For a detailed list of the latest changes see the Subversion change log.
SolvableIdeal, and new structures for solvable
 polynomial rings in classes SolvableQuotient,
 SolvableResidue and the corresponding factories
 SolvableQuotientRing,
 SolvableResidueRing. New theme for Ruby rdoc
 documentation. Adaption to a newer version of jruby (1.7.3). Further
 small fixes and improvments.
GBFactory and added new option to select Gebauer &
 Möller critical pair handling in
 GBAlgorithmBuilder.  Switch to DECIMAL128 as default in
 BigDecimal.  Improved
 GreatestCommonDivisorHensel by using integer evaluation
 points and other optimizations.
scaleSubtractMultiple(b, g, a, e, S) to compute the expression b
 xg this - a xe S in one rush.  There is now first
 version of an Android App. The JAS App uses its JRuby
 scripting interface and runs within the Ruby IRB Android App 
 Ruboto.
GroebnerBaseDistributedMPJ for the pure distributed
 version and GroebnerBaseDistributedHybridMPJ for the
 distributed and multi-threaded version. 
WordGroebnerBase
 and new classes WordGroebnerBaseAbstract and
 WordGroebnerBaseSeq. jython and jruby access to
 non-commutative polynomials in WordPolyRing and
 WordIdeal. Improved selection of (commutative)
 Gröbner base algorithm implementations in class
 GBAlgorithmBuilder. For example in case of rational
 number coefficients a fraction free algorithm with optimization of
 the variable order can be requested by gbab.fractionFree()
 .optimize() .build().
Clonable from Element and renamed
 clone() to copy(). New classes for free
 non-commutative associative rings in GenWordPolynomial
 and GenWordPolynomialRing.
CharacteristicSetWu. Unit tests are in
 CharSetTest. jython and jruby script access to
 characteristic set algorithms in methods CS(),
 isCS(), csReduction().  Small fixes and
 improvements.
PolyRing are now
 injecting the polynomial ring variables into the top level
 interpreter environment by default. New class
 GroebnerBaseFGLM to compute a Gröbner base
 according to the "FGLM" algorithm. It computes a Gröbner base
 with respect to a graded term order and then constructs the
 Gröbner base with respect to the requested term order via linear
 algebra in the residue class ring. Changes from '{}' to
 '()' in GenPolynomial to string conversion.
 New launcher shell script jas.  Small fixes, improvements
 and a missing method implemented and in PolyUtilApp.
edu.jas.ufdroot to remove cyclic
 package dependencies again. Improved selection of factorization
 implementations in FactorFactory classes and better
 suited constructors of the factorization implementations.  Small
 fixes and improvements.
PolyGBUtil.  Small fixes and improvements.
GreatestCommonDivisor* classes in the
 edu.jas.ufd package. Fixed ModLong to
 ModInteger conversion. Small fixes, improvements and
 refactorings of methods to right classes.
jas.py in JAS for the
 required methods.  More JRuby examples. Small improvements and
 fixes.
factorsSquarefreeHensel() in class
 FactorInteger. Improved multivariate Hensel lifting in
 class HenselMultUtil.  Small improvements and fixes.
complexAlgebraicRoots() in class
 PolyUtilApp.  Simple isolating interval refinement for
 real and complex roots.  Alternative factoring of univariate
 polynomials over algebraic number fields via prime ideal
 decomposition in class FactorAlgebraicPrim.  Improved
 parsing of complex numbers.  Forced term orders in some situations
 and further small improvements and fixes.
RealAlgebraicNumber and RealAlgebraicRing
 in package edu.jas.application.  New experimental
 RootFactory with methods to compute complex roots for
 polynomials with coefficients in some complex algebraic extension
 field of the rational numbers. Uses the respective classes form
 package edu.jas.root in a recursive setting.
 New generic factorization classes FactorRealAlgebraic
 and FactorRealReal. Small improvement for reduced / minimal
 Gröbner base computation.
ResidueRing. Jruby and Jython versions and examples of
 the extension field builder. Small improvements and bug fixes for
 latest Eclipse and Java 1.7 version.
ExtensionFieldBuilder with methods for algebraic and
 transcendental field extensions.  Improvements in real and complex
 algebraic numbers.  Improved polynomial parser for recursive
 representations. Small bug fixes.
HenselMultUtil for multivariate Hensel lifting.
 Will be used in polyomial factorization in the future.
 Some parts of greatest common divisor using multivariate Hensel lifting.
 The JAS source (r3408) compiles on Apache Harmony 6.0 (r991881). The
 unit tests pass with the exception of test cases involving object
 serialization.
toScript() methods rewritten to reflect the Ruby
 language requirements and to differentiate between Ruby and Python.
 More precise exceptions for modular computations to return also the
 discovered factors.
GenPolynomialTokenizer
 to RingFactoryTokenizer. Some artificial code was
 required to use solvable polynomials as ring elements since solvable
 polynomials cannot implement
 RingElem<GenSolvablePolynomial<C>>.  This
 resulted in some cases in wrong method dispatch for the
 multiply() method due to compiler optimizations. A work
 around to detect and repair this is now implemented in class
 GenPolynomial.
OrderedSyzPairlist. Refactoring of Gröbner base
 classes to optionally use the new pair selection.  Back port of some
 JDK 1.6 constructs to be again compatible with JDK 1.5.  Small
 improvements in Kronecker factor combination in class
 FactorAbstract. Fixed race condition in
 ThreadPool and improved termination detection in
 Terminator.  Fixes in parallel reduced Gröbner base
 computations. Fixed univariate polynomial construction in
 Ideal.  
 
