h5check
[OPTIONS]
file
h5check
is a validation tool designed to verify that an HDF5 file is encoded
according to the HDF5 File Format
Specification. The purpose is to ensure data model integrity and
long-term compatibility between evolving versions of the HDF5 Library.
Independent Verification Tool:
Note that h5check is designed to operate independently of the
HDF5 Library:
- It verifies the validity of an HDF5 file directly against the HDF5 File Format Specification without reference to or any use of the HDF5 Library.
h5checkis distributed separately; see “HDF5 Tools and Software.”
h5check scans through the encoded content,
verifying it against the defined library format.
If it finds any non-compliance, h5check prints the error and
the reason behind the non-compliance; if possible, it continues the scanning.
If h5check does not find any non-compliance, it prints an
approval statement upon completion.
By default, the file is verified against the latest version of the
file format; as of this writing, that is the format recognized by the
HDF5 Release 1.8.x series. A format version can be explicitly specified
with the -fn
(or --format=n) option.
For example, -f16 (or --format=16) would specify
verification against the format recognized by the HDF5 Release 1.6.x series.
-h, --help- Print usage message and exit.
-V, --version- Print version number and exit.
-vn, --verbose n- Set verbose mode:
n=0Terse Indicate only whether file is compliant. n=1Normal Print progress and all errors found. (Default) n=2Verbose Print all known information; usually used for debugging. -e, --external- Validate external links existing in the file.
-fn, --format n- Set library release version against which the file is to be
validated:
n=16Validate according to HDF5 Release 1.6.x series. n=18Validate according to HDF5 Release 1.8.x series. (Default) -oa, --object a- Check object header, where
ais the address of the object header to be validated.
0
| Succeeded. |
1
| Command failures, such as argument errors. |
2
| Format compliance errors found. |
| Release | Change |
| 1.8.5 | Tool first distributed shortly before this release. |
- Last modified: 24 April 2014
- Tool Name: h5perf
- Syntax:
- Tool Name: h5perf
h5perf[-h|--help]h5perf[options]- Purpose:
- Tests Parallel HDF5 performance.
- Description:
h5perfis a tool for testing the performance of the Parallel HDF5 Library. The tool can perform testing with 1-dimensional and 2-dimensional buffers and datasets. For details regarding data organization and access, see the “h5perf User Guide.”The following environment variables have the following effects on
h5perfbehavior:HDF5_NOCLEANUPIf set, h5perfdoes not remove data files.
(Default: Data files are removed.)HDF5_MPI_INFOMust be set to a string containing a list of semi-colon separated key=valuepairs for the MPIINFOobject.
Example:HDF5_PARAPREFIXSets the prefix for parallel output data files. - Options and Parameters:
These terms are used as follows in this section: file A filename size A size specifier, expressed as an integer greater than or equal to 0 (zero) followed by a size indicator:
Kfor kilobytes (1024 bytes)
Mfor megabytes (1048576 bytes)
Gfor gigabytes (1073741824 bytes)
Example:37Mspecifies 37 megabytes or 38797312 bytes.N An integer greater than or equal to 0 (zero)
-h,--helpPrints a usage message and exits. -asize,--align=sizeSpecifies the alignment of objects in the HDF5 file.
(Default:1)-Aapi_list,--api=api_listSpecifies which APIs to test. api_list is a comma-separated list with the following valid values:
(Default: All APIs)phdf5Parallel HDF5 mpiioMPI-I/O posixPOSIX
Example,--api=mpiio,phdf5specifies that the MPI I/O and Parallel HDF5 APIs are to be monitored.-Bsize,--block-size=sizeControls the block size within the transfer buffer.
(Default: Half the number of bytes per process per dataset)Block size versus transfer buffer size:
The transfer buffer size is the size of a buffer in memory. The data in that buffer is broken into block size pieces and written to the file.Transfer buffer size is discussed below with the
-x (or--min-xfer-size) and-X(or--max-xfer-size) options.The pattern in which the blocks are written to the file is described in the discussion of the
-I(or--interleaved) option.-c,--chunkCreates HDF5 datasets in chunked layout.
(Default: Off)-C,--collectiveUse collective I/O for the MPI I/O and Parallel HDF5 APIs.
