ThirdParty-6/scotch_6.0.3/INSTALL.txt

Scotch 6.0 installation instructions
====================================


1) Mandatory tools
==================

In order for you to compile Scotch and/or PT-Scotch, you must have GNU
Make installed on your system, as well as an implementation of the MPI
message-passing library in the case of PT-Scotch. Lex and Yacc are
optional. There is a possibility to install Scotch without having Lex
or Yacc, but it may require the tuning of sample Flex and Bison (i.e.,
the GNU equivalents of Lex and Yacc) outputs created on a Linux
system, which may need some tricky work to compile on other systems,
because of different C library implementations.

To check if GNU Make is installed and is found first, please type:

%prompt% make --version

It should read:
% GNU Make x.xx
% Copyright (C) 20xx  Free Software Foundation, Inc.
etc, etc.


Alternatively, if GNU Make is installed but its directory does
not appear first in the PATH variable that is searched for
executables, you can try to locate it using the which command:

%prompt% which make

If several occurences of make are found, one might be GNU Make,
so try to figure out which of them.

To see if lex and yacc are present, type
%prompt% which lex
%prompt% which yacc    (or "bison", the GNU flavor of yacc)

If some of these are missing, please:
- check your path variable (just in case they are located in
  some unusual place, such as /usr/local/bin, /opt/bin,
  /opt/local/bin/, /opt/gnu/bin, etc). Tools such as "which",
  "locate" or "find" may help you find them;
- ask your system administrator (highly recommended);
- install a copy of GNU Make of your own (less recommended,
  please ask your system administrator first). GNU Make is
  available from the FSF website, at:
  http://www.gnu.org/software/make/ and
  http://ftp.gnu.org/pub/gnu/make/ .
  A GNU version of lex and yacc is also available from the
  very same FSF website, at:
  http://www.gnu.org/software/flex/
  http://ftp.gnu.org/non-gnu/flex/
  http://www.gnu.org/software/bison/
  http://ftp.gnu.org/pub/gnu/bison/ ;
- use the "last resort" files placed in a directory judiciously
  called "last_resort", located in subdirectory "src/libscotch".
  These files are:
  . parser_ll.c
  . parser_ly.h
  . parser_yy.c .
  They should be copied in the directory where object files are
  created, and "touch"ed so that their modification date is more
  recent than those of the corresponding "parser_ll.l" and
  "parser_yy.y" files. Then cross your fingers and hope it
  compiles properly on your system. Else, you will have to dig in
  their code to have them compile properly...
  The Makefile of the libScotch library has been designed so as
  to copy the last_resort/* files automatically when the lex or
  yacc tools are not found.
  In this case, depending on your platform, you may also have to set
  the "-DSCOTCH_RENAME_PARSER" flag in order for all symbols to be
  properly redefined (see Section 2.2).


2) Configuration
================

2.1) Creating the "Makefile.inc" file
-------------------------------------

Go to the "src/" directory.

Look in the "Make.inc/" subdirectory for a configuration
file which matches your system configuration. If there
is none, build a proper one in the "Make.inc/" subdirectory,
basing on the structure of existing ones.

In particular, the Makefile.inc file contains three variables
which specify which C compiler to use. Their semantic is as
follows: the compiler command in variable CCS is used to compile
the sequential (hence the "S" in "CCS") Scotch distribution. The
compiler command in CCP is used to compile the parallel ("P")
PT-Scotch distribution. The compiler command in CCD is used to compile
the version of the "dummysizes" ("D") executable used for compiling
PT-Scotch, as explained below.

Create a symbolic link from the configuration file to the
current "src/" working directory, renaming it as "Makefile.inc":

%prompt% ln -s Make.inc/Makefile.inc.xxxx_xxx_xxx Makefile.inc

If symbolic links are not available on your system, make a
plain copy of the file to a file named "Makefile.inc" in the
current "src/" working directory:

%prompt% cp Make.inc/Makefile.inc.xxxx_xxx_xxx Makefile.inc

Some additional scripts, designed to ease the installation of Scotch
on specific platforms, are also present in subdirectories of the
Make.inc directory. This is for instance the case for the mingw32
platform.


