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README

                      MPE (Multi-Processing Environment)
                      ----------------------------------

                          Version 2.4.9b. December, 2015

                    Mathematics and Computer Science Division
                           Argonne National Laboratory

I.  INTRODUCTION
----------------

The Multi-Processing Environment (MPE) attempts to provide programmers with 
a complete suite of performance analysis tools for their MPI programs based
on post processing approach.  These tools include a set of profiling libraries, 
a set of utility programs, and a set of graphical tools.

The first set of tools to be used with user MPI programs is profiling libraries
which provide a collection of routines that create log files.  These log files
can be created manually by inserting MPE calls in the MPI program, or 
automatically by linking with the appropriate MPE libraries, or by combining 
the above two methods.  Currently, the MPE offers the following 4 profiling 
libraries.

   1) Tracing Library - Traces all MPI calls.  Each MPI call is preceded by a 
      line that contains the rank in MPI_COMM_WORLD of the calling process, 
      and followed by another line indicating that the call has completed.
      Most send and receive routines also indicate the values of count, tag,
      and partner (destination for sends, source for receives).  Output is to
      standard output.

   2) Animation Libraries - A simple form of real-time program animation 
      that requires X window routines.  

   3) Logging Libraries - The most useful and widely used profiling libraries 
      in MPE.  These libraries form the basis to generate log files from 
      user MPI programs.  There are several different log file formats
      available in MPE.  The default log file format is CLOG2.  It is a low
      overhead logging format, a simple collection of single timestamp events.
      The old format ALOG, which is not being developed for years, is not
      distributed here.  The powerful visualization format is SLOG-2, stands 
      for Scalable LOGfile format version II which is a total redesign of the
      original SLOG format.  SLOG-2 allows for much improved scalability for 
      visualization purpose.  CLOG2 file can be easily converted to 
      SLOG-2 file through the new SLOG-2 viewer, Jumpshot-4.  The MPI logging
      library is now thread-safe through the use of a global mutex over the
      the MPE logging library which is not yet thread-safe.

   4) Collective and datatype checking library - An argument consistency 
      checking library for MPI collective calls.  It checks for datatype,
      root, and various argument consistency in MPI collective calls.
      If an error is detected, a backtrace of the callstack (on the supported
      platform) will be printed to locate the offended call.

The set of utility programs in MPE includes log format converter (e.g. 
clogTOslog2), logfile print (e.g. slog2print) and logfile viewer and
convertor (e.g. jumpshot).  These new tools, clog2TOslog2, slog2print and
jumpshot(Jumpshot-4) replace old tools, clog2slog, slog_print and logviewer
(i.e. Jumpshot-2 and Jumpshot-3).  For more information of various
logfile formats and their viewers, see 

http://www.mcs.anl.gov/perfvis



II. CONFIGURATION
-----------------

MPE can be configured and installed as an extension to most MPI standard
-compliant MPI implementations, e.g. MPICH-2, MPICH, OpenMPI, LAM/MPI,
SGI's MPI, HP-UX's MPI, IBM's MPI, Cray's MPI and NEC's MPI.  
MPE has been integrated into MPICH and MPE2 has been integrated seamlessly
into MPICH-2, so MPEx will be installed automatically during MPICHx's
installation process.  

For details of configuration of MPE, see the INSTALL or INSTALL.cross file.



III. INSTALLATION INSTRUCTIONS
-------------------------------

For details of installation instruction/examples of MPE, see the INSTALL file.



IV.  EXAMPLE PROGRAMS
----------------------

As previously noted, the MPE library is composed of 3 different profiling
libraries.  During configure, the compiler's library linkage flags and 
appropriate libraries are determined.  These variables are first substituted
in the Makefiles in the directories, mpe2/src/wrappers/test,
mpe2/src/graphics/contrib/test and mpe2/src/collchk/test.  The Makefiles for
mpe2/src/wrappers/test and mpe2/src/graphics/contrib/test are then installed
into directory share/ as examples/logging/ and examples/graphics/ during the 
final installation process.  The following are some of the crucial variables:

LOG_LIBS     = library flag that links with the logging libraries
TRACE_LIBS   = library flag that links with the tracing library
ANIM_LIBS    = library flag that links with the animation library
COLLCHK_LIBS = library flag that links with the collective and datatype
               checking library

The variable FLIB_PATH is the compiler's library path needed to link fortran 
MPI programs with the logging library.

