Update README.md

specfem3d/README.md

 # Specfem 3D globe -- Bench readme
 
-Note that this guide is still a work in progress and is currently being reviewed.
-
 ## Get the source
 
 Clone the repository in a location of your choice, let's say $HOME.
@@ -62,7 +60,8 @@ during the last benchmark campaign
 ## Compile specfem
 
 As arrays are staticaly declared, you will need to compile specfem once for each
-test case with the right `Par_file`
+test case with the right `Par_file`. Indeed, input for the mesher (and the solver) is provided through the parameter file Par_file, which resides in the
+subdirectory DATA of specfem3D\_Globe. Before running the mesher, a number of parameters need to be set in the Par\_file. In our case, the Par\_file for each test case is provided in the subdirectories test_cases.
 On some environement, depending on MPI configuration you will need to replace
 `use mpi` statement with `include mpif.h`, use the script and prodedure commented
 below.
@@ -73,10 +72,9 @@ First you will have to configure.
 configure:`--build=ppc64 --with-cuda=cuda5`.
 
 ```shell
-cp -r $HOME/specfem3d_globe specfem_compil_${test_case_id}
-cp $HOME/bench_spec/test_case_${test_case_id}/DATA/Par_file specfem_compil_${test_case_id}/DATA/
-
-cd specfem_compil_${test_case_id}
+cp -r $HOME/specfem3d_globe specfem_build_${test_case_id}
+cp $HOME/ueabs/specfem3d/test_cases/SPECFEM3D_${test_case_id}/Par_file specfem_build_${test_case_id}/DATA/
+cd specfem_build_${test_case_id}
 
 ### replace `use mpi` if needed ###
 # cd utils
@@ -84,27 +82,35 @@ cd specfem_compil_${test_case_id}
 # cd ..
 ####################################
 
-./configure --prefix=$PWD
-```
+# GPU platform
+./configure --prefix=$PWD --build=ppc64 --with-cuda=cuda5
+# Otherwise
+#./configure --prefix=$PWD --enable-openmp
 
-**On Xeon Phi**, since support is recent you should replace the following variables
-values in the generated Makefile:
+```
 
-```Makefile
-FCFLAGS = -g -O3 -qopenmp -xMIC-AVX512 -DUSE_FP32 -DOPT_STREAMS -align array64byte  -fp-model fast=2 -traceback -mcmodel=large
+Depending on the architecture you will have to export (before configuring) different options for the environment variables related to the compilation (CFLAGS, CPPFLAGS, FCFLAGS...) (or you can modify the values of the variables in the generated Makefile).
+Here is an example of the variables to (re)define **On Xeon Phi** 
+```Makefile/environnment
+FCFLAGS=" -g -O3 -qopenmp -xMIC-AVX512 -DUSE_FP32 -DOPT_STREAMS -fp-model fast=2 -traceback -mcmodel=large -fma -align array64byte -finline-functions -ipo"
+CFLAGS=" -g -O3  -xMIC-AVX512 -fma -align -finline-functions -ipo"
 FCFLAGS_f90 = -mod ./obj -I./obj -I.  -I. -I${SETUP} -xMIC-AVX512
 CPPFLAGS = -I${SETUP}  -DFORCE_VECTORIZATION  -xMIC-AVX512
 ```
+Another example for **Skylake** architecture:
+```Makefile/environnment
+export FCFLAGS=" -g -O3 -qopenmp -xCORE-AVX512 -mtune=skylake -ipo -DUSE_FP32 -DOPT_STREAMS -fp-model fast=2 -traceback -mcmodel=large"
+export CFLAGS=" -g -O3  -xCORE-AVX512 -mtune=skylake -ipo"
+```
 Note: Be careful, in most machines login node does not have the same instruction set so, in order to compile with the right instruction set, you'll have to compile on a compute node (salloc + ssh)
 
-
 Finally compile with make:
 ```shell
 make clean
 make all
 ```
 
-**-> You will find in the specfem folder of ueabs repository the file "compile.sh" which is an compilation script template for several machines (different architectures : KNL, SKL, Haswell and GPU)**
+**-> You will find in the specfem folder of ueabs repository the file "compile.sh" which is an compilation script template for several machines (different architectures : KNL, SKL, Power 8, Haswell and GPU)**
 
 ## Launch specfem
 
@@ -117,16 +123,5 @@ You can use or be inspired by the submission script template in the job_script f
 
 ## Gather results
 
-The relevant metric for this benchmark is time for the solver. Using slurm, it is
-easy to gather as each `mpirun` or `srun` is interpreted as a step wich is already
-timed. So the command line `sacct -j <job_id>` allows you to catch the metric.
-
-Or you can find more precise timing info at the end of this output file : specfem3d_globe/OUTPUT_FILES/output_solver.txt
-
-
-
-
-
-
-
-
+The relevant metric for this benchmark is time for the solver, you can find it at the end of this output file : specfem3d_globe/OUTPUT_FILES/output_solver.txt.
+Using slurm, it is easy to gather as each `mpirun` or `srun` is interpreted as a step wich is already timed. So the command line `sacct -j <job_id>` allows you to catch the metric.