2.2) Parser symbol conflicts
----------------------------

Since Scotch uses a parser to analyze its strategy strings, it may
happen that the symbols of this parser conflict with those of
another parser used in a third-party library. All "Makefile.inc.*"
platform configuration files which base on flex / bison are already
tailored so as to prevent such conflicts. If you use other parsing
tools, you may have to provide other options. Another solution is to
use the pre-processed parser files of the "src/libscotch/last_resort"
subdirectory (corresponding operation instructions are given in
Section 1).


2.3) Integer size issues
------------------------

By default, all integers used in Scotch and PT-Scotch are of the "int"
C type, corresponding to the "INTEGER" type in Fortran. To coerce the
size of the Scotch integer type to 32 or 64 bits, add the "-DINTSIZE32"
or "-DINTSIZE64" flags, respectively, to the C compiler flags in the
Makefile.inc configuration file. If you do so, make sure to use
integer types of equivalent size to declare variables passed to Scotch
routines from caller C and Fortran procedures. Also, when running on
32_64-bit architectures (that is, integer types are 32-bit wide,
while address types are 64-bit wide), some integer array indices
returned by the Fortran interface have to be of a size equivalent to
those of memory addresses, that is, 64 bits. The size of these
variables is determined by the "-DIDXSIZE32" and "-DIDXSIZE64" flags,
respectively. When none of them is provided, the size of the indices
is assumed to be equivalent to that of the Scotch integer type.

For instance, on a 32-bit architecture, you can use 64-bit integers in
Scotch by just setting the "-DINTSIZE64" flag, because addresses will
remain on 32 bits. On a 32_64 architecture, you can use either 32-bit
or 64-bit integers in Scotch, by setting the "-DINTSIZE32" or
"-DINTSIZE64" flags accordingly, but in all cases you must set the
"-DIDXSIZE64" flag in order for some of the routines of the Fortran
interface to operate properly, because the array indices returned by
these routines have to be stored as 64-bit quantities.

Of course, on 64-bit architectures, another possibility is to tune
your C and Fortran compilers to make them interpret all "int" and
"INTEGER" types as 64 bit values. This solution is the simplest one,
as there is no need to use any of the aforementioned flags, nor to
hard-code type lengths in user's code. Yet, it prevents mixing 32 and
64-bit features, and may create problems when linking PT-Scotch if a
corresponding MPI library is not available.

Be careful not to mismatch the 32-bit and 64-bit versions of the
"scotch.h" and "ptscotch.h" include files that are generated at
compile time. When several versions of Scotch are simultaneously
present on a system, Make sure to place the corresponding include and
library files in separate directories. Most Scotch data structures
will have different sizes, depending on integer or pointer
sizes. Consequently, compiling a 64-bit executable with the 32-bit
version of "scotch.h" may lead to unpredictable behavior because of
memory overflow.


2.4) Compression libraries
--------------------------

The binaries of the Scotch distribution can handle compressed
graphs in input or output. Three compressed graph formats are
currently supported: bzip2, gzip and lzma. In order for them to be
actually activated, the proper libraries must be available on your
system. On a Linux platform, they are called "zlib" for the gzip
format, "libbz2" for the bzip2 format, and "liblzma" for the lzma
format. Note that it is the "development" version (also called
"devel", for short, within package names) of each of these libraries
which is required for the compilation to succeed.
According to the libraries installed on your system, you may set
flags "-DCOMMON_FILE_COMPRESS_BZ2", "-DCOMMON_FILE_COMPRESS_GZ" and/or
"-DCOMMON_FILE_COMPRESS_LZMA" in the CFLAGS variable of your
Makefile.inc configuration file, to have these formats and their
respective extensions ".bz2", ".gz" and ".lzma", recognized and
handled by Scotch.

