Hdf5 How To Install
The actual name of the hdf5 installation package is 'libhdf5-dev' (not 'hdf5'). Running the following command should return package information. Dpkg -s libhdf5-dev. If that doesn't give any results, you can check for any hdf5 installation by doing: dpkg -l grep hdf5. Apr 21, 2016 Yes, you are right, hdf.repo contains only Kafka, Storm and Zookeeper and a package called hdf-select most likely used to select current HDF versions. So, to install NiFi you can download what's in the docs called 'HDF (NiFi only)'.
The OLCAO package requires an installation of HDF5 that is configured to include Fortran interfaces and the deflate filter. You should check what your computer has installed. If your computer uses the modules program then just type 'module avail' to see if there is an HDF5 module available.
Then try 'module list' to see if you have it loaded already. If not, then 'module load ' where instead of you type the appropriate name of the module that you saw from 'module avail'. Then run 'h5fc -showconfig' to see if it has Fortran interfaces and if the deflate filter is available. If not, you should first ask your system administrator to install it for you. You should also ask that the administrator install it with the particular Fortran compiler that you intend to use to compile OLCAO with. If your system does not have it and you are having trouble getting it, then you can install it yourself as instructed below.
Make sure that you have zlib installed. This is required for the compression (deflate) HDF5 filter. To check if it is installed, see if it exists in your library (e.g. In /usr/lib or /usr/lib64). An easy way to check this is by running the command ls /usr/lib grep 'libz'.
Conda Hdf5
This is a very standard package and so if you don't have it you should contact your system administrator to learn where he/she has installed it. (Note that the library name is 'zlib' but the file name is usually something like 'libz.so'. Hence that confusing position of the letter z.). Download the latest HDF5 source files from the. Transfer this tar file to the cluster on which you'd like to install, and untar it using the command tar -xvf.tar. This will create a new directory. If you downloaded the bzip2 then use -xvjf options and if you downloaded the gzip then use -xvzf options.
Anaconda Hdf5
Compiling HDF5 requires a Fortran compiler for the Fortran interface which is necessary for use with OLCAO. You will want to set your environment variable FC to whatever Fortran compiler you plan to use when you compile OLCAO. So you might issues a command like export FC=ifort or export FC=gfortran before continuing. Go to the newly created directory, and issue the following command:./configure -enable-fortran -enable-static -disable-shared -disable-hd -prefix=$HOME. (Note that this may take quite a while depending on the capabilities of your computer. A long estimate is 30 minutes a short one is 5-10 minutes.). The above command prints a lot of information to the screen.
Hdf5 Install Python
Make sure that towards the very end, the parameter 'deflate' is turned on. After the above command finishes, you can make and make install to install HDF5. (Again, this process will take some time. A long estimate is 1 hour and a short one is 15 minutes.). Before you proceed to install OLCAO, you will need to change the FC environment variable to points to the HDF5 compiler wrapper. To do that issue the command export FC=h5fc. You may want to put that line into your /.bashprofile file so that it is executed every time you log in.
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Therefore you should not compile HDF5 with gfortran and then compile OLCAO with ifort or vice-versa because the HDF5 mod files will not correctly integrate. This is a real pain so watch out for it.If you go to your home directory, you should be able to see many executables starting with h5 in your bin directory. 'ls /bin/h5.' Note that if your cluster had a previous install of HDF5 executables, you need to make sure that your install is invoked and not theirs.
To do so, make sure that you add the following line to your.bashrc (or.profile) file in your home directory: export PATH=$HOME/bin:$PATH.That should be it. You can test with 'which h5fc' and 'h5fc -showconfig' to make sure that the settings are correct.