...
Installing the hdf5-libraries at HLRN
| Auszug |
|---|
HDF5 - hierarchical data format |
Documentation
HDF5 is a data model, library, and file format for storing and managing data. It can represent very complex data objects and a wide variety of metadata. For a documentation visit the HDF group
support portal
Documentation
Installed versions
Serial HDF-5
Parallel HDF-5
...
1.10.6
...
intel/18.0.6, openmpi/intel/3.1.6
...
1.10.5
...
gcc/8.3.0, openmpi/gcc.9/3.1.5
...
1.10.6
...
The libraries are threadsafe and can be used in omp-parallel codes. To see configure-details on the installed libraries, load a hdf5-module and issue cat $HDF5DIR/libhdf5.settings!
Modules and Prerequisites
...
Loading a module adds the path to some hdf5-binaries to $PATH. For convenience, some other environmental variables are extended or defined, which satisfies the needs of several software packages for linking the hdf5-libraries:
PATH, LD_RUN_PATH
C_INCLUDE_PATH, CPLUS_INCLUDE_PATH,
HDF5DIR, HDF5INCLUDE, HDF5LIB
HDF5_HOME, HDF5_ROOT
The module files do not require any prerequisites. All dynamically linked libraries are found, since RPATH is defined in libraries and binaries. For an example, consider
- readelf -a $HDF5DIR/libhdf5_hl.so | grep RPATH
Linking the hdf5-libraries in user programs
Loading a hdf5-module does not link the libraries automatically, when compiling some other software. hdf5 does not deliver any standard way to detect the path to the libraries like pkg-config. So you have to configure Makefiles or install-scripts "by hand". The environment variables exported by the modules should allow short and flexible notation.
hdf5-modules do not have any effect during the runtime of your binaries. If the hdf5-libraries are linked dynamically, it is recommended to set RPATH in the binary. Otherwise the hdf5-libraries (and others) will not be found, during runtime. This can be done with the compiler option -Wl,-rpath=$LD_RUN_PATH, which passes the rpath to the linker.
hdf5 compiler wrapper
The compiler wrapper h5cc, h5fc (parallel h5pcc and h5pfc) can be used to build programs linking the hdf5-libraries. These wrappers set rpath for all libraries to be linked dynamically for hdf5.
Installing the hdf5-libraries at HLRN
| Auszug |
|---|
HDF5 - hierarchical data format |
Documentation
HDF5 is a data model, library, and file format for storing and managing data. It can represent very complex data objects and a wide variety of metadata. For a documentation visit the HDF group support portal
Installed versions
Serial HDF-5
Parallel HDF-5
...
1.10.6
...
intel/18.0.6, openmpi/intel/3.1.6
...
1.10.5
...
gcc/8.3.0, openmpi/gcc.9/3.1.5
...
1.10.6
...
The libraries are threadsafe and can be used in omp-parallel codes. To see configure-details on the installed libraries, load a hdf5-module and issue cat $HDF5DIR/libhdf5.settings!
Modules and Prerequisites
...
Loading a module adds the path to some hdf5-binaries to $PATH. For convenience, some other environmental variables are extended or defined, which satisfies the needs of several software packages for linking the hdf5-libraries:
PATH, LD_RUN_PATH
C_INCLUDE_PATH, CPLUS_INCLUDE_PATH,
HDF5DIR, HDF5INCLUDE, HDF5LIB
HDF5_HOME, HDF5_ROOT
The module files do not require any prerequisites. All dynamically linked libraries are found, since RPATH is defined in libraries and binaries. For an example, consider
- readelf -a $HDF5DIR/libhdf5_hl.so | grep RPATH
Linking the hdf5-libraries in user programs
Loading a hdf5-module does not link the libraries automatically, when compiling some other software. hdf5 does not deliver any standard way to detect the path to the libraries like pkg-config. So you have to configure Makefiles or install-scripts "by hand". The environment variables exported by the modules should allow short and flexible notation.
hdf5-modules do not have any effect during the runtime of your binaries. If the hdf5-libraries are linked dynamically, it is recommended to set RPATH in the binary. Otherwise the hdf5-libraries (and others) will not be found, during runtime. This can be done with the compiler option -Wl,-rpath=$LD_RUN_PATH, which passes the rpath to the linker.
hdf5 compiler wrapper
The compiler wrapper h5cc, h5fc (parallel h5pcc and h5pfc) can be used to build programs linking the hdf5-libraries. These wrappers set rpath for all libraries to be linked dynamically for hdf5.
Installing the hdf5-libraries at HLRN
| Auszug |
|---|
HDF5 - hierarchical data format |
Documentation
HDF5 is a data model, library, and file format for storing and managing data. It can represent very complex data objects and a wide variety of metadata. For a documentation visit the HDF group support portal
Documentation
Installed versions
Serial HDF-5
Parallel HDF-5
...
1.10.6
...
intel/18.0.6, openmpi/intel/3.1.6
...
1.10.5
...
gcc/8.3.0, openmpi/gcc.9/3.1.5
...
1.10.6
...
The libraries are threadsafe and can be used in omp-parallel codes. To see configure-details on the installed libraries, load a hdf5-module and issue cat $HDF5DIR/libhdf5.settings!
Modules and Prerequisites
...
Loading a module adds the path to some hdf5-binaries to $PATH. For convenience, some other environmental variables are extended or defined, which satisfies the needs of several software packages for linking the hdf5-libraries:
PATH, LD_RUN_PATH
C_INCLUDE_PATH, CPLUS_INCLUDE_PATH,
HDF5DIR, HDF5INCLUDE, HDF5LIB
HDF5_HOME, HDF5_ROOT
The module files do not require any prerequisites. All dynamically linked libraries are found, since RPATH is defined in libraries and binaries. For an example, consider
- readelf -a $HDF5DIR/libhdf5_hl.so | grep RPATH
Linking the hdf5-libraries in user programs
Loading a hdf5-module does not link the libraries automatically, when compiling some other software. hdf5 does not deliver any standard way to detect the path to the libraries like pkg-config. So you have to configure Makefiles or install-scripts "by hand". The environment variables exported by the modules should allow short and flexible notation.
hdf5-modules do not have any effect during the runtime of your binaries. If the hdf5-libraries are linked dynamically, it is recommended to set RPATH in the binary. Otherwise the hdf5-libraries (and others) will not be found, during runtime. This can be done with the compiler option -Wl,-rpath=$LD_RUN_PATH, which passes the rpath to the linker.
hdf5 compiler wrapper
The compiler wrapper h5cc, h5fc (parallel h5pcc and h5pfc) can be used to build programs linking the hdf5-libraries. These wrappers set rpath for all libraries to be linked dynamically for hdf5.