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Merge pull request ESMCI#1370 from NCAR/ejh_bug_fix
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Fixing memory leak in test_darray_async_many.c
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@edhartnett
edhartnett authored Mar 23, 2019
2 parents 3289961 + 64496c8 commit 5596b4d
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Showing 7 changed files with 126 additions and 100 deletions.
2 changes: 2 additions & 0 deletions .travis.yml
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Expand Up @@ -41,8 +41,10 @@ env:

script:
- autoreconf -i
- export CFLAGS='-std=c99 -fsanitize=address -fno-omit-frame-pointer'
- ./configure
- make -j distcheck
- export CFLAGS='-std=c99'
- rm -rf build
- mkdir build
- cd build
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3 changes: 2 additions & 1 deletion README.md
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Expand Up @@ -4,7 +4,8 @@ A high-level Parallel I/O Library for structured grid applications

## Website

For complete documentation, see our website at [http://ncar.github.io/ParallelIO/](http://ncar.github.io/ParallelIO/).
For complete documentation, see our website at
[http://ncar.github.io/ParallelIO/](http://ncar.github.io/ParallelIO/).

## Mailing List

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13 changes: 3 additions & 10 deletions src/clib/pio_lists.c
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Expand Up @@ -23,18 +23,12 @@ static file_desc_t *current_file = NULL;
*/
void pio_add_to_file_list(file_desc_t *file)
{
file_desc_t *cfile;

assert(file);

/* Get a pointer to the global list of files. */
cfile = pio_file_list;

/* Keep a global pointer to the current file. */
current_file = file;

/* If there is nothing in the list, then file will be the first
* entry. Otherwise, move to end of the list. */
/* Add file to list. */
HASH_ADD_INT(pio_file_list, pio_ncid, file);
}

Expand Down Expand Up @@ -279,10 +273,10 @@ int pio_delete_iodesc_from_list(int ioid)
io_desc_t *ciodesc;

ciodesc = pio_get_iodesc_from_id(ioid);
if(ciodesc)
if (ciodesc)
{
HASH_DEL(pio_iodesc_list, ciodesc);
if (current_iodesc = ciodesc)
if (current_iodesc == ciodesc)
current_iodesc = pio_iodesc_list;
free(ciodesc);
return PIO_NOERR;
Expand Down Expand Up @@ -367,7 +361,6 @@ int get_var_desc(int varid, var_desc_t **varlist, var_desc_t **var_desc)
int delete_var_desc(int varid, var_desc_t **varlist)
{
var_desc_t *v;
var_desc_t *prev = NULL;
int ret;

/* Check inputs. */
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1 change: 0 additions & 1 deletion src/clib/pio_rearrange.c
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Expand Up @@ -991,7 +991,6 @@ int rearrange_io2comp(iosystem_desc_t *ios, io_desc_t *iodesc, void *sbuf,
int niotasks;
int mpierr; /* Return code from MPI calls. */
int ret;
void *tmparray;

/* Check inputs. */
pioassert(ios && iodesc, "invalid input", __FILE__, __LINE__);
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186 changes: 104 additions & 82 deletions tests/cunit/test_darray_async_many.c
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Original file line number Diff line number Diff line change
Expand Up @@ -62,6 +62,63 @@ int my_type[NTYPE] = {PIO_BYTE, PIO_CHAR, PIO_SHORT, PIO_INT, PIO_FLOAT,
/* Names of the dimensions. */
char dim_name[NDIM4][PIO_MAX_NAME + 1] = {"time", "vert_level", "lat", "lon"};

int
check_4d_vars(int my_rank, int ncid, int *varid_4d)
{
void *data_in2 = NULL;
int expected_int_4d[VERT_LEN * LAT_LEN * LON_LEN] = {1, 0, 2, 1, 2, 1, 3, 2, 3, 2, 4, 3};
float expected_float_4d[VERT_LEN * LAT_LEN * LON_LEN] = {1, 0, 2, 1.5, 2, 1, 3, 2.5, 3, 2, 4, 3.5};
int ret;

for (int v = 0; v < NUM_4D_VARS; v++)
{
int xtype;
PIO_Offset size;

/* Get the type of the 4d var. */
if ((ret = PIOc_inq_vartype(ncid, varid_4d[v], &xtype)))
BAIL(ret);

/* Get the size of this type. */
if ((ret = PIOc_inq_type(ncid, xtype, NULL, &size)))
BAIL(ret);

