ross-org url (and whitespace)

codes-vis-readme.md

 ## README for using ROSS instrumentation with CODES
 
-For details about the ROSS instrumentation, see the [ROSS Instrumentation blog post](http://carothersc.github.io/ROSS/instrumentation/instrumentation.html) 
+For details about the ROSS instrumentation, see the [ROSS Instrumentation blog post](http://ross-org.github.io/instrumentation/instrumentation.html)
 on the ROSS webpage.
- 
+
 
 There are currently 4 types of instrumentation: GVT-based, real time sampling, virtual time sampling, and event tracing.
 See the ROSS documentation for more info on the specific options or use `--help` with your model.
 To collect data about the simulation engine, no changes are needed to model code for any of the instrumentation modes.
 Some additions to the model code is needed in order to turn on any model-level data collection.
-See the "Model-level data sampling" section on [ROSS Instrumentation blog post](http://carothersc.github.io/ROSS/instrumentation/instrumentation.html).
+See the "Model-level data sampling" section on [ROSS Instrumentation blog post](http://ross-org.github.io/instrumentation/instrumentation.html).
 Here we describe CODES specific details.
 
 ### Register Instrumentation Callback Functions
@@ -37,13 +37,13 @@ The second pointer is for the data to be sampled at the GVT or real time samplin
 In this case the LPs have different function pointers since we want to collect different types of data for the two LP types.
 For the terminal, I set the appropriate size of the data to be collected, but for the router, the size of the data is dependent on the radix for the dragonfly configuration being used, which isn't known until runtime.
 
-*Note*: You can only reuse the function for event tracing for LPs that use the same type of message struct.  
+*Note*: You can only reuse the function for event tracing for LPs that use the same type of message struct.
 For example, the dragonfly terminal and router LPs both use the `terminal_message` struct, so they can
-use the same functions for event tracing.  
-However the model net base LP uses the `model_net_wrap_msg` struct, so it gets its own event collection function and `st_trace_type` struct, in order to read the event type correctly from the model. 
+use the same functions for event tracing.
+However the model net base LP uses the `model_net_wrap_msg` struct, so it gets its own event collection function and `st_trace_type` struct, in order to read the event type correctly from the model.
 
-In the ROSS instrumentation documentation, there are two methods provided for letting ROSS know about these `st_model_types` structs.  
-In CODES, this step is a little different, as `codes_mapping_setup()` calls `tw_lp_settype()`.  
+In the ROSS instrumentation documentation, there are two methods provided for letting ROSS know about these `st_model_types` structs.
+In CODES, this step is a little different, as `codes_mapping_setup()` calls `tw_lp_settype()`.
 Instead, you add a function to return this struct for each of your LP types:
 ```C
 static const st_model_types *dragonfly_get_model_types(void)
@@ -73,7 +73,7 @@ static void router_register_model_types(st_model_types *base_type)
 At this point, there are two different steps to follow depending on whether the model is one of the model-net models or not.
 
 ##### Model-net Models
-In the `model_net_method` struct, two fields have been added: `mn_model_stat_register` and `mn_get_model_stat_types`.  
+In the `model_net_method` struct, two fields have been added: `mn_model_stat_register` and `mn_get_model_stat_types`.
 You need to set these to the functions described above.  For example:
 