(Default: Off, i.e., independent I/O)If this option is set and the MPI-I/O and PHDF5 APIs are in use, all the blocks of every process will be written at once with an MPI derived type.
-dN,--num-dsetsNSets the number of datasets per file.
(Default:1)-Ddebug_flags,--debug=debug_flagsSets the debugging level. debug_flags is a comma-separated list of debugging flags with the following valid values:
(Default: No debugging)1Minimal debugging 2Moderate debugging (“not quite everything”) 3Extensive debugging (“everything”) 4All possible debugging (“the kitchen sink”) rRaw data I/O throughput information tTimes, in additions to throughputs vVerify data correctness Example:
--debug=2,r,tspecifies to run a moderate level of debugging while collecting raw data I/O throughput information and verifying the correctness of the data.Throughput values are computed by dividing the total amount of transferred data (excluding metadata) over the time spent by the slowest process. Several time counters are defined to measure the data transfer time and the total elapsed time; the latter includes the time spent during file open and close operations. A number of iterations can be specified with the option
-i(or--num-iterations) to create the desired population of measurements from which maximum, minimum, and average values can be obtained. The timing scheme is the following:for each iteration initialize elapsed time counter initialize data transfer time counter for each file start and accumulate elapsed time counter file open start and accumulate data transfer time counter access entire file stop data transfer time counter file close stop elapsed time counter end file save elapsed time counter save data transfer time counter end iterationThe reported write throughput is based on the accumulated data transfer time, while the write open-close throughput uses the accumulated elapsed time.
-esize,--num-bytes=sizeSpecifies the number of bytes per process per dataset.
(Default:256Kfor 1D,8Kfor 2D)Depending on the selected geometry, each test dataset can be a linear array of size bytes-per-process * num-processes or a square array of size (bytes-per-process * num-processes) × (bytes-per-process * num-processes). The number of processes is set by the
-p(or--min-num-processes) and-P(or--max-num-processes) options.-FN,--num-files=NSpecifies the number of files.
(Default:1)-g,--geometrySelects 2D geometry for testing.
(Default: Off, i.e., 1D geometry)-iN,--num-iterations=NSets the number of iterations to perform.
(Default:1)-I,--interleavedSets interleaved block I/O.
(Default: Contiguous block I/O)Interleaved and contiguous patterns in 1D geometry:
When a contiguous access pattern is chosen, the dataset is evenly divided into num-processes regions and each process writes data to its assigned region. When interleaved blocks are written to a dataset, space for the first block of the first process is allocated in the dataset, then space is allocated for the first block of the second process, etc., until space is allocated for the first block of each process, then space is allocated for the second block of the first process, the second block of the second process, etc.For example, with a three process run, 512KB bytes-per-process, 256KB transfer buffer size, and 64KB block size, each process must issue two transfer requests to complete access to the dataset.
Contiguous blocks of the first transfer request are written as follows:
1111----2222----3333----Interleaved blocks of the first transfer request are written as follows:
123123123123------------The actual number of I/O operations involved in a transfer request depends on the access pattern and communication mode. When using independent I/O with an interleaved access pattern, each process performs four small non-contiguous I/O operations per transfer request. If collective I/O is turned on, the combined content of the buffers of the three processes will be written using one collective I/O operation per transfer request.
For details regarding the impact of performance and access patterns in 2D, see the “h5perf User Guide.”
-m,--mpi-posixThis option is no longer available. -n,--no-fillSpecifies to not write fill values to HDF5 datasets. This option is supported only in HDF5 Release v1.6 or later.
(Default: Off, i.e., write fill values)-ofile,--output=fileSets the output file for raw data to file.
(Default: None)-pN,--min-num-processes=NSets the minimum number of processes to be used.
(Default:1)-PN,--max-num-processes=N
Sets the maximum number of processes to be used.
(Default: AllMPI_COMM_WORLDprocesses)-Tsize,--threshold=sizeSets the threshold for alignment of objects in the HDF5 file.
(Default:1)-w,--write-onlyPerforms only write tests, not read tests.
(Default: Read and write tests)-xsize,--min-xfer-size=sizeSets the minimum transfer buffer size.
