Merge pull request ESMCI#1752 from NCAR/ejh_bget

Remove bget

.github/workflows/a4.yml

@@ -117,6 +117,21 @@ jobs:
         make
         sudo make install
         popd
+    - name: cmake build
+      run: |
+        set -x
+        gcc --version
+        echo 'export PATH=/home/runner/mpich/bin:$PATH' > .bashrc
+        source .bashrc
+        export CC=/home/runner/mpich/bin/mpicc
+        export FC=/home/runner/mpich/bin/mpifort
+        export LD_LIBRARY_PATH="/home/runner/netcdf-c/lib:/home/runner/mpich/lib:/home/runner/hdf5/lib:/home/runner/netcdf-fortran/lib:/home/runner/pnetcdf/lib:$LD_LIBRARY_PATH"
+        mkdir build
+        cd build
+        cmake -Wno-dev -DNetCDF_C_LIBRARY=/home/runner/netcdf-c/lib/libnetcdf.so -DNetCDF_C_INCLUDE_DIR=/home/runner/netcdf-c/include -DPnetCDF_PATH='/home/runner/pnetcdf' -DPIO_ENABLE_FORTRAN=Off -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off .. || (cat CMakeFiles/CMakeOutput.log && cat CMakeFiles/CMakeError.log)
+        make VERBOSE=1
+        make tests VERBOSE=1
+#        ctest -VV
     - name: autotools build
       run: |
         set -x
@@ -129,3 +144,4 @@ jobs:
         ./configure --enable-fortran
         make -j check
         
+        

CMakeLists.txt

@@ -91,7 +91,6 @@ option (PIO_INTERNAL_DOC     "Enable PIO developer documentation"           OFF)
 option (PIO_TEST_BIG_ENDIAN  "Enable test to see if machine is big endian"  ON)
 option (PIO_USE_MPIIO        "Enable support for MPI-IO auto detect"        ON)
 option (PIO_USE_MPISERIAL    "Enable mpi-serial support (instead of MPI)"   OFF)
-option (PIO_USE_MALLOC       "Use native malloc (instead of bget package)"  ON)
 option (PIO_USE_PNETCDF_VARD       "Use pnetcdf put_vard "  OFF)
 option (WITH_PNETCDF         "Require the use of PnetCDF"                   ON)
 
@@ -103,11 +102,7 @@ else()
 endif()
 
 # Set a variable that appears in the config.h.in file.
-if(PIO_USE_MALLOC)
-  set(USE_MALLOC 1)
-else()
-  set(USE_MALLOC 0)
-endif()
+set(USE_MALLOC 1)
 
 # Set a variable that appears in the config.h.in file.
 if(PIO_ENABLE_LOGGING)

src/clib/CMakeLists.txt

@@ -7,7 +7,7 @@ project (PIOC C)
 #==============================================================================
 
 set (src topology.c pio_file.c pioc_support.c pio_lists.c
-  pioc.c pioc_sc.c pio_spmd.c pio_rearrange.c pio_nc4.c bget.c
+  pioc.c pioc_sc.c pio_spmd.c pio_rearrange.c pio_nc4.c 
   pio_nc.c pio_put_nc.c pio_get_nc.c pio_getput_int.c pio_msg.c
   pio_darray.c pio_darray_int.c pio_get_vard.c pio_put_vard.c pio_error.c)
 if (NETCDF_INTEGRATION)

src/clib/Makefile.am

@@ -19,10 +19,10 @@ libpioc_la_LDFLAGS = -version-info 4:1:3
 include_HEADERS = pio.h uthash.h pio_meta.h
 
 # The library soure files.
-libpioc_la_SOURCES = bget.c pioc_sc.c pio_darray.c pio_file.c		\
+libpioc_la_SOURCES = pioc_sc.c pio_darray.c pio_file.c			\
 pio_getput_int.c pio_msg.c pio_nc.c pio_rearrange.c pioc.c		\
 pioc_support.c pio_darray_int.c pio_get_nc.c pio_lists.c pio_nc4.c	\
 pio_put_nc.c pio_spmd.c pio_get_vard.c pio_put_vard.c pio_error.c	\
-pio_internal.h bget.h uthash.h pio_error.h
+pio_internal.h uthash.h pio_error.h
 