Compression and decompression are handled either by extra threads
or by fork'ed child processes if threads are not available. On
systems which do not provide a functional fork() system call,
compressed files cannot be handled when the "-DCOMMON_PTHREAD" flag
is not set (see below).


2.5) Multi-threading
--------------------

Scotch can also take advantage of Posix threads when they are
available. They are used in several places:

- to compress and uncompress file data. This can be done either
  by launching a service thread, or else by creating a separate
  process by means of a Posix fork() system call. This choice is
  controlled by the "-DCOMMON_PTHREAD" flag: if it is set, threads
  will be used, else fork() calls will be performed. For systems
  which do not support the fork() system call, such as the MinGW32
  platform, one can set the "-DCOMMON_STUB_FORK" flag, which creates
  a stub fork() routine which always returns an error. Therefore,
  without both fork() and threads, one must set the
  "-DCOMMON_STUB_FORK" flag without setting "-DCOMMON_PTHREAD", so
  that compilation will successfully complete; however, in this case,
  compressed graphs shall not be handled in practice.

- to create distributed graphs in parallel. Since this task involves
  concurrent MPI communications, the MPI library must support the
  MPI_THREAD_MULTIPLE level. The use of threads within Scotch itself
  is controlled by the "-DSCOTCH_PTHREAD" flag, which is completely
  independent from the "-DCOMMON_PTHREAD" flag. Any of them can be set
  without setting the other.

  Note that if you compile Scotch with the "-DSCOTCH_PTHREAD" flag,
  you will have to initialize your communication subsystem by using
  the MPI_Init_thread() MPI call, not MPI_Init(), and the provided
  thread support level value returned by the routine must be
  checked carefully.
  If you have doubts on the stability of your MPI implementation, it
  is better not to set "-DSCOTCH_PTHREAD". For instance, on Linux
  platforms, concurrency problems have been experienced with MPICH2
  versions prior to 1.0.7 using TCP; consequently, if the MPI
  implementation on your platform is based on an older MPICH2 version,
  do not set the "-DSCOTCH_PTHREAD" flag.

  Note that since the Scotch and PT-Scotch libraries are distinct, you
  can still compile Scotch with threads enabled, and compile PT-Scotch
  with threads disabled. However, since PT-Scotch calls Scotch
  routines when operating on a single process, threaded routines will
  be used on each process, without interfering with MPI.

- to run in a multi-threaded way several key algorithms of the Scotch
  (no longer really) sequential library, such as graph coarsening and
  k-way diffusion. More algorithms will be re-coded in a threaded way
  in future versions.

To date, thread management is performed in a very rudimentary way.
The available number of threads can only be set at compile-time, and
the assignment of threads to cores is performed in increasing order,
starting from 0, which may not always prove to be the most efficient
mapping in terms of memory affinity. We plan to add a mechanism for
dynamic thread allocation in the near future, based upon the hwloc
library.

The compilation flags used to manage threads are the following:

"-DCOMMON_PTHREAD" enables threads for algorithms not related to
graph management, partitioning and/or ordering, e.g. compressed
file handling.

"-DCOMMON_PTHREAD_BARRIER" creates a replacement for missing
pthread_barrier_t implementations, which unfortunately happens on some
systems.

"-DSCOTCH_PTHREAD" is necessary to enable multi-threaded algorithms
in Scotch and/or PT-Scotch.

"-DSCOTCH_PTHREAD_AFFINITY_LINUX" enables Linux extensions for
handling thread affinity. As said above, this may not prove
efficient in all cases. More options will be provided in the
near future.

"-DSCOTCH_PTHREAD_NUMBER=x" sets the overall number of threads to be
used by multi-threaded algorithms. This number may not necessary be a
power of two. Since some algorithms have had to be reformulated to
accomodate for multi-threading, some algorithms will most probably be
much more efficient than sequential processing only for a number of
threads strictly greater than 2. Setting "-DSCOTCH_PTHREAD_NUMBER=1"
allows one to run sequential algorithms instead of multi-threaded
ones, while benefitting from multi-threading for file compression and
distributed graph handling.