Quotient* to package edu.jas.ufd. 
 Fixed small bugs and cosmetic.
MultiVarPowerSeries 
 and MultiVarPowerSeriesRing. Mora's tangent cone reduction
 algorithm and standard base computation for power series in package 
 edu.jas.ps. Iterator over exponent vectors. 
BigDecimal
 coefficients. Removed the use of the underscore for algebraic number
 coefficients in the polynomial parser. Now every recursive call of
 parse() from a ring factory is triggered by braces which
 can be nested to any depth. Fixed synchronization bug in solvable
 polynomial relation tables and a parallelization bug in parallel
 solvable polynomial Gröbner base computation. Use of unbounded
 thread pools to avoid dead-locks. Added remaining parts for the
 square-free decomposition in polynomial rings of characteristic p
 > 0.  Changed the script representation of AN
 (AlgebraicNumbers).
edu.jas.kern.TimeStatus to provide user feedback for 
 long running tasks via method checkTime().
 Implemented some missing extGB() methods. GBFactory for 
 the selection of appropriate Gröbner base implementations.
 New method isFinite() for all ElemFactorys and usage 
 in SquarefreeFactory.  Added some missing parts for the factorization 
 in polynomial rings of characteristic p > 0 and ideal decomposition.
GBFactory.
 New GBProxy like GCDProxy to run a sequential and a parallel 
 Gröbner base computation concurrently.
 Primitive element computation via normalPositionFor() in
 methods primitiveElement() together with several
 conversion methods convertToPrimitiveElem().  A new 
 index of all algorithms from the book 
 Gröbner bases to their JAS equivalents.
Ideal with methods
 radicalDecomposition(),
 decomposition(),
 primeDecomposition() and
 primaryDecomposition().
 Computation of extension and contraction ideals.
 Unit tests for the decomposition methods.
 Fixed a bug in multivariate polynomial factorization in Kronecker's method.
 
