source: CIVL/examples/xsbench/README.txt

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                                   Version 13

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Contact Information
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Organization:     Center for Exascale Simulation of Advanced Reactors (CESAR)
                  Argonne National Laboratory

Development Lead: John Tramm   <jtramm@anl.gov>
                  Ron Rahaman  <rahaman@anl.gov>
                  Amanda Lund  <alund@anl.gov>

==============================================================================
What is XSBench?
==============================================================================

XSBench is a mini-app representing a key computational kernel of the
Monte Carlo neutronics application OpenMC.

A full explanation of the theory and purpose of XSBench is provided in
docs/XSBench_Theory.pdf.

==============================================================================
Quick Start Guide
==============================================================================

Download----------------------------------------------------------------------

        For the most up-to-date version of XSBench, we recommend that you
        download from our git repository. This can be accomplished via
        cloning the repository from the command line, or by downloading a zip
        from our github page. Alternatively, you can download a tar file from
        the CESAR website directly.

        Git Repository Clone:
                
                Use the following command to clone XSBench to your machine:

                >$ git clone https://github.com/jtramm/XSBench.git

                Once cloned, you can update the code to the newest version
                using the following command (when in the XSBench directory):

                >$ git pull
        
        Git Zip Download:

                Simply use the "zip download" option on our webpage at:

                https://github.com/jtramm/XSBench
        
        CESAR Tar Download:

                A tar of the XSBench source code is available
                on the CESAR website at the following URL:
                
                https://cesar.mcs.anl.gov/content/software/neutronics

                Once downloaded, you can decompress XSBench using the following
                command on a linux or Mac OSX system:

                >$ tar -xvf XSBench-11.tar

                This will decompress the tar file into a directory called
                XSBench-11.

                To begin use of the XSBench code, you will have to navigate to
                the src directory:

                >$ cd XSBench-11/src

Compilation-------------------------------------------------------------------

        To compile XSBench with default settings, use the following
        command:

        >$ make

Running XSBench---------------------------------------------------------------

        To run XSBench with default settings, use the following command:

        >$ ./XSBench

        For non-default settings, XSBench supports the following command line
        options:        

        Usage: ./XSBench <options>
        Options include:
          -t <threads>     Number of OpenMP threads to run
          -s <size>        Size of H-M Benchmark to run (small, large, XL, XXL)
          -g <gridpoints>  Number of gridpoints per nuclide
          -l <lookups>     Number of Cross-section (XS) lookups
        Default (no arguments given) is equivalent to: -s large -l 15000000

        -t <threads>

                Sets the number of OpenMP threads to run. By default, XSBench
                will run with 1 thread per hardware core. If the architecture
                supports hyperthreading, multiple threads will be run per
                core.

                If running in MPI mode, this will be the number of threads
                per MPI rank.

        -s <size>
                
                Sets the size of the Hoogenboom-Martin reactor model. There
                are four options: 'small', 'large', 'XL', and 'XXL'. By default,
                the 'large' option is selected. 

                The H-M size corresponds to the number of nuclides present
                in the fuel region.  The small version has 34 fuel nuclides,
                whereas the large version has 321 fuel nuclides. This
                significantly slows down the runtime of the program as the
                data structures are much larger, and more lookups are required
                whenever a lookup occurs in a fuel material.  Note that the
                program defaults to "Large" if no specification is made.

                The additional size options, "XL" and "XXL", do not directly correspond
                to any particular physical model. They are similar to the H-M
                "large" option, except the number of gridpoints per nuclide
                has been increased greatly. This creates an extremely
                large energy grid data structure (XL: 120GB, XXL: 252GB), which is
                unlikely to fit on a single node, but is useful for experimentation
                purposes on novel architectures.

        -g <gridpoints>

                Sets the number of gridpoints per nuclide. By default, this
                value is set to 11,303. This corresponds to the average number
                of actual gridpoints per nuclide in the H-M Large model as run
                by OpenMC with the actual ACE ENDF cross-section data. 

                Note that this option will override the number of default grid
                -points as set by the '-s' option.

        -l <lookups>
                
                Sets the number of cross-section (XS) lookups to perform. By
                default, this value is set to 15,000,000. Users may want to
                increase this value if they wish to extend the runtime of
                XSBench, perhaps to produce more reliable performance counter
                data - as extending the run will decrease the percentage of
                runtime spent on initialization.

==============================================================================
Debugging, Optimization & Profiling
==============================================================================

There are also a number of switches that can be set in the makefile.

Here is a sample of the control panel at the top of the makefile:

COMPILER  = gnu
OPTIMIZE  = yes
DEBUG     = no
PROFILE   = no
MPI       = no
PAPI      = no
VEC_INFO  = no
VERIFY    = no
PAUSE     = no
BENCHMARK = no
BINARY_DUMP = no
BINARY_READ = no

-> Optimization enables the -O3 optimization flag.

-> Debugging enables the -g flag.

-> Profiling enables the -pg flag.

-> MPI enables MPI support in the code.

-> The PAPI flag is explained below.

-> VEC_INFO enables some additional information regarding the success or
   failure of the compiler's use of vectorization techniques during
   compilation.

-> VERIFY enables a verification mode, the details of which are explained below.