When compiling under mingw32 on Windows systems, it is possible to
benefit from multi-threading by including the "semaphore.h" and
"pthread.h" files, included in the "src/misc" subdirectory, at compile
time. These files have been kindly provided by Samuel Thibault, under
a BSD 2-Clause License. These files will not work for Cygwin. This is
not a problem, as Cygwin provides its own implementation of Posix
threads.


2.6) Monitoring memory allocation
---------------------------------

Some memory allocation information can be aggregated if PT-Scotch is
compiled with the -DCOMMON_MEMORY_TRACE flag. When this flag is set,
the "-va" option will make dgmap, dgord and dgpart output the minimum,
maximum and average peak amount of memory used over all processes.

Several API routines will also be made available to report the current
and maximum amount of memory used by Scotch within the process they
are called: SCOTCH_memCur() and SCOTCH_memMax(), respectively.

A rudimentary memory checking mechanism is available for platforms
that do not have efficient memory checking and debugging tools such as
Valgrind or gdb. It can be activated through the
"-DCOMMON_MEMORY_CHECK=x" flag. This is almost only for internal
debugging purposes. The value of the "-DCOMMON_MEMORY_CHECK" is 1 if
memory checking should be enabled by default, and 0 else. This
mechanism is absolutely NOT thread-safe at the time being.


2.7) Randomness
---------------

Many algorithms in Scotch and PT-Scotch are based on the random
selection of vertices (e.g. seed vertices for graph growing
algorithms, vertices to be mated for coarsening algorithms,
etc.). This selection is performed by using integer pseudo-random
generators to produce seemingly uncorrelated vertex indices.

The advantage of pseudo-randomness over pure randomness is that the
same pseudo-random seed will always yield the same sequence of
pseudo-random numbers. Consequently, while using a different random
seed for each run is likely to explore better the solution space,
using a fixed random seed eases the debugging of programs, because
algorithms behave identically across multiple runs (save for
asynchronousness issues, see next section). By default, Scotch is
compiled with the "-DCOMMON_RANDOM_FIXED_SEED" flag set, so that
multiple executions of the same sequential programs will always yield
the same results.

Prior to version 6.0, Scotch relied on the operating system
pseudo-random generator. While this posed no problem for most
sequential programs, parallel runs of PT-Scotch were not reproducible
on some systems, because the MPI implementation also used this
pseudo-random generator for its own purposes. In order to avoid this
problem, Scotch now uses its own pseudo-random generator. Users that
want to go on using the operating system pseudo-random generator
(e.g. for regression testing with respect to version 5.x) can still do
so, by compiling with the "-DCOMMON_RANDOM_SYSTEM" flag set. In this
case, the "-DCOMMON_RANDOM_RAND" flag allows one to use the srand()
routine instead of the default srandom() routine.


2.8) Deterministic behavior
---------------------------

When Scotch is compiled with the "-DCOMMON_RANDOM_FIXED_SEED"
flag set, multiple executions of the same sequential programs
will always yield the same results. Yet, non-deterministic
multi-threaded and/or parallel algorithms may still introduce
some variability in the produced results, due to operating system
artifacts.

To ease the tracking down of bugs, it is possible to coerce Scotch to
exhibit a deterministic behavior by setting the
"-DSCOTCH_DETERMINISTIC" flag. This option makes sure that two
consecutive runs of Scotch on the same graph and same number of
processes and/or threads will always yield the same result. However,
it does not mean that two executions of Scotch on different numbers of
processes and/or threads will always yield the same result. Indeed,
changing the number of processes impacts graph data distribution and
consequently the order in which vertices are processed. Consequently,
coarsening algorithms are likely to produce different coarse graphs,
leading to different partitions.

