Patent Application: US-63634209-A

Abstract:
xml parsing can be improved using multicore cpus , enhancing its suitability for scientific data . one approach is to divide the xml document into equal - sized chunks , and parse each chunk in parallel . xml parsing is inherently potentially dependent on all preceding characters . the skeleton , an outline of the document generated during a fast preparse , is used to guide full parallel parsing . the preparse is a sequential phase that limits scalability , and this phase can also be parallelized using a meta - dfa mechanism . for each state q of the original preparser the meta - dfa incorporates a complete copy of the preparser state machine as a sub - dfa which starts in state q running multiple instances of the preparser simultaneously when parsing a chunk , with each possible preparser state at the beginning of a chunk represented by an instance . by pursuing all possibilities simultaneously , the meta - dfa allows each chunk to be preparsed independently in parallel .

Description:
preparsing is a sequential stage before the parallel parsing , and limits the scalability of the pxp technique to about four cores . by parallelizing the preparsing stage , additional improvements in performance may be obtained . fundamentally , preparsing is sequential because the state of the preparser at the beginning of each chunk cannot be determined without preparsing all preceding chunks . such limitation cannot be eliminated , but can be addressed in a manner such that parallel preparsing is still feasible . a model of xml parsing is initially defined which includes the parallel preparser . it is assumed that an xml parser is based on a deterministic , finite state automata ( dfa ). at every state , a number of transitