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Merge pull request #425 in HDFFV/hdf5 from ~LRKNOX/hdf5_lrk:hdf5_1_10 to hdf5_1_10

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* commit 'b03e41146a3e15c7a287ab98f1963bf7944719a8':
  Skip tests for page buffering in test/fheap.c for parallel build Skip the two tests for page buffering in test/fheap.c because this feature is disabled in parallel. Activate full testing when this feature is re-enabled in the future for parallel build.
  Due to HDFVIEW-19 add read VL as string function
  Fix URL name
  updated with README changes
  DAILYTEST-250 change test props to reduce timeout
  Combined the README_DEVEL and README, and removed out-dated README material
  Fix for H5Dset_extent test failure with extensive array indexing (HDFFV-9771) 1) Calculate chunk index for extensive array index based on swizzled max chunks when unlim_dim > 0 2) Minor fixes to test/fheap.c that somehow were missed from last check in.  See pull request #396 review comments.
This commit is contained in:
Larry Knox 2017-04-13 16:40:56 -05:00
commit b77e601996
7 changed files with 190 additions and 221 deletions
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1
MANIFEST
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@ -247,7 +247,6 @@
./fortran/src/HDF5.F90 ./fortran/src/HDF5.F90
./fortran/src/Makefile.am ./fortran/src/Makefile.am
./fortran/src/README ./fortran/src/README
./fortran/src/README_DEVELOPEMENT _DO_NOT_DISTRIBUTE_
./fortran/src/h5fc.in ./fortran/src/h5fc.in
./fortran/src/hdf5_fortrandll.def.in ./fortran/src/hdf5_fortrandll.def.in

256
fortran/src/README
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@ -1,122 +1,18 @@
===================================
README for the Fortran APIs to HDF5
===================================
README for the FORTRAN90 Prototype APIs to HDF5 This directory contains Fortran APIs for HDF5 Library functionality.
A complete list of implemented Fortran subroutines can be found in the HDF5
Reference Manual.
This distribution contains the HDF5 FORTRAN90 APIs source code (prototype)
based on the HDF5 1.2.2 release (ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current),
tests and examples.
This prototype supports a selected subset of the HDF5 Library functionality.
A complete list of the Fortran subroutines can be found in the HDF5
Reference Manual provided with this release.
Check the online documentation at http://hdf.ncsa.uiuc.edu/HDF5/doc (select
the "HDF5 Fortran90 Docs" link at the bottom of the left-hand column) or
H5_F90.R1.2.2.RefMan.tar at ftp://hdf.ncsa.uiuc.edu/HDF5/fortran .
Changes since last release (October 1999)
=========================================
* Support for Linux
* Support for parallel features (tested on O2K platform only)
* Most of the functions from the H5R, H5P, H5T, H5E and H5I interfaces were
implemented. See Reference Manual for complete list. The new functions
include support for object and dataset region references, and for
compound datatypes.
* This prototype supports more predefined types. See list below in
the "About the Fortran APIs" section.
* This prototype supports T3E and T3E with mpt 1.3. One has to modify
H5Dff.f90, H5Aff.f90, H5Pff.f90 to comment lines with the module procedures for
double precision datatypes. See source code.
Supported platforms
===================
The FORTRAN90 APIs provided here are known to work with the
following platforms and compilers:
* SunOS 5.6 with WorkshopCompilers 4.2 Fortran 90 1.2
* SunOS 5.7 with WorkshopCompilers 5.0 Fortran 90 2.0
* OSF1 V4.0 with Digital Fortran 90 4.1
* Linux RedHat 6.1, Kernel 2.2.12 with PGF90
* T3E with Cray Fortran: Version 3.4.0.0
with mpt 1.3
Compilation
===========
1. Install HDF5 Release 1.2.2 on your system
(ftp://ftp.ncsa.uiuc.edu/HDF/HDF5/current). If you are using a
binary distribution provided by the HDF group, make sure that a GZIP
library is installed on your system. If you do not have a GZIP library,
you may copy it from the HDF FTP server.
2. In the src directory copy H5fortran_types.f90_<system> to
H5fortran_types.f90, where <system> is one of the following:
solaris
digunix
linux
Example: On Digital Unix systems use the following command
cp H5fortran_types.f90_digunix H5fortran_types.f90
3. Edit Makefile_<system >in the src/, test/ and examples/ directories
to specify the locations of the HDF5 C Library, the GZIP Library, and the
corresponding include files on your system.
4. In the src directory, run make to create the HDF5 FORTRAN90 library
hdf5_fortran.a
make -f Makefile_<system>
Example: On Solaris run
make -f Makefile_solaris
The Fortran library hdf5_fortran.a will be created.
5. In the test directory, build tests by running
make -f Makefile_<system>
This command will build fortranlib_test, fflush1 and fflush2 executables.
Run those executables to make sure that the library works on your system.
6. In the examples directory, run
make -f Makefile_<system>
to build the following examples:
fileexample - creates an HDF5 file
dsetexample - creates an empty dataset of integers
rwdsetexample - writes and reads to the dataset created by dsetexample
groupexample - creates a group in the file
grpsexample - creates groups using absolute and relative names
grpdsetexample - creates datasets in the groups
hyperslabexample - writes and reads a hyperslab
selectele - writes element selections
attrexample - creates and writes a dataset attribute
compound - creates, writes and reads one dim array of structures
mountexample - shows how to use mounting files to access a dataset
refobjexample - creates and stores references to the objects
refregexample - creates and stores references to the dataset regions
The script run_example.sh runs the examples in the appropriate order.
Use the HDF5 utility, h5dump, to see the content of the created HDF5 files.
7. Install the HDF5 Reference Manual (in HTML format). The manual
can be found in the Unix tar file H5_F90.R1.2.2.RefMan.tar
on the ftp server and is served over the Web from
http://hdf.ncsa.uiuc.edu/HDF5/doc/ (select the "HDF5 Fortran90 Docs"
link at the bottom of the left-hand column).
8. Send bug reports and comments to hdfhelp@ncsa.uiuc.edu
User's Guide Notes
+++++++++++++++++++
About the source code organization About the source code organization
================================== ==================================
The Fortran APIs are organized in modules parallel to the HDF5 Interfaces. The Fortran APIs are organized in modules parallel to the HDF5 Interfaces.
Each module is in a separate file with the name H5*ff.f. Corresponding C Each module is in a separate file with the name H5*ff.F90. Corresponding C
stubs are in the H5*f.c files. For example, the Fortran File APIs are in stubs are in the H5*f.c files. For example, the Fortran File APIs are in
the file H5Fff.f and the corresponding C stubs are in the file H5Ff.c. the file H5Fff.F90 and the corresponding C stubs are in the file H5Ff.c.
Each module contains Fortran definitions of the constants, interfaces to Each module contains Fortran definitions of the constants, interfaces to
the subroutines if needed, and the subroutines themselves. the subroutines if needed, and the subroutines themselves.
@ -124,31 +20,29 @@ the subroutines if needed, and the subroutines themselves.
Users must use constant names in their programs instead of the numerical Users must use constant names in their programs instead of the numerical
values, as the numerical values are subject to change without notice. values, as the numerical values are subject to change without notice.
About the Fortran APIs Quick overview of the Fortran APIs
======================= ==============================================
* An in-depth description of each Fortran API and its parameters can
be found in the HDF5 Reference Manual.
* The Fortran APIs come in the form of Fortran subroutines. * The Fortran APIs come in the form of Fortran subroutines.
* Each Fortran subroutine name is derived from the corresponding C function * Each Fortran subroutine name is derived from the corresponding C function
name by adding "_f" to the name. For example, the name of the C function name by adding "_f" to the name. For example, the name of the C function
to create an HDF5 file is H5Fcreate; the corresponding Fortran subroutine to create an HDF5 file is H5Fcreate; the corresponding Fortran subroutine
is h5fcreate_f. is h5fcreate_f.
* A description of each Fortran subroutine and its parameters can be found * The parameter list for each Fortran subroutine usually has two more parameters
following the description of the corresponding C function in the than the corresponding C function. These additional parameters typically hold
Reference Manual provided with this release. The manual can be found in
the Unix tar file H5_F90.R1.2.2.tar in this directory and
is served over the Web from http://hdf.ncsa.uiuc.edu/HDF5/doc/ (select
the "HDF5 Fortran90 Docs" link at the bottom of the left-hand column).
* The parameter list for each Fortran subroutine has two more parameters
than the corresponding C function. These additional parameters hold
the return value and an error code. The order of the Fortran subroutine the return value and an error code. The order of the Fortran subroutine
parameters may differ from the order of the C function parameters. parameters may differ from the order of the C function parameters.
The Fortran subroutine parameters are listed in the following order:
The Fortran subroutine parameters are usually listed in the following order:
-- required input parameters, -- required input parameters,
-- output parameters, including return value and error code, and -- output parameters, including return value and error code, and
-- optional input parameters. optional input parameters.
For example, the C function to create a dataset has the following For example, the C function to create a dataset has the following
prototype: prototype:
@ -158,72 +52,35 @@ About the Fortran APIs
The corresponding Fortran subroutine has the following form: The corresponding Fortran subroutine has the following form:
SUBROUTINE h5dcreate_f(loc_id, name, type_id, space_id, dset_id, SUBROUTINE h5dcreate_f(loc_id, name, type_id, space_id, dset_id, &
hdferr, creation_prp) hdferr, dset_creation_prp, link_creation_prp, dset_access_prop)
The first four parameters of the Fortran subroutine correspond to the The first four parameters of the Fortran subroutine correspond to the
C function parameters. The fifth parameter dset_id is an output C function parameters. The fifth parameter dset_id is an output
parameter and contains a valid dataset identifier if the value of the parameter and contains a valid dataset identifier if the value of the
sixth output parameter hdferr indicates successful completion. sixth output parameter, hdferr, indicates successful completion.
(Error code descriptions are provided with the subroutine descriptions (Error code descriptions are provided with the subroutine descriptions
in the Reference Manual.) The seventh input parameter creation_prp in the Reference Manual.) The last three input parameters are optional
is optional, and may be omitted when the default creation property and may be omitted, resulting in default values being used.
list is used.
(XXX: Update this! - QAK)
* Parameters to the Fortran subroutines have one of the following * Parameters to the Fortran subroutines typically include
predefined datatypes (see the file H5fortran_types.f90 for KIND predefined datatypes (see the build-time generated file
definitions): H5fortran_types.F90 for a complete listing):
INTEGER(HID_T) compares with hid_t type in HDF5 C APIs INTEGER(HID_T) compares with hid_t type in HDF5 C APIs
INTEGER(HSIZE_T) compares with hsize_t in HDF5 C APIs INTEGER(HSIZE_T) compares with hsize_t in HDF5 C APIs
INTEGER(HSSIZE_T) compares with hssize_t in HDF5 C APIs INTEGER(HSSIZE_T) compares with hssize_t in HDF5 C APIs
INTEGER(SIZE_T) compares with the C size_t type INTEGER(SIZE_T) compares with the C size_t type
These integer types usually correspond to 4 or 8 byte integers, These integer types usually correspond to 4 or 8 byte integers,
depending on the FORTRAN90 compiler and corresponding HDF5 depending on the Fortran compiler and corresponding HDF5
C library definitions. C library definitions.
The H5R module defines two types: * Each Fortran application must call the h5open_f subroutine to
TYPE(HOBJ_REF_T_F) compares to the hobj_ref_t in HDF5 C API
TYPE(HDSET_REG_REF_T_F) compares to hdset_reg_ref_t in HDF5 C API
These types are represented by character arrays now.