 EXTRA_DIST = CMakeLists.txt topology.c pio_meta.h.in

src/clib/pio_darray.c

@@ -274,7 +274,7 @@ PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int nvars,
     if (rlen > 0)
     {
         /* Allocate memory for the buffer for all vars/records. */
-        if (!(file->iobuf = bget(iodesc->mpitype_size * (size_t)rlen)))
+        if (!(file->iobuf = malloc(iodesc->mpitype_size * (size_t)rlen)))
             return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
         PLOG((3, "allocated %lld bytes for variable buffer", (size_t)rlen * iodesc->mpitype_size));
 
@@ -294,7 +294,7 @@ PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int nvars,
         /* this assures that iobuf is allocated on all iotasks thus
            assuring that the flush_output_buffer call above is called
            collectively (from all iotasks) */
-        if (!(file->iobuf = bget(1)))
+        if (!(file->iobuf = malloc(1)))
             return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
         PLOG((3, "allocated token for variable buffer"));
     }
@@ -341,7 +341,7 @@ PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int nvars,
         if (file->iobuf)
         {
             PLOG((3,"freeing variable buffer in pio_darray"));
-            brel(file->iobuf);
+            free(file->iobuf);
             file->iobuf = NULL;
         }
     }
@@ -365,9 +365,9 @@ PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int nvars,
 
         /* Get a buffer. */
         if (ios->io_rank == 0)
-            vdesc0->fillbuf = bget(iodesc->maxholegridsize * iodesc->mpitype_size * nvars);
+            vdesc0->fillbuf = malloc(iodesc->maxholegridsize * iodesc->mpitype_size * nvars);
         else if (iodesc->holegridsize > 0)
-            vdesc0->fillbuf = bget(iodesc->holegridsize * iodesc->mpitype_size * nvars);
+            vdesc0->fillbuf = malloc(iodesc->holegridsize * iodesc->mpitype_size * nvars);
 
         /* copying the fill value into the data buffer for the box
          * rearranger. This will be overwritten with data where
@@ -403,7 +403,7 @@ PIOc_write_darray_multi(int ncid, const int *varids, int ioid, int nvars,
             /* Free resources. */
             if (vdesc0->fillbuf)
             {
-                brel(vdesc0->fillbuf);
+                free(vdesc0->fillbuf);
                 vdesc0->fillbuf = NULL;
             }
         }
@@ -718,7 +718,7 @@ PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *arra
     if (!wmb)
     {
         /* Allocate a buffer. */
-        if (!(wmb = bget((bufsize)sizeof(wmulti_buffer))))
+        if (!(wmb = malloc(sizeof(wmulti_buffer))))
             return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
 
         /* Set pointer to newly allocated buffer and initialize.*/
@@ -808,22 +808,22 @@ PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *arra
     /* Get memory for data. */
     if (arraylen > 0)
     {
-        if (!(wmb->data = bgetr(wmb->data, (1 + wmb->num_arrays) * arraylen * iodesc->mpitype_size)))
+        if (!(wmb->data = realloc(wmb->data, (1 + wmb->num_arrays) * arraylen * iodesc->mpitype_size)))
             return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
         PLOG((2, "got %ld bytes for data", (1 + wmb->num_arrays) * arraylen * iodesc->mpitype_size));
     }
 #endif
 
     /* vid is an array of variable ids in the wmb list, grow the list
      * and add the new entry. */
-    if (!(wmb->vid = bgetr(wmb->vid, sizeof(int) * (1 + wmb->num_arrays))))
+    if (!(wmb->vid = realloc(wmb->vid, sizeof(int) * (1 + wmb->num_arrays))))
         return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
 
     /* wmb->frame is the record number, we assume that the variables
      * in the wmb list may not all have the same unlimited dimension
      * value although they usually do. */
     if (vdesc->record >= 0)
-        if (!(wmb->frame = bgetr(wmb->frame, sizeof(int) * (1 + wmb->num_arrays))))
+        if (!(wmb->frame = realloc(wmb->frame, sizeof(int) * (1 + wmb->num_arrays))))
             return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
 
