X-Git-Url: http://bilbo.iut-bm.univ-fcomte.fr/pub/gitweb/simgrid.git/blobdiff_plain/325f3e852ae3ca8c9e4c2a6d3ba26317c33b0ace..40ee10e13b61bfb28374d96ade010a262b5abd44:/docs/source/Configuring_SimGrid.rst

diff --git a/docs/source/Configuring_SimGrid.rst b/docs/source/Configuring_SimGrid.rst
index 77a615f34c..d06882f609 100644
--- a/docs/source/Configuring_SimGrid.rst
+++ b/docs/source/Configuring_SimGrid.rst
@@ -5,7 +5,7 @@ Configuring SimGrid
 
 .. raw:: html
 
-   <object id="TOC" data="graphical-toc.svg" width="100%" type="image/svg+xml"></object>
+   <object id="TOC" data="graphical-toc.svg" type="image/svg+xml"></object>
    <script>
    window.onload=function() { // Wait for the SVG to be loaded before changing it
      var elem=document.querySelector("#TOC").contentDocument.getElementById("ConfigBox")
@@ -32,17 +32,17 @@ The most common way is to use the ``--cfg`` command line argument. For
 example, to set the item ``Item`` to the value ``Value``, simply
 type the following on the command-line:
 
-.. code-block:: shell
-		
-   my_simulator --cfg=Item:Value (other arguments)
+.. code-block:: console
+
+   $ my_simulator --cfg=Item:Value (other arguments)
 
 Several ``--cfg`` command line arguments can naturally be used. If you
 need to include spaces in the argument, don't forget to quote the
-argument. You can even escape the included quotes (write @' for ' if
-you have your argument between ').
+argument. You can even escape the included quotes (write ``@'`` for ``'`` if
+you have your argument between simple quotes).
 
 Another solution is to use the ``<config>`` tag in the platform file. The
-only restriction is that this tag must occure before the first
+only restriction is that this tag must occur before the first
 platform element (be it ``<zone>``, ``<cluster>``, ``<peer>`` or whatever).
 The ``<config>`` tag takes an ``id`` attribute, but it is currently
 ignored so you don't really need to pass it. The important part is that
@@ -52,41 +52,44 @@ can be done by adding the following to the beginning of your platform
 file:
 
 .. code-block:: xml
-		
+
   <config>
     <prop id="Item" value="Value"/>
   </config>
 
 A last solution is to pass your configuration directly in your program
-with :cpp:func:`simgrid::s4u::Engine::set_config` or :cpp:func:`MSG_config`.
+with :cpp:func:`simgrid::s4u::Engine::set_config`.
 
 .. code-block:: cpp
-		
+
    #include <simgrid/s4u.hpp>
 
    int main(int argc, char *argv[]) {
      simgrid::s4u::Engine e(&argc, argv);
-     
-     e->set_config("Item:Value");
-     
+
+     simgrid::s4u::Engine::set_config("Item:Value");
+
      // Rest of your code
    }
 
 .. _options_list:
-   
+
 Existing Configuration Items
 ----------------------------
 
 .. note::
   The full list can be retrieved by passing ``--help`` and
-  ``--help-cfg`` to an executable that uses SimGrid.
+  ``--help-cfg`` to an executable that uses SimGrid. Try passing
+  ``help`` as a value to get the list of values accepted by a given
+  option. For example, ``--cfg=plugin:help`` will give you the list
+  of plugins available in your installation of SimGrid.
 
-- **clean-atexit:** :ref:`cfg=clean-atexit`
+- **bmf/max-iterations:** :ref:`cfg=bmf/max-iterations`
+- **bmf/precision:** :ref:`cfg=bmf/precision`
 
 - **contexts/factory:** :ref:`cfg=contexts/factory`
 - **contexts/guard-size:** :ref:`cfg=contexts/guard-size`
 - **contexts/nthreads:** :ref:`cfg=contexts/nthreads`
-- **contexts/parallel-threshold:** :ref:`cfg=contexts/parallel-threshold`
 - **contexts/stack-size:** :ref:`cfg=contexts/stack-size`
 - **contexts/synchro:** :ref:`cfg=contexts/synchro`
 
@@ -94,34 +97,31 @@ Existing Configuration Items
 - **cpu/model:** :ref:`options_model_select`
 - **cpu/optim:** :ref:`Cpu Optimization Level <options_model_optim>`
 
+- **debug/breakpoint:** :ref:`cfg=debug/breakpoint`
+- **debug/clean-atexit:** :ref:`cfg=debug/clean-atexit`
+- **debug/verbose-exit:** :ref:`cfg=debug/verbose-exit`
+
 - **exception/cutpath:** :ref:`cfg=exception/cutpath`
 
 - **host/model:** :ref:`options_model_select`
 
-- **maxmin/precision:** :ref:`cfg=maxmin/precision`
 - **maxmin/concurrency-limit:** :ref:`cfg=maxmin/concurrency-limit`
 
-- **msg/debug-multiple-use:** :ref:`cfg=msg/debug-multiple-use`
-
 - **model-check:** :ref:`options_modelchecking`
-- **model-check/checkpoint:** :ref:`cfg=model-check/checkpoint`
 - **model-check/communications-determinism:** :ref:`cfg=model-check/communications-determinism`
 - **model-check/dot-output:** :ref:`cfg=model-check/dot-output`
-- **model-check/hash:** :ref:`cfg=model-checker/hash`
 - **model-check/max-depth:** :ref:`cfg=model-check/max-depth`
-- **model-check/property:** :ref:`cfg=model-check/property`
-- **model-check/record:** :ref:`cfg=model-check/record`
 - **model-check/reduction:** :ref:`cfg=model-check/reduction`
 - **model-check/replay:** :ref:`cfg=model-check/replay`
 - **model-check/send-determinism:** :ref:`cfg=model-check/send-determinism`
-- **model-check/sparse-checkpoint:** :ref:`cfg=model-check/sparse-checkpoint`
-- **model-check/termination:** :ref:`cfg=model-check/termination`
+- **model-check/setenv:** :ref:`cfg=model-check/setenv`
 - **model-check/timeout:** :ref:`cfg=model-check/timeout`
-- **model-check/visited:** :ref:`cfg=model-check/visited`
 
 - **network/bandwidth-factor:** :ref:`cfg=network/bandwidth-factor`
 - **network/crosstraffic:** :ref:`cfg=network/crosstraffic`
 - **network/latency-factor:** :ref:`cfg=network/latency-factor`
+- **network/loopback-lat:** :ref:`cfg=network/loopback`
+- **network/loopback-bw:** :ref:`cfg=network/loopback`
 - **network/maxmin-selective-update:** :ref:`Network Optimization Level <options_model_optim>`
 - **network/model:** :ref:`options_model_select`
 - **network/optim:** :ref:`Network Optimization Level <options_model_optim>`
@@ -129,22 +129,27 @@ Existing Configuration Items
 - **network/weight-S:** :ref:`cfg=network/weight-S`
 
 - **ns3/TcpModel:** :ref:`options_pls`
+- **ns3/seed:** :ref:`options_pls`
 - **path:** :ref:`cfg=path`
 - **plugin:** :ref:`cfg=plugin`
 
-- **simix/breakpoint:** :ref:`cfg=simix/breakpoint`
-
 - **storage/max_file_descriptors:** :ref:`cfg=storage/max_file_descriptors`
 
-- **surf/precision:** :ref:`cfg=surf/precision`
+- **precision/timing:** :ref:`cfg=precision/timing`
+- **precision/work-amount:** :ref:`cfg=precision/work-amount`
 
 - **For collective operations of SMPI,** please refer to Section :ref:`cfg=smpi/coll-selector`
+- **smpi/auto-shared-malloc-thresh:** :ref:`cfg=smpi/auto-shared-malloc-thresh`
 - **smpi/async-small-thresh:** :ref:`cfg=smpi/async-small-thresh`
-- **smpi/bw-factor:** :ref:`cfg=smpi/bw-factor`
+- **smpi/barrier-finalization:** :ref:`cfg=smpi/barrier-finalization`
+- **smpi/barrier-collectives:** :ref:`cfg=smpi/barrier-collectives`
+- **smpi/buffering:** :ref:`cfg=smpi/buffering`
 - **smpi/coll-selector:** :ref:`cfg=smpi/coll-selector`
 - **smpi/comp-adjustment-file:** :ref:`cfg=smpi/comp-adjustment-file`
 - **smpi/cpu-threshold:** :ref:`cfg=smpi/cpu-threshold`
+- **smpi/display-allocs:** :ref:`cfg=smpi/display-allocs`
 - **smpi/display-timing:** :ref:`cfg=smpi/display-timing`
+- **smpi/errors-are-fatal:** :ref:`cfg=smpi/errors-are-fatal`
 - **smpi/grow-injected-times:** :ref:`cfg=smpi/grow-injected-times`
 - **smpi/host-speed:** :ref:`cfg=smpi/host-speed`
 - **smpi/IB-penalty-factors:** :ref:`cfg=smpi/IB-penalty-factors`
@@ -152,11 +157,11 @@ Existing Configuration Items
 - **smpi/iprobe-cpu-usage:** :ref:`cfg=smpi/iprobe-cpu-usage`
 - **smpi/init:** :ref:`cfg=smpi/init`
 - **smpi/keep-temps:** :ref:`cfg=smpi/keep-temps`
-- **smpi/lat-factor:** :ref:`cfg=smpi/lat-factor`
 - **smpi/ois:** :ref:`cfg=smpi/ois`
 - **smpi/or:** :ref:`cfg=smpi/or`
 - **smpi/os:** :ref:`cfg=smpi/os`
 - **smpi/papi-events:** :ref:`cfg=smpi/papi-events`
+- **smpi/pedantic:** :ref:`cfg=smpi/pedantic`
 - **smpi/privatization:** :ref:`cfg=smpi/privatization`
 - **smpi/privatize-libs:** :ref:`cfg=smpi/privatize-libs`
 - **smpi/send-is-detached-thresh:** :ref:`cfg=smpi/send-is-detached-thresh`
@@ -165,11 +170,11 @@ Existing Configuration Items
 - **smpi/simulate-computation:** :ref:`cfg=smpi/simulate-computation`
 - **smpi/test:** :ref:`cfg=smpi/test`
 - **smpi/wtime:** :ref:`cfg=smpi/wtime`
+- **smpi/list-leaks** :ref:`cfg=smpi/list-leaks`
 
 - **Tracing configuration options** can be found in Section :ref:`tracing_tracing_options`
 
 - **storage/model:** :ref:`options_model_select`
-- **verbose-exit:** :ref:`cfg=verbose-exit`
 
 - **vm/model:** :ref:`options_model_select`
 
@@ -183,7 +188,7 @@ Configuring the Platform Models
 Choosing the Platform Models
 ............................
 
-SimGrid comes with several network, CPU and storage models built in,
+SimGrid comes with several network, CPU and disk models built in,
 and you can change the used model at runtime by changing the passed
 configuration. The three main configuration items are given below.
 For each of these items, passing the special ``help`` value gives you
@@ -193,13 +198,13 @@ models). Also, ``--help-models`` should provide information about all
 models for all existing resources.
 