The internal representation can be changed in the future.
* Each Fortran application must call the h5init_types subroutine to
initialize the Fortran predefined datatypes before calling the HDF5 Fortran initialize the Fortran predefined datatypes before calling the HDF5 Fortran
subroutines. The application must call the h5close_types subroutine subroutines. The application should call the h5close_f subroutine
after all calls to the HDF5 Fortran Library. after all calls to the HDF5 Fortran Library.
* The following predefined types are implemented in this prototype:
H5T_NATIVE_INTEGER
H5T_NATIVE_REAL
H5T_NATIVE_DOUBLE
H5T_NATIVE_CHARACTER
H5T_STD_REF_OBJ
H5T_STD_REF_DSETREG
H5T_IEEE_F32BE
H5T_IEEE_F32LE
H5T_IEEE_F64BE
H5T_IEEE_F64LE
H5T_STD_I8BE
H5T_STD_I8LE
H5T_STD_I16BE
H5T_STD_I16LE
H5T_STD_I32BE
H5T_STD_I32LE
H5T_STD_I64BE
H5T_STD_I64LE
H5T_STD_U8BE
H5T_STD_U8LE
H5T_STD_U16BE
H5T_STD_U16LE
H5T_STD_U32BE
H5T_STD_U32LE
H5T_STD_U64BE
H5T_STD_U64LE
* When a C application reads data stored from a Fortran program, the data * When a C application reads data stored from a Fortran program, the data
will appear to be transposed due to the difference in the C - Fortran will appear to be transposed due to the difference in the C - Fortran
storage order. For example, if Fortran writes a 4x6 two-dimensional dataset storage order. For example, if Fortran writes a 4x6 two-dimensional dataset
@ -233,6 +90,45 @@ About the Fortran APIs
* Fortran indices are 1 based. * Fortran indices are 1 based.
* Compound datatype datasets can be written or read by atomic fields only. ============================
FOR DEVELOPERS
============================
Procedure to add a new function
----------------------------------
(1) Edit the fortran/src/H5*ff.F90 file
(2) Edit the fortran/src/H5*f.c file
(3) Edit the fortran/src/H5f90proto.h file
(4) Add the new function to fortran/src/hdf5_fortrandll.def.in
Procedure for passing C variables to Fortran
---------------------------------------------
(1) Find the C struct name you are interested in:
(a) src/H5public.h if it is a generic type, i.e. H5_*
or
(b) src/H5*public.h if is a specific type, i.e. H5*_
(2) Put that structure into an array that will be passed to fortran in:
(a) fortran/src/H5_f.c (add to nh5init_flags_c subroutine)
(b) edit fortran/src/H5f90proto.h and edit nh5init_flags_c interface call
(3) Edit the function call in fortran/src/H5_ff.F90
(a) edit the call: FUNCTION h5init_flags_c
(b) edit h5init_flags_c call in h5open_f to match the number of arguments passing
(4) add the size of the array and array to fortran/src/H5f90global.F90
- must match the size found it H5_f.c
NOTE: To just add a default C value argument, do steps (2a) and (4)
Procedure for adding a new file to the repository
--------------------------------------------------
Add the name of the file to the:
(1) Makefile.am located in the same directory as the newfile
(2) CMakeLists.txt located in the same directory as the newfile
(3) MANIFEST located in the top level directory
Not all of the APIs provided with this prototype have been fully tested.