     /* If we need a fill value, get it. If we are using the subset
@@ -832,7 +832,7 @@ PIOc_write_darray(int ncid, int varid, int ioid, PIO_Offset arraylen, void *arra
     if (iodesc->needsfill)
     {
         /* Get memory to hold fill value. */
-        if (!(wmb->fillvalue = bgetr(wmb->fillvalue, iodesc->mpitype_size * (1 + wmb->num_arrays))))
+        if (!(wmb->fillvalue = realloc(wmb->fillvalue, iodesc->mpitype_size * (1 + wmb->num_arrays))))
             return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
 
         memcpy((char *)wmb->fillvalue + iodesc->mpitype_size * wmb->num_arrays,
@@ -961,7 +961,7 @@ PIOc_read_darray(int ncid, int varid, int ioid, PIO_Offset arraylen,
 
     /* Allocate a buffer for one record. */
     if (ios->ioproc && rlen > 0)
-        if (!(iobuf = bget(iodesc->mpitype_size * rlen)))
+        if (!(iobuf = malloc(iodesc->mpitype_size * rlen)))
             return pio_err(ios, file, PIO_ENOMEM, __FILE__, __LINE__);
 
     /* Call the correct darray read function based on iotype. */
@@ -1018,7 +1018,7 @@ PIOc_read_darray(int ncid, int varid, int ioid, PIO_Offset arraylen,
 
     /* Free the buffer. */
     if (rlen > 0)
-        brel(iobuf);
+        free(iobuf);
 
 #ifdef USE_MPE
     pio_stop_mpe_log(DARRAY_READ, __func__);

src/clib/pio_darray_int.c

@@ -23,7 +23,7 @@
 extern PIO_Offset pio_buffer_size_limit;
 
 /** Initial size of compute buffer. */
-bufsize pio_cnbuffer_limit = 33554432;
+long pio_cnbuffer_limit = 33554432;
 
 /** Global buffer pool pointer. */
 extern void *CN_bpool;
@@ -1339,8 +1339,8 @@ pio_read_darray_nc(file_desc_t *file, io_desc_t *iodesc, int vid, void *iobuf)
 
                 if (tmp_bufsize > 0)
                 {
-                    startlist[rrlen] = bget(fndims * sizeof(PIO_Offset));
-                    countlist[rrlen] = bget(fndims * sizeof(PIO_Offset));
+                    startlist[rrlen] = malloc(fndims * sizeof(PIO_Offset));
+                    countlist[rrlen] = malloc(fndims * sizeof(PIO_Offset));
 
                     for (int j = 0; j < fndims; j++)
                     {
@@ -1380,8 +1380,8 @@ pio_read_darray_nc(file_desc_t *file, io_desc_t *iodesc, int vid, void *iobuf)
                     /* Release the start and count arrays. */
                     for (int i = 0; i < rrlen; i++)
                     {
-                        brel(startlist[i]);
-                        brel(countlist[i]);
+                        free(startlist[i]);
+                        free(countlist[i]);
                     }
                 }
             }
@@ -1825,7 +1825,7 @@ flush_output_buffer(file_desc_t *file, bool force, PIO_Offset addsize)
         if (file->iobuf)
         {
             PLOG((3,"freeing variable buffer in flush_output_buffer"));
-            brel(file->iobuf);
+            free(file->iobuf);
             file->iobuf = NULL;
         }
 
@@ -1835,7 +1835,7 @@ flush_output_buffer(file_desc_t *file, bool force, PIO_Offset addsize)
                 return pio_err(NULL, file, ierr, __FILE__, __LINE__);
             if (vdesc->fillbuf)
             {
-                brel(vdesc->fillbuf);
+                free(vdesc->fillbuf);
                 vdesc->fillbuf = NULL;
             }
         }
@@ -1845,82 +1845,6 @@ flush_output_buffer(file_desc_t *file, bool force, PIO_Offset addsize)
     return ierr;
 }
 