(Default: Half the number of bytes per processor per dataset)This option and the
-Xsize option (or--max-xfer-size=size) control transfer-buffer-size, the size of the transfer buffer in memory. In 1D geometry, the transfer buffer is a linear array of size transfer-buffer-size. In 2D geometry, the transfer buffer is a rectangular array of size block-size × transfer-buffer-size, or transfer-buffer-size × block-size if the interleaved access pattern is selected.-Xsize,--max-xfer-size=sizeSets the maximum transfer buffer size.
(Default: The number of bytes per processor per dataset)- Exit Status:
0 Succeeded. >0 An error occurred. - History:
Release Change 1.6.0 Tool introduced in this release. 1.6.8 and 1.8.0 Option -g,--geometryintroduced in this release.
- Tool Name: h5perf_serial
- Syntax:
h5perf_serial[-h|--help]h5perf_serial[options]- Purpose:
- Tests HDF5 serial performance.
- Description:
h5perf_serialprovides tools for testing the performance of the HDF5 Library in serial mode.See “h5perf_serial, a Serial File System Benchmarking Tool” for a complete description of this tool.
The following environment variable can be set to control the specfied aspect of
h5perf_serialbehavior:HDF5_NOCLEANUPIf set, h5perf_serialdoes not remove data files.
(Default: Data files are removed.)HDF5_PREFIXSets the prefix for output data files. - Options and Parameters:
-
The term size specifier is used
as follows in this section:
- Exit Status:
0 Succeeded. >0 An error occurred. - History:
Release Command Line Tool 1.8.1 Tool introduced in this release.
A size specifier is an integer greater than or equal to 0 (zero) followed by a size indicator:
Kfor kilobytes (1024 bytes)
Mfor megabytes (1048576 bytes)
Gfor gigabytes (1073741824 bytes)
Example:37Mspecifies 37 megabytes or 38797312 bytes.-Aapi_listSpecifies which APIs to test. api_list is a comma-separated list with the following valid values:
(Default: All APIs are monitored.)hdf5HDF5 Library APIs posixPOSIX APIs Example:
-A hdf5,posixspecifies that the HDF5 and POSIX APIs are to be monitored.-cchunk_size_listSpecifies chunked storage and defines chunks dimensions and sizes.
(Default: Chunking is off.)chunk_size_list is a comma-separated list of size specifiers. For example, a chunk_size_list value of
2K,4K,6M
specifies that chunking is turned on and that chunk size is 2 kilobytes by 4 kilobytes by 6 megabytes.-edataset_size_listSpecifies dataset dimensionality and dataset dimension sizes.
(Default dataset size is 100x200, or100,200.)dataset_size_list is a comma-separated list of size specifiers, which are defined above.
For example, a dataset_size_list value of
2K,4K,6M
specifies a 2 kilobytes by 4 kilobytes by 6 megabytes dataset.-iiterationsSpecifies the number of iterations to perform.
(Default: A single iteration,1, is performed.)iterations is an integer specifying the number of iterations.
-raccess_orderSpecifies dimension access order.
(Default:1,2)access_order is a comma-separated list of integers specifying the order of access. For example,
-r 1,3,2
specifies the traversal of dimension 1 first, then dimension 3, and finally dimension 2.-tSelects extendable HDF5 dataset dimensions.
(Default: Datasets are fixed size.)-vfile_driverSelects HDF5 driver to be used for HDF5 file access.
(Default:sec2)Valid values are as follows:
sec2
stdio
core
split
multi
family
direct-wSpecifies the performance of write tests only, read performance will not be tested.
(Default: Both write and read tests are performed.)-xbuffer_size_listSpecifies transfer buffer dimensions and sizes.
(Default:10,20)
- Last modified: 5 May 2016
- Tool Name: h5clear
- Syntax:
h5clear [OPTIONS] file- Purpose:
- To clear the
status_flagsfield in the superblock of the file specified in the command line or to remove the metadata cache image from the file.
- Description:
- The
h5cleartool can either clear thestatus_flagsfield in the superblock of the file or close a metadata cache image in the specified file.With the implementation of file locking, the library uses the
status_flagsfield in the superblock to mark a file as in writing or SWMR writing mode when a file is opened. The library will clear this field when the file closes.