During make, small test programs cpi.c, cpilog.c and fpilog.f will be linked
with each of the above libraries.  In the output from Make, a message will be 
printed to indicate the status of each attempted link test.  The success 
of these linkage tests will also be included in the Make output.  If the
linkage tests are successful, then these library linkage flags can be used
for your programs as well.   

The following example programs are also included in the distribution:

    mpe/src/graphics/contrib/mandel is a Mandelbrot program that uses the MPE 
    graphics package.

    mpe/src/graphics/contrib/mastermind is a program for solving the Mastermind
    puzzle in parallel.

These programs should work on all MPI implementations, but have not been
extensively tested.





V.  MPEINSTALL
--------------

A 'mpeinstall' script is created during configuration.  If configuring with
MPICH and MPICH2, then the 'mpiinstall' script will invoke the 'mpeinstall'
script.  However, 'mpeinstall' can also be used by itself.  This is only 
optional and is of use only if you wish to install the MPE library in a 
public place so that others may use it.  Final install directory will 
consist of an include, lib, bin, sbin and share subdirectories.  Examples 
and various logfile viewers will be installed under share.





VI. USAGE
---------

The final install directory contains the following subdirectories.

    include/ contains all the include files that user program needs to read.
    lib/     contains all the libraries that user program needs to link with.
    bin/     contains all the utility programs that user needs to use.
    doc/     contains available MPE documentation, e.g. Jumpshot-4's userguide.
    sbin/    contains the MPE uninstall script to uninstall the installation.
    share/   contains user read-only data.  Besides share/examples/logging/,
             share/examples/graphics/, share/examples/collchk, and
             share/examples/logfiles, user usually does NOT need to know
             the details of other subdirectories.

In terms of usage of MPE, user usually only need to know about the files
that have been installed in include/, lib/ and bin/.  



VI. a) CUSTOMIZING LOGFILES
---------------------------

In addition to using the predefined MPE logging libraries to log all MPI 
calls, MPE logging calls can be inserted into user's MPI program to define
and log states.  These states are called User-Defined states.  States may 
be nested, allowing one to define a state describing a user routine that 
contains several MPI calls, and display both the user-defined state and 
the MPI operations contained within it.

The simplest way to insert user-defined states is as follows:
1) Get handles from MPE logging library: MPE_Log_get_state_eventIDs()
   has to be used to get unique event IDs (MPE logging handles).
   This is important if you are writing a library that uses
   the MPE logging routines from the MPE system.  

   PS. Hardwiring the eventIDs is considered a bad idea since it may cause
   eventID confict and so the practice isn't supported.  Older MPE libraries 
   provide MPE_Log_get_event_number() which is still being supported but
   has been deprecated.  Users are strongly urged to use
   MPE_Log_get_state_eventIDs() instead.
2) Set the logged state's characteristics: MPE_Describe_state() sets the
   name and color of the states.
3) Log the events of the logged states: MPE_Log_event() are called twice
   to log the user-defined states.

Below is a simple example that uses the 3 steps outlined above.

\begin{verbatim}

int eventID_begin, eventID_end;
...
MPE_Log_get_state_eventIDs( &eventID_begin, &eventID_end );
...
MPE_Describe_state( eventID_begin, eventID_end, "Multiplication", "red" );
...
MyAmult( Matrix m, Vector v )
{
    /* Log the start event of the red "Multiplication" state */
    MPE_Log_event( eventID_begin, 0, NULL );
    ...
    ... Amult code, including MPI calls ...
    ...
    /* Log the end event of the red "Multiplication" state */
    MPE_Log_event( eventID_end, 0, NULL );
}

\end{verbatim}

The logfile generated by this code will have the MPI routines nested within
the routine MyAmult().