 Fixed a bug in squarefree decomposition in inseparable case. 
 Added NO_THREADS flag to edu.jas.kern.ComputerThreads
 to avoid (some) thread creation for usage in Google app engine.
Ideal with methods
 zeroDimRadicalDecomposition(),
 zeroDimDecomposition(),
 zeroDimPrimeDecomposition(),
 zeroDimPrimaryDecomposition() and
 zeroDimRootDecomposition().  Exact 0-dim ideal real root
 computation and approximation in methods
 PolyUtilApp.realAlgebraicRoots() and
 decimalApproximation(). Small enhancements to Javadoc
 comments.
edu.jas.ufd,
 simplified and improved the factory classes.  Refactorings of
 parallel Gröbner bases computations for solvable polynomial
 rings. Improved logging for distributed Gröbner bases and
 distributed middle-ware.
PrimeList.
 Construction of minimal univariate polynomials in zero dimensional ideals.
 Supersets of complex and real roots of zero dimensional ideals. More unit tests for 
 real and complex roots of univariate polynomials and zero dimensional ideal roots.
 Minor enhancements and fixes.
GroebnerBasePartial.
 Small enhancements: polynomial recursive coefficient parser and a
 matrix parser. Book-keeping of all used polynomial variable names.
 New and improved unit tests.
Complex coefficients via algebraic 
 coefficients in Q(i).
 New classes ModLong and ModLongRing for faster modular arithmetic.
 New interfaces Modular and ModularRingFactory implemented also by
 ModInteger to make both interchangable.
 Improved factorization and serveral refactorings. Factorization mod p = 2 is now implemented.
ComplexRoots, ComplexRootsAbstract, 
 ComplexRootsSturm.
 The implementation provides an exact infallible method which follows the numeric method of Wilf.
 It uses Sturm sequences following the Routh-Hurwitz Method 
 to count the number of complex roots within a rectangle in the complex plane.
MultiplicativeSet, in sub-classes
 polynomials made co-prime in MultiplicativeSetCoPrime, 
 polynomials made co-prime and squarefree in MultiplicativeSetSquarefree
 and polynomials made irreducible in MultiplicativeSetFactors.
 New distributed hybrid Gröbner base computation with new class 
 TaggedMesageChannel to handle multiple message types and partners over 
 one socket connection. Improved object serialization in distributed hash table.
 Adapter updated for JLinAlg version 0.6.
ToRational used for BigRational 
 and RealAlgebraicNumber to remove type case distinctions 
 in Interval.
 clone() removed from Element interface because 
 of compiler changes.
Squarefree, abstract class is
 SquarefreeAbstract.  Other main classes are
 SquarefreeFieldChar0, SquarefreeFiniteFieldCharP 
 and SquarefreeInfiniteFieldCharP.
FactorAlgebraic can now also handle factorizations over 
 multiple algebraic extensions like for example Q(i)(sqrt(2)). 
 Class FactorAbsolute is now also extended
 by FactorAlgebraic, so that absolute factorizations can
 be computed over algebraic extensions of Q. Added new containers for
 absolute factorization results and tests for correct absolute
 factorizations.  More toScript() methods and
 improvements in Jython script interface.  Minor additions and fixes.
ZZ, ZM, QQ, DD, CC, Quat, Oct,
 PolyRing, AN, RealN, RF, RC, LC, SolvPolyRing
 and RR, PS, Vec, Mat for the construction of rings and elements.
 Added generic Complex class and ComplexRing factory. 
 Fixed a programming bug in factorization code.
factory() method to Element interface to have an uniform way to 
 obtain a corresponing ring object.
 Improved RealAlgebraicNumber so that it can be used as polynomial coefficients,
 for example GenPolynomial<RealAlgebricNumber<BigRational>>.
 Real root isolation can now also be used for polynomials with real algebraic coefficients,
 for example RealRootsSturm<RealAlgebraicNumber<BigRational>>.
edu.jas.root during CISIS/ECDS 2009.
 Reached 100.000 lines of Java code.
edu.jas.ring to edu.jas.gb
 and edu.jas.module to edu.jas.gbmod.
Factorization interface with FactorAbstract class for common codes.