However, a situation may occur where an open file is closed without going through the normal library file closing procedure, and this field will not be cleared as a result. An example would be if an application program crashed. This situation will prevent a user from opening the file. Theh5cleartool will clear thestatus_flagsfield, and the user can then open the file.When used to close a metadata cache image,
h5clearwill open the supplied HDF5 file in Read-Write (R/W) mode, check to see if it contains a cache image, and then close it. If the file does not contain a cache image,h5clearwill generate a warning message to that effect. -
- File Options:
-h, --helpPrint a usage message and exit -V, --versionPrint version number and exit -s, --statusClear the status_flagsfield in the file's superblock-m, --imageRemove the metadata cache image from the file - Exit Status:
0 Succeeded. > 0 An error occurred. - History:
Release Change 1.10.1 -m,--imageoption added to remove the metadata cache image.1.10.0 Tool introduced in this release.
- Tool Name:
h5watch - Syntax:
h5watch [OPTIONS] OBJECT- Purpose:
- Outputs new records appended to a dataset as the dataset grows.
- Motivation:
h5watchcan be used to watch data that is added to a dataset. The functionality is similar to the Unix user commandtailwith the follow option, which outputs appended data as the file grows.- Current Limitations:
- The current limitations are the following:
h5watchcan only be used on chunked datasets with unlimited dimension(s) or a fixed dimension with a maximum dimension setting.- While monitoring a dataset, users need to ensure that data that is being written to the dataset is flushed to the file.
- Options and Parameters:
- Options:
- The following optional command-line options can be used with
h5watch: Long Format Comments --helpPrint a usage message and exit. --versionPrint the version of HDF5 and exit. --labelLabel members of a compound datatyped dataset. --simpleUse a machine-readable output format. --dimMonitor changes in dimension size of the dataset only. --width=NSet the number of columns to N for output. A value of 0 sets the number of columns to the maximum (65535). The default width is 80 columns. --polling=NSet the polling interval to N (in seconds) when the dataset will be checked for appended data. The default polling interval is 1. --fields=list_of_fieldsDisplay data for the fields specified in list_of_fieldsfor a compound datatype.list_of_fieldcan be specified as follows:- A comma-separated list of field names in a compound data type.
- A single field name in a compound data type. This option can be used multiple times to select multiple fields in a compound data type.
Object:OBJECTis the dataset to be monitored and is specified with the following format:-
filename/path_to_dataset/dsetname
Each element in this specification of OBJECTis defined as follows:filenameThe name of the HDF5 file.
May be preceded by a path separated by slashes to the specified HDF5 file.path_to_datasetThe path within the HDF5 file separated by slashes to the specified dataset dsetnameThe name of the dataset to be monitored. - Exit Status:
-
0 Succeeded. > 0 An error occurred. - Example Usage:
-
The default use is to include the tool name and the name of the dataset that will be watched. The output will describe any change and will list the changes.
Suppose there is a dataset called dsetA in an HDF5 file called example.h5, and this dataset is a one-dimensional dataset with three records. After
h5watchis run with a command line ofh5watch example.h5/dsetA, the dimension size in the file is changed from three to five, and data is written to the dataset. The output fromh5watchwould be the following:dims[0]: 3->5 Data: (3): record (4): recordFor more examples, see the h5watch Examples document.
- See Also:
- History:
-
Release Change 1.10.0 Tool introduced in this release.
- Last modified: 26 May 2016
- Tool Name: h5format_convert
- Syntax:
h5format_convert [OPTIONS] file_name- Purpose:
- Converts the layout format version and chunked indexing types of datasets created with a 1.10.x version of the library so that applications built with a 1.8.x version of the library can access these datasets.
- Motivation:
- When datasets are created in a 1.10.x HDF5 file accessed with the latest format, the library will use the latest layout format version for the datasets. This will allow users to take advantage of new features such as virtual storage and the latest index types for chunked datasets. However, applications built with 1.8.x versions of the library will not be able to access these datasets.
- Description:
- When run, the tool will investigate datasets in
the file
file_name. It will convert datasets as follows:- A chunked dataset: convert the chunk indexing type to version 1 B-tree if the type is not already a version 1 B-tree
- A compact or contiguous dataset: downgrade the layout version to 3 if the layout version is not already version 3
- A virtual dataset: no action
If errors are encountered, no further conversion will be performed, and the tool will exit with failure.