Besides user-defined states, MPE2 also provides support for user-defined
events which can be defined through use of MPE_Log_get_solo_eventID()
and MPE_Describe_event.  For more details, e.g. see cpilog.c.

If the MPE logging library, liblmpe.a, is NOT linked with the user program, 
MPE_Init_log() and MPE_Finish_log() need to be used before and after all 
the MPE calls.   Sample programs cpilog.c and fpilog.f are available to 
illustrate the use of these MPE routines.  They are in the MPE 
source directory, mpe2/src/wrappers/test or the installed directory, 
share/examples/logging to illustrate the use of these MPE routines.  
For futher linking information, see section "Convenient Compiler Wrappers".

For undefined user-defined state, i.e. corresponding MPE_Describe_state() 
has not been issued, new jumpshot (Jumpshot-4) may display the legend name as
"UnknownType-INDEX" where INDEX is the internal MPE category index.



VI. b) ENVIRONMENTAL VARIABLES
------------------------------

For MPE logging, MPE_TMPDIR and MPE_LOGFILE_PREFIX are 2 environment variables
that most users find to be very useful.  So it is recommended to set these
2 env. variables before launching the MPI program during logging :

CLOG_BLOCK_SIZE: The integer value determines the clog2 buffer block size
                 which set the least minimum clog2 file size.  If
                 CLOG_BLOCK_SIZE is not set, 64K per block is assumed.

CLOG_BUFFERED_BLOCKS: The integer value determines the number of blocks
                      witin the CLOG2's internal buffer.  Together with
                      CLOG_BLOCK_SIZE, CLOG_BUFFERED_BLOCKS determines how
                      often the internal buffer is flushed to the disk.  
                      The total buffer size is determined by the product of
                      CLOG_BLOCK_SIZE and CLOG_BUFFERED_BLOCKS.  These 2
                      environmental variables allows user to minimize MPE2
                      logging overhead when large local memory is available.
                      The default value is 128.

MPE_TMPDIR: MPE_TMPDIR takes precedence over TMPDIR.  It specifies a
            directory to be used as temporary storage for each process.
            By default, when MPE_TMPDIR and TMPDIR are NOT set,
            /tmp will be used.  When user needs to generate a very large
            logfile for long-running MPI job, user needs to make sure that
            MPE_TMPDIR(or TMPDIR) is big enough to hold the temporary local
            logfile which will be deleted if the merged logfile can be
            created successfully.  In order to minimize the overhead of the
            logging to the MPI program, it is highly recommended user to
            use a *local* file system for TMPDIR.

             Note : The final merged logfile will be written back to the 
                    file system where process 0 is.

MPE_SAME_TMPDIR: The boolean value determines whether MPE_TMPDIR will be
                 the same across the whole MPI_COMM_WORLD. By default,
                 MPE_SAME_TMPDIR is set to true and only rank 0's MPE_TMPDIR
                 will be broadcasted to every process. There is scalability
                 implication on whether MPE_SAME_TMPDIR is true.  When
                 MPE_SAME_TMPDIR=false, MPE_TMPDIR could be set differently
                 on different processes and hence mkstemp() will be called
                 once on each process to create temporary filename.  Calling
                 mkstemp() on the same filesystem, e.g. $HOME, for each process
                 is not scalable, i.e. the shared filesystem may be hanging.
                 MPE_SAME_TMPDIR=false is provided for cases that MPE_TMPDIR
                 has to be set differently on different process but it is
                 in general not scalable when MPI_COMM_WORLD's size >> 1K.

MPE_DELETE_LOCALFILE:  The boolean value determines whether to delete the
                       temporary local clog2 file.  When this flag is
                       set to true, user needs to collect from the temporary
                       clog2 files from each slave node's MPE_TMPDIR.
                       Then separate serial programs, clog2_join and 
                       clog2_repair, can be used to merge the local clog2 
                       files.  This process is useful e.g. when MPI_Finalize()
                       fails to complete properly, e.g.  due to user program
                       overwritten to MPE/MPI internal data structures.