 ```C
@@ -115,21 +115,21 @@ static void svr_register_model_types()
 int main(int argc, char **argv)
 {
     // ... some set up removed for brevity
-    
+
     model_net_register();
     svr_add_lp_type();
-    
+
     if (g_st_ev_trace || g_st_model_stats)
         svr_register_model_types();
-        
+
     codes_mapping_setup();
-    
+
     //...
 }
 ```
 
 `g_st_ev_trace` is a ROSS flag for determining if event tracing is turned on and `g_st_model_stats` determines if the GVT-based or real time instrumentation
-modes are collecting model-level data as well.  
+modes are collecting model-level data as well.
 
 
 ### CODES LPs that currently have event type collection implemented:
@@ -144,4 +144,3 @@ If you're using any of the following CODES models, you don't have to add anythin
 - slimfly router and terminal LPs (slimfly.c)
 - fat tree switch and terminal LPs (fat-tree.c)
 - model-net-base-lp (model-net-lp.c)
- 

doc/BUILD_STEPS

@@ -2,12 +2,12 @@ NOTE: see bottom of this file for suggested configurations on particular ANL
 machines.
 
 0 - Checkout, build, and install the trunk version of ROSS
-(https://github.com/carothersc/ROSS). At the time of
+(https://github.com/ross-org/ROSS). At the time of
 release (0.6.0), ROSS's latest commit hash was 10d7a06b2d, so this revision is
 "safe" in the unlikely case incompatible changes come along in the future. If
 working from the CODES master branches, use the ROSS master branch.
 
-    git clone http://github.com/carothersc/ROSS.git
+    git clone http://github.com/ross-org/ROSS.git
     # if using 0.5.2 release: git checkout d3bdc07
     cd ROSS
     mkdir build
@@ -22,7 +22,7 @@ working from the CODES master branches, use the ROSS master branch.
     ROSS/install/ directory>
 
     For more details on installing ROSS, go to
-    https://github.com/carothersc/ROSS/blob/master/README.md .
+    https://github.com/ross-org/ROSS/blob/master/README.md .
 
     If using ccmake to configure, don't forget to set CMAKE_C_COMPILER and
     CMAKE_CXX_COMPILER to mpicc/mpicxx

doc/GETTING_STARTED

@@ -14,7 +14,7 @@ https://lists.mcs.anl.gov/mailman/listinfo/codes-ross-users
 
 == CODES
 
-* main site: http://www.mcs.anl.gov/projects/codes/ 
+* main site: http://www.mcs.anl.gov/projects/codes/
 * repositories:
   * "base" (this repository): git.mcs.anl.gov:radix/codes-base
   * codes-net (networking component of CODES): git.mcs.anl.gov:radix/codes-net
@@ -22,11 +22,11 @@ https://lists.mcs.anl.gov/mailman/listinfo/codes-ross-users
 
 == ROSS
 
-* main site, repository, etc.: https://github.com/carothersc/ROSS
+* main site, repository, etc.: https://github.com/ross-org/ROSS
   * both the site and repository contain good documentation as well - refer to
     it for an in-depth introduction and overview of ROSS proper
 
-= Components of CODES 
+= Components of CODES
 
 == Configuration
 
@@ -36,7 +36,7 @@ structured configuration file. The configuration format allows categories, and
 optionally subgroups within the category, of key-value pairs for configuration.
 The LPGROUPS category defines the LP configuration. The PARAMS category is
 currently used for networking and ROSS-specific parameters. User-defined
-categories can also be used. 
+categories can also be used.
 
 The configuration system additionally allows LP specialization via the usage of
 "annotations". This allows two otherwise identical LPs to have different
@@ -125,7 +125,7 @@ The format of the metadata file is a set of lines containing:
   <group ID> <start ID> <end ID inclusive> <kernel file>
 where:
 * <group ID> is the ID of this group (see restrictions)
-* <start ID> and <end ID> form the range of logical client IDs that will 
+* <start ID> and <end ID> form the range of logical client IDs that will
   perform the given workload. Note that the end ID is inclusive, so a start,
   end pair of 0, 3 will include IDs 0, 1, 2, and 3. An <end ID> of -1 indicates
   to use the remaining number of clients as specified by the user.
@@ -288,7 +288,7 @@ lsm
 }
 
 The API can be found at codes/local-storage-model.h and example usage can be
-seen in tests/local-storage-model-test.c and tests/conf/lsm-test.conf. 
+seen in tests/local-storage-model-test.c and tests/conf/lsm-test.conf.
 
 The queueing policy of LSM is currently FIFO, and the default mode uses an
 implicit queue, simply incrementing counters and scheduling future events when