- Options and Parameters:
- Options:
-
Short and Long Forms Comments -h
--helpThe tool will print a usage message and exit with success. -V
--versionThe tool will print the version # and exit with success. -v
--verboseThis will enable the verbose mode. The tool will print the steps being done while converting a dataset. -d dataset_name
--dname=dataset_name
This is the name including its path of the dataset to be converted (the links from the root group to the dataset). If no conversion is needed, the tool will exit with success. Only one dataset can be specified with this option each time the tool is run. If this option is not used, the tool will attempt to convert every dataset in file_name.-n
--noopNoop is short for no operation. The file will not be modified. The tool will perform all the steps except the actual conversion and exit with success. When errors are encountered along the way, the tool will exit with failure. - Parameter:
-
file_name
The name of the file that the tool will operate on. - See Also:
- HDF5 File Format Specification
- History:
Release Change 1.10.0 Tool introduced in this release.
- Last modified: 10 May 2013
- Tool Name: h5redeploy
- Syntax:
- Tool Name: h5redeploy
h5redeploy[help|-help]h5redeploy[-echo] [-force] [-prefix=dir] [-exec-prefix=dir] [-libdir=dir] [-includedir=dir] [-tool=tool] [-show]- Purpose:
- Updates HDF5 compiler tools after an HDF5 software installation
in a new location.
- Description:
h5redeployupdates the HDF5 compiler tools after the HDF5 software has been installed in a new location.- Options and Parameters:
help,-helpPrints a help message. -echoShows all the shell commands executed. -forcePerforms the requested action without offering any prompt requesting confirmation. -prefix=dirSpecifies a new directory in which to find the HDF5 subdirectories lib/andinclude/.
(Default: current working directory)-exec-prefix=dir
Specifies a new directory in which to find the HDF5 lib/subdirectory.
(Default:prefix)-libdir=dirSpecifies a new directory for the HDF5 lib/directory.
(Default:exec-prefix/lib)-includedir=dirSpecifies a new directory for the HDF5 include/directory.
(Default:prefix/include)-tool=toolSpecifies the tool to update.
tool must be in the current directory and must be writable.
(Default:h5cc h5pcc h5fc h5pfc h5c++)-showShows all of the shell commands to be executed without actually executing them. - Exit Status:
0 Succeeded. > 0 An error occurred. - History:
Release Command Line Tool 1.8.11 -exec-prefix,-libdir, and-includediroptions added.1.8.5 Tool exit status codes updated. 1.6.0 Tool introduced in this release.
- Last modified: 25 September 2013
- Tool Name: h5cc and h5pcc
- Syntax:
- Tool Name: h5cc and h5pcc
h5cc [OPTIONS]<compile line>h5pcc [OPTIONS]<compile_line>- Purpose:
- Helper scripts to compile HDF5 applications.
- Description:
h5ccandh5pcccan be used in much the same way asmpiccby MPICH is used to compile an HDF5 program. These tools take care of specifying on the command line the locations of the HDF5 header files and libraries.h5ccis for use in serial computing environments;h5pccis for parallel environments.h5ccandh5pccsubsume all other compiler scripts in that if you have used a set of scripts to compile the HDF5 library, thenh5ccandh5pccalso use those scripts. For example, when compiling an MPICH program, you use thempiccscript. If you have built HDF5 using MPICH, thenh5ccuses the MPICH program for compilation.Some programs use HDF5 in only a few modules. It is not necessary to use
h5ccorh5pccto compile those modules which do not use HDF5. In fact, sinceh5ccandh5pccare only convenience scripts, you can still compile HDF5 modules in the normal manner, though you will have to specify the HDF5 libraries and include paths yourself. Use the-showoption to see the details. For example, runningh5ccfor an HDF5 library built usinggccwith--disable-shared,zlibandszlib, all installed in/usr/local/libwould provide this compile command:gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE \ -D_BSD_SOURCE -L/usr/local/lib /usr/local/lib/libhdf5_hl.a \ /usr/local/lib/libhdf5.a /usr/local/lib/libsz.a /usr/local/lib/libz.a \ -lm -W1,-rpath -W1,/usr/local/lib [OPTIONS] <compile line>An example of how to use
h5ccto compile the programhdf_prog, which consists of the modulesprog1.candprog2.cand uses the HDF5 shared library, would be as follows.h5pccis used in an identical manner.# h5cc -c prog1.c # h5cc -c prog2.c # h5cc -shlib -o hdf_prog prog1.o prog2.o- Options and Parameters:
-helpPrints a help message. -echoShow all the shell commands executed. -prefix=DIRUse the directory DIRto find the HDF5lib/andinclude/subdirectories.