MPE_CLOCKS_SYNC: The boolean value determines the behavior of
                 MPE_Log_sync_clocks() and the default clock synchronization
                 at the end of logging.  Users may way to force MPE
                 clock synchronization when the MPI implementation has
                 buggy clock synchronization mechanism, e.g. Some versions
                 of BG/L MPI's MPI_WTIME_IS_GLOBAL is incorrectly set
                 to true when 64-ways or 256-ways partition is used.

MPE_SYNC_ALGORITHM: specifies the clock synchronization algorithm.  The
                    accepted values are "DEFAULT", "SEQ", "BITREE" 
                    and "ALTNGBR".
                    SEQ: a O(N) steps algorithm and is non-scalable and slowest
                         but is also the most accurate.
                    BITREE: a O(log2(N)) steps algorithm, scalable and much
                            faster than SEQ but less accurate than SEQ.
                            A good compromise.
                    ALTNGBR: a O(1) steps algorithm, perfectly parallel
                             is the fastest of 3 algorithms supported.
                             It is also the least accurate.
                    DEFAULT: uses SEQ when the number of processes <= 16.
                             uses BITREE when number of processes > 16.

MPE_SYNC_FREQUENCY: specifies the number of iterations of selected clock
                    synchronization.  In general, the higher of
                    MPI_SYNC_FREQUENCY, the higher the probability of
                    obtaining a accurate measurement of all the clocks,
                    i.e. less error.  Keep in mind, this is generally
                    not a guarantee and is highly dependent of the system
                    noise.  The default is 3.

MPE_LOGFILE_PREFIX: specifies the filename prefix of the output logfile.
                    The file extension will be determined by the output
                    logfile format, i.e. MPE_LOG_FORMAT.

MPE_LOG_FORMAT: determines the format of the logfile generated from the 
                execution of application linked with MPE logging libraries.  
                The allowed value for MPE_LOG_FORMAT is CLOG2 only.
                So there is no need to use this variable at the moment.

MPE_LOG_OVERHEAD: The boolean value determines to log MPE/CLOG2's internal
                  profiling state CLOG_Buffer_write2disk(). The default
                  setting is yes.  CLOG_Buffer_write2disk labels region
                  in each process that MPE/CLOG2 spends on flushing logging
                  data in the memory to the disk.  The frequency and location
                  of CLOG_Buffer_write2disk state can be altered by changing
                  CLOG_BLOCK_SIZE and/or CLOG_BUFFERED_BLOCKS.

MPE_LOG_RANK2PROCNAME: The boolean value determines if a .clog2.pnm file
                       that contains the MPI_COMM_WORLD rank to processor
                       name determined by MPI_Get_processor_name().  The
                       default is No.

MPE_WRAPPERS_ADD_LDFLAGS: The variable tells MPE wrappers, mpecc/mpefc
                          (includes mpich2's mpicc and friends), to use
                          LDFLAGS added by MPE, e.g. -Wl,--export-dynamic.
                          The default is yes.  User can override it by
                          setting it to "no" or "false".

MPE_USE_FCONSTS_IN_MPIH : The boolean value determines if MPI_F_* constants
                          from mpi.h will be used.  By default, MPE computes
                          the MPI_F_* constants instead of reading from mpi.h.
                          The affected constants are MPI_F_STATUS(ES)_IGNORE.

Possible boolean values are "true", "false", "yes" and "no" in either
all lower or upper cases.


For MPE X11 graphics, environment variables DISPLAY set in each process
is read during MPE_Open_graphics.

DISPLAY: determines where MPE X11 graphics on each process is connected to.



VI. c) EXAMPLE MAKEFILE 
-----------------------

The install directories, share/examples/logging, share/examples/graphics and
share/examples/collchk contain some very useful and simple example programs.
The Makefiles in these directories illustrate the usage of MPE routines
and how to link with various MPE libraries. In most cases, users can simply
copy the share/examples/logging/Makefile to their home directory, and do a
"make" to compile the suggested targets.  Users don't need to copy the
.c and .f files when MPE has been compiled with a MAKE that has VPATH
support.  The created executables can be launched with mpiexec or mpirun
from the MPI implementation to generate sample logfiles.



