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gw4-isambard · Feb 19, 2024 · 0f16e44 · 0f16e44
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diff --git a/_sources/applications/arepo.rst.txt b/_sources/applications/arepo.rst.txt
@@ -0,0 +1,159 @@
+Arepo
+=====
+
+Useful links
+------------
+
+- `Arepo homepage <https://arepo-code.org>`_
+
+Licensing
+---------
+
+Arepo is released under GPLv3 (see the `Arepo licence <https://gitlab.mpcdf.mpg.de/vrs/arepo/-/blob/master/LICENSE>`_).
+
+Version
+-------
+
+Latest version on Arepo
+
+Building
+--------
+We should load the Cray hdf5 module
+
+.. code-block:: bash
+
+    module load cray-hdf5
+
+So on XCI system you can:
+
+Install GSL with:
+
+.. code-block:: bash
+
+    wget https://ftp.gnu.org/gnu/gsl/gsl-latest.tar.gz
+
+    tar xxvf gsl-latest.tar.gz
+
+    cd gsl-*
+
+    ./configure --prefix=$HOME/gsl CC=cc
+
+    make -j
+
+    make install
+
+ 
+
+Then in Arepo specify in Makefile.systype
+
+
+.. code-block:: bash
+                               
+    SYSTYPE="XCI"
+
+ 
+
+And in Makefile
+
+
+.. code-block:: bash
+
+    # Isambard XCI
+
+    ifeq ($(SYSTYPE),"XCI")
+    CC=cc
+
+    # compiler and its optimization options
+    OPTIMIZE  =
+                               
+    # overwrite default:
+
+    MPICH_INCL=
+    MPICH_LIB =
+    GSL_INCL  = -I$(HOME)/gsl/include
+    GSL_LIB   = -L$(HOME)/gsl/lib -lgsl -lgslcblas
+    HWLOC_LIB =
+
+    # libraries that are included on demand, depending on Config.sh options
+
+    FFTW_INCL =
+    FFTW_LIBS =
+    HDF5_INCL = -DH5_USE_16_API
+    HDF5_LIB  =
+    HWLOC_INCL=
+
+    endif
+
+ 
+
+Then:
+
+.. code-block:: bash
+
+    module load cray-hdf5
+
+    module load cray-fftw
+
+    make
+
+ 
+
+Then it should compile an Arepo executable.
+
+To use and build examples a venv is required:
+
+.. code-block:: bash
+
+    module load cray-python
+
+    python -m venv venv
+
+    . venv/bin/activate
+
+    pip install “numpy<1.20”
+
+    pip install h5py
+
+
+(numpy<1.20 needed due to broken code using np.int)
+
+
+
+Then followed docs on using examples.
+
+Running
+-------
+
+Example Job Submission Script
+.............................
+
+Arm
+...
+
+.. code-block:: bash
+
+    #!/bin/bash
+
+    # Select 1 nodes (maximum of 64 cores)
+    #PBS -l select=1
+
+    # Set maximum job walltime
+    #PBS -l walltime=00:30:00
+
+    # Change to the directory the script was submitted from
+    cd $PBS_O_WORKDIR
+
+    # Load required GSL
+    export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HOME/gsl/lib
+
+    # Launch 8192 MPI ranks (64 per node, 1 per core)
+    # Launch 1 OpenMP threads per rank (NOT using 4-way hyperthreading)
+    export OMP_NUM_THREADS=1
+    aprun -n 64 -d 1 -j 1 Arepo
+      
+
+Notes
+.....
+
+For maximum performance, you may wish to tune the MPI/OpenMP decomposition.
+At large scale, you may find that reducing the number of MPI ranks and increasing the number of OpenMP threads yields better performance.
diff --git a/applications/README.html b/applications/README.html
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   <title>GW4 Isambard Application Documentation &mdash; GW4-Isambard  documentation</title>