Default: prefix specified when configuring HDF5.-showShow the commands without executing them. -shlibCompile using shared HDF5 libraries.
Default for HDF5 built without static libraries.-noshlibCompile using static HDF5 libraries.
Default for HDF5 built with static libraries.<compile line> The normal compile line options for your compiler. h5ccandh5pccuse the the same compiler you used to compile HDF5. Check your compiler's manual for more information on which options are needed.- Environment Variables:
- When set, these environment variables override some of the built-in
h5ccandh5pccdefaults.HDF5_CCUse a different C compiler. HDF5_CLINKERUse a different linker. HDF5_USE_SHLIB=[yes|no]Use shared version of the HDF5 library.
Default: no, except when HDF5 built with only shared libraries.HDF5_CPPFLAGSUse additional preprocessor flags. HDF5_CFLAGSUse additional C compiler flags. HDF5_LDFLAGSUse additional library paths. HDF5_LIBSUse additional libraries. The last four of these environment variables have corresponding variables with names ending in
BASEthat can also be set by editing their values in the "Things You Can Modify to Override HDF5 Library Build Components" section of theh5ccandh5pccscripts.Note that adding library paths to
HDF5_LDFLAGSwhere another HDF5 version is located may link your program with that other HDF5 Library version. - Exit Status:
0 Succeeded. > 0 An error occurred. - History:
Release Change 1.8.12 Tool modified to switch default to link to shared libraries when HDF5 configured with --disable-static.1.8.6 Four compiler flags and environment variables added. 1.8.5 Tool exit status codes updated.
- Last modified: 25 September 2013
- Tool Name: h5fc and h5pfc
- Syntax:
- Tool Name: h5fc and h5pfc
h5fc [OPTIONS]<compile line>h5pfc [OPTIONS]<compile_line>- Purpose:
- Helper scripts to compile HDF5 Fortran applications.
- Description:
h5fcandh5pfccan be used in much the same waympif90by MPICH is used to compile an HDF5 program. These tools take care of specifying on the command line the locations of the HDF5 header files and libraries.h5fcis for use in serial computing environments;h5pfcis for parallel environments.h5fcandh5pfcsubsume all other compiler scripts in that if you have used a set of scripts to compile the HDF5 Fortran library, thenh5fcandh5pfcalso use those scripts. For example, when compiling an MPICH program, you use thempif90script. If you have built HDF5 using MPICH, thenh5fcuses the MPICH program for compilation.Some programs use HDF5 in only a few modules. It is not necessary to use
h5fcandh5pfcto compile those modules which do not use HDF5. In fact, sinceh5fcandh5pfcare only convenience scripts, you can still compile HDF5 Fortran modules in the normal manner, though you will have to specify the HDF5 libraries and include paths yourself. Use the-showoption to see the details.An example of how to use
h5fcto compile the programhdf_prog, which consists of the modulesprog1.f90andprog2.f90and uses the HDF5 Fortran library, would be as follows.h5pfcis used in an identical manner.# h5fc -c prog1.f90 # h5fc -c prog2.f90 # h5fc -o hdf_prog prog1.o prog2.o- Options and Parameters:
-helpPrints a help message. -echoShow all the shell commands executed. -prefix=DIRUse the directory DIRto find HDF5lib/andinclude/subdirectories.
Default: prefix specified when configuring HDF5.-showShow the commands without executing them. -shlibCompile using shared HDF5 libraries.
Default for HDF5 built without static libraries.-noshlibCompile using static HDF5 libraries.
Default for HDF5 built with static libraries.<compile line> The normal compile line options for your compiler.
h5fcandh5pfcuse the the same compiler you used to compile HDF5. Check your compiler's manual for more information on which options are needed.- Environment Variables:
- When set, these environment variables override some of the built-in
h5fcandh5pfcdefaults.HDF5_FCUse a different Fortran compiler. HDF5_FLINKERUse a different linker. HDF5_USE_SHLIB=[yes|no]Use shared version of the HDF5 library.