VI. d) UTILITY PROGRAMS
-----------------------

In bin/, user can find several useful utility programs when manipulating 
logfiles.  These includes log format converters, log format print programs,
and logfile display program,


Log Format Converters
---------------------

clog2TOslog2 : a CLOG2 to SLOG-2 logfile convertor.  For more details,
              do "clog2TOslog2 -h".

rlogTOslog2 : a RLOG to SLOG-2 logfile convertor.  For more details,
              do "rlogTOslog2 -h".  Where RLOG is an internal MPICH2 logging
              format.

logconvertor : a standalone GUI based convertor that invokes clog2TOslog2
               or rlogTOslog2 based on logfile extension.  The GUI also
               shows the progress of the conversion.  The same convertor
               can be invoked from within the logfile viewer, jumpshot.

slog2filter : a SLOG-2 to SLOG-2 logfile convertor.  It allows for removal
              unwanted categories (when used with slog2print -c).  It also
              allows for changing of the SLOG-2 internal structure, e.g.
              modify the duration of preview drawable.  The tool reads
              and writes SLOG-2 file of same version.

slog2updater: a SLOG-2 file format update utility.  It is essentially
              a slog2filter that reads in older SLOG-2 file and writes
              out the latest SLOG-2 file format.


Log Format Print Programs
-------------------------

clog2_print : a stdout print program for CLOG file.
              Java version is named as clogprint.

clog2_join  : a clog2 serial merging program that merges clog2 files
              1) temporary local clog2 files which all are from the
                 same MPI_COMM_WORLD.
              2) merged clog2 files from each MPI_COMM_WORLDs
                 (Incomplete!, timestamps are not sync'ed yet.)

clog2_repair : a clog2 repair program that tries to fix the missing data
               of a clog2 file (when the MPI program that is being profiled
               aborts) so that the file can be processed by other tools
               like clog2TOslog2.

rlog_print  : a stdout print program for SLOG-2 file.

slog2print  : a stdout print program for SLOG-2 file.



Log File Display Program 
------------------------

jumpshot : the Jumpshot-4 launcher script.  Jumpshot-4 does logfile
           conversion as well as visualization.

To view a logfile, say fpilog.slog2, do

jumpshot fpilog.slog2

The command will select and invoke Jumpshot-4 to display the content
of SLOG-2 file if Jumpshot-4 has been built and installed successfully.

One can also do

jumpshot fpilog.clog2

or

jumpshot barrier.rlog

Both will invoke the logfile convertor first before visualization.


Collective and Datatype Checking
--------------------------------

Linking an MPI application with the collective and datatype checking library
as follows

mpicc -o mpi_pgm *.o -L<mpe2_libdir> -lmpe_collchk.

Or using compiler wrappers (more details in next section), e.g.

(with mpich2's compiler wrapper)
mpicc -mpe=mpicheck -o mpi_pgm *.o

(with MPE's compiler wrapper)
mpecc -mpe=mpicheck -o mpi_pgm *.o


Convenient Compiler Wrappers
----------------------------

Standalone MPE installation with non-MPICH2 will see 2 convenient compiler
wrappers mpecc and mpefc which mimic the typical usage of mpicc/mpif77/mpif90
in MPICH* by providing convenient compilation and linking switches.
mpecc is for C program, and mpefc is for Fortran program.  Typically,
user can use mpecc as follows:

mpecc -mpilog -o cpilog cpilog.c

which is equivalent to doing

mpicc -o cpilog cpilog.c -L<mpe2_libdir> -llmpe -lmpe

Available MPE profiling options for "mpecc" and "mpefc" are as follows:

    -mpilog     : Automatic MPI and MPE user-defined states logging.
                  This links against -llmpe -lmpe.