 Factorization of univariate polynomials with several coefficient rings: 
 modulo primes in class FactorModular,
 over integers in class FactorInteger,
 over rational numbers in class FactorRational and
 over algebraic numbers in class FactorAlgebraic<C> 
 (where C can be ModInteger or BigRational).
 Multivatiate polynomials are reduced to the univariate polynomials via Kronecker substitution 
 and are therefore not very efficient.
 Refactorings and fixes.
compareTo to be transitive as required by 
 Javas SortedMap implementations.
 Implemented an adaptor package for Apache Log4j to delegate logging calls to native Java logging.
RingElem and RingFactory types 
 in package edu.jas.ps 
 in classes UnivPowerSeries and UnivPowerSeriesRing.
 The implementation follows the "Infinite Streams in Java" paper of D. Gruntz
 in PPPJ2006.
Condition
 and ColoredSystem classes. 
 Conditions consist of an ideal 
 (with lazy Groebner base computation) for the conditions equal to zero 
 and a multiplicative set for the conditions not equal to zero.
 Non-zero condition polynomials are reduced modulo the ideal of 
 condition zero polynomials. 
 The squarefree part from both condition polynomials is used.
 It differs from the MAS implementation by Schoenfeld, Pesch and others 
 by the ideal used to store the zero conditions and some more details. 
long, 
 int (now the default, as seems to be the fastest), 
 short and byte.
 The respective classes are ExpVectorLong, 
 ExpVectorInteger,
 ExpVectorShort and ExpVectorByte.
RGroebnerBaseSeq and RGroebnerBasePseudoSeq.
 Refactorings and fixes.
Product and RegularRingElem.
 Added fraction free pseudo reduction and Groebner bases
 GroebnerBasePseudoSeq.
 Minor refactorings and fixes.
DGroebnerBaseSeq and EGroebnerBaseSeq.
 Added test methods for reducibility and refactored sequential 
 Groebner base implementations.
Implemented noncommutative product for solvable polynomials, together with relation tables. SolvableOrderedMapPolynomial extends OrderedMapPolynomial. RatSolvableOrderedMapPolynomial extends SolvableOrderedMapPolynomial. Interface SolvablePolynomial extends Ordered Polynomial. Some more left multiplication methods, left reduction and left Groebner Bases, twosided Groebner Base test and computation. Pairlist class changed to avoid usage of criterion 4 if running for SolvablePolynomials, also criterion4() method itself checks for SolvablePolynomials.
| run / n | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| first | 3 | 13 | 32 | 92 | 128 | 188 | 274 | 420 | 683 | 1126 | 1795 | 2793 | 4380 | 6741 | 
| second | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 8 | 10 | 13 | 16 | 21 | 27 | 35 | 
Timings in ms on AMD XP 2800+. Computation of (Y^n) * (X^n) with respect to the relation Y * X = X Y - H. In the first run the relation table is populated with the products Y^i * X^i, i = 2,...,n. In the second run the relations are reused, showing almost no computing time anymore for the products.
| run / n | 2 | 3 | 4 | 5 | 6 | 7 | 
|---|---|---|---|---|---|---|
| first | 28 | 94 | 303 | 1234 | 5185 | 24647 | 
| second | 1 | 12 | 107 | 782 | 4569 | 23897 | 
Second example shows the computation of ( Xa + Xb + Xc + Ya + Yb + Yc + Ha + Hb )^n in U(sl_3). Since in the relation table only products of two variables are stored, the improvement is minimal (for low n).
| # Threads CPUs | # JVMs | time (sec) | #put | #remove | % total | 
|---|---|---|---|---|---|
| 1, seq | 1 | 160.2 | 70 | 327 | 13.5 | 
| 1, par | 1 | 157.0 | 70 | 327 | 13.5 | 
| 2, par | 1 | 82.2 | 72 | 329 | 12.7 | 
| 1, dist | 1 | 177.2 | 77 | 334 | 11.4 | 
| 2, dist | 2 | 92.2 | 90 | 347 | 8.6 | 
| 4, dist | 2 | 56.2 | 112 | 369 | 5.9 | 
| 8, dist | 2 | 58.9 | 255 | 516 | 1.5 | 
| 4, dist | 4 | 51.2 | 117 | 374 | 5.5 | 
| 6, dist | 4 | 43.7 | 129 | 386 | 4.6 | 
| 8, dist | 4 | 62.9 | 259 | 519 | 1.5 | 
Timings taken on a 16 CPU Intel Xeon SMP computer running 
   at 2.7 GHz and with 32 GB RAM. 
   JVM 1.4.2 started with AggressiveHeap and UseParallelGC. 
   
