IMPROVE gpaw formating

gpaw/README.md

@@ -89,23 +89,23 @@ are two additional steps compared to a standard installation:
 2. Edit your GPAW setup script (customize.py) to add correct link and compile
    options for CUDA. The relevant lines are e.g.:
 
-   ```python
-   define_macros += [('GPAW_CUDA', '1')]
-   libraries += [
-           'gpaw-cuda',
-           'cublas',
-           'cudart',
-           'stdc++'
-   ]
-   library_dirs += [
-           './c/cuda',
-           '/path/to/cuda/lib64'
-   ]
-   include_dirs += [
-           '/path/to/cuda/include'
-   ]
-
-   ```
+    ```python
+    define_macros += [('GPAW_CUDA', '1')]
+    libraries += [
+            'gpaw-cuda',
+            'cublas',
+            'cudart',
+            'stdc++'
+    ]
+    library_dirs += [
+            './c/cuda',
+            '/path/to/cuda/lib64'
+    ]
+    include_dirs += [
+            '/path/to/cuda/include'
+    ]
+
+    ```
 
 
 ## Xeon Phi MICs
@@ -158,31 +158,31 @@ In addition, pyMIC requires:
 In addition to using Intel compilers, there are three additional steps apart
 from standard installation:
 
-1) Compile and install Numpy with a suitable site.cfg to use MKL, e.g.
+1. Compile and install Numpy with a suitable site.cfg to use MKL, e.g.
 
-```python
-[mkl]
-library_dirs = /path/to/mkl/lib/intel64
-include_dirs = /path/to/mkl/include
-lapack_libs =
-mkl_libs = mkl_rt
-```
+    ```python
+    [mkl]
+    library_dirs = /path/to/mkl/lib/intel64
+    include_dirs = /path/to/mkl/include
+    lapack_libs =
+    mkl_libs = mkl_rt
+    ```
 
-2) Compile and install pyMIC before GPAW.
+2. Compile and install pyMIC before GPAW.
 
-3) Edit your GPAW setup script (customize.py) to add correct link and compile
-options for offloading. The relevant lines are e.g.:
+3. Edit your GPAW setup script (customize.py) to add correct link and compile
+   options for offloading. The relevant lines are e.g.:
 
-```python
-# offload to KNC
-extra_compile_args += ['-qoffload-option,mic,compiler,"-qopenmp"']
-extra_compile_args += ['-qopt-report-phase=offload']
+    ```python
+    # offload to KNC
+    extra_compile_args += ['-qoffload-option,mic,compiler,"-qopenmp"']
+    extra_compile_args += ['-qopt-report-phase=offload']
 
-# linker settings for MKL on KNC
-mic_mkl_lib = '/path/to/mkl/lib/mic/'
-extra_link_args += ['-offload-option,mic,link,"-L' + mic_mkl_lib \
-        + ' -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread"']
-```
+    # linker settings for MKL on KNC
+    mic_mkl_lib = '/path/to/mkl/lib/mic/'
+    extra_link_args += ['-offload-option,mic,link,"-L' + mic_mkl_lib \
+            + ' -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -lpthread"']
+    ```
 
 
 
@@ -211,11 +211,14 @@ To improve performance, one may also link to Intel TBB to benefit from an
 optimised memory allocator (tbbmalloc). This can be done during installation
 or at run-time by setting environment variable LD_PRELOAD to point to the
 correct libraries, i.e. for example:
-  export LD_PRELOAD=$TBBROOT/lib/intel64/gcc4.7/libtbbmalloc_proxy.so.2
-  export LD_PRELOAD=$LD_PRELOAD:$TBBROOT/lib/intel64/gcc4.7/libtbbmalloc.so.2
+
+```shell
+export LD_PRELOAD=$TBBROOT/lib/intel64/gcc4.7/libtbbmalloc_proxy.so.2
+export LD_PRELOAD=$LD_PRELOAD:$TBBROOT/lib/intel64/gcc4.7/libtbbmalloc.so.2
+```
 
 It may also be beneficial to use hugepages together with tbbmalloc
-(export TBB_MALLOC_USE_HUGE_PAGES=1).
+(export TBB_MALLOC_USE_HUGE_PAGES=1`).
 
 
 ## Run instructions for PRACE Accelerator Benchmark for GPAW
@@ -257,19 +260,22 @@ Input file: copper-filament/input.py
 No special command line options or environment variables are needed to run the
 benchmarks on GPGPUs or KNL (Xeon Phi Knights Landing) MICs. One can simply
 say e.g.
-  mpirun -np 256 gpaw-python input.py
+  `mpirun -np 256 gpaw-python input.py`
 
 
 For KNCs (Xeon Phi Knights Corner), one needs to use a wrapper script to set
 correct affinities for pyMIC (see setup/affinity-wrapper.sh for an example)
 and to set two environment variables for GPAW:
-  GPAW_OFFLOAD=1  (to turn on offloading)
-  GPAW_PPN=<no. of MPI tasks per node>
+```shel
+GPAW_OFFLOAD=1  (to turn on offloading)
+GPAW_PPN=<no. of MPI tasks per node>
+```
 
 For example, in a SLURM system, this could be:
-  GPAW_PPN=12 GPAW_OFFLOAD=1 mpirun -np 256 -bootstrap slurm \
+```shell
+GPAW_PPN=12 GPAW_OFFLOAD=1 mpirun -np 256 -bootstrap slurm \
     ./affinity-wrapper.sh gpaw-python input.py
-
+```
 
 Example job scripts (setup/job-*.sh) for different accelerator architectures
 are provided together with related machine specifications (setup/specs.*) that