38
fortran/src/README_DEVELOPEMENT
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@ -1,38 +0,0 @@
Procedure to add a new function
---------------------------------
(1) Edit the fortran/src/H5*ff.f90 file
(2) Edit the fortran/src/H5*f.c file
(3) Edit the fortran/src/H5f90proto.h file
(4) Add the new function to fortran/src/hdf5_fortrandll.def.in
Procedure for passing C variables to Fortran
---------------------------------------------
(1) Find the C struct name you are interested in:
(a) src/H5public.h if it is a generic type, i.e. H5_*
or
(b) src/H5*public.h if is a specific type, i.e. H5*_
(2) Put that structure into an array that will be passed to fortran in:
(a) fortran/src/H5_f.c (add to nh5init_flags_c subroutine)
(b) edit fortran/src/H5f90proto.h and edit nh5init_flags_c interface call
(3) Edit the function call in fortran/src/H5_ff.f90
(a) edit the call: FUNCTION h5init_flags_c
(b) edit h5init_flags_c call in h5open_f to match the number of arguments passing
(4) add the size of the array and array to fortran/src/H5f90global.f90
- must match the size found it H5_f.c
NOTE: To just add a default C value argument, do steps (2a) and (4)
Procedure for adding a new file to the repository
--------------------------------------------------
Add the name of the file to the:
(1) Makefile.am located in the same directory as the newfile
(2) CMakeLists.txt located in the same directory as the newfile
(3) MANIFEST located in the top level directory

3
java/src/hdf/hdf5lib/H5.java
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@ -1798,6 +1798,9 @@ public class H5 implements java.io.Serializable {
return H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true); return H5Dread_short(dataset_id, mem_type_id, mem_space_id, file_space_id, xfer_plist_id, buf, true);
} }
public synchronized static native int H5DreadVL(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, Object[] buf) throws HDF5LibraryException, NullPointerException;
public synchronized static native int H5Dread_string(long dataset_id, long mem_type_id, long mem_space_id, public synchronized static native int H5Dread_string(long dataset_id, long mem_type_id, long mem_space_id,
long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException; long file_space_id, long xfer_plist_id, String[] buf) throws HDF5LibraryException, NullPointerException;

91
java/src/jni/h5dImp.c
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@ -55,6 +55,7 @@ extern jobject visit_callback;
/* Local Prototypes */ /* Local Prototypes */
/********************/ /********************/
static herr_t H5DreadVL_asstr (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
static herr_t H5DreadVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); static herr_t H5DreadVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
static herr_t H5DreadVL_array (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); static herr_t H5DreadVL_array (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
static herr_t H5DwriteVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf); static herr_t H5DwriteVL_str (JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf);
@ -992,6 +993,96 @@ Java_hdf_hdf5lib_H5_H5Dwrite_1double
return (jint)status; return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dwrite_1double */ } /* end Java_hdf_hdf5lib_H5_H5Dwrite_1double */
/*
* Class: hdf_hdf5lib_H5
* Method: H5DreadVL
* Signature: (JJJJJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5DreadVL
(JNIEnv *env, jclass clss, jlong dataset_id, jlong mem_type_id, jlong mem_space_id,
jlong file_space_id, jlong xfer_plist_id, jobjectArray buf)
{
herr_t status = -1;
htri_t isVlenStr=0;
if (buf == NULL) {
h5nullArgument(env, "H5DreadVL: buf is NULL");
} /* end if */
else {