   #JVMs = number of distinct Java virtual machines.
   #put = number of polynomials put to pair list.
   #remove = number of pairs removed from pair list, 
             i.e. after application of criterions, 
             but including nulls up to now.
   % total = per cent of removed pairs from total pairs generated,
             #remove / ( #put * (#put-1) / 2 ) * 100.
| # Threads CPUs | # JVMs | time (sec) | #put | #remove | % total | 
|---|---|---|---|---|---|
| 1, dist | 1 | 24726.2 | 140 | 781 | 8.0 | 
| 2, dist | 2 | 12356.1 | 165 | 806 | 5.9 | 
| 4, dist | 4 | 6859.3 | 218 | 859 | 3.6 | 
| 8, dist | 4 | 7465.1 | 411 | 1054 | 1.2 | 
| 8, dist | 8 | 6412.9 | 344 | 986 | 1.6 | 
| 8, dist | 8 | 7173.3 | 399 | 1041 | 1.3 | 
Overhead for distributed variant is about 10% in Katsura 6 (G). Distributed 1 means one distributed process is running for the reduction of S-polynomials. There is always a master process handling polynomial input / output, setup and management of distributed workers and handling of the pair list. Communication between master and workers is always via TCP/IP with object serialization, even if running on one computer.
New classes implementing a distributed hash table to hold the polynomials in distributed GB. Index of polynomials in Pairlist is used as hash key. Communication is now using message types GBTransportMess. Now polynomials are only transported once to each reducer since only polynomial hash indexes are transported. Distributed list is asynchronous and late updated, so some duplicate H-polynomials (head terms) could be (are) produced. Solution by local put to hash table with dummy index? Timings are not dramatically better.
Todo: check reduction algorithm to use later arriving polynomials.
-Xms200M -Xmx400M -XX:+AggressiveHeap -XX:+UseParallelGCMemory must be adjusted with respect to your situation.
Seperated versions with Pair Sequence Respecting Order (PS) and normal versions. PS versions try to keep the order of reduced polynomials added to the ideal base the same as in the sequential version. Normal versions now running OK on parallel computer with the right JVM options. Refactoring with Eclipse (organize imports, static methods).
| # Threads CPUs | Katsura 6 TO(G) load* | Katsura 6 TO(G) empty* | Katsura 7 TO(G) load* | Katsura 7 TO(G) empty* | 
|---|---|---|---|---|
| seq | 184.5 | 153.3 | ||
| 1 | 181.5 | 4% / 159.7 | 28418.6 | |
| 2 | 118.6 | s2.02 / p2.11 / 75.6 | p2.06 / 13760.0 | |
| 4 | 76.8 | s3.79 / p3.95 / 40.4 | 6256.9 | p4.56 / 6225.1 | 
| 8 | 43.2 | s7.19 / p7.49 / 21.3 | 3240.7 | p8.56/ 3318.8 | 
| 10 | 42.5 | |||
| 12 | 40.5 | 2288.1 | p9.90 / 2868.4 | |
| 14 | 31.2 | |||
| 16 | 51.9 | s8.19 / p8.54 / 18.7 | 5376.4 | p12.59 / 2256.1 | 
Timings taken on a 16 CPU Intel Xeon SMP computer running 
   at 2.7 GHz and with 32 GB RAM. 
   JVM 1.4.2 started with AggressiveHeap and UseParallelGC. 
   