-/**
- * Print out info about the buffer for debug purposes. This should
- * only be called when logging is enabled.
- *
- * @param ios pointer to the IO system structure
- * @param collective true if collective report is desired
- * @ingroup PIO_write_darray_c
- * @author Jim Edwards
- */
-void
-cn_buffer_report(iosystem_desc_t *ios, bool collective)
-{
-    int mpierr;  /* Return code from MPI functions. */
-
-    PLOG((2, "cn_buffer_report ios->iossysid = %d collective = %d CN_bpool = %d",
-          ios->iosysid, collective, CN_bpool));
-    if (CN_bpool)
-    {
-        long bget_stats[5];
-        long bget_mins[5];
-        long bget_maxs[5];
-
-        bstats(bget_stats, bget_stats+1,bget_stats+2,bget_stats+3,bget_stats+4);
-        if (collective)
-        {
-            PLOG((3, "cn_buffer_report calling MPI_Reduce ios->comp_comm = %d", ios->comp_comm));
-            if ((mpierr = MPI_Reduce(bget_stats, bget_maxs, 5, MPI_LONG, MPI_MAX, 0, ios->comp_comm)))
-                check_mpi(NULL, NULL, mpierr, __FILE__, __LINE__);
-            PLOG((3, "cn_buffer_report calling MPI_Reduce"));
-            if ((mpierr = MPI_Reduce(bget_stats, bget_mins, 5, MPI_LONG, MPI_MIN, 0, ios->comp_comm)))
-                check_mpi(NULL, NULL, mpierr, __FILE__, __LINE__);
-            if (ios->compmaster == MPI_ROOT)
-            {
-                PLOG((1, "Currently allocated buffer space %ld %ld", bget_mins[0], bget_maxs[0]));
-                PLOG((1, "Currently available buffer space %ld %ld", bget_mins[1], bget_maxs[1]));
-                PLOG((1, "Current largest free block %ld %ld", bget_mins[2], bget_maxs[2]));
-                PLOG((1, "Number of successful bget calls %ld %ld", bget_mins[3], bget_maxs[3]));
-                PLOG((1, "Number of successful brel calls  %ld %ld", bget_mins[4], bget_maxs[4]));
-            }
-        }
-        else
-        {
-            PLOG((1, "Currently allocated buffer space %ld", bget_stats[0]));
-            PLOG((1, "Currently available buffer space %ld", bget_stats[1]));
-            PLOG((1, "Current largest free block %ld", bget_stats[2]));
-            PLOG((1, "Number of successful bget calls %ld", bget_stats[3]));
-            PLOG((1, "Number of successful brel calls  %ld", bget_stats[4]));
-        }
-    }
-}
-
-/**
- * Free the buffer pool. If malloc is used (that is, PIO_USE_MALLOC is
- * non zero), this function does nothing.
- *
- * @param ios pointer to the IO system structure.
- * @ingroup PIO_write_darray_c
- * @author Jim Edwards
- */
-void
-free_cn_buffer_pool(iosystem_desc_t *ios)
-{
-#if !PIO_USE_MALLOC
-    PLOG((2, "free_cn_buffer_pool CN_bpool = %d", CN_bpool));
-    /* Note: it is possible that CN_bpool has been freed and set to NULL by bpool_free() */
-    if (CN_bpool)
-    {
-        cn_buffer_report(ios, false);
-        bpoolrelease(CN_bpool);
-        PLOG((2, "free_cn_buffer_pool done!"));
-        free(CN_bpool);
-        CN_bpool = NULL;
-    }
-#endif /* !PIO_USE_MALLOC */
-}
-
 /**
  * Flush the buffer.
  *
@@ -1958,21 +1882,21 @@ flush_buffer(int ncid, wmulti_buffer *wmb, bool flushtodisk)
         wmb->num_arrays = 0;
 
         /* Release the list of variable IDs. */
-        brel(wmb->vid);
+        free(wmb->vid);
         wmb->vid = NULL;
 
         /* Release the data memory. */
-        brel(wmb->data);
+        free(wmb->data);
         wmb->data = NULL;
 
         /* If there is a fill value, release it. */
         if (wmb->fillvalue)
-            brel(wmb->fillvalue);
+            free(wmb->fillvalue);
         wmb->fillvalue = NULL;
 
         /* Release the record number. */
         if (wmb->frame)
-            brel(wmb->frame);
+            free(wmb->frame);
         wmb->frame = NULL;
 
         if (ret)

src/clib/pio_file.c

@@ -419,7 +419,7 @@ PIOc_sync(int ncid)
                 if (wmb->num_arrays > 0)
                     flush_buffer(ncid, wmb, true);
                 HASH_DEL(file->buffer, wmb);
-                brel(wmb);
+                free(wmb);
 
             }
             file->buffer = NULL;

src/clib/pio_internal.h

@@ -13,7 +13,6 @@
 #include <config.h>
 #include <pio.h>
 #include <pio_error.h>
-#include <bget.h>
 #include <limits.h>
 #include <math.h>
 #include <netcdf.h>