 - ``network/model``: specify the used network model. Possible values:
-  
+
   - **LV08 (default one):** Realistic network analytic model
     (slow-start modeled by multiplying latency by 13.01, bandwidth by
     .97; bottleneck sharing uses a payload of S=20537 for evaluating
     RTT). Described in `Accuracy Study and Improvement of Network
     Simulation in the SimGrid Framework
-    <http://mescal.imag.fr/membres/arnaud.legrand/articles/simutools09.pdf>`_.     
+    <http://mescal.imag.fr/membres/arnaud.legrand/articles/simutools09.pdf>`_.
   - **Constant:** Simplistic network model where all communication
     take a constant time (one second). This model provides the lowest
     realism, but is (marginally) faster.
@@ -216,36 +221,23 @@ models for all existing resources.
     without corrective factors. The timings of small messages are thus
     poorly modeled. This model is described in `A Network Model for
     Simulation of Grid Application
-    <ftp://ftp.ens-lyon.fr/pub/LIP/Rapports/RR/RR2002/RR2002-40.ps.gz>`_.
-  - **Reno/Reno2/Vegas:** Models from Steven H. Low using lagrange_solve instead of
-    lmm_solve (experts only; check the code for more info).
-  - **NS3** (only available if you compiled SimGrid accordingly): 
+    <https://hal.inria.fr/inria-00071989/document>`_.
+  - **ns-3** (only available if you compiled SimGrid accordingly):
     Use the packet-level network
-    simulators as network models (see :ref:`pls_ns3`).
+    simulators as network models (see :ref:`models_ns3`).
     This model can be :ref:`further configured <options_pls>`.
-    
-- ``cpu/model``: specify the used CPU model.  We have only one model
-  for now:
-
-  - **Cas01:** Simplistic CPU model (time=size/power)
-
-- ``host/model``: The host concept is the aggregation of a CPU with a
-  network card. Three models exists, but actually, only 2 of them are
-  interesting. The "compound" one is simply due to the way our
-  internal code is organized, and can easily be ignored. So at the
-  end, you have two host models: The default one allows to aggregate
-  an existing CPU model with an existing network model, but does not
-  allow parallel tasks because these beasts need some collaboration
-  between the network and CPU model. That is why, ptask_07 is used by
-  default when using SimDag.
-  
-  - **default:** Default host model. Currently, CPU:Cas01 and
-    network:LV08 (with cross traffic enabled)
-  - **compound:** Host model that is automatically chosen if
-    you change the network and CPU models
-  - **ptask_L07:** Host model somehow similar to Cas01+CM02 but
-    allowing "parallel tasks", that are intended to model the moldable
-    tasks of the grid scheduling literature.
+
+- ``cpu/model``: specify the used CPU model.  We have only one model for now:
+
+  - **Cas01:** Simplistic CPU model (time=size/speed)
+
+- ``host/model``: we have two such models for now. 
+
+  - **default:** Default host model. It simply uses the otherwise configured models for cpu, disk and network (i.e. CPU:Cas01,
+    disk:S19 and network:LV08 by default)
+  - **ptask_L07:** This model is mandatory if you plan to use parallel tasks (and useless otherwise). ptasks are intended to
+    model the moldable tasks of the grid scheduling literature. A specific host model is necessary because each such activity
+    has a both compute and communicate components, so the CPU and network models must be mixed together.
 
 - ``storage/model``: specify the used storage model. Only one model is
   provided so far.
@@ -254,17 +246,37 @@ models for all existing resources.
 
 .. todo: make 'compound' the default host model.
 
+.. _options_model_solver:
+
+Solver
+......
+
+The different models rely on a linear inequalities solver to share
+the underlying resources. SimGrid allows you to change the solver, but
+be cautious, **don't change it unless you are 100% sure**.
+
+  - items ``cpu/solver``, ``network/solver``, ``disk/solver`` and  ``host/solver``
+    allow you to change the solver for each model:
+
+    - **maxmin:** The default solver for all models except ptask. Provides a
+      max-min fairness allocation.
+    - **fairbottleneck:** The default solver for ptasks. Extends max-min to
+      allow heterogeneous resources.
+    - **bmf:** More realistic solver for heterogeneous resource sharing.
+      Implements BMF (Bottleneck max fairness) fairness. To be used with
+      parallel tasks instead of fair-bottleneck.
+
 .. _options_model_optim:
 
 Optimization Level
 ..................
 
-The network and CPU models that are based on lmm_solve (that
+The network and CPU models that are based on linear inequalities solver (that
 is, all our analytical models) accept specific optimization
 configurations.
 
   - items ``network/optim`` and ``cpu/optim`` (both default to 'Lazy'):
-    
+
     - **Lazy:** Lazy action management (partial invalidation in lmm +
       heap in action remaining).
     - **TI:** Trace integration. Highly optimized mode when using
@@ -272,7 +284,7 @@ configurations.
       now).
     - **Full:** Full update of remaining and variables. Slow but may be
       useful when debugging.
-      
+
   - items ``network/maxmin-selective-update`` and
     ``cpu/maxmin-selective-update``: configure whether the underlying
     should be lazily updated or not. It should have no impact on the
@@ -286,14 +298,16 @@ configurations.
     the dependency induced by the backbone), but through a complicated
     and slow pattern that follows the actual dependencies.
 
-.. _cfg=maxmin/precision:
-.. _cfg=surf/precision:
+.. _cfg=bmf/precision:
+.. _cfg=precision/timing:
+.. _cfg=precision/work-amount:
 
 Numerical Precision
 ...................
 
-**Option** ``maxmin/precision`` **Default:** 0.00001 (in flops or bytes) |br|
-**Option** ``surf/precision`` **Default:** 0.00001 (in seconds)
+**Option** ``precision/timing`` **Default:** 1e-9 (in seconds) |br|
+**Option** ``precision/work-amount`` **Default:** 1e-5 (in flops or bytes) |br|
+**Option** ``bmf/precision`` **Default:** 1e-12 (no unit)
 
 The analytical models handle a lot of floating point values. It is
 possible to change the epsilon used to update and compare them through
@@ -322,6 +336,17 @@ Such limitations help both to the simulation speed and simulation accuracy
 on highly constrained scenarios, but the simulation speed suffers of this
 setting on regular (less constrained) scenarios so it is off by default.
 
+.. _cfg=bmf/max-iterations:
+
+BMF settings
+............
+
+**Option** ``bmf/max-iterations`` **Default:** 1000
+
+It may happen in some settings that the BMF solver fails to converge to
+a solution, so there is a hard limit on the amount of iteration count to
+avoid infinite loops.
+
 .. _options_model_network:
 
 Configuring the Network Model
@@ -334,47 +359,143 @@ Maximal TCP Window Size
 
 **Option** ``network/TCP-gamma`` **Default:** 4194304
 
-The analytical models need to know the maximal TCP window size to take
-the TCP congestion mechanism into account.  On Linux, this value can
-be retrieved using the following commands. Both give a set of values,
-and you should use the last one, which is the maximal size.
+The analytical models need to know the maximal TCP window size to take the TCP congestion mechanism into account (see
+:ref:`this page <understanding_cm02>` for details). On Linux, this value can be retrieved using the following commands.
+Both give a set of values, and you should use the last one, which is the maximal size.
 
-.. code-block:: shell
-		
-   cat /proc/sys/net/ipv4/tcp_rmem # gives the sender window
-   cat /proc/sys/net/ipv4/tcp_wmem # gives the receiver window
+.. code-block:: console
+
+   $ cat /proc/sys/net/ipv4/tcp_rmem # gives the sender window
+   $ cat /proc/sys/net/ipv4/tcp_wmem # gives the receiver window
+
+If you want to disable the TCP windowing mechanism, set this parameter to 0.
 
-.. _cfg=smpi/IB-penalty-factors:
 .. _cfg=network/bandwidth-factor:
 .. _cfg=network/latency-factor:
 .. _cfg=network/weight-S:
-   
-Correcting Important Network Parameters
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-SimGrid can take network irregularities such as a slow startup or
-changing behavior depending on the message size into account.  You
-should not change these values unless you really know what you're
-doing.  The corresponding values were computed through data fitting
-one the timings of packet-level simulators, as described in `Accuracy
-Study and Improvement of Network Simulation in the SimGrid Framework
-<http://mescal.imag.fr/membres/arnaud.legrand/articles/simutools09.pdf>`_.
+Manual calibration factors
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+SimGrid can take network irregularities such as a slow startup or changing behavior depending on the message size into account.
+The values provided by default were computed a long time ago through data fitting one the timings of either packet-level
+simulators or direct experiments on real platforms. These default values should be OK for most users, but if simulation realism
+is really important to you, you probably want to recalibrate the models (i.e., devise sensible values for your specific
+settings). This section only describes how to pass new values to the models while the calibration process involved in the
+computation of these values is described :ref:`in the relevant chapter <models_calibration>`.
+
+We found out that many networking effects can be realistically accounted for with the three following correction factors. They
+were shown to be enough to capture slow-start effects, the different transmission modes of MPI systems (eager vs. rendez-vous
+mode), or the non linear effects of wifi sharing.
+
+**Option** ``network/latency-factor`` **Default:** 1.0, but overridden by most models
+
+This option specifies a multiplier to apply to the *physical* latency (i.e., the one described in the platform) of the set of
+links involved in a communication. The factor can either be a constant to apply to any communication, or it may depend on the
+message size. The ``CM02`` model does not use any correction factor, so the latency-factor remains to 1. The ``LV08`` model sets
+it to 13.01 to model slow-start, while the ``SMPI`` model has several possible values depending on the interval in which the
+message size falls. The default SMPI setting given below specifies for example that a message smaller than 257 bytes will get a
+latency multiplier of 2.01467 while a message whose size is in [15424, 65472] will get a latency multiplier of 3.48845. The
+``wifi`` model goes further and uses a callback in the program to compute the factor that must be non-linear in this case.
+
+This multiplier is applied to the latency computed from the platform, that is the sum of all link *physical* latencies over the
+:ref:`network path <platform_routing>` used by the considered communication, to derive the *effective* end-to-end latency.
+
+Constant factors are easy to express, but the interval-based syntax used in SMPI is somewhat complex. It expects a set of
+factors separated by semicolons, each of the form ``boundary:factor``. For example if your specification is
+``0:1;1000:2;5000:3``, it means that on [0, 1000) the factor is 1. On [1000,5000), the factor is 2 while the factor is 3 for
+5000 and beyond. If your first interval does include size=0, then the default value of 1 is used before. Changing the factor
+callback is not possible from the command line and must be done from your code, as shown in `this example
+<https://framagit.org/simgrid/simgrid/tree/master/examples/cpp/network-factors/s4u-network-factors.cpp>`_. Note that the chosen
+model only provides some default settings. You may pick a ``LV08`` model to get some of the settings, and override the latency
+with interval-based values.
+
+SMPI default value: 65472:11.6436; 15424:3.48845; 9376:2.59299; 5776:2.18796; 3484:1.88101; 1426:1.61075; 732:1.9503;
+257:1.95341;0:2.01467 (interval boundaries are sorted automatically). These values were computed by data fitting on the Stampede
+Supercomputer at TACC, with optimal deployment of processes on nodes. To accurately model your settings, you should redo the
+:ref:`calibration <models_calibration>`.
+
+**Option** ``network/bandwidth-factor`` **Default:** 1.0, but overridden by most models
+
+Setting this option automatically adjusts the *effective* bandwidth (i.e., the one perceived by the application) used by any
+given communication. As with latency-factor above, the value can be a constant (``CM02`` uses 1 -- no correction -- while
+``LV08`` uses 0.97 to discount TCP headers while computing the payload bandwidth), interval-based (as the default provided by
+the ``SMPI``), or using in-program callbacks (as with ``wifi``).
 
+SMPI default value: 65472:0.940694;15424:0.697866;9376:0.58729;5776:1.08739;3484:0.77493;1426:0.608902;732:0.341987;257:0.338112;0:0.812084
+This was also computed on the Stampede Supercomputer.
 