  *) timing taken with other load on the CPUs.
  +) timing taken with no other load on the CPUs.
   
   Speedup: s = relative to sequential, 
            p = relative to parallel with one thread / CPU.
   
   Scaling from 8 to 16 CPUs is bad, but also observed on 
   non CA / GB Examples (Java and C/FORTRAN).
| N vars = N+1 | TermOrder | Seconds | TermOrder | Seconds | 
|---|---|---|---|---|
| 7 | G | 32044.204 | L | |
| 6 | G | 112.641 | L | |
| 5 | G | 4.195 | L | |
| 4 | G | 0.431 | L | 11.650 | 
| 3 | G | 0.153 | L | 0.310 | 
| 2 | G | 0.031 | L | 0.032 | 
putParallel(), removeParallel() and 
  helper methods. Sequence numbers are generated and reduced polynomials 
  are only put to the pair list if corresponding pair number is in 
  correct (sequential) sequence. 
  The ordered list / queue pairsequence (TreeMap/SortedMap) 
  keeps track of the polynomials not yet put to the pairlist.
  ExecutableServer) for remote execution 
  of objects implementing the RemoteExecutable interface.
  New setup for the distributed computation of GBs: the GB master now sends the client code to some ExecutableSevers based on a maschine file with host and port infos about the distributed environment.
Improved the PolynomialTokenizer so that it can read almost unedited
  old MAS GB input files: ** exponents and parenthesis 
  around polynomials. 
  Lines starting with # are treated as comments.
  Comments (* *) and parenthesis within polynomials are 
  still not supported.
  
Implemented a common driver for GB computations RunGB.
  Sequential, thread parallel and distributed computation can be selected
  by command line parameters. The input is taken from a file. The number 
  of threads respectively the number of distributed clients can be specified.
  For distributed execution the host and port information is taken from 
  a maschines file.
  
Usage: RunGB [seq|par|dist|cli] <file> #procs [machinefile]
Added methods putCount() and remCount()
  in OrderedPairlist to count the number of polynomials
  put and get from the pair data structure.
  
| # Threads | 1 seq | 1 par | 2 par | 2 par | 3 par | 4 par | 5 par | 1 dist | 2 dist | 3 dist | 4 dist | 4 dist | 4 dist | 5 dist | 
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| # put | 22 | 22 | 43 | 26 | 28 | 28 | 28 | 22 | 25 | 28 | 37 | 40 | 33 | 27 | 
| # remove | 25 | 25 | 61 | 30 | 32 | 32 | 41 | 26 | 33 | 42 | 47 | 61 | 54 | 69 | 
Timings @ 500 MHz on one CPU and one maschine and log4j level INFO are: 
  ca. 2.5 - 3.5 seconds for sequential GB,
  ca. 2.5 - 6 seconds for parallel GB,
  ca. 5.5 - 9 seconds plus 5 seconds sync time for distributed GB. 
  Network shuffling of polynomials seems to account for 3 seconds in 
  this example.
  
Problem uncovered: the distributed version of GB needs an avarage of 5 seconds to sync with all clients (on one maschine). This is way to much for execution times in the range of 2 to 8 seconds.
Redesign of DistributedList, now using TreeMap to keep the list 
  entries in proper sequence. As key a natural number is used, which is 
  assigned by the server to successive add() requests.
  The server now also holds a copy of the list by itself. So the 
  retransmission of list elements to late arriving clients is possible.
  This doubles the space required to store polynomials, but removes 
  initial delays to sync all clients to receive all list elements.
  
  By retransmission the DistributedList synchronization delay during 
  DistributedGB could be removed.
  However the problem of about 5 seconds delay in startup 
  of DistributedGB still remains. It is not visible where and why this
  delay occurs.
  