This option is likely to have adverse impact on performance, since all
non-deterministic multi-threaded algorithms will be disabled. In the
case of Scotch, the multi-threaded matching algorithm for coarsening
will be replaced by its sequential counterpart, whatever the available
number of threads is. In the case of PT-Scotch, point-to-point
messages will be received in a fixed order rather than being processed
on a first-come, first-serve basis.

Setting this flag automatically results in setting the
"-DCOMMON_RANDOM_FIXED_SEED" flag. Users are also strongly advised to
compile without setting the "-DCOMMON_RANDOM_SYSTEM" flag, in order to
avoid any interference with third-party libraries that might use the
operating system pseudo-random generator.


2.9) Point-to-point or collective communications
------------------------------------------------

Since distributed graph vertices can have any initial distribution
across processes, communication rounds are likely to involve all of
the processes in an almost all-to-all scheme. In order to speed-up
running time, most of these communications are performed by means of
asynchronous sends and receives, which allows computations to overlap
with communications. However, for large numbers of processes, this can
lead to the saturation of the communication network of the target
parallel machine. To avoid this, communication consuming routines also
have a collective communication based version. The use of this version
is enabled by default, as it greatly improves scalability for large
numbers of processes. To disable it, set the "-DSCOTCH_PTOP" flag at
compile time.


2.10) MeTiS compatibility library
---------------------------------

In order to ease the adoption of Scotch/PT-Scotch by people who
already developed code based on the MeTiS/ParMeTiS interface, a MeTiS
V3 compatibility library is included in the Scotch package. It
provides stubs for the graph partitioning and ordering routines of
MeTiS/ParMeTiS, but not for the service routines that are comprised
in this package. Consequently, for people willing to use both
libraries, that is, experiment with the graph partitioning features of
Scotch while using the service routines of the genuine MeTiS package,
special measures have to be taken.

A first solution can be to coerce the linker to pick partitioning
routines from the libscotch, and service routines from the
libmetis. This can be done by placing the library names in this
order as arguments to the linker command. Yet, some linkers may still
report an error, as some symbols are multiply defined.

Alternately, the names of the compatibility routines can be changed so
as to avoid conflicts. When the "-DSCOTCH_METIS_PREFIX" flag is set at
compile time, all Scotch versions of the MeTiS routines are prefixed
with "SCOTCH_". Of course, this will require an equivalent change in
the user's application code.

An advantage of the Scotch/PT-Scotch stubs over the genuine
MeTiS/ParMeTiS V3 routines is that they can be available in a 64-bit
version. In this case, all int's that were passed to MeTiS/ParMeTiS
routines must be replaced by 64-bit integer values (even the option
configuration values). However, in this case, one will not be able to
link against the service routines of the genuine MeTiS/ParMeTiS V3
library, as the latter is only available as a 32-bit implementation.


3) Compilation
==============

Once you have performed the configuration of the "Makefile.inc" file,
compile the Scotch distribution by typing "make scotch", or just
"make", in the current "src/" working directory. To compile the
PT-Scotch distribution, type "make ptscotch" in the same "src/"
directory. This can be done in any order. Typing "make scotch
ptscotch" to compile both is equivalent to typing "make ptscotch"
alone, since PT-Scotch requires Scotch.

The most common problem you may encounter when trying to compile
PT-Scotch on a new platform relates to the "dummysizes" and
"ptdummysizes" executables. The purpose of these programs is to
determine, on the target platform, the sizes of the opaque data
structures of Scotch and PT-Scotch, respectively. They have to be
compiled and run before any library function can be compiled. The
sequential case poses no specific problems, as "dummysizes" is always
compiled with the same command as the one used to compile the
sequential Scotch package (hence, "CCD=$(CCS)" when executing "make
scotch"). In the parallel case, "ptdummysizes" has to take into
account the sizes of some MPI data structures, such as MPI_Comm, and
the most common way to have access to this information is to use some
flavor of MPI-aware compilers such as "mpicc" which automatically
refer to "mpi.h". Therefore, "CCD=mpicc" will work for most systems
and MPI implementations. Yet, on some platforms, programs compiled for
parallel execution cannot be run interactively. Moreover,
"ptdummysizes" itself does not contain any MPI calls, as it just wants
to know the sizes of the data structures, and the communication
susbystem of the platform may not want to run it. In any of these
cases, compilation will break. It is possible to solve this problem by
specifying, in the CCD variable of "Makefile.inc", how to compile
"ptdummysizes" sequentially but with knowledge of the location of the
"mpi.h" include file, for instance with the following line: "CCD =
my_sequential_cc -I/path/to/my/mpi/implementation/include/dir/".