-If you are using the SMPI model, these correction coefficients are
-themselves corrected by constant values depending on the size of the
-exchange.  By default SMPI uses factors computed on the Stampede
-Supercomputer at TACC, with optimal deployment of processes on
-nodes. Again, only hardcore experts should bother about this fact.
+**Option** ``network/weight-S`` **Default:** depends on the model
+
+Value used to account for RTT-unfairness when sharing a bottleneck (network connections with a large RTT are generally penalized
+against those with a small one). See :ref:`models_TCP` and also this scientific paper: `Accuracy Study and Improvement of Network
+Simulation in the SimGrid Framework <http://mescal.imag.fr/membres/arnaud.legrand/articles/simutools09.pdf>`_
+
+Default values for ``CM02`` is 0. ``LV08`` sets it to 20537 while both ``SMPI`` and ``IB`` set it to 8775.
+
+.. _cfg=network/loopback:
+
+Configuring loopback link
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Several network models provide an implicit loopback link to account for local
+communication on a host. By default it has a 10GBps bandwidth and a null latency.
+This can be changed with ``network/loopback-lat`` and ``network/loopback-bw``
+items. Note that this loopback is conveniently modeled with a :ref:`single FATPIPE link  <pf_loopback>`
+for the whole platform. If modeling contention inside nodes is important then you should
+rather add such loopback links (one for each host) yourself.
+
+.. _cfg=smpi/IB-penalty-factors:
+
+Infiniband model
+^^^^^^^^^^^^^^^^
 
 InfiniBand network behavior can be modeled through 3 parameters
-``smpi/IB-penalty-factors:"βe;βs;γs"``, as explained in `this PhD
-thesis
-<http://mescal.imag.fr/membres/jean-marc.vincent/index.html/PhD/Vienne.pdf>`_.
+``smpi/IB-penalty-factors:"βe;βs;γs"``, as explained in `the PhD
+thesis of Jérôme Vienne
+<http://mescal.imag.fr/membres/jean-marc.vincent/index.html/PhD/Vienne.pdf>`_ (in French)
+or more concisely in `this paper <https://hal.inria.fr/hal-00953618/document>`_,
+even if that paper does only describe models for myrinet and ethernet.
+You can see in Fig 2 some results for Infiniband, for example. This model
+may be outdated by now for modern infiniband, anyway, so a new
+validation would be good.
+
+The three paramaters are defined as follows:
+
+- βs: penalty factor for outgoing messages, computed by running a simple send to
+  two nodes and checking slowdown compared to a single send to one node,
+  dividing by 2
+- βe: penalty factor for ingoing messages, same computation method but with one
+  node receiving several messages
+- γr: slowdown factor when communication buffer memory is saturated. It needs a
+  more complicated pattern to run in order to be computed (5.3 in the thesis,
+  page 107), and formula in the end is γr = time(c)/(3×βe×time(ref)), where
+  time(ref) is the time of a single comm with no contention).
+
+Once these values are computed, a penalty is assessed for each message (this is
+the part implemented in the simulator) as shown page 106 of the thesis. Here is
+a simple translation of this text. First, some notations:
+
+- ∆e(e) which corresponds to the incoming degree of node e, that is to say the number of communications having as destination node e.
+- ∆s (s) which corresponds to the degree outgoing from node s, that is to say the number of communications sent by node s.
+- Φ (e) which corresponds to the number of communications destined for the node e but coming from a different node.
+- Ω (s, e) which corresponds to the number of messages coming from node s to node e. If node e only receives communications from different nodes then Φ (e) = ∆e (e). On the other hand if, for example, there are three messages coming from node s and going from node e then Φ (e) 6 = ∆e (e) and Ω (s, e) = 3
 
-.. todo:: This section should be rewritten, and actually explain the
-	  options network/bandwidth-factor, network/latency-factor,
-	  network/weight-S.
+To determine the penalty for a communication, two values need to be calculated. First, the penalty caused by the conflict in transmission, noted ps.
+
+
+- if ∆s (i) = 1 then ps = 1.
+- if ∆s (i) ≥ 2 and ∆e (i) ≥ 3 then ps = ∆s (i) × βs × γr
+- else, ps = ∆s (i) × βs
+
+
+Then,  the penalty caused by the conflict in reception (noted pe) should be computed as follows:
+
+- if ∆e (i) = 1 then pe = 1
+- else, pe = Φ (e) × βe × Ω (s, e)
+
+Finally, the penalty associated with the communication is:
+p = max (ps ∈ s, pe)
 
 .. _cfg=network/crosstraffic:
 
@@ -399,43 +520,49 @@ Note that with the default host model this option is activated by default.
 
 .. _cfg=smpi/async-small-thresh:
 
-Simulating Asyncronous Send
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-(this configuration item is experimental and may change or disapear)
+Simulating Asynchronous Send
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-It is possible to specify that messages below a certain size will be
+It is possible to specify that messages below a certain size (in bytes) will be
 sent as soon as the call to MPI_Send is issued, without waiting for
-the correspondant receive. This threshold can be configured through
+the correspondent receive. This threshold can be configured through
 the ``smpi/async-small-thresh`` item. The default value is 0. This
 behavior can also be manually set for mailboxes, by setting the
 receiving mode of the mailbox with a call to
-:cpp:func:`MSG_mailbox_set_async`. After this, all messages sent to
+:cpp:func:`sg_mailbox_set_receiver`. After this, all messages sent to
 this mailbox will have this behavior regardless of the message size.
 
 This value needs to be smaller than or equals to the threshold set at
-@ref options_model_smpi_detached , because asynchronous messages are
-meant to be detached as well.
+:ref:`cfg=smpi/send-is-detached-thresh`, because asynchronous messages
+are meant to be detached as well.
 
 .. _options_pls:
 
-Configuring NS3
-^^^^^^^^^^^^^^^
+Configuring ns-3
+^^^^^^^^^^^^^^^^
 
-**Option** ``ns3/TcpModel`` **Default:** "default" (NS3 default)
+**Option** ``ns3/NetworkModel`` **Default:** "default" (ns-3 default TCP)
 
-When using NS3, there is an extra item ``ns3/TcpModel``, corresponding
-to the ``ns3::TcpL4Protocol::SocketType`` configuration item in
-NS3. The only valid values (enforced on the SimGrid side) are
-'default' (no change to the NS3 configuration), 'NewReno' or 'Reno' or
-'Tahoe'.
+When using ns-3, the item ``ns3/NetworkModel`` can be used to switch between TCP or UDP, and switch the used TCP variante. If
+the item is left unchanged, ns-3 uses the default TCP implementation. With a value of "UDP", ns-3 is set to use UDP instead.
+With the value of either 'NewReno' or 'Cubic', the ``ns3::TcpL4Protocol::SocketType`` configuration item in ns-3 is set to the
+corresponding protocol.
+
+**Option** ``ns3/seed`` **Default:** "" (don't set the seed in ns-3)
+
+This option is the random seed to provide to ns-3 with
+``ns3::RngSeedManager::SetSeed`` and ``ns3::RngSeedManager::SetRun``.
+
+If left blank, no seed is set in ns-3. If the value 'time' is
+provided, the current amount of seconds since epoch is used as a seed.
+Otherwise, the provided value must be a number to use as a seed.
 
 Configuring the Storage model
 .............................
 
 .. _cfg=storage/max_file_descriptors:
 
-File Descriptor Cound per Host
+File Descriptor Count per Host
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 **Option** ``storage/max_file_descriptors`` **Default:** 1024
@@ -449,7 +576,7 @@ application requires it or to reduce it to save memory space.
 Activating Plugins
 ------------------
 
-SimGrid plugins allow to extend the framework without changing its
+SimGrid plugins allow one to extend the framework without changing its
 source code directly. Read the source code of the existing plugins to
 learn how to do so (in ``src/plugins``), and ask your questions to the
 usual channels (Stack Overflow, Mailing list, IRC). The basic idea is
@@ -463,117 +590,101 @@ modification to your simulation code. For example, you can activate
 the host energy plugin by adding ``--cfg=plugin:host_energy`` to your
 command line.
 
-Here is the full list of plugins that can be activated this way:
+Here is a partial list of plugins that can be activated this way. You can get
+the full list by passing ``--cfg=plugin:help`` to your simulator.
 
- - **host_energy:** keeps track of the energy dissipated by
-   computations. More details in @ref plugin_energy.
- - **link_energy:** keeps track of the energy dissipated by
-   communications. More details in @ref SURF_plugin_energy.
- - **host_load:** keeps track of the computational load. 
-   More details in @ref plugin_load.
+  - :ref:`Host Energy <plugin_host_energy>`: models the energy dissipation of the compute units.
+  - :ref:`Link Energy <plugin_link_energy>`: models the energy dissipation of the network.
+  - :ref:`Host Load <plugin_host_load>`: monitors the load of the compute units.
 
 .. _options_modelchecking:
-   
+
 Configuring the Model-Checking
 ------------------------------
 
-To enable the SimGrid model-checking support the program should
+To enable SimGrid's model-checking support, the program should
 be executed using the simgrid-mc wrapper:
 
-.. code-block:: shell
-		
-   simgrid-mc ./my_program
+.. code-block:: console
+
+   $ simgrid-mc ./my_program
 
 Safety properties are expressed as assertions using the function
 :cpp:func:`void MC_assert(int prop)`.
 
-.. _cfg=model-check/property:
-     
-Specifying a liveness property
-..............................
+.. _cfg=smpi/buffering:
 
-**Option** ``model-check/property`` **Default:** unset
+Specifying the MPI buffering behavior
+.....................................
 
-If you want to specify liveness properties, you have to pass them on
-the command line, specifying the name of the file containing the
-property, as formatted by the ltl2ba program.
+**Option** ``smpi/buffering`` **Default:** infty
 
+Buffering in MPI has a huge impact on the communication semantic. For example,
+standard blocking sends are synchronous calls when the system buffers are full
+while these calls can complete immediately without even requiring a matching
+receive call for small messages sent when the system buffers are empty.
 
-.. code-block:: shell
-		
-   simgrid-mc ./my_program --cfg=model-check/property:<filename>
+In SMPI, this depends on the message size, that is compared against two thresholds:
 
-.. _cfg=model-check/checkpoint:
-   
-Going for Stateful Verification
-...............................
+- if (size < :ref:`smpi/async-small-thresh <cfg=smpi/async-small-thresh>`) then
+  MPI_Send returns immediately, and the message is sent even if the
+  corresponding receive has not be issued yet.  This is known as the eager mode.
+- if (:ref:`smpi/async-small-thresh <cfg=smpi/async-small-thresh>` < size <
+  :ref:`smpi/send-is-detached-thresh <cfg=smpi/send-is-detached-thresh>`) then
+  MPI_Send also returns immediately, but SMPI waits for the corresponding
+  receive to be posted, in order to perform the communication operation.
+- if (:ref:`smpi/send-is-detached-thresh <cfg=smpi/send-is-detached-thresh>` < size) then
+  MPI_Send returns only when the message has actually been sent over the network. This is known as the rendez-vous mode.
+
+The ``smpi/buffering`` (only valid with MC) option gives an easier interface to choose between these semantics. It can take two values:
 
-By default, the system is backtracked to its initial state to explore
-another path instead of backtracking to the exact step before the fork
-that we want to explore (this is called stateless verification). This
-is done this way because saving intermediate states can rapidly
-exhaust the available memory. If you want, you can change the value of
-the ``model-check/checkpoint`` item. For example,
-``--cfg=model-check/checkpoint:1`` asks to take a checkpoint every
-step.  Beware, this will certainly explode your memory. Larger values
-are probably better, make sure to experiment a bit to find the right
-setting for your specific system.
+- **zero:** means that buffering should be disabled. All communications are actually blocking.
+- **infty:** means that buffering should be made infinite. All communications are non-blocking.
 
 .. _cfg=model-check/reduction:
 
 Specifying the kind of reduction
 ................................
 
+**Option** model-check/reduction **Default:** "dpor"
+
 The main issue when using the model-checking is the state space
-explosion. To counter that problem, you can chose a exploration
-reduction techniques with
+explosion. You can activate some reduction technique with
 ``--cfg=model-check/reduction:<technique>``. For now, this
 configuration variable can take 2 values:
 
- - **none:** Do not apply any kind of reduction (mandatory for now for
-   liveness properties)
- - **dpor:** Apply Dynamic Partial Ordering Reduction. Only valid if
-   you verify local safety properties (default value for safety
-   checks).
-
-There is unfortunately no silver bullet here, and the most efficient
-reduction techniques cannot be applied to any properties. In
-particular, the DPOR method cannot be applied on liveness properties
-since our implementation of DPOR may break some cycles, while cycles
-are very important to the soundness of the exploration for liveness
-properties.
+ - **none:** Do not apply any kind of reduction
+ - **dpor:** Apply Dynamic Partial Ordering Reduction. Only valid if you verify local safety properties (default value for
+   safety checks).
+ - **sdpor:** Source-set DPOR, as described in "Source Sets: A Foundation for Optimal Dynamic Partial Order Reduction"
+    by Abdulla et al.
+ - **odpor:** Optimal DPOR, as described in "Source Sets: A Foundation for Optimal Dynamic Partial Order Reduction"
+    by Abdulla et al.
 
-.. _cfg=model-check/visited:
+Our current DPOR implementation could be improved in may ways. We are
+currently improving its efficiency (both in term of reduction ability
+and computational speed).
 