  Further improvements would be the removal of list elements or the 
  clearing of the list.
  Next steps could be distributed HashMap or TreeMap.
  
  An important improvement would be to keep serialized copies of the 
  list elements (polynomials) at the server and to 
  avoid many time serialization during broadcast.
  
mpirun,
  a daemon to run on a distributed system to work with the launcher,
  solvable polynomials and non-commutative GBs.
With one thread the time is 30.6 h. Besides the better CPU speed, this makes a 5 % improvement on JDK 1.4 compared to the older timings from a JDK 1.3 and the new polynomial implementation.
Multiplication with ordered polynomials is about 8-10 times faster than the multiplication with unordered polynomials. Also the multiplication with semi-ordered polynomials (LinkedHashMap) with orderpreserving addition is about 7-8 times slower than multiplication with ordered polynomials.
All implementations are based on Map interface and classes. The Map maps exponent vectors (from some monoid) to coefficients (from some domain). This is in sync with the mathematical definition of multivariate polynomials as mappings from some monoid to some domain. Term orders are represented by a TermOrder class which provides the desired Comparator classes for the SortedMap implementation.
  However the merging add/subtact implementation is a factor of 
  2 slower than the TreeMap implementation. 
  Complexity for a+b is 
  2*(length(a)+length(b)) 
    for access and merging pre sorted polynomials and 
  
  2*length(a)+length(b)+length(b)*log2(length(a+b)) 
    for TreeMap clone, access and insertion.
  
  The merging multiplication implementation is by a factor of 
  10 slower than the TreeMap implementation. 
  Polynomial size was ~100 terms and the product contained ~8000 terms.
  Complexity for a*b is 
  
  lab = length(a)*length(b) coefficient multiplications for both implementations
  
  plus 2*length(a*b)*length(b) for merging summands, respectively 
  
  plus length(a)*length(b)*log2(length(a*b)) for TreeMap insertion.
  Since for sparse polynomials length(a*b) = lab, the TreeMap complexity 
  is asymptotically better in this case:
     2*length(a)*length(b)*length(b) =>= length(a)*length(b)*log2(length(a*b))
  
  For dense polynomials with length(a*b) ~ length(a)[+length(b)], then 
  the LinkedHashMap complexity is asymptotically better:
  
     2*length(a)*length(b) =<= length(a)*length(b)*log2(length(a*b))
  
Parallel computations with the Rose example are at 18 h with 4 threads on 2 Pentium 4 @ 2.4 GHz hyperthreading CPUs. With one thread the time is 40 h.
Does this influence the validity of criterion 3? Access to pairlist is synchronized. Pairs are marked as reduced as soon they are taken from the list. But the algorithm terminates only after all reductions of pairs have terminated. So criterion 3 holds.
New implementation of parallel version of GB. Removal of pairs is now also in parallel. But ordering of pair insertion is no more preserved
Timings are more stable and slightly better than that of sequential GB.
Todo: unit tests, comments, ...
Improved parallel version of GB.
Todo: CVS, comments, polynomial implementation using LinkedList, parallel GB simplify
With the improved algorithm the running time of the parallel GB becomes more stable and not slower than the sequential GB. However there is still no significant speedup.
| # Threads | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 16 | 
|---|---|---|---|---|---|---|---|---|---|
| # Reductions | 25 | 25 | 27 | 25 | 25 | 25 | 25 | 25 | 25 | 
| # Threads | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 16 | 
|---|---|---|---|---|---|---|---|---|---|
| # Reductions | 22 | 24 | 30, 28, 24, 29 | 28 | 29 | 42 | 32 | 32 | 37 | 
    parallel results: 
    Trinks 7: mas 0.598 sec, jas 0.918 sec, jas par 0.955 sec 
    Trinks 6: mas 26.935 sec, jas 3.211 sec, jas par 3.656 sec 
    mas: including startup and gc time,
    jas: excluding startup of jvm and including gc time,
    jas par on single processor
    timing on P-3@450
    