If no error occurs, all of the relevant header, library and executable
files will be created and copied to the "../include/", "../lib/" and
"../bin/" directories, relatively to your current "src/" working
directory. Headers, libraries and binaries of Scotch and PT-Scotch can
coexist in these directories without any interference.

Then, typing "make install" will perform a GNU-like installation, with
header, library, binary and man files copied to the "include", "lib",
"bin" and "man" subdirectories of the path specified in the "prefix"
variable, which is set by default to "/usr/local". For instance,
typing "make prefix=/home/myself/usr/ install" will install the
Scotch/PT-Scotch files in a subtree of directory "/home/myself/usr/".


4) Checking 
===========

A set of test programs is available in the "src/check" directory. They
serve as non-regression checks for both sequential and parallel
features of Scotch and PT-Scotch. They can be launched by typing "make
check" and/or "make ptcheck" in the "src/" directory.

In the case of "ptcheck", programs will be run in debug mode; user
action is required (by typing ENTER whenever necessary) for launching
the parallel programs.

One might look at these programs for examples of how to use the Scotch
and PT-Scotch libraries. However, some of these programs test internal
features, and interact with the library through non-standard and
non-documented procedures. It is therefore recommended NOT to imitate
these calling practices and rather to follow the guidelines provided in
the Scotch and PT-Scotch user manuals.


5) Use
======

Users willing to use the features of the sequential (but possibly
threaded) libScotch library have to include "scotch.h" and to link
against the "libscotch" library, plus an error handling package such
as "libscotcherr" or "libscotcherrexit".

Users willing to use the features of the distributed-memory parallel
libPTScotch library have to include "ptscotch.h" (which itself
includes "scotch.h") and to link against both the "libptscotch" and
"libscotch" libraries (in this order whenever order is significant),
plus an error handling package such as "libptscotcherr" or
"libptscotcherrexit".

In the case of complex programs, which may run as sequential programs
but may also call parallel routines, it is necessary to link only once
against a Scotch error handling routine, and this routine cannot call
MPI routines. Hence, the "libscotcherr" or "libscotcherrexit"
libraries must be used. This will not impact the behavior of the
parallel routines, but process numbers will not be displayed in case
of an error.


6) Documentation and use
========================

The Scotch and PT-Scotch user's manuals are available in the "doc/"
directory. They describe how to use the libscotch and libptscotch
libraries, as well as the standalone programs of the Scotch and
PT-Scotch distributions.


7) Note to packagers
====================

Since version 6.0, the Scotch and PT-Scotch packages can be made
independent. The libScotch will not be tied by any dependency against
any MPI package, while the libPTScotch has to depend on the one with
which it has been compiled, in addition to the libScotch package that
it uses.

In versions 5.x, the libPTScotch also contained a modified copy of the
libScotch. It is no longer the case, which will result in lower disk
footprint.

Regarding the use of threads, since Scotch is at the time being  not
dynamically configurable, one has to decide whether to compile it with
threads enabled or not and, additionally, with which number of threads
it will run. Based on the current processor market, I recommend to
compile with -DSCOTCH_PTHREAD_NUMBER=2 (and, of course,
-DSCOTCH_PTHREAD_AFFINITY_LINUX whenever possible). The penalty for
single-thread CPUs will not be too high, while hyper-threaded and
many-core CPUs will benefit from the extra thread.