isVlenStr = H5Tdetect_class((hid_t)mem_type_id, H5T_STRING);
if (isVlenStr)
h5badArgument(env, "H5DreadVL: type is not variable length non-string");
else
status = H5DreadVL_asstr(env, (hid_t)dataset_id, (hid_t)mem_type_id,
(hid_t)mem_space_id, (hid_t)file_space_id,
(hid_t)xfer_plist_id, buf);
} /* end else */
return (jint)status;
} /* end Java_hdf_hdf5lib_H5_H5Dread_1VLStrings */
herr_t
H5DreadVL_asstr
(JNIEnv *env, hid_t did, hid_t tid, hid_t mem_sid, hid_t file_sid, hid_t xfer_plist_id, jobjectArray buf)
{
jint i;
jint n;
jstring jstr;
h5str_t h5str;
hvl_t *rdata;
size_t size;
size_t max_len = 0;
herr_t status = -1;
n = ENVPTR->GetArrayLength(ENVPAR buf);
rdata = (hvl_t*)HDcalloc((size_t)n, sizeof(hvl_t));
if (rdata == NULL) {
h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buff for read");
} /* end if */
else {
status = H5Dread(did, tid, mem_sid, file_sid, xfer_plist_id, rdata);
if (status < 0) {
H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
HDfree(rdata);
h5JNIFatalError(env, "H5DreadVL_notstr: failed to read data");
} /* end if */
else {
max_len = 1;
for (i=0; i < n; i++) {
if ((rdata + i)->len > max_len)
max_len = (rdata + i)->len;
}
size = H5Tget_size(tid) * max_len;
HDmemset(&h5str, 0, sizeof(h5str_t));
h5str_new(&h5str, 4 * size);
if (h5str.s == NULL) {
H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
HDfree(rdata);
h5JNIFatalError(env, "H5DreadVL_notstr: failed to allocate buf");
} /* end if */
else {
for (i=0; i < n; i++) {
h5str.s[0] = '\0';
h5str_sprintf(&h5str, did, tid, rdata+i, 0);
jstr = ENVPTR->NewStringUTF(ENVPAR h5str.s);
ENVPTR->SetObjectArrayElement(ENVPAR buf, i, jstr);
} /* end for */
h5str_free(&h5str);
H5Dvlen_reclaim(tid, mem_sid, xfer_plist_id, rdata);
HDfree(rdata);
} /* end else */
} /* end else */
} /* end else */
return status;
}
/* /*
* Class: hdf_hdf5lib_H5 * Class: hdf_hdf5lib_H5
* Method: H5Dread_string * Method: H5Dread_string

9
java/src/jni/h5dImp.h
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@ -204,6 +204,15 @@ JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5Dwrite_1double Java_hdf_hdf5lib_H5_H5Dwrite_1double
(JNIEnv*, jclass, jlong, jlong, jlong, jlong, jlong, jdoubleArray, jboolean); (JNIEnv*, jclass, jlong, jlong, jlong, jlong, jlong, jdoubleArray, jboolean);
/*
* Class: hdf_hdf5lib_H5
* Method: H5DreadVL
* Signature: (JJJJJ[Ljava/lang/String;)I
*/
JNIEXPORT jint JNICALL
Java_hdf_hdf5lib_H5_H5DreadVL
(JNIEnv*, jclass, jlong, jlong, jlong, jlong, jlong, jobjectArray);
/* /*
* Class: hdf_hdf5lib_H5 * Class: hdf_hdf5lib_H5
* Method: H5Dread_string * Method: H5Dread_string

13
test/fheap.c
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@ -16388,14 +16388,23 @@ main(void)
/* /*
* Caution when turning on ExpressMode 0: * Caution when turning on ExpressMode 0:
* It will activate testing with different combinations of * It will activate testing with different combinations of
* page buffering and file space strategy and the * page buffering and file space strategy and the
* running time will be long. * running time will be long.
* For parallel build, the last two tests for page buffering
* are skipped because this feature is disabled in parallel.
* Activate full testing when this feature is re-enabled
* in the future for parallel build.
*/ */
if(ExpressMode > 1) if(ExpressMode > 1)
HDprintf("***Express test mode on. Some tests may be skipped\n"); HDprintf("***Express test mode on. Some tests may be skipped\n");
else if(ExpressMode == 0) else if(ExpressMode == 0) {
#ifdef H5_HAVE_PARALLEL
num_pb_fs = NUM_PB_FS - 2;
#else
num_pb_fs = NUM_PB_FS; num_pb_fs = NUM_PB_FS;
#endif
}
/* Initialize heap creation parameters */ /* Initialize heap creation parameters */
init_small_cparam(&small_cparam); init_small_cparam(&small_cparam);