    -mpitrace   : Trace MPI program with printf.
                  This links against -ltmpe.

    -mpianim    : Animate MPI program in real-time.
                  This links against -lampe -lmpe.

    -mpicheck   : Check MPI Program with the Collective & Datatype
                  Checking library.  This links against -lmpe_collchk.

    -graphics   : Use MPE graphics routines with X11 library.
                  This links against -lmpe <X11 libraries>.

    -log        : MPE user-defined states logging.
                  This links against -lmpe.

    -nolog      : Nullify MPE user-defined states logging.
                  This links against -lmpe_null.

    -help       : Print this help page.


MPE has been seamlessly integrated into MPICH2 and MPICH distributions,

In MPICH2, all the convenient compilation and linking switches described above
are provided through -mpe= option in mpicc/mpicxx/mpif77/mpif90.  For instance,
to compile and link cpilog with automatic MPI logging library can be done
as follows

mpicc -mpe=mpilog -o cpilog cpilog.c

which is equivalent to the mpecc command

mpecc -mpilog -o cpilog cpilog.c


In MPICH(the old one), the compiler wrappers, mpicc/mpiCC/mpif77/mpif90 
do not provide all the convenient switches listed above, only 3 of them
are available.  These options are :

-mpitrace   - to compile and link with tracing library.
-mpianim    - to compile and link with animation libraries.
-mpilog     - to compile and link with logging libraries.

For instance, the following command creates executable, {\tt fpilog}, which
generates logfile when it is executed.

mpif77 -mpilog -o fpilog fpilog.f 




VII. Using MPE in MPICHx
------------------------

VII. a) Inheritance of Environmental Variables
----------------------------------------------
MPE relies on certain environmental variables (e.g. MPE_TMPDIR).  These
variables determine how MPE behaves.  It is important to make sure that
all the MPI processes receive the intended value of environmental variables.
The complication of this issue comes from the fact that different MPI
implementations have different ways of passing environmental varaiable.  For
instance, MPICH contains many different devices for different platforms,
some of these devices have their unique way of passing of environmental
variables to other processes.  The often used devices, like ch_p4 and ch_shmem,
do not require special attention to pass the value of the environmental 
variable to spawned processes.  The spawned process inherits the value from
the launching process when the environmental variable in the launching
process has been set.  But this is NOT true for all the devices, for instance,
the ch_p4mpd device requires special option of mpirun to set environmental
variables to all processes.

mpirun -np N fpilog -MPDENV- MPE_LOGFILE_PREFIX=fpilog

In this example, the option -MPDENV- is needed to make sure
that all processes have their environmental variable, MPE_LOGFILE_PREFIX,
set to the desirable output logfile prefix.


In MPICH2, when using MPD as a process manage, passing MPE_LOGFILE_PREFIX
and MPE_TMPDIR can be done as follows:

mpiexec -env MPE_LOGFILE_PREFIX <output-logname-prefix> \
        -env MPE_TMPDIR <local-tmp-dir> -n 32 <executable-name>

Also, with MPE X11 graphics library, the local DISPLAY variable set on each
process is read (so ssh tunnelling can be used), for examples assume
an mpd ring has been set up by on 2 machines, schwinn and triumph, as follows:

cat > mpd.hosts << EOF
schwinn
triumph
EOF

mpdboot -n 2 -f mpd.hosts

Now launch MPE X11 graphics sample code, cxgraphics, as follows:

mpiexec -host schwinn -env DISPLAY <display_0> cxgraphics : \
        -host triumph -env DISPLAY <display_1> cxgraphics

Where <display_0> and <display_1> are the local DISPLAY variable
echoed from consoles connected to schwinn and triumph respectively.


For other MPI implementations, how environmental variables are passed
remains unchanged.  User needs to get familar with the runtime environment
and set the environmental variables appropriately.


VII. b) Viewing Logfiles
------------------------
MPE's install directory structure is the same as MPICH's and MPICH-2's.
So all MPE's utility programs will be located in the bin/ directory of 
MPICH and MPICH-2.