@@ -359,7 +359,7 @@ model-net LPs, like any other LP in CODES/ROSS, require specification in the
 configuration file as well as LP-specific parameters. To identify model-net LPs
 to CODES, we use the naming scheme of prefixing model-net LP names with the
 string "modelnet_". For example, the "simplenet" LP (see "model-net models")
-would be specified in the LPGROUPS section as "modelnet_simplenet". 
+would be specified in the LPGROUPS section as "modelnet_simplenet".
 
 Currently, model-net LPs expect their configuration values in the PARAMS
 section. This is due to historical precedent and may be changed in the future
@@ -389,7 +389,7 @@ program, they will be printed to the specified directory.
 = model-net models
 
 Currently, model-net contains a combination of analytical models and specific
-models for high-performance networking, with an HPC bent. 
+models for high-performance networking, with an HPC bent.
 
 Configuration files for each model can be found in tests/conf, under the name
 "model-net-test*.conf".
@@ -402,7 +402,7 @@ infinite packet buffering when routing. These are best used for models that
 require little fidelity out of the network performance. SimpleP2P is the same
 model as Simplenet, except it provides heterogeneous link capacities from point
 to point. Rather than a single entry, it requires files containing a matrix of
-point-to-point bandwidths and latencies. 
+point-to-point bandwidths and latencies.
 
 Simplenet models require two configuration parameters: "net_startup_ns" and
 "net_bw_mbps", which define the startup and bandwidth costs in nanoseconds and
@@ -426,7 +426,7 @@ The only configuration entry the LogGP model requires is
 configuration file.
 
 For more details on gathering parameters for the LogGP model, as well as it's
-usage and caveats, see the document src/model-net/doc/README.loggp.txt. 
+usage and caveats, see the document src/model-net/doc/README.loggp.txt.
 
 == Torus
 
@@ -454,7 +454,7 @@ The configuration parameters are a little trickier here, as additional LPs
 other than the "modelnet_dragonfly" LP must be specified. "modelnet_dragonfly"
 represent the node LPs (terminals), while a second type "dragonfly_router"
 represents a physical router. At least one "dragonfly_router" LP must be
-present in every LP group with a "modelnet_dragonfly" LP. 
+present in every LP group with a "modelnet_dragonfly" LP.
 
 Further configuration and model setup can be found at
 src/model-net/doc/README.dragonfly.txt.
@@ -509,7 +509,7 @@ section of the example.conf config file.
 == Server state and event handlers
 
 The server LP state maintains a count of the number of remote messages it has
-sent and received as well as the number of local completion messages.   
+sent and received as well as the number of local completion messages.
 
 For the server event message, we have four message types: KICKOFF, REQ, ACK and
 LOCAL. With a KICKOFF event, each LP sends a message to itself to begin the
@@ -517,7 +517,7 @@ simulation proper. To avoid event ties, we add a small amount of random noise
 using codes_local_latency. The REQ message is sent by a server to its
 neighboring server and when received, neighboring server sends back a message
 of type ACK. We've shown a hard-coded direct communication method which
-directly computes the LP ID, and a codes-mapping API-based method. 
+directly computes the LP ID, and a codes-mapping API-based method.
 
 == Server reverse computation
 
@@ -533,19 +533,19 @@ conservative modes, so reverse computation may not be necessary if the
 simulation is not compute- or memory-intensive.
 
 For our example program, recall the "forward" event handlers. They perform the
-following: 
+following:
 * Kickoff: send a message to the peer server, and increment sender LP's
     count of sent messages.
 * Request (received from peer server): increment receiver count of
     received messages, and send an acknowledgement to the sender.
 * Acknowledgement (received from message receiver): send the next
     message to the receiver and increment messages sent count. Set a flag
-    indicating whether a message has been sent.  
+    indicating whether a message has been sent.
 * Local model-net callback: increment the local model-net
     received messages count.
 
 In terms of LP state, the four operations are simply modifying counts. Hence,
-the "reverse" event handlers need to merely roll back those changes: 