-Size of Cycle Detection Set
-...........................
+.. _cfg=model-check/strategy:
 
-In order to detect cycles, the model-checker needs to check if a new
-explored state is in fact the same state than a previous one. For
-that, the model-checker can take a snapshot of each visited state:
-this snapshot is then used to compare it with subsequent states in the
-exploration graph.
-
-The ``model-check/visited`` item is the maximum number of states which
-are stored in memory. If the maximum number of snapshotted state is
-reached, some states will be removed from the memory and some cycles
-might be missed. Small values can lead to incorrect verifications, but
-large value can exhaust your memory, so choose carefully.
-
-By default, no state is snapshotted and cycles cannot be detected.
-
-.. _cfg=model-check/termination:
-
-Non-Termination Detection
-.........................
+Guiding strategy
+................
 
-The ``model-check/termination`` configuration item can be used to
-report if a non-termination execution path has been found. This is a
-path with a cycle which means that the program might never terminate.
+**Option** model-check/strategy **Default:** "none"
 
-This only works in safety mode, not in liveness mode.
+Even after the DPOR's reduction, the state space that we have to explore remains huge. SimGrid provides several guiding
+strategies aiming at converging faster toward bugs. By default, none of these strategy is enabled, and SimGrid does a regular
+DFS exploration.
 
-This options is disabled by default.
+ - **max_match_comm**: Try to minimize the number of in-fly communication by appairing matching send and receive. This tend to
+   produce nicer backtraces, in particular when a user-level ``send`` is broken down internally into a ``send_async`` + ``wait``.
+   This strategy will ensure that the ``wait`` occures as soon as possible, easing the understanding of the user who do not
+   expect her ``send`` to be split.
+ - **min_match_comm**: Try to maximize the number of in-fly communication by not appairing matching send and receive. This is
+   the exact opposite strategy, but it is still useful as it tend to explore first the branches where the risk of deadlock is
+   higher.
+ - **uniform**: this is a boring random strategy where choices are based on a uniform sampling of possible choices.
+   Surprisingly, it gives really really good results.
 
 .. _cfg=model-check/dot-output:
 
@@ -581,30 +692,29 @@ Dot Output
 ..........
 
 If set, the ``model-check/dot-output`` configuration item is the name
-of a file in which to write a dot file of the path leading the found
-property (safety or liveness violation) as well as the cycle for
-liveness properties. This dot file can then fed to the graphviz dot
-tool to generate an corresponding graphical representation.
+of a file in which to write a dot file of the path leading to the
+property violation discovered (safety violation). This dot file can then be fed to the
+graphviz dot tool to generate a corresponding graphical representation.
 
 .. _cfg=model-check/max-depth:
 
 Exploration Depth Limit
 .......................
 
-The ``model-checker/max-depth`` can set the maximum depth of the
-exploration graph of the model-checker. If this limit is reached, a
+The ``model-check/max-depth`` can set the maximum depth of the
+exploration graph of the model checker. If this limit is reached, a
 logging message is sent and the results might not be exact.
 
-By default, there is not depth limit.
+By default, the exploration is limited to the depth of 1000.
 
 .. _cfg=model-check/timeout:
 
 Handling of Timeouts
 ....................
 
-By default, the model-checker does not handle timeout conditions: the `wait`
+By default, the model checker does not handle timeout conditions: the `wait`
 operations never time out. With the ``model-check/timeout`` configuration item
-set to **yes**, the model-checker will explore timeouts of `wait` operations.
+set to **yes**, the model checker will explore timeouts of `wait` operations.
 
 .. _cfg=model-check/communications-determinism:
 .. _cfg=model-check/send-determinism:
@@ -614,120 +724,154 @@ Communication Determinism
 
 The ``model-check/communications-determinism`` and
 ``model-check/send-determinism`` items can be used to select the
-communication determinism mode of the model-checker which checks
+communication determinism mode of the model checker, which checks
 determinism properties of the communications of an application.
 
-.. _cfg=model-check/sparse-checkpoint:
+.. _cfg=model-check/setenv:
 
-Incremental Checkpoints
-.......................
+Passing environment variables
+.............................
 
-When the model-checker is configured to take a snapshot of each
-explored state (with the ``model-checker/visited`` item), the memory
-consumption can rapidly reach GiB ou Tib of memory. However, for many
-workloads, the memory does not change much between different snapshots
-and taking a complete copy of each snapshot is a waste of memory.
-
-The ``model-check/sparse-checkpoint`` option item can be set to
-**yes** to avoid making a complete copy of each snapshot. Instead,
-each snapshot will be decomposed in blocks which will be stored
-separately.  If multiple snapshots share the same block (or if the
-same block is used in the same snapshot), the same copy of the block
-will be shared leading to a reduction of the memory footprint.
-
-For many applications, this option considerably reduces the memory
-consumption.  In somes cases, the model-checker might be slightly
-slower because of the time taken to manage the metadata about the
-blocks. In other cases however, this snapshotting strategy will be
-much faster by reducing the cache consumption.  When the memory
-consumption is important, by avoiding to hit the swap or reducing the
-swap usage, this option might be much faster than the basic
-snapshotting strategy.
-
-This option is currently disabled by default.
+You can specify extra environment variables to be set in the verified application
+with ``model-check/setenv``. For example, you can preload a library as follows:
+``-cfg=model-check/setenv:LD_PRELOAD=toto;LD_LIBRARY_PATH=/tmp``.
+
+.. _options_mc_perf:
 
 Verification Performance Considerations
 .......................................
 
 The size of the stacks can have a huge impact on the memory
 consumption when using model-checking. By default, each snapshot will
-save a copy of the whole stacks and not only of the part which is
+save a copy of the whole stacks and not only of the part that is
 really meaningful: you should expect the contribution of the memory
-consumption of the snapshots to be @f$ @mbox{number of processes}
-@times @mbox{stack size} @times @mbox{number of states} @f$.
-
-The ``model-check/sparse-checkpoint`` can be used to reduce the memory
-consumption by trying to share memory between the different snapshots.
+consumption of the snapshots to be:
+:math:`\text{number of processes} \times \text{stack size} \times \text{number of states}`.
 
 When compiled against the model checker, the stacks are not
 protected with guards: if the stack size is too small for your
-application, the stack will silently overflow on other parts of the
+application, the stack will silently overflow into other parts of the
 memory (see :ref:`contexts/guard-size <cfg=contexts/guard-size>`).
 
-.. _cfg=model-checker/hash:
-
-State Hashing
-.............
-
-Usually most of the time of the model-checker is spent comparing states. This
-process is complicated and consumes a lot of bandwidth and cache.
-In order to speedup the state comparison, the experimental ``model-checker/hash``
-configuration item enables the computation of a hash summarizing as much
-information of the state as possible into a single value. This hash can be used
-to avoid most of the comparisons: the costly comparison is then only used when
-the hashes are identical.
-
-Currently most of the state is not included in the hash because the
-implementation was found to be buggy and this options is not as useful as
-it could be. For this reason, it is currently disabled by default.
-
-.. _cfg=model-check/record:
 .. _cfg=model-check/replay:
 
-Record/Replay of Verification
-.............................
-
-As the model-checker keeps jumping at different places in the execution graph,
-it is difficult to understand what happens when trying to debug an application
-under the model-checker. Event the output of the program is difficult to
-interpret. Moreover, the model-checker does not behave nicely with advanced
-debugging tools such as valgrind. For those reason, to identify a trajectory
-in the execution graph with the model-checker and replay this trajcetory and
-without the model-checker black-magic but with more standard tools
-(such as a debugger, valgrind, etc.). For this reason, Simgrid implements an
-experimental record/replay functionnality in order to record a trajectory with
-the model-checker and replay it without the model-checker.
+Replaying buggy execution paths from the model checker
+......................................................
 
-When the model-checker finds an interesting path in the application
-execution graph (where a safety or liveness property is violated), it
-can generate an identifier for this path. To enable this behavious the
-``model-check/record`` must be set to **yes**, which is not the case
-by default.
+Debugging the problems reported by the model checker is challenging because
+the model checker may explore several execution paths before encountering the issue,
+the output very difficult to understand. Fortunately, SimGrid provides
+the execution path leading to any reported issue so that you can replay
+this path reported by the model checker, restoring a classical experience of debugging.
 
-Here is an example of output:
+When the model checker finds an interesting path in the application
+execution graph (where a safety property is violated), it
+generates an identifier for this path. Here is an example of the output:
 
-.. code-block:: shell
+.. code-block:: console
 
    [  0.000000] (0:@) Check a safety property
    [  0.000000] (0:@) **************************
    [  0.000000] (0:@) *** PROPERTY NOT VALID ***
    [  0.000000] (0:@) **************************
    [  0.000000] (0:@) Counter-example execution trace:
+   [  0.000000] (0:@)   [(1)Tremblay (app)] MC_RANDOM(3)
+   [  0.000000] (0:@)   [(1)Tremblay (app)] MC_RANDOM(4)
    [  0.000000] (0:@) Path = 1/3;1/4
-   [  0.000000] (0:@) [(1)Tremblay (app)] MC_RANDOM(3)
-   [  0.000000] (0:@) [(1)Tremblay (app)] MC_RANDOM(4)
    [  0.000000] (0:@) Expanded states = 27
    [  0.000000] (0:@) Visited states = 68
    [  0.000000] (0:@) Executed transitions = 46
 