/* Allocate memory for data. */
if (!(data_in2 = malloc(size * VERT_LEN * LAT_LEN * LON_LEN * NREC)))
BAIL(PIO_ENOMEM);

/* Read the data. */
if ((ret = PIOc_get_var(ncid, varid_4d[v], data_in2)))
BAIL(ret);

/* Check each element of data. */
for (int r = 0; r < LAT_LEN * LON_LEN * NREC; r++)
{
switch (xtype)
{
case PIO_INT:
if (((int *)data_in2)[r] != expected_int_4d[r % (VERT_LEN * LAT_LEN * LON_LEN)])
BAIL(ERR_WRONG);
break;
case PIO_FLOAT:
if (((float *)data_in2)[r] != expected_float_4d[r % (VERT_LEN * LAT_LEN * LON_LEN)])
BAIL(ERR_WRONG);
break;
default:
BAIL(ERR_WRONG);
}
}
free(data_in2);
data_in2 = NULL;
}

exit:
if (data_in2)
free(data_in2);

return ret;
}

/* Check the file that was created in this test. */
int check_darray_file(int iosysid, char *data_filename, int iotype, int my_rank,
int *rec_varid, int *norec_varid, int num_types, int *varid_4d)
Expand All @@ -88,42 +145,40 @@ int check_darray_file(int iosysid, char *data_filename, int iotype, int my_rank,
9223372036854775827ULL, 9223372036854775828ULL,
9223372036854775837ULL, 9223372036854775838ULL};
#endif /* _NETCDF4 */
int expected_int_4d[VERT_LEN * LAT_LEN * LON_LEN] = {1, 0, 2, 1, 2, 1, 3, 2, 3, 2, 4, 3};
float expected_float_4d[VERT_LEN * LAT_LEN * LON_LEN] = {1, 0, 2, 1.5, 2, 1, 3, 2.5, 3, 2, 4, 3.5};
void *data_in = NULL;
void *norec_data_in = NULL;

/* Reopen the file. */
if ((ret = PIOc_openfile(iosysid, &ncid, &iotype, data_filename, NC_NOWRITE)))
ERR(ret);
BAIL(ret);

/* Check metadata. */
int ndims_in, nvars_in, ngatts_in, unlimdimid_in;
if ((ret = PIOc_inq(ncid, &ndims_in, &nvars_in, &ngatts_in, &unlimdimid_in)))
ERR(ret);
BAIL(ret);
if (ndims_in != NDIM4 || nvars_in != num_types * 2 + NUM_4D_VARS || ngatts_in != 0 || unlimdimid_in != 0)
ERR(ERR_WRONG);
BAIL(ERR_WRONG);

/* Check the vars. */
for (int t = 0; t < num_types; t++)
{
void *data_in;
void *norec_data_in;
PIO_Offset type_size;

/* Find size of type. */
if ((ret = PIOc_inq_type(ncid, my_type[t], NULL, &type_size)))
ERR(ret);
BAIL(ret);

/* Allocate buffers to hold data. */
if (!(data_in = malloc(LAT_LEN * LON_LEN * NREC * type_size)))
ERR(PIO_ENOMEM);
BAIL(PIO_ENOMEM);
if (!(norec_data_in = malloc(LAT_LEN * LON_LEN * type_size)))
ERR(PIO_ENOMEM);
BAIL(PIO_ENOMEM);

/* Read record and non-record vars for this type. */
if ((ret = PIOc_get_var(ncid, rec_varid[t], data_in)))
ERR(ret);
BAIL(ret);
if ((ret = PIOc_get_var(ncid, norec_varid[t], norec_data_in)))
ERR(ret);
BAIL(ret);

