User-guide.md

@@ -18,9 +18,9 @@ The EAR development team had worked also with OAR and PBSPro batch schedulers, b
 
 [[_TOC_]]
 
-## Use cases
+# Use cases
 
-### MPI applications
+## MPI applications
 
 EARL is automatically loaded with MPI applications when EAR is enabled by
 default (check `ear-info`). EAR supports the utilization of both
@@ -32,12 +32,12 @@ When using specific MPI flavour commands to start applications (e.g., `mpirun`,
 `mpiexec.hydra`), there are some keypoints which you must take account.
 See [next sections](#using-mpirunmpiexec-command) for examples and more details.
 
-#### Hybrid MPI + (OpenMP, CUDA, MKL) applications
+### Hybrid MPI + (OpenMP, CUDA, MKL) applications
 
 EARL automatically supports this use case.
 `mpirun`/`mpiexec` and `srun` are supported in the same manner as explained above.
 
-#### Python MPI applications
+### Python MPI applications
 
 EARL cannot detect automatically MPI symbols when Python is used.
 On that case, an environment variable used to specify which MPI flavour is provided.
@@ -46,9 +46,9 @@ Export [`SLURM_EAR_LOAD_MPI_VERSION`](EAR-environment-variables#ear_load_mpi_ver
 values, e.g., `export SLURM_EAR_LOAD_MPI_VERSION="open mpi"`, whose are the two MPI
 implementations 100% supported by EAR.
 
-#### Running MPI applications on SLURM systems
+### Running MPI applications on SLURM systems
 
-##### Using `srun` command
+#### Using `srun` command
 
 Running MPI applications with EARL on SLURM systems using `srun` command is the most
 straightforward way to start using EAR.
@@ -62,12 +62,12 @@ They are provided by EAR's SLURM SPANK plug-in.
 When using SLURM commands for job submission, both Intel and OpenMPI implementations are
 supported.
 
-##### Using `mpirun`/`mpiexec` command
+#### Using `mpirun`/`mpiexec` command
 
 To provide an automatic loading of the EAR library, the only requirement from
 the MPI library is to be coordinated with the scheduler.
 
-###### Intel MPI
+##### Intel MPI
 
 Recent versions of Intel MPI offers two environment variables that can be used
 to guarantee the correct scheduler integrations:
@@ -79,7 +79,7 @@ These arguments are passed to SLURM, and they can be all the same as EAR's SPANK
 
 You can read [here](https://www.intel.com/content/www/us/en/develop/documentation/mpi-developer-reference-linux/top/environment-variable-reference/hydra-environment-variables.html) the Intel environment variables guide.
 
-###### OpenMPI
+##### OpenMPI
 
 For joining OpenMPI and EAR it is highly recommended to use SLURM's `srun` command.
 When using `mpirun`, as OpenMPI is not fully coordinated with the scheduler, EARL
@@ -89,7 +89,7 @@ will be reported.
 To provide support for this workflow, EAR provides [`erun`](EAR-commands#erun) command.
 Read the corresponding [examples section](User-guide.md#openmpi-1) for more information about how to use this command.
 
-###### MPI4PY
+##### MPI4PY
 
 To use MPI with Python applications, the EAR Loader cannot automatically detect symbols to classify
 the application as Intel or OpenMPI. In order to specify it, the user has
@@ -97,9 +97,9 @@ to define the `SLURM_LOAD_MPI_VERSION` environment variable with the values _int
 _open mpi_. It is recommended to add in Python modules to make it easy for
 final users.
 
-### Non-MPI applications
+## Non-MPI applications
 
-#### Python
+### Python
 
 Since version 4.1 EAR automatically executes the Library with Python applications,
 so no action is needed.
@@ -107,14 +107,14 @@ You must run the application with `srun` command to pass through the EAR's SLURM
 SPANK plug-in in order to enable/disable/tuning EAR.
 See [EAR submission flags](#ear-job-submission-flags) provided by EAR SLURM integration.
 
-#### OpenMP, CUDA and Intel MKL
+### OpenMP, CUDA and Intel MKL
 
 To load EARL automatically with non-MPI applications it is required to have it compiled
 with dynamic symbols and also it must be executed with `srun` command.
 For example, for CUDA applications the `--cudart=shared` option must be used at compile time.
 EARL is loaded for OpenMP, MKL and CUDA programming models when symbols are dynamically detected.
 