-> Benchmark mode tests all possible thread configurations on the given
   computer. I.e., if your computer supports 16 threads, XSBench will
   automatically do 1 <= nthreads <= 16 lookup loops

-> Binary dump mode writes a binary file containing a randomized data set
   of cross sections. This can be used in tandem with the binary read mode
   to skip generation of cross section data every time the program is run.

-> Binary read mode reads the binary file created by the binary dump mode
   as a (usually) much faster substitution for randomly generating XS
   data on-the-fly. This mode is particularly useful if running on
   simulators where walltime minimization is extremely critical for
   logistical reasons.

==============================================================================
MPI Support
==============================================================================

While XSBench is primarily used to investigate "on node parallelism" issues,
some systems provide power & performance statistics batched in multi-node
configurations. To accommodate this, XSBench provides an MPI mode which
runs the code on all MPI ranks simultaneously. There is no decomposition
across ranks of any kind, and all ranks accomplish the same work. There is
only one point of MPI communication (a reduce) at the end, which aggregates
the timing statistics and averages them across MPI ranks before printing them
out.

MPI support can be enabled with the makefile flag "MPI". If you are not using
the mpicc wrapper on your system, you may need to alter the makefile to
make use of your desired compiler.


==============================================================================
Verification Support
==============================================================================

XSBench has the ability to verify that consistent and correct results are
achieved. This mode is enabled by altering the "VERIFY" setting to 'yes' in
the makefile, i.e.:

VERIFY = yes

Once enabled, the code will generate a hash of the results and display it
with the other data once the code has completed executing. This hash can
then be verified against hashes that other versions or configurations of
the code generate. For instance, running XSBench with 4 threads vs 8 threads
(on a machine that supports that configuration) should generate the
same hash number. Changing the model / run parameters should NOT generate
the same hash number (i.e., increasing the number of lookups, number
of gridpoints, etc, will result in different hashes). 

Verification mode uses a RNG with a static seed. The randomized lookup
parameters are generated within a critical region. This ensures that the
same set of lookups are performed regardless of the number of threads
used. Then, after each lookup is completed, the lookup parameters and
the cross section vector are hashed together. This local hash is then
atomically added to a global running hash.

Note that the verification mode runs much slower, due to the use of
atomics within the threading loop. 

Below are the expected checksums for default runs of each size (-s):

small : 74966788162
large : 74994938929 

==============================================================================
PAPI Performance Counters
==============================================================================

PAPI performance counters is a performance counting library that can
offer information regarding the frequency of specific events (such as
memory loads, cache misses, branch prediction failures, etc) that occur
when the code is executed. XSBench supports use of these performance
counters, although it is left to the user to select the particular
performance counters and locations to instrument.

By default, PAPI is disabled.

To enable PAPI, set in the makefile:

PAPI = yes

Note that you may need to change the relevant library paths for papi to
work (as these are dependent on your machine).  The library path can be
specified in the makefile, and the header path is specified in the
XSBench_header.h file.

To select the performance counters you are interested in, open
the file papi.c and alter the events[] array to the events
you would like to count. 

==============================================================================
Binary File Support
==============================================================================

The flags:

BINARY_DUMP = no
BINARY_READ = no

Can be set to yes in order to write or read a binary file containing
a randomized XS data set (both nuclide grids and unionized grids). This
feature may be extremely useful for users running on simulators where
walltime minimization is critical for logistical purposes, or for users
who are doing many sequential runs.

Note that identical input parameters (problem size, etc) must be used
when reading and writing a binary file. No runtime checks are made
to validate that the file correctly corresponds to the selected input
parameters.

==============================================================================
Running on ANL BlueGene/Q (Vesta & Mira)
==============================================================================

Compilation is done using the included makefile, as follows:

>$ make MACHINE=bluegene

Note that the INFO macro in the XSbench_header.h file should be set to
0 when running on BG/Q to remove the run status portions of the output,
which cuts down on unnecessary file I/O, i.e.:

#define INFO 0

Also, note that you may need to add the following line to your .soft
file in order to use the mpicc compiler wrapper:

+mpiwrapper-gcc

Then, be sure to use the "resoft" command to update your software, i.e.,:

>$ resoft

When running in c16 mode, the maximum number of gridpoints per nuclide
is 900 (when running in "Large" mode). More points will cause the 1GB
memory limit to be broken.

A basic test run on 1 node can be achieved (assuming you have an allocation)
using the makefile and the following command:

>$ make bgqrun

Further information on queuing can be found at:

https://www.alcf.anl.gov/resource-guides/vesta-queuing

==============================================================================
Citing XSBench
==============================================================================

Papers citing the XSBench program in general should refer to:

J. R. Tramm, A. R. Siegel, T. Islam, and M. Schulz, “XSBench - The
Development and Verification of a Performance Abstraction for Monte
Carlo Reactor Analysis,” presented at PHYSOR 2014 - The Role
of Reactor Physics toward a Sustainable Future, Kyoto.

A PDF of this paper can be accessed directly at this link:

http://www.mcs.anl.gov/papers/P5064-0114.pdf

Bibtex Entry:

@inproceedings{Tramm:wy,
author = {Tramm, John R and Siegel, Andrew R and Islam, Tanzima and Schulz, Martin},
title = {{XSBench - The Development and Verification of a Performance Abstraction for Monte Carlo Reactor Analysis}},
booktitle = {PHYSOR 2014 - The Role of Reactor Physics toward a Sustainable Future},
address = {Kyoto}
}

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