implemented edu.jas.arith.BigInteger which implements Coefficient, tested with IntPolynomial which extends Polynomial
todo: alternative Implementations, cleanup RatPolynomial, parallel GB, conversion RatPolynomial <--> IntPolynomial
    second results (with new criterion 3 in jas): 
    Trinks 7: mas 0.598 sec, jas 1.159 sec 
    Trinks 6: mas 26.935 sec, jas 6.468 sec 
    mas: including startup and gc time,
    jas: excluding startup of jvm and including gc time 
    
    third results (with new criterion 3 in jas and GBminimal): 
    Trinks 7: mas 0.598 sec, jas 0.918 sec 
    Trinks 6: mas 26.935 sec, jas 3.211 sec 
    mas: including startup and gc time,
    jas: excluding startup of jvm and including gc time 
    timing on P-3@450
    
this makes for a factor of 8-9 better, all tests with output to files, startup of JVM is approx. 1.0-1.2 sec, most time is spent in BigInteger:
java -Xrunhprof:cpu=times,format=a CPU TIME (ms) BEGIN (total = 136) Thu Jan 2 18:33:53 2003 rank self accum count trace method 1 15,44% 15,44% 596610 21 java.math.MutableBigInteger.rightShift 2 13,24% 28,68% 582132 15 java.math.MutableBigInteger.difference 3 12,50% 41,18% 612760 19 java.math.MutableBigInteger.getLowestSetBit 4 9,56% 50,74% 2 9 java.lang.Object.wait 5 9,56% 60,29% 5271 22 java.math.MutableBigInteger.binaryGCD 6 6,62% 66,91% 612760 23 java.math.BigInteger.trailingZeroCnt 7 5,88% 72,79% 592152 18 java.math.BigInteger.bitLen 8 5,88% 78,68% 6018 20 java.math.MutableBigInteger.binaryGCD 9 5,15% 83,82% 578887 25 java.math.MutableBigInteger.normalize 10 4,41% 88,24% 550992 24 java.math.MutableBigInteger.primitiveRightShift 11 4,41% 92,65% 1 10 java.lang.Object.wait 12 3,68% 96,32% 582132 12 java.math.MutableBigInteger.compare 13 0,74% 97,06% 35965 13 edu.jas.poly.ExpVector.EVILCP 14 0,74% 97,79% 11612 14 java.math.BigInteger.divide 15 0,74% 98,53% 5866 11 java.math.MutableBigInteger.divide 16 0,74% 99,26% 9032 16 java.math.MutableBigInteger.divide 17 0,74% 100,00% 9032 17 java.math.BigInteger.divide CPU TIME (ms) END
    first results (without criterion 3 in jas): 
    Trinks 7: mas 0.598 sec, jas 1.373 sec 
    Trinks 6: mas 26.935 sec, jas 30.935 sec 
    mas: including startup and gc time, 
    jas: excluding startup of jvm and including gc time.
    timing on P-3@450
    
Implemented and testet ExpVector based on Javas int arrays.
Implemented and testet RatPolynomial based on Javas TreeMap. 
       static methods: DIRPDF, DIRPWR via toString, DIRPON, DIRPMC, 
       DIRPPR, DIRPSM, DIRRAS.
       Consider replacing keySet/get by entrySet/getval where appropriate.
       Can there be an generic Polynomial class?
    
This will be the end of list processing for Jas.
   DIPRNGB needs DIRPDF, DIRPWR, DIRPON, DIRPMC, DIRPPR, DIRPSM.
   These need RNDIF, RNDWR, RNINT, RNSIGN, ISRNONE, RNONE, RNZERO,
         RNINV (and DIRPRP), RNPROD, RNSUM.
   
Last modified: Mon Apr 29 20:46:06 CEST 2013