-### Other application types or frameworks
+## Other application types or frameworks
 
 For other programming models or sequential apps not supported by default, EARL can
 be forced to be loaded by setting [`SLURM_EAR_LOADER_APPLICATION`](EAR-environment-variables#ear_loader_application)
@@ -128,7 +128,7 @@ export SLURM_EAR_LOADER_APPLICATION=my_app
 srun my_app
 ```
 
-## Retrieving EAR data
+# Retrieving EAR data
 
 As a job accounting and monitoring tool, EARL collects some metrics that you can
 get to see or know your applications behaviour.
@@ -185,7 +185,7 @@ how to generate Paraver traces.
 > Contact with [ear-support@bsc.es](mailto:ear-support@bsc.es) if you want to get more details
 about how to deal with EAR data with Paraver.
 
-## EAR job submission flags
+# EAR job submission flags
 
 The following EAR options can be specified when running `srun` and/or `sbatch`,
 and are supported with `srun`/`sbatch`/`salloc`:
@@ -217,7 +217,7 @@ the output files to be generated, it will be automatically created if needed.
 > You can always check the avaiable EAR submission flags provided by EAR's SLURM SPANK
 plug-in by typing `srun --help`.
 
-### CPU frequency selection
+## CPU frequency selection
 
 The [EAR configuration file](www.example.org) supports the specification of *EAR authorized users*,
 who can ask for a more privileged submission options. The most relevant ones are the possibility
@@ -227,7 +227,7 @@ with sysadmin or helpdesk team to become an authorized user.
 - The `--ear-policy=policy_name` flag asks for _policy_name_ policy. Type `srun --help` to see policies currently installed in your system.
 - The `--ear-cpufreq=value` (_value_ must be given in kHz) asks for a specific CPU frequency.
 
-### GPU frequency selection
+## GPU frequency selection
 
 EAR version 3.4 and upwards supports GPU monitoring for NVIDIA devices from the
 point of view of the application and node monitoring. GPU frequency optimization
@@ -242,9 +242,9 @@ To see the list of available frequencies of the GPU you will work on, you can ty
 nvidia-smi -q -d SUPPORTED_CLOCKS
 ```
 
-## Examples
+# Examples
 
-### `srun` examples
+## `srun` examples
 
 Having an MPI application asking for one node and 24 tasks, the following is a
 simple case of job submission.
@@ -288,7 +288,7 @@ srun --ear-cpufreq=2000000 --ear-policy=monitoring --ear-verbose=1 -J test -N 1
 
 For `--ear-cpufreq` to have any effect, you must specify the `--ear-policy` option even if you want to run your application with the default policy.
 
-### `sbatch` + EARL + srun
+## `sbatch` + EARL + srun
 
 When using `sbatch` EAR options can be specified in the same way. If more than one
 `srun` is included in the job submission, EAR options can be inherited from `sbatch` to the different `srun` instances or they can be specifically modified on each individual `srun`.
@@ -318,9 +318,9 @@ mkdir ear_metrics
 srun --ear-user-db=ear_metrics/app_metrics application
 ```
 
-### EARL + `mpirun`
+## EARL + `mpirun`
 
-#### Intel MPI
+### Intel MPI
 
 When running EAR with `mpirun` rather than `srun`, we have to specify the utilization of `srun` as bootstrap. Version 2019 and newer offers two environment variables for bootstrap server specification and arguments.
 ```
@@ -329,7 +329,7 @@ export I_MPI_HYDRA_BOOTSTRAP_EXEC_EXTRA_ARGS="--ear-policy=monitoring --ear-verb
 mpiexec.hydra -n 10 application
 ```
 
-#### OpenMPI
+### OpenMPI
 
 Bootstrap is an Intel(R) MPI option but not an OpenMPI option. For OpenMPI
 `srun` must be used for an automatic EAR support.
@@ -355,7 +355,7 @@ time per job or node, like SLURM does with its plugins.
 **IMPORTANT NOTE** If you are going to launch `n` applications with `erun` command through a sbatch job, you must set the environment variable `SLURM_STEP_ID` to values from `0` to `n-1` before each `mpirun` call.
 By this way `erun` will inform the EARD the correct step ID to be stored then to the Database.
 
-## EAR job Accounting (`eacct`)
+# EAR job Accounting (`eacct`)
 
 The [`eacct`](EAR-commands#ear-job-accounting-eacct) command shows accounting information stored in the EAR DB for
 jobs (and steps) IDs.
@@ -363,7 +363,7 @@ The command uses EAR's configuration file to determine if the user running it is
 privileged or not, as **non-privileged users can only access their information**.
 It provides the following options.
 
-### Usage examples
+## Usage examples
 
 The basic usage of `eacct` retrieves the last 20 applications (by default) of the
 user executing it.
@@ -428,7 +428,7 @@ Please, read the [commands section page](EAR-commands) to see which of them are
  Successfully written applications to csv. Only applications with EARL will have its information properly written.
 ```
 
-## Job energy optimization: EARL policies
+# Job energy optimization: EARL policies
 
 The core component of EAR at the user's job level is the EAR Library (EARL).
 The Library deals with job monitoring and is the component which implements and applies