Default: no, except when HDF5 built with only shared libraries.HDF5_FFLAGSUse additional Fortran compiler flags. HDF5_LDFLAGSUse additional library paths. HDF5_LIBSUse additional libraries. The last three of these environment variables have corresponding variables with names ending in
BASEthat can also be set by editing their values in the "Things You Can Modify to Override HDF5 Library Build Components" section of theh5fcandh5pfcscripts.Note that adding library paths to
HDF5_LDFLAGSwhere another HDF5 version is located may link your program with that other HDF5 Library version. - Exit Status:
0 Succeeded. > 0 An error occurred. - History:
Release Change 1.8.12 Tool modified to switch default to link to shared libraries when HDF5 configured with --disable-static.1.8.11 Tool updated to recognize .f95,.f03, and.f08file extensions.1.8.6 Three compiler flags and environment variables added. 1.8.5 Tool exit status codes updated. 1.6.0 Tool introduced in this release.
- Last modified: 25 September 2013
- Tool Name: h5c++
- Syntax:
- Tool Name: h5c++
h5c++ [OPTIONS]<compile line>- Purpose:
- Helper script to compile HDF5 C++ applications.
- Description:
h5c++can be used in much the same way MPIch is used to compile an HDF5 program. It takes care of specifying where the HDF5 header files and libraries are on the command line.h5c++supersedes all other compiler scripts in that if you've used one set of compiler scripts to compile the HDF5 C++ library, thenh5c++uses those same scripts. For example, when compiling an MPIch program, you use thempiCCscript.Some programs use HDF5 in only a few modules. It isn't necessary to use
h5c++to compile those modules which don't use HDF5. In fact, sinceh5c++is only a convenience script, you are still able to compile HDF5 C++ modules in the normal way. In that case, you will have to specify the HDF5 libraries and include paths yourself. Use the-showoption to see the details.An example of how to use
h5c++to compile the programhdf_prog, which consists of modulesprog1.cppandprog2.cppand uses the HDF5 C++ library, would be as follows:# h5c++ -c prog1.cpp # h5c++ -c prog2.cpp # h5c++ -o hdf_prog prog1.o prog2.o- Options and Parameters:
-helpPrints a help message. -echoShow all the shell commands executed. -prefix=DIRUse the directory DIRto find HDF5lib/andinclude/subdirectories
Default: prefix specified when configuring HDF5.-showShow the commands without executing them. -shlibCompile using shared HDF5 libraries.
Default for HDF5 built without static libraries.-noshlibCompile using static HDF5 libraries.
Default for HDF5 built with static libraries.<compile line>
The normal compile line options for your compiler. h5c++uses the same compiler you used to compile HDF5. Check your compiler's manual for more information on which options are needed.- Environment Variables:
- When set, these environment variables override some of the built-in
defaults of
h5c++.HDF5_CXXUse a different C++ compiler. HDF5_CXXLINKERUse a different linker. HDF5_USE_SHLIB=[yes|no]Use shared version of the HDF5 library.
Default: no, except when HDF5 built with only shared libraries.HDF5_CPPFLAGSUse additional preprocessor flags. HDF5_CXXFLAGSUse additional C++ compiler flags. HDF5_LDFLAGSUse additional library paths. HDF5_LIBSUse additional libraries. The last four of these environment variables have corresponding variables with names ending in
BASEthat can also be set by editing their values in the "Things You Can Modify to Override HDF5 Library Build Components" section of theh5c++script.Note that adding library paths to
HDF5_LDFLAGSwhere another HDF5 version is located may link your program with that other HDF5 Library version. - Exit Status:
0 Succeeded. > 0 An error occurred. - History:
Release Command Line Tool 1.8.12 Tool modified to switch default to link to shared libraries when HDF5 configured with --disable-static.1.8.6 Four compiler flags and environment variables added. 1.8.5 Tool exit status codes updated. 1.6.0 Tool introduced in this release.
The HDF Group Help Desk: 
Describes HDF5 Release 1.10. |
Copyright by
The HDF Group
and the Board of Trustees of the University of Illinois |