ios, NULL, ret, __FILE__, __LINE__);
 
     /* Pass the sindex from each compute task to its associated IO task. */
     if ((mpierr = MPI_Gatherv(iodesc->sindex, iodesc->scount[0], PIO_OFFSET,

src/clib/pioc.c

@@ -595,10 +595,6 @@ PIOc_InitDecomp(int iosysid, int pio_type, int ndims, const int *gdimlen, int ma
     /* Remember the maplen. */
     iodesc->maplen = maplen;
 
-    /* check if the decomp is valid for write or is read-only */
-    /* this check is expensive and memory intensive on compute task 0 */
-//    iodesc->readonly = check_compmap(ios, iodesc, compmap);
-
     /* Remember the map. */
     if (!(iodesc->map = malloc(sizeof(PIO_Offset) * maplen)))
         return pio_err(ios, NULL, PIO_ENOMEM, __FILE__, __LINE__);
@@ -661,6 +657,10 @@ PIOc_InitDecomp(int iosysid, int pio_type, int ndims, const int *gdimlen, int ma
     /* Is this the subset rearranger? */
     if (iodesc->rearranger == PIO_REARR_SUBSET)
     {
+        /* check if the decomp is valid for write or is read-only */
+        /* this check is expensive and may be memory intensive on compute task 0 */
+        iodesc->readonly = check_compmap(ios, iodesc, compmap);
+
         iodesc->num_aiotasks = ios->num_iotasks;
         PLOG((2, "creating subset rearranger iodesc->num_aiotasks = %d",
               iodesc->num_aiotasks));

src/clib/pioc_support.c

@@ -3283,7 +3283,7 @@ bool check_compmap(iosystem_desc_t *ios, io_desc_t *iodesc,const PIO_Offset *com
     if(ios->compproc) 
     {
         int *gmaplen;
-        if(ios->compmaster)
+        if(ios->compmaster == MPI_ROOT)
             gmaplen = malloc(ios->num_comptasks * sizeof(int));
         else
             gmaplen = NULL;
@@ -3292,9 +3292,9 @@ bool check_compmap(iosystem_desc_t *ios, io_desc_t *iodesc,const PIO_Offset *com
             return check_mpi(ios, NULL, ierr, __FILE__,__LINE__);
 
         int *displs;
-        int gcompmaplen;
+        int gcompmaplen=0;
         int *gcompmaps;
-        if(ios->compmaster)
+        if(ios->compmaster == MPI_ROOT)
         {
             displs = malloc(ios->num_comptasks * sizeof(int));
             displs[0] = 0;
@@ -3304,16 +3304,16 @@ bool check_compmap(iosystem_desc_t *ios, io_desc_t *iodesc,const PIO_Offset *com
             }
             gcompmaplen = displs[ios->num_comptasks-1] + gmaplen[ios->num_comptasks-1];
             gcompmaps = malloc(gcompmaplen * sizeof(PIO_Offset)); 
-            printf("gcompmaplen %d\n",gcompmaplen);
-            for(int i=0;i<ios->num_comptasks; i++)
-                printf("gmaplen=%d displs[%d]=%d\n",gmaplen[i], i,displs[i]);
+//            printf("gcompmaplen %d\n",gcompmaplen);
+//            for(int i=0;i<ios->num_comptasks; i++)
+//                printf("gmaplen=%d displs[%d]=%d\n",gmaplen[i], i,displs[i]);
         }
 
         /* next gather the compmap arrays */
         if ((ierr = MPI_Gatherv(compmap, iodesc->maplen, MPI_OFFSET, gcompmaps, gmaplen, displs, MPI_OFFSET, 0, ios->comp_comm)))
             return check_mpi(ios, NULL, ierr, __FILE__,__LINE__);
 
-        if(ios->compmaster)
+        if(ios->compmaster == MPI_ROOT)
         {
             /* sort */
             qsort(gcompmaps, gcompmaplen, sizeof(MPI_OFFSET), offsetsort);
@@ -3332,6 +3332,6 @@ bool check_compmap(iosystem_desc_t *ios, io_desc_t *iodesc,const PIO_Offset *com
         }
 
     }
-    MPI_Bcast(&readonly, 1, MPI_CHAR, ios->compmaster, ios->intercomm);
+    MPI_Bcast(&readonly, 1, MPI_CHAR, ios->comproot, ios->my_comm);
     return readonly;
 }