-This path can then be replayed outside of the model-checker (and even
-in non-MC build of simgrid) by setting the ``model-check/replay`` item
-to the given path. The other options should be the same (but the
-model-checker should be disabled).
-
-The format and meaning of the path may change between different
-releases so the same release of Simgrid should be used for the record
-phase and the replay phase.
+The interesting line is ``Path = 1/3;1/4``, which means that you should use
+``--cfg=model-check/replay:1/3;1/4`` to replay your application on the buggy
+execution path. All options (but the model checker related ones) must
+remain the same. In particular, if you ran your application with
+``smpirun -wrapper simgrid-mc``, then remove the ``-wrapper simgrid-mc`` part 
+(you may want to use valgrind or gdb as wrappers instead). Also remove all
+MC-related options, keep non-MC-related ones and add
+``--cfg=model-check/replay:???``.
+
+Things are very similar if you are using sthread. Simply drop ``simgrid-mc`` from your command line, as follows:
+
+.. code-block:: console
+
+   $ LD_PRELOAD=../../lib/libsthread.so ./pthread-mutex-simpledeadlock --cfg=model-check/replay:'2;2;3;2;3;3'
+   sthread is intercepting the execution of ./pthread-mutex-simpledeadlock
+   [0.000000] [xbt_cfg/INFO] Configuration change: Set 'model-check/replay' to '2;2;3;2;3;3'
+   [0.000000] [mc_record/INFO] path=2;2;3;2;3;3
+   All threads are started.
+   [0.000000] [mc_record/INFO] ***********************************************************************************
+   [0.000000] [mc_record/INFO] * Path chunk #1 '2/0' Actor thread 1(pid:2): MUTEX_ASYNC_LOCK(mutex_id:0 owner:none)
+   [0.000000] [mc_record/INFO] ***********************************************************************************
+   Backtrace (displayed in actor thread 1):
+     ->  #0 simgrid::s4u::Mutex::lock() at ../../src/s4u/s4u_Mutex.cpp:26
+     ->  #1 sthread_mutex_lock at ../../src/sthread/sthread_impl.cpp:188
+     ->  #2 pthread_mutex_lock at ../../src/sthread/sthread.c:141
+     ->  #3 thread_fun1 at ../../examples/sthread/pthread-mutex-simpledeadlock.c:21
+   
+   [0.000000] [mc_record/INFO] ***********************************************************************************
+   [0.000000] [mc_record/INFO] * Path chunk #2 '2/0' Actor thread 1(pid:2): MUTEX_WAIT(mutex_id:0 owner:2)
+   [0.000000] [mc_record/INFO] ***********************************************************************************
+   Backtrace (displayed in actor thread 1):
+     ->  #0 simgrid::s4u::Mutex::lock() at ../../src/s4u/s4u_Mutex.cpp:29
+     ->  #1 sthread_mutex_lock at ../../src/sthread/sthread_impl.cpp:188
+     ->  #2 pthread_mutex_lock at ../../src/sthread/sthread.c:141
+     ->  #3 thread_fun1 at ../../examples/sthread/pthread-mutex-simpledeadlock.c:21
+   
+   [0.000000] [mc_record/INFO] ***********************************************************************************
+   [0.000000] [mc_record/INFO] * Path chunk #3 '3/0' Actor thread 2(pid:3): MUTEX_ASYNC_LOCK(mutex_id:1 owner:none)
+   [0.000000] [mc_record/INFO] ***********************************************************************************
+   Backtrace (displayed in actor thread 2):
+     ->  #0 simgrid::s4u::Mutex::lock() at ../../src/s4u/s4u_Mutex.cpp:26
+     ->  #1 sthread_mutex_lock at ../../src/sthread/sthread_impl.cpp:188
+     ->  #2 pthread_mutex_lock at ../../src/sthread/sthread.c:141
+     ->  #3 thread_fun2 at ../../examples/sthread/pthread-mutex-simpledeadlock.c:31
+   
+   [0.000000] [mc_record/INFO] ***********************************************************************************
+   [0.000000] [mc_record/INFO] * Path chunk #4 '2/0' Actor thread 1(pid:2): MUTEX_ASYNC_LOCK(mutex_id:1 owner:3)
+   [0.000000] [mc_record/INFO] ***********************************************************************************
+   Backtrace (displayed in actor thread 1):
+     ->  #0 simgrid::s4u::Mutex::lock() at ../../src/s4u/s4u_Mutex.cpp:26
+     ->  #1 sthread_mutex_lock at ../../src/sthread/sthread_impl.cpp:188
+     ->  #2 pthread_mutex_lock at ../../src/sthread/sthread.c:141
+     ->  #3 thread_fun1 at ../../examples/sthread/pthread-mutex-simpledeadlock.c:22
+   
+   [0.000000] [mc_record/INFO] ***********************************************************************************
+   [0.000000] [mc_record/INFO] * Path chunk #5 '3/0' Actor thread 2(pid:3): MUTEX_WAIT(mutex_id:1 owner:3)
+   [0.000000] [mc_record/INFO] ***********************************************************************************
+   Backtrace (displayed in actor thread 2):
+     ->  #0 simgrid::s4u::Mutex::lock() at ../../src/s4u/s4u_Mutex.cpp:29
+     ->  #1 sthread_mutex_lock at ../../src/sthread/sthread_impl.cpp:188
+     ->  #2 pthread_mutex_lock at ../../src/sthread/sthread.c:141
+     ->  #3 thread_fun2 at ../../examples/sthread/pthread-mutex-simpledeadlock.c:31
+   
+   [0.000000] [mc_record/INFO] ***********************************************************************************
+   [0.000000] [mc_record/INFO] * Path chunk #6 '3/0' Actor thread 2(pid:3): MUTEX_ASYNC_LOCK(mutex_id:0 owner:2)
+   [0.000000] [mc_record/INFO] ***********************************************************************************
+   Backtrace (displayed in actor thread 2):
+     ->  #0 simgrid::s4u::Mutex::lock() at ../../src/s4u/s4u_Mutex.cpp:26
+     ->  #1 sthread_mutex_lock at ../../src/sthread/sthread_impl.cpp:188
+     ->  #2 pthread_mutex_lock at ../../src/sthread/sthread.c:141
+     ->  #3 thread_fun2 at ../../examples/sthread/pthread-mutex-simpledeadlock.c:32
+   
+   [0.000000] [mc_record/INFO] The replay of the trace is complete. DEADLOCK detected.
+   [0.000000] [ker_engine/INFO] 3 actors are still running, waiting for something.
+   [0.000000] [ker_engine/INFO] Legend of the following listing: "Actor <pid> (<name>@<host>): <status>"
+   [0.000000] [ker_engine/INFO] Actor 1 (main thread@Lilibeth) simcall ActorJoin(pid:2)
+   [0.000000] [ker_engine/INFO] Actor 2 (thread 1@Lilibeth) simcall MUTEX_WAIT(mutex_id:1 owner:3)
+   [0.000000] [ker_engine/INFO] Actor 3 (thread 2@Lilibeth) simcall MUTEX_WAIT(mutex_id:0 owner:2)
+   [0.000000] [sthread/INFO] All threads exited. Terminating the simulation.
+   [0.000000] ../../src/kernel/EngineImpl.cpp:265: [ker_engine/WARNING] Process called exit when leaving - Skipping cleanups
+   [0.000000] ../../src/kernel/EngineImpl.cpp:265: [ker_engine/WARNING] Process called exit when leaving - Skipping cleanups
+
+Currently, if the path is of the form ``X;Y;Z``, each number denotes
+the actor's pid that is selected at each indecision point. If it's of
+the form ``X/a;Y/b``, the X and Y are the selected pids while the a
+and b are the return values of their simcalls. In the previous
+example, ``1/3;1/4``, you can see from the full output that the actor
+1 is doing MC_RANDOM simcalls, so the 3 and 4 simply denote the values
+that these simcall return on the execution branch leading to the
+violation.
 
 Configuring the User Code Virtualization
 ----------------------------------------
@@ -745,7 +889,7 @@ process requires a blocking action (such as sending a message), it is
 interrupted, and only gets released when the simulated clock reaches
 the point where the blocking operation is done. This is explained
 graphically in the `relevant tutorial, available online
-<http://simgrid.gforge.inria.fr/tutorials/simgrid-simix-101.pdf>`_.
+<https://simgrid.org/tutorials/simgrid-simix-101.pdf>`_.
 
 In SimGrid, the containers in which user processes are virtualized are
 called contexts. Several context factory are provided, and you can
@@ -756,11 +900,8 @@ should be the most effcient one (please report bugs if the
 auto-detection fails for you). They are approximately sorted here from
 the slowest to the most efficient:
 
- - **thread:** very slow factory using full featured threads (either
-   pthreads or windows native threads). They are slow but very
-   standard. Some debuggers or profilers only work with this factory.
- - **java:** Java applications are virtualized onto java threads (that
-   are regular pthreads registered to the JVM)
+ - **thread:** very slow factory using full featured, standard threads.
+   They are slow but very standard. Some debuggers or profilers only work with this factory.
  - **ucontext:** fast factory using System V contexts (Linux and FreeBSD only)
  - **boost:** This uses the `context
    implementation <http://www.boost.org/doc/libs/1_59_0/libs/context/doc/html/index.html>`_
@@ -768,14 +909,14 @@ the slowest to the most efficient:
    raw implementation.
    |br| Install the relevant library (e.g. with the
    libboost-contexts-dev package on Debian/Ubuntu) and recompile
-   SimGrid. 
+   SimGrid.
  - **raw:** amazingly fast factory using a context switching mechanism
    of our own, directly implemented in assembly (only available for x86
    and amd64 platforms for now) and without any unneeded system call.
 
-The main reason to change this setting is when the debugging tools get
+The main reason to change this setting is when the debugging tools become
 fooled by the optimized context factories. Threads are the most
-debugging-friendly contextes, as they allow to set breakpoints
+debugging-friendly contexts, as they allow one to set breakpoints
 anywhere with gdb and visualize backtraces for all processes, in order
 to debug concurrency issues. Valgrind is also more comfortable with
 threads, but it should be usable with all factories (Exception: the
@@ -798,8 +939,16 @@ stacks), leading to segfaults with corrupted stack traces.
 If you want to push the scalability limits of your code, you might
 want to reduce the ``contexts/stack-size`` item. Its default value is
 8192 (in KiB), while our Chord simulation works with stacks as small
-as 16 KiB, for example. For the thread factory, the default value is
-the one of the system but you can still change it with this parameter.
+as 16 KiB, for example. You can ensure that some actors have a specific
+size by simply changing the value of this configuration item before
+creating these actors. The :cpp:func:`simgrid::s4u::Engine::set_config`
+functions are handy for that.
+
+This *setting is ignored* when using the thread factory (because there
+is no way to modify the stack size with C++ system threads). Instead,
+you should compile SimGrid and your application with
+``-fsplit-stack``. Note that this compilation flag is not compatible
+with the model checker right now.
 
 The operating system should only allocate memory for the pages of the
 stack which are actually used and you might not need to use this in
@@ -811,50 +960,39 @@ model checker (see :ref:`options_mc_perf`).
 Disabling Stack Guard Pages
 ...........................
 
-**Option** ``contexts/guard-size`` **Default** 1 page in most case (0 pages on Windows or with MC)
+**Option** ``contexts/guard-size`` **Default** 1 page in most case (0 pages with MC)
 
-A stack guard page is usually used which prevents the stack of a given
-actor from overflowing on another stack. But the performance impact
-may become prohibitive when the amount of actors increases.  The
-option ``contexts/guard-size`` is the number of stack guard pages
-used.  By setting it to 0, no guard pages will be used: in this case,
-you should avoid using small stacks (with :ref:`contexts/stack-size
-<cfg=contexts/stack-size>`) as the stack will silently overflow on
-other parts of the memory.
+Unless you use the threads context factory (see
+:ref:`cfg=contexts/factory`), a stack guard page is usually used
+which prevents the stack of a given actor from overflowing on another
+stack. But the performance impact may become prohibitive when the
+amount of actors increases.  The option ``contexts/guard-size`` is the
+number of stack guard pages used.  By setting it to 0, no guard pages
+will be used: in this case, you should avoid using small stacks (with
+:ref:`contexts/stack-size <cfg=contexts/stack-size>`) as the stack
+will silently overflow on other parts of the memory.
 
 When no stack guard page is created, stacks may then silently overflow
 on other parts of the memory if their size is too small for the
 application.
 
 .. _cfg=contexts/nthreads:
-.. _cfg=contexts/parallel-threshold:
 .. _cfg=contexts/synchro:
-  
+
 Running User Code in Parallel
 .............................
 
 Parallel execution of the user code is only considered stable in
-SimGrid v3.7 and higher, and mostly for MSG simulations. SMPI
+SimGrid v3.7 and higher, and mostly for S4U simulations. SMPI
 simulations may well fail in parallel mode. It is described in
 `INRIA RR-7653 <http://hal.inria.fr/inria-00602216/>`_.
 
 If you are using the **ucontext** or **raw** context factories, you can
 request to execute the user code in parallel. Several threads are
-launched, each of them handling as much user contexts at each run. To
-actiave this, set the ``contexts/nthreads`` item to the amount of
-cores that you have in your computer (or lower than 1 to have
-the amount of cores auto-detected).
-
-Even if you asked several worker threads using the previous option,
-you can request to start the parallel execution (and pay the
-associated synchronization costs) only if the potential parallelism is
-large enough. For that, set the ``contexts/parallel-threshold``
-item to the minimal amount of user contexts needed to start the
-parallel execution. In any given simulation round, if that amount is
-not reached, the contexts will be run sequentially directly by the
-main thread (thus saving the synchronization costs). Note that this
-option is mainly useful when the grain of the user code is very fine,
-because our synchronization is now very efficient.
+launched, each of them handling the same number of user contexts at each
+run. To activate this, set the ``contexts/nthreads`` item to the amount
+of cores that you have in your computer (or lower than 1 to have the
+amount of cores auto-detected).
 
 When parallel execution is activated, you can choose the
 synchronization schema used with the ``contexts/synchro`` item,
@@ -871,49 +1009,45 @@ which value is either:
    your machine for no good reason. You probably prefer the other less
    eager schemas.
 
-   
 Configuring the Tracing
 -----------------------
 
-The :ref:`tracing subsystem <outcomes_vizu>` can be configured in
-several different ways depending on the nature of the simulator (MSG,
-SimDag, SMPI) and the kind of traces that need to be obtained. See the
+The :ref:`tracing subsystem <outcome_vizu>` can be configured in
+several different ways depending on the used interface (S4U, SMPI)
+and the kind of traces that needs to be obtained. See the
 :ref:`Tracing Configuration Options subsection
-<tracing_tracing_options>` to get a detailed description of each
+<tracing_tracing_options>` for a full description of each
 configuration option.
 
 We detail here a simple way to get the traces working for you, even if
 you never used the tracing API.
 
 
-- Any SimGrid-based simulator (MSG, SimDag, SMPI, ...) and raw traces:
+- Any SimGrid-based simulator (S4U, SMPI, ...) and raw traces:
 
-  .. code-block:: shell
+  .. code-block:: none
 
-     --cfg=tracing:yes --cfg=tracing/uncategorized:yes --cfg=triva/uncategorized:uncat.plist
+     --cfg=tracing:yes --cfg=tracing/uncategorized:yes
 
-  The first parameter activates the tracing subsystem, the second
+  The first parameter activates the tracing subsystem, and the second
   tells it to trace host and link utilization (without any
-  categorization) and the third creates a graph configuration file to
-  configure Triva when analysing the resulting trace file.
+  categorization).
 