+the "reverse" event handlers need to merely roll back those changes:
 * Kickoff: decrement sender LP's count of sent messages.
 * Request (received from peer server): decrement receiver count of
     received messages.

doc/RELEASE_NOTES

@@ -16,7 +16,7 @@ per compute node or one multi-port NIC per node.
 
 Adding a generic template for building new network models. For simplest case,
 only 2 functions and premable changes should suffice to add a new network.
-Updated Express Mesh network model to serve as an example. For details, see 
+Updated Express Mesh network model to serve as an example. For details, see
 
 Darshan workload generator has been updated to use Darshan version 3.x.
 
@@ -28,11 +28,11 @@ https://xgitlab.cels.anl.gov/codes/codes/wikis/Using-ROSS-Instrumentation-with-C
 Compatible with ROSS version that enables statistics collection of simulation
 performance. For details see:
 
-http://carothersc.github.io/ROSS/instrumentation/instrumentation.html
+http://ross-org.github.io/instrumentation/instrumentation.html
 
 Online workload replay functionality has been added that allows SWM workloads
 to be simulated insitu on the network models. WIP to integrate Conceptual
-domain specific language for network communication.  
+domain specific language for network communication.
 
 Multiple traffic patterns were added in the background traffic generation
 including stencil, all-to-all and random permutation.
@@ -93,7 +93,7 @@ Background network communication using uniform random workload can now be
 generated. The traffic generation gets automatically shut off when the main workload
 finishes.
 
-Collectives can now be translated into point to point using the CoRTex library. 
+Collectives can now be translated into point to point using the CoRTex library.
 
 Performance of MPI_AllReduce is reported when debug_cols option is enabled.
 

doc/codes-best-practices.tex

@@ -121,7 +121,7 @@ xleftmargin=6ex
 % IEEEtran.cls handling of captions and this will result in nonIEEE style
 % figure/table captions. To prevent this problem, be sure and preload
 % caption.sty with its "caption=false" package option. This is will preserve
-% IEEEtran.cls handing of captions. Version 1.3 (2005/06/28) and later 
+% IEEEtran.cls handing of captions. Version 1.3 (2005/06/28) and later
 % (recommended due to many improvements over 1.2) of subfig.sty supports
 % the caption=false option directly:
 %\usepackage[caption=false,font=footnotesize]{subfig}
@@ -188,7 +188,7 @@ easily shared and reused.  It also includes a few tips to help avoid common
 simulation bugs.
 
 For more information, ROSS has a bunch of documentation available in their
-repository/wiki - see \url{https://github.com/carothersc/ROSS}.
+repository/wiki - see \url{https://github.com/ross-org/ROSS}.
 \end{abstract}
 
 \section{CODES: modularizing models}
@@ -394,7 +394,7 @@ action upon the completion of them. More generally, the problem is: an event
 issuance (an ack to the client) is based on the completion of more than one
 asynchronous/parallel events (local write on primary server, forwarding write to
 replica server). Further complicating the matter for storage simulations, there
-can be any number of outstanding requests, each waiting on multiple events. 
+can be any number of outstanding requests, each waiting on multiple events.
 
 In ROSS's sequential and conservative parallel modes, the necessary state can
 easily be stored in the LP as a queue of statuses for each set of events,
@@ -488,7 +488,7 @@ Most core ROSS examples are design to intentionally hit
 the end timestamp for the simulation (i.e. they are modeling a continuous,
 steady state system). This isn't necessarily true for other models. Quite
 simply, set g\_tw\_ts\_end to an arbitrary large number when running simulations
-that have a well-defined end-point in terms of events processed. 
+that have a well-defined end-point in terms of events processed.
 
 Within the LP finalize function, do not call tw\_now. The time returned may not
 be consistent in the case of an optimistic simulation.
@@ -515,7 +515,7 @@ section(s).
         \item generating multiple concurrent events makes rollback more difficult
     \end{enumerate}
 
-    \item use dummy events to work around "event-less" advancement of simulation time 
+    \item use dummy events to work around "event-less" advancement of simulation time
 
     \item add a small amount of time "noise" to events to prevent ties