/* Check each value of non-record data. */
for (int r = 0; r < LAT_LEN * LON_LEN; r++)
Expand All @@ -132,52 +187,52 @@ int check_darray_file(int iosysid, char *data_filename, int iotype, int my_rank,
{
case PIO_BYTE:
if (((signed char *)norec_data_in)[r] != expected_byte[r])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_CHAR:
if (((char *)norec_data_in)[r] != expected_char[r])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_SHORT:
if (((short *)norec_data_in)[r] != expected_short[r])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_INT:
if (((int *)norec_data_in)[r] != expected_int[r])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_FLOAT:
if (((float *)norec_data_in)[r] != expected_float[r])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_DOUBLE:
if (((double *)norec_data_in)[r] != expected_double[r])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
#ifdef _NETCDF4
case PIO_UBYTE:
if (((unsigned char *)norec_data_in)[r] != expected_ubyte[r])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_USHORT:
if (((unsigned short *)norec_data_in)[r] != expected_ushort[r])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_UINT:
if (((unsigned int *)norec_data_in)[r] != expected_uint[r])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_INT64:
if (((long long *)norec_data_in)[r] != expected_int64[r])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_UINT64:
if (((unsigned long long *)norec_data_in)[r] != expected_uint64[r])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
#endif /* _NETCDF4 */
default:
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
}
}

Expand All @@ -188,109 +243,76 @@ int check_darray_file(int iosysid, char *data_filename, int iotype, int my_rank,
{
case PIO_BYTE:
if (((signed char *)data_in)[r] != expected_byte[r % (LAT_LEN * LON_LEN)])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_CHAR:
if (((char *)data_in)[r] != expected_char[r % (LAT_LEN * LON_LEN)])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_SHORT:
if (((short *)data_in)[r] != expected_short[r % (LAT_LEN * LON_LEN)])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_INT:
if (((int *)data_in)[r] != expected_int[r % (LAT_LEN * LON_LEN)])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_FLOAT:
if (((float *)data_in)[r] != expected_float[r % (LAT_LEN * LON_LEN)])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_DOUBLE:
if (((double *)data_in)[r] != expected_double[r % (LAT_LEN * LON_LEN)])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
#ifdef _NETCDF4
case PIO_UBYTE:
if (((unsigned char *)data_in)[r] != expected_ubyte[r % (LAT_LEN * LON_LEN)])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_USHORT:
if (((unsigned short *)data_in)[r] != expected_ushort[r % (LAT_LEN * LON_LEN)])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_UINT:
if (((unsigned int *)data_in)[r] != expected_uint[r % (LAT_LEN * LON_LEN)])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_INT64:
if (((long long *)data_in)[r] != expected_int64[r % (LAT_LEN * LON_LEN)])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
case PIO_UINT64:
if (((unsigned long long *)data_in)[r] != expected_uint64[r % (LAT_LEN * LON_LEN)])
ERR(ERR_WRONG);
BAIL(ERR_WRONG);
break;
#endif /* _NETCDF4 */
default:
ERR(ERR_WRONG);
}
}

/* Check the 4D vars. */
for (int v = 0; v < NUM_4D_VARS; v++)
{
void *data_in;
int xtype;
PIO_Offset size;

/* Get the type of the 4d var. */
if ((ret = PIOc_inq_vartype(ncid, varid_4d[v], &xtype)))
ERR(ret);

/* Get the size of this type. */
if ((ret = PIOc_inq_type(ncid, xtype, NULL, &size)))
ERR(ret);

/* Allocate memory for data. */
if (!(data_in = malloc(size * VERT_LEN * LAT_LEN * LON_LEN * NREC)))
ERR(PIO_ENOMEM);

/* Read the data. */
if ((ret = PIOc_get_var(ncid, varid_4d[v], data_in)))
ERR(ret);

/* Check each element of data. */
for (int r = 0; r < LAT_LEN * LON_LEN * NREC; r++)
{
switch (xtype)
{
case PIO_INT:
if (((int *)data_in)[r] != expected_int_4d[r % (VERT_LEN * LAT_LEN * LON_LEN)])
ERR(ERR_WRONG);
break;
case PIO_FLOAT:
if (((float *)data_in)[r] != expected_float_4d[r % (VERT_LEN * LAT_LEN * LON_LEN)])
ERR(ERR_WRONG);
break;
default:
ERR(ERR_WRONG);
}
BAIL(ERR_WRONG);
}

/* Release memory. */
free(data_in);
}

/* Free memory. */
free(data_in);
data_in = NULL;
free(norec_data_in);
norec_data_in = NULL;

/* Check the 4D vars. */
if ((ret = check_4d_vars(my_rank, ncid, varid_4d)))
BAIL(ret);
}

/* Close the file. */
if ((ret = PIOc_closefile(ncid)))
ERR(ret);

return 0;
exit:
if (data_in)
free(data_in);
if (norec_data_in)
free(norec_data_in);
return ret;
}

/* Run a simple test using darrays with async. */
Expand Down
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