-- MSG or SimDag-based simulator and categorized traces (you need to
-  declare categories and classify your tasks according to them) 
+- S4U-based simulator and categorized traces (you need to
+  declare categories and classify your tasks according to them)
 
-  .. code-block:: shell
+  .. code-block:: none
 
-     --cfg=tracing:yes --cfg=tracing/categorized:yes --cfg=triva/categorized:cat.plist
+     --cfg=tracing:yes --cfg=tracing/categorized:yes
 
-  The first parameter activates the tracing subsystem, the second
-  tells it to trace host and link categorized utilization and the
-  third creates a graph configuration file to configure Triva when
-  analysing the resulting trace file.
+  The first parameter activates the tracing subsystem, and the second
+  tells it to trace host and link categorized utilization.
 
 - SMPI simulator and traces for a space/time view:
 
-  .. code-block:: shell
-     
-     smpirun -trace ...
+  .. code-block:: console
+
+     $ smpirun -trace ...
 
   The `-trace` parameter for the smpirun script runs the simulation
   with ``--cfg=tracing:yes --cfg=tracing/smpi:yes``. Check the
@@ -925,41 +1059,25 @@ reproduce an experiment. You have two ways to do that:
 
 - Add a string on top of the trace file as comment:
 
-  .. code-block:: shell
+  .. code-block:: none
 
      --cfg=tracing/comment:my_simulation_identifier
 
 - Add the contents of a textual file on top of the trace file as comment:
 
-  .. code-block:: shell
-		  
+  .. code-block:: none
+
      --cfg=tracing/comment-file:my_file_with_additional_information.txt
 
 Please, use these two parameters (for comments) to make reproducible
 simulations. For additional details about this and all tracing
 options, check See the :ref:`tracing_tracing_options`.
 
-Configuring MSG
----------------
-
-.. _cfg=msg/debug-multiple-use:
-
-Debugging MSG Code
-..................
-
-**Option** ``msg/debug-multiple-use`` **Default:** off
-
-Sometimes your application may try to send a task that is still being
-executed somewhere else, making it impossible to send this task. However,
-for debugging purposes, one may want to know what the other host is/was
-doing. This option shows a backtrace of the other process.
-
 Configuring SMPI
 ----------------
 
 The SMPI interface provides several specific configuration items.
-These are uneasy to see since the code is usually launched through the
-``smiprun`` script directly.
+These are not easy to see with ``--help-cfg``, since SMPI binaries are usually launched through the ``smiprun`` script.
 
 .. _cfg=smpi/host-speed:
 .. _cfg=smpi/cpu-threshold:
@@ -975,28 +1093,34 @@ a ``MPI_Send()``, SMPI will automatically benchmark the duration of
 this code, and create an execution task within the simulator to take
 this into account. For that, the actual duration is measured on the
 host machine and then scaled to the power of the corresponding
-simulated machine. The variable ``smpi/host-speed`` allows to specify
-the computational speed of the host machine (in flop/s) to use when
-scaling the execution times. It defaults to 20000, but you really want
-to update it to get accurate simulation results.
-
-When the code is constituted of numerous consecutive MPI calls, the
+simulated machine. The variable ``smpi/host-speed`` allows one to
+specify the computational speed of the host machine (in flop/s by
+default) to use when scaling the execution times.
+
+The default value is ``smpi/host-speed=20kf`` (= 20,000 flop/s). This
+is probably underestimated for most machines, leading SimGrid to
+overestimate the amount of flops in the execution blocks that are
+automatically injected in the simulator. As a result, the execution
+time of the whole application will probably be overestimated until you
+use a realistic value.
+
+When the code consists of numerous consecutive MPI calls, the
 previous mechanism feeds the simulation kernel with numerous tiny
 computations. The ``smpi/cpu-threshold`` item becomes handy when this
-impacts badly the simulation performance. It specifies a threshold (in
+impacts badly on the simulation performance. It specifies a threshold (in
 seconds) below which the execution chunks are not reported to the
 simulation kernel (default value: 1e-6).
 
 .. note:: The option ``smpi/cpu-threshold`` ignores any computation
    time spent below this threshold. SMPI does not consider the
-   `amount` of these computations; there is no offset for this. Hence,
-   a value that is too small, may lead to unreliable simulation
-   results.
+   `amount of time` of these computations; there is no offset for
+   this. Hence, a value that is too small, may lead to unreliable
+   simulation results.
 
 In some cases, however, one may wish to disable simulation of
-application computation. This is the case when SMPI is used not to
-simulate an MPI applications, but instead an MPI code that performs
-"live replay" of another MPI app (e.g., ScalaTrace's replay tool,
+the computation of an application. This is the case when SMPI is used not to
+simulate an MPI application, but instead an MPI code that performs
+"live replay" of another MPI app (e.g., ScalaTrace's replay tool, or
 various on-line simulators that run an app at scale). In this case the
 computation of the replay/simulation logic should not be simulated by
 SMPI. Instead, the replay tool or on-line simulator will issue
@@ -1004,16 +1128,16 @@ SMPI. Instead, the replay tool or on-line simulator will issue
 being replayed/simulated. At the moment, these computation events can
 be simulated using SMPI by calling internal smpi_execute*() functions.
 
-To disable the benchmarking/simulation of computation in the simulated
+To disable the benchmarking/simulation of a computation in the simulated
 application, the variable ``smpi/simulate-computation`` should be set
-to no.  This option just ignores the timings in your simulation; it
+to **no**.  This option just ignores the timings in your simulation; it
 still executes the computations itself. If you want to stop SMPI from
-doing that, you should check the SMPI_SAMPLE macros, documented in 
-Section :ref:`SMPI_adapting_speed`.
+doing that, you should check the SMPI_SAMPLE macros, documented in
+Section :ref:`SMPI_use_faster`.
 
 +------------------------------------+-------------------------+-----------------------------+
 |  Solution                          | Computations executed?  | Computations simulated?     |
-+====================================+=========================+=============================+   
++====================================+=========================+=============================+
 | --cfg=smpi/simulate-computation:no | Yes                     | Never                       |
 +------------------------------------+-------------------------+-----------------------------+
 | --cfg=smpi/cpu-threshold:42        | Yes, in all cases       | If it lasts over 42 seconds |
@@ -1032,7 +1156,7 @@ This option allows you to pass a file that contains two columns: The
 first column defines the section that will be subject to a speedup;
 the second column is the speedup. For instance:
 
-.. code-block:: shell
+.. code-block:: none
 
   "start:stop","ratio"
   "exchange_1.f:30:exchange_1.f:130",1.18244559422142
@@ -1041,7 +1165,7 @@ The first line is the header - you must include it.  The following
 line means that the code between two consecutive MPI calls on line 30
 in exchange_1.f and line 130 in exchange_1.f should receive a speedup
 of 1.18244559422142. The value for the second column is therefore a
-speedup, if it is larger than 1 and a slow-down if it is smaller
+speedup, if it is larger than 1 and a slowdown if it is smaller
 than 1. Nothing will be changed if it is equal to 1.
 
 Of course, you can set any arbitrary filenames you want (so the start
@@ -1052,29 +1176,15 @@ Please note that you must pass the ``-trace-call-location`` flag to
 smpicc or smpiff, respectively. This flag activates some internal
 macro definitions that help with obtaining the call location.
 
-.. _cfg=smpi/bw-factor:
-
-Bandwidth Factors
-.................
-
-**Option** ``smpi/bw-factor``
-|br| **Default:** 65472:0.940694;15424:0.697866;9376:0.58729;5776:1.08739;3484:0.77493;1426:0.608902;732:0.341987;257:0.338112;0:0.812084
-
-The possible throughput of network links is often dependent on the
-message sizes, as protocols may adapt to different message sizes. With
-this option, a series of message sizes and factors are given, helping
-the simulation to be more realistic. For instance, the current default
-value means that messages with size 65472 and more will get a total of
-MAX_BANDWIDTH*0.940694, messages of size 15424 to 65471 will get
-MAX_BANDWIDTH*0.697866 and so on (where MAX_BANDWIDTH denotes the
-bandwidth of the link).
+Bandwidth and latency factors
+.............................
 
-An experimental script to compute these factors is available online. See
-http://simgrid.gforge.inria.fr/contrib/smpi-calibration-doc.html
-http://simgrid.gforge.inria.fr/contrib/smpi-saturation-doc.html
+Adapting the bandwidth and latency acurately to the network conditions is of a paramount importance to get realistic results.
+This is done through the :ref:`network/bandwidth-factor <cfg=network/bandwidth-factor>` and :ref:`network/latency-factor
+<cfg=network/latency-factor>` items. You probably also want to read the following section: :ref:`models_calibration`.
 
 .. _cfg=smpi/display-timing:
-       
+
 Reporting Simulation Time
 .........................
 
@@ -1087,6 +1197,23 @@ code, making it difficult to report the simulated time when the
 simulation ends. If you enable the ``smpi/display-timing`` item,
 ``smpirun`` will display this information when the simulation
 ends.
+SMPI will also display information about the amout of real time spent
+in application code and in SMPI internals, to provide hints about the
+need to use sampling to reduce simulation time.
+
+.. _cfg=smpi/display-allocs:
+
+Reporting memory allocations
+............................
+
+**Option** ``smpi/display-allocs`` **Default:** 0 (false)
+
+SMPI intercepts malloc and calloc calls performed inside the running
+application, if it wasn't compiled with SMPI_NO_OVERRIDE_MALLOC.
+With this option, SMPI will show at the end of execution the amount of
+memory allocated through these calls, and locate the most expensive one.
+This helps finding the targets for manual memory sharing, or the threshold
+to use for smpi/auto-shared-malloc-thresh option (see :ref:`cfg=smpi/auto-shared-malloc-thresh`).
 
 .. _cfg=smpi/keep-temps:
 
@@ -1096,39 +1223,24 @@ Keeping temporary files after simulation
 **Option** ``smpi/keep-temps`` **default:** 0 (false)
 
 SMPI usually generates a lot of temporary files that are cleaned after
-use. This option request to preserve them, for example to debug or
+use. This option requests to preserve them, for example to debug or
 profile your code. Indeed, the binary files are removed very early
-under the dlopen privatization schema, which tend to fool the
+under the dlopen privatization schema, which tends to fool the
 debuggers.
 
-.. _cfg=smpi/lat-factor:
-
-Latency factors
-...............
-
-**Option** ``smpi/lat-factor`` |br|
-**default:** 65472:11.6436;15424:3.48845;9376:2.59299;5776:2.18796;3484:1.88101;1426:1.61075;732:1.9503;257:1.95341;0:2.01467
-
-The motivation and syntax for this option is identical to the motivation/syntax
-of :ref:`cfg=smpi/bw-factor`.
-
-There is an important difference, though: While smpi/bw-factor `reduces` the
-actual bandwidth (i.e., values between 0 and 1 are valid), latency factors
-increase the latency, i.e., values larger than or equal to 1 are valid here.
-
 .. _cfg=smpi/papi-events:
-       
+
 Trace hardware counters with PAPI
 .................................
 
 **Option** ``smpi/papi-events`` **default:** unset
 
-When the PAPI support was compiled in SimGrid, this option takes the
+When the PAPI support is compiled into SimGrid, this option takes the
 names of PAPI counters and adds their respective values to the trace
 files (See Section :ref:`tracing_tracing_options`).
 
 .. warning::
-   
+
    This feature currently requires superuser privileges, as registers
    are queried.  Only use this feature with code you trust! Call
    smpirun for instance via ``smpirun -wrapper "sudo "
@@ -1140,7 +1252,7 @@ It is planned to make this feature available on a per-process (or per-thread?) b
 The first draft, however, just implements a "global" (i.e., for all processes) set
 of counters, the "default" set.
 
-.. code-block:: shell
+.. code-block:: none
 
    --cfg=smpi/papi-events:"default:PAPI_L3_LDM:PAPI_L2_LDM"
 
@@ -1151,14 +1263,14 @@ Automatic Privatization of Global Variables
 
 **Option** ``smpi/privatization`` **default:** "dlopen" (when using smpirun)
 
-MPI executables are usually meant to be executed in separated
+MPI executables are usually meant to be executed in separate
 processes, but SMPI is executed in only one process. Global variables
-from executables will be placed in the same memory zone and shared
+from executables will be placed in the same memory region and shared
 between processes, causing intricate bugs.  Several options are
 possible to avoid this, as described in the main `SMPI publication
 <https://hal.inria.fr/hal-01415484>`_ and in the :ref:`SMPI
 documentation <SMPI_what_globals>`. SimGrid provides two ways of
-automatically privatizing the globals, and this option allows to
+automatically privatizing the globals, and this option allows one to
 choose between them.
 
   - **no** (default when not using smpirun): Do not automatically
@@ -1189,11 +1301,11 @@ Multiple libraries can be given, semicolon separated.
 
 This configuration option can only use either full paths to libraries,
 or full names.  Check with ldd the name of the library you want to
-use.  Example:
+use.  For example:
+
+.. code-block:: console
 
-.. code-block:: shell
-		  
-   ldd allpairf90
+   $ ldd allpairf90
       ...
       libgfortran.so.3 => /usr/lib/x86_64-linux-gnu/libgfortran.so.3 (0x00007fbb4d91b000)
       ...
@@ -1211,9 +1323,9 @@ Simulating MPI detached send
 
 This threshold specifies the size in bytes under which the send will
 return immediately. This is different from the threshold detailed in
-:ref:`options_model_network_asyncsend` because the message is not
-effectively sent when the send is posted. SMPI still waits for the
-correspondant receive to be posted to perform the communication
+:ref:`cfg=smpi/async-small-thresh` because the message is not
+really sent when the send is posted. SMPI still waits for the
+corresponding receive to be posted, in order to perform the communication
 operation.
 
 .. _cfg=smpi/coll-selector:
@@ -1226,15 +1338,84 @@ Simulating MPI collective algorithms
 SMPI implements more than 100 different algorithms for MPI collective
 communication, to accurately simulate the behavior of most of the
 existing MPI libraries. The ``smpi/coll-selector`` item can be used to
-use the decision logic of either OpenMPI or MPICH libraries (by
-default SMPI uses naive version of collective operations).
+select the decision logic either of the OpenMPI or the MPICH libraries. (By
+default SMPI uses naive version of collective operations.)
 
-Each collective operation can be manually selected with a
-``smpi/collective_name:algo_name``. Available algorithms are listed in
-:ref:`SMPI_use_colls`.
+Each collective operation can be manually selected with a ``smpi/collective_name:algo_name``. For example, if you want to use
+the Bruck algorithm for the Alltoall algorithm, you should use ``--cfg=smpi/alltoall:bruck`` on the command-line of smpirun. The
+reference of all available algorithms are listed in :ref:`SMPI_use_colls`, and you can get the full list implemented in your
+version using ``smpirun --help-coll``.
 
-.. TODO:: All available collective algorithms will be made available
-          via the ``smpirun --help-coll`` command.
+.. _cfg=smpi/barrier-collectives:
+
+Add a barrier in all collectives
+................................
+
+**Option** ``smpi/barrier-collectives`` **default:** off
+
+This option adds a simple barrier in some collective operations to catch dangerous
+code that may or may not work depending on the MPI implementation: Bcast, Exscan,
+Gather, Gatherv, Scan, Scatter, Scatterv and Reduce.
+
+For example, the following code works with OpenMPI while it deadlocks in MPICH and
+Intel MPI. Broadcast seem to be "fire and forget" in OpenMPI while other
+implementations expect to receive a message.
+
+.. code-block:: C
+
+  if (rank == 0) {
+    MPI_Bcast(buf1, buff_size, MPI_CHAR, 0, newcom);
+    MPI_Send(&buf2, buff_size, MPI_CHAR, 1, tag, newcom);
+  } else if (rank==1) {
+    MPI_Recv(&buf2, buff_size, MPI_CHAR, 0, tag, newcom, MPI_STATUS_IGNORE);
+    MPI_Bcast(buf1, buff_size, MPI_CHAR, 0, newcom);
+  }
+
+The barrier is only simulated and does not involve any additional message (it is a S4U barrier).
+This option is disabled by default, and activated by the `-analyze` flag of smpirun.
+
+.. _cfg=smpi/barrier-finalization:
+
+Add a barrier in MPI_Finalize
+.............................
+
+**Option** ``smpi/finalization-barrier`` **default:** off
+
+By default, SMPI processes are destroyed as soon as soon as their code ends,
+so after a successful MPI_Finalize call returns. In some rare cases, some data
+might have been attached to MPI objects still active in the remaining processes,
+and can be destroyed eagerly by the finished process.
+If your code shows issues at finalization, such as segmentation fault, triggering
+this option will add an explicit MPI_Barrier(MPI_COMM_WORLD) call inside the
+MPI_Finalize, so that all processes will terminate at almost the same point.
+It might affect the total timing by the cost of a barrier.
+
+.. _cfg=smpi/errors-are-fatal:
+
+Disable MPI fatal errors
+........................
+
+**Option** ``smpi/errors-are-fatal`` **default:** on
+
+By default, SMPI processes will crash if a MPI error code is returned. MPI allows
+to explicitely set MPI_ERRORS_RETURN errhandler to avoid this behaviour. This flag
+will turn on this behaviour by default (for all concerned types and errhandlers).
+This can ease debugging by going after the first reported error.
+
+.. _cfg=smpi/pedantic:
+
+Disable pedantic MPI errors
+...........................
+
+**Option** ``smpi/pedantic`` **default:** on
+
+By default, SMPI will report all errors it finds in MPI codes. Some of these errors
+may not be considered as errors by all developers. This flag can be turned off to
+avoid reporting some usually harmless mistakes.
+Concerned errors list (will be expanded in the future):
+
+ - Calling MPI_Win_fence only once in a program, hence just opening an epoch without
+   ever closing it.
 
 .. _cfg=smpi/iprobe:
 
@@ -1255,10 +1436,10 @@ Reduce speed for iprobe calls
 **Option** ``smpi/iprobe-cpu-usage`` **default:** 1 (no change)
 
 MPI_Iprobe calls can be heavily used in applications. To account
-correctly for the energy cores spend probing, it is necessary to
+correctly for the energy that cores spend probing, it is necessary to
 reduce the load that these calls cause inside SimGrid.
 
-For instance, we measured a max power consumption of 220 W for a
+For instance, we measured a maximum power consumption of 220 W for a
 particular application but only 180 W while this application was
 probing. Hence, the correct factor that should be passed to this
 option would be 180/220 = 0.81.
@@ -1303,7 +1484,7 @@ values, for example ``1:3:2;10:5:1``.  The sections are divided by ";"
 so this example contains two sections.  Furthermore, each section
 consists of three values.
 
-1. The first value denotes the minimum size for this section to take effect;
+1. The first value denotes the minimum size in bytes for this section to take effect;
    read it as "if message size is greater than this value (and other section has a larger
    first value that is also smaller than the message size), use this".
    In the first section above, this value is "1".
@@ -1317,7 +1498,7 @@ consists of three values.
    and hence accounts also for larger messages. In the first
    section of the example above, this value is "2".
 
-Now, SMPI always checks which section it should take for a given
+Now, SMPI always checks which section it should use for a given
 message; that is, if a message of size 11 is sent with the
 configuration of the example above, only the second section will be
 used, not the first, as the first value of the second section is
@@ -1348,7 +1529,7 @@ Inject constant times for MPI_Test
 By setting this option, you can control the amount of time a process
 sleeps when MPI_Test() is called; this is important, because SimGrid
 normally only advances the time while communication is happening and
-thus, MPI_Test will not add to the time, resulting in a deadlock if
+thus, MPI_Test will not add to the time, resulting in deadlock if it is
 used as a break-condition as in the following example:
 
 .. code-block:: cpp
@@ -1358,8 +1539,8 @@ used as a break-condition as in the following example:
        ...
    }
 
-To speed up execution, we use a counter to keep track on how often we
-already checked if the handle is now valid or not. Hence, we actually
+To speed up execution, we use a counter to keep track of how often we
+checked if the handle is now valid or not. Hence, we actually
 use counter*SLEEP_TIME, that is, the time MPI_Test() causes the
 process to sleep increases linearly with the number of previously
 failed tests. This behavior can be disabled by setting
@@ -1376,36 +1557,36 @@ Factorize malloc()s
 
 If your simulation consumes too much memory, you may want to modify
 your code so that the working areas are shared by all MPI ranks. For
-example, in a bloc-cyclic matrix multiplication, you will only
-allocate one set of blocs, and every processes will share them.
+example, in a block-cyclic matrix multiplication, you will only
+allocate one set of blocks, and all processes will share them.
 Naturally, this will lead to very wrong results, but this will save a
-lot of memory so this is still desirable for some studies. For more on
+lot of memory. So this is still desirable for some studies. For more on
 the motivation for that feature, please refer to the `relevant section
 <https://simgrid.github.io/SMPI_CourseWare/topic_understanding_performance/matrixmultiplication>`_
 of the SMPI CourseWare (see Activity #2.2 of the pointed
-assignment). In practice, change the call to malloc() and free() into
+assignment). In practice, change the calls for malloc() and free() into
 SMPI_SHARED_MALLOC() and SMPI_SHARED_FREE().
 
-SMPI provides two algorithms for this feature. The first one, called 
-``local``, allocates one bloc per call to SMPI_SHARED_MALLOC() in your
-code (each call location gets its own bloc) and this bloc is shared
-amongst all MPI ranks.  This is implemented with the shm_* functions
+SMPI provides two algorithms for this feature. The first one, called
+``local``, allocates one block per call to SMPI_SHARED_MALLOC()
+(each call site gets its own block) ,and this block is shared
+among all MPI ranks.  This is implemented with the shm_* functions
 to create a new POSIX shared memory object (kept in RAM, in /dev/shm)
-for each shared bloc.
+for each shared block.
 
 With the ``global`` algorithm, each call to SMPI_SHARED_MALLOC()
-returns a new adress, but it only points to a shadow bloc: its memory
-area is mapped on a 1MiB file on disk. If the returned bloc is of size
-N MiB, then the same file is mapped N times to cover the whole bloc.
-At the end, no matter how many SMPI_SHARED_MALLOC you do, this will
+returns a new address, but it only points to a shadow block: its memory
+area is mapped on a 1 MiB file on disk. If the returned block is of size
+N MiB, then the same file is mapped N times to cover the whole block.
+At the end, no matter how many times you call SMPI_SHARED_MALLOC, this will
 only consume 1 MiB in memory.
 
 You can disable this behavior and come back to regular mallocs (for
-example for debugging purposes) using @c "no" as a value.
+example for debugging purposes) using ``no`` as a value.
 
 If you want to keep private some parts of the buffer, for instance if these
 parts are used by the application logic and should not be corrupted, you
-can use SMPI_PARTIAL_SHARED_MALLOC(size, offsets, offsets_count). Example:
+can use SMPI_PARTIAL_SHARED_MALLOC(size, offsets, offsets_count). For example:
 
 .. code-block:: cpp
 
@@ -1417,22 +1598,40 @@ mem[100..199] are shared while other area remain private.
 Then, it can be deallocated by calling SMPI_SHARED_FREE(mem).
 
 When smpi/shared-malloc:global is used, the memory consumption problem
-is solved, but it may induce too much load on the kernel's pages table. 
-In this case, you should use huge pages so that we create only one
-entry per Mb of malloced data instead of one entry per 4k.
+is solved, but it may induce too much load on the kernel's pages table.
+In this case, you should use huge pages so that the kernel creates only one
+entry per MB of malloced data instead of one entry per 4 kB.
 To activate this, you must mount a hugetlbfs on your system and allocate
 at least one huge page:
 
-.. code-block:: shell
-		
-    mkdir /home/huge
-    sudo mount none /home/huge -t hugetlbfs -o rw,mode=0777
-    sudo sh -c 'echo 1 > /proc/sys/vm/nr_hugepages' # echo more if you need more
+.. code-block:: console
+
+    $ mkdir /home/huge
+    $ sudo mount none /home/huge -t hugetlbfs -o rw,mode=0777
+    $ sudo sh -c 'echo 1 > /proc/sys/vm/nr_hugepages' # echo more if you need more
 
 Then, you can pass the option
 ``--cfg=smpi/shared-malloc-hugepage:/home/huge`` to smpirun to
 actually activate the huge page support in shared mallocs.
 
+.. _cfg=smpi/auto-shared-malloc-thresh:
+
+Automatically share allocations
+...............................
+
+**Option** ``smpi/auto-shared-malloc-thresh:`` **Default:** 0 (false)
+   This value in bytes represents the size above which all allocations
+   will be "shared" by default (as if they were performed through
+   SMPI_SHARED_MALLOC macros). Default = 0 = disabled feature.
+   The value must be carefully chosen to only select data buffers which
+   will not modify execution path or cause crash if their content is false.
+   Option :ref:`cfg=smpi/display-allocs` can be used to locate the largest
+   allocation detected in a run, and provide a good starting threshold.
+   Note : malloc, calloc and free are overridden by smpicc/cxx by default.
+   This can cause some troubles if codes are already overriding these. If this
+   is the case, defining SMPI_NO_OVERRIDE_MALLOC in the compilation flags can
+   help, but will make this feature unusable.
+
 .. _cfg=smpi/wtime:
 
 Inject constant times for MPI_Wtime, gettimeofday and clock_gettime
@@ -1443,39 +1642,49 @@ Inject constant times for MPI_Wtime, gettimeofday and clock_gettime
 This option controls the amount of (simulated) time spent in calls to
 MPI_Wtime(), gettimeofday() and clock_gettime(). If you set this value
 to 0, the simulated clock is not advanced in these calls, which leads
-to issue if your application contains such a loop:
+to issues if your application contains such a loop:
 
 .. code-block:: cpp
-		
+
    while(MPI_Wtime() < some_time_bound) {
         /* some tests, with no communication nor computation */
    }
 
 When the option smpi/wtime is set to 0, the time advances only on
-communications and computations, so the previous code results in an
+communications and computations. So the previous code results in an
 infinite loop: the current [simulated] time will never reach
 ``some_time_bound``.  This infinite loop is avoided when that option
-is set to a small amount, as it is by default since SimGrid v3.21.
+is set to a small value, as it is by default since SimGrid v3.21.
 
 Note that if your application does not contain any loop depending on
 the current time only, then setting this option to a non-zero value
 will slow down your simulations by a tiny bit: the simulation loop has
-to be broken and reset each time your code ask for the current time.
+to be broken out of and reset each time your code asks for the current time.
 If the simulation speed really matters to you, you can avoid this
 extra delay by setting smpi/wtime to 0.
 
+.. _cfg=smpi/list-leaks:
+
+Report leaked MPI objects
+.........................
+
+**Option** ``smpi/list-leaks`` **default:** 0
+
+This option controls whether to report leaked MPI objects.
+The parameter is the number of leaks to report.
+
 Other Configurations
 --------------------
 
-.. _cfg=clean-atexit:
+.. _cfg=debug/clean-atexit:
 
 Cleanup at Termination
 ......................
 
-**Option** ``clean-atexit`` **default:** on
+**Option** ``debug/clean-atexit`` **default:** on
 
 If your code is segfaulting during its finalization, it may help to
-disable this option to request SimGrid to not attempt any cleanups at
+disable this option to request that SimGrid not attempt any cleanups at
 the end of the simulation. Since the Unix process is ending anyway,
 the operating system will wipe it all.
 
@@ -1486,40 +1695,40 @@ Search Path
 
 **Option** ``path`` **default:** . (current dir)
 
-It is possible to specify a list of directories to search into for the
+It is possible to specify a list of directories to search in for the
 trace files (see :ref:`pf_trace`) by using this configuration
 item. To add several directory to the path, set the configuration
 item several times, as in ``--cfg=path:toto --cfg=path:tutu``
 
-.. _cfg=simix/breakpoint:
+.. _cfg=debug/breakpoint:
 
 Set a Breakpoint
 ................
 
-**Option** ``simix/breakpoint`` **default:** unset
+**Option** ``debug/breakpoint`` **default:** unset
 
 This configuration option sets a breakpoint: when the simulated clock
 reaches the given time, a SIGTRAP is raised.  This can be used to stop
 the execution and get a backtrace with a debugger.
 
 It is also possible to set the breakpoint from inside the debugger, by
-writing in global variable simgrid::simix::breakpoint. For example,
+writing in global variable simgrid::kernel::cfg_breakpoint. For example,
 with gdb:
 
-.. code-block:: shell
+.. code-block:: none
 
-   set variable simgrid::simix::breakpoint = 3.1416
+   set variable simgrid::kernel::cfg_breakpoint = 3.1416
+
+.. _cfg=debug/verbose-exit:
 
-.. _cfg=verbose-exit:
-   
 Behavior on Ctrl-C
 ..................
 
-**Option** ``verbose-exit`` **default:** on
+**Option** ``debug/verbose-exit`` **default:** on
 
 By default, when Ctrl-C is pressed, the status of all existing actors
 is displayed before exiting the simulation. This is very useful to
-debug your code, but it can reveal troublesome if you have many
+debug your code, but it can become troublesome if you have many
 actors. Set this configuration item to **off** to disable this
 feature.
 
@@ -1532,14 +1741,126 @@ Truncate local path from exception backtrace
 
 This configuration option is used to remove the path from the
 backtrace shown when an exception is thrown. This is mainly useful for
-the tests: the full file path makes the tests not reproducible because
-the path of source files depend of the build settings. That would
-break most of our tests as we keep comparing output.
+the tests: the full file path would makes the tests non-reproducible because
+the paths of source files depend of the build settings. That would
+break most of the tests since their output is continually compared.
 
-Logging Configuration
+.. _logging_config:
+
+Logging configuration
 ---------------------
 
-It can be done by using XBT. Go to :ref:`XBT_log` for more details.
+As introduced in :ref:`outcome_logs`, the SimGrid logging mechanism allows to configure at runtime the messages that should be displayed and those that should be omitted. Each
+message produced in the code is given a category (denoting its topic) and a priority. Then at runtime, each category is given a threshold (only messages of priority higher than
+that threshold are displayed), a layout (deciding how the messages in this category are formatted), and an appender (deciding what to do with the message: either print on stderr or
+to a file).
+
+This section explains how to configure this logging features. You can also refer to the documentation of the :ref:`programmer's interface <logging_prog>`, that allows to produce
+messages from your code.
+
+Most of the time, the logging mechanism is configured at runtime using the ``--log`` command-line argument, even if you can also use :c:func:`xbt_log_control_set()` to control it from
+your program. To pass configure more than one setting, you can either pass several ``--log`` arguments, or separate your settings with spaces, that must be quoted accordingly. In
+practice, the following is equivalent to the above settings: ``--log=root.thresh:error --log=s4u_host.thresh:debug``.
+
+If you want to specify more than one setting, you can either pass several ``--log`` argument to your program as above, or separate them with spaces. In this case, you want to quote
+your settings, as in ``--log="root.thresh:error s4u_host.thresh:debug"``. The parameters are interpreted in order, from left to right.
+
+
+Threshold configuration
+.......................
+
+The keyword ``threshold`` controls which logging event will get displayed in a given category. For example, ``--log=root.threshold:debug`` displays *every* message produced in the
+``root`` category and its subcategories (i.e., every message produced -- this is *extremely* verbose), while ``--log=root.thres:critical`` turns almost everything off. As you can
+see, ``threshold`` can be abbreviated here.
+
+Existing thresholds:
+
+ - ``trace`` some functions display a message at this level when entering or returning
+ - ``debug`` output that is mostly useful when debugging the corresponding module.
+ - ``verbose`` verbose output that is only mildly interesting and can easily be ignored
+ - ``info`` usual output (this is the default threshold of all categories)
+ - ``warning`` minor issue encountered
+ - ``error`` issue encountered
+ - ``critical`` major issue encountered, such as assertions failures
+
+.. _log/fmt:
+
+Format configuration
+....................
+
+The keyword ``fmt`` controls the layout (the format) of a logging category. For example, ``--log=root.fmt:%m`` reduces the output to the user-message only, removing any decoration such
+as the date, or the actor ID, everything. Existing format directives:
+
+ - %%: the % char
+ - %n: line separator (LOG4J compatible)
+ - %e: plain old space (SimGrid extension)
+
+ - %m: user-provided message
+
+ - %c: Category name (LOG4J compatible)
+ - %p: Priority name (LOG4J compatible)
+
+ - %h: Hostname (SimGrid extension)
+ - %a: Actor name (SimGrid extension -- note that with SMPI this is the integer value of the process rank)
+ - %i: Actor PID (SimGrid extension -- this is a 'i' as in 'i'dea)
+ - %t: Thread "name" (LOG4J compatible -- actually the address of the thread in memory)
+
+ - %F: file name where the log event was raised (LOG4J compatible)
+ - %l: location where the log event was raised (LOG4J compatible, like '%%F:%%L' -- this is a l as in 'l'etter)
+ - %L: line number where the log event was raised (LOG4J compatible)
+ - %M: function name (LOG4J compatible -- called method name here of course).
+
+ - %d: date (UNIX-like epoch)
+ - %r: application age (time elapsed since the beginning of the application)
+
+
+``--log=root.fmt:'[%h:%a:(%i) %r] %l: %m%n'`` gives you the default layout used for info messages while ``--log=root.fmt:'[%h:%a:(%i) %r] %l: [%c/%p] %m%n'`` gives you the default
+layout for the other priorities (it adds the source code location). Also, the actor identification is omitted by the default layout for the messages coming directly from the
+SimGrid kernel, so info messages are formatted with ``[%r] [%c/%p] %m%n`` in this case. When specifying the layout manually, such distinctions are currently impossible, and the
+provided layout is used for every messages.
+
+As with printf, you can specify the precision and width of the fields. For example, ``%.4r`` limits the date precision to four digits while ``%15h`` limits the host name to at most
+15 chars.
+
+
+If you want to have spaces in your log format, you should protect it. Otherwise, SimGrid will consider that this is a space-separated list of several parameters. But you should
+also protect it from the shell that also splits command line arguments on spaces. At the end, you should use something such as ``--log="'root.fmt:%l: [%p/%c]: %m%n'"``.
+Another option is to use the ``%e`` directive for spaces, as in ``--log=root.fmt:%l:%e[%p/%c]:%e%m%n``.
+
+Category appender
+.................
+
+The keyword ``app`` controls the appended of a logging category. For example ``--log=root.app:file:mylogfile`` redirects every output to the file ``mylogfile``.
+
+With the ``splitfile`` appender, a new file is created when the size of the output reaches the specified size. The format is ``--log=root.app:splitfile:<size>:<file name>``. For
+example, ``--log=root.app:splitfile:500:mylog_%`` creates log files of at most 500 bytes, using the names ``mylog_0``, ``mylog_1``, ``mylog_2``, etc.
+
+The ``rollfile`` appender uses one file only, but the file is emptied and recreated when its size reaches the specified maximum. For example, ``--log=root.app:rollfile:500:mylog``
+ensures that the log file ``mylog`` will never overpass 500 bytes in size.
+
+Any appender setup this way have its own layout format, that you may change afterward. When specifying a new appender, its additivity is set to false to prevent log event displayed
+by this appender to "leak" to any other appender higher in the hierarchy. You can naturally change that if you want your messages to be displayed twice.
+
+Category additivity
+...................
+
+The keyword ``add`` controls the additivity of a logging category. By default, the messages are only passed one appender only: the more specific, i.e. the first one found when
+climbing the tree from the category in which they were produced. In Log4J parlance, it is said that the default additivity of appenders is false. If you change this setting to
+``on`` (or ``yes`` or ``1``), the produced messages will also be passed to the upper appender.
+
+Let's consider a more complex example: ``--log="root.app:file:all.log s4u.app:file:iface.log xbt.app:file:xbt.log xbt.add:yes``. Here, the logging of s4u will be sent to the
+``iface.log`` file; the logging of the xbt toolbox will be sent to both the ``xbt.log`` file and the ``all.log`` file (because xbt additivity was enabled); and every other loggings
+will only be sent to ``all.log``.
+
+Other options
+.............
+
+``--help-logs`` displays a complete help message about logging in SimGrid.
+
+``--help-log-categories`` displays the actual hierarchy of log categories for this binary.
+
+``--log=no_loc`` hides the source locations (file names and line numbers) from the messages. This is useful to make tests reproducible.
+
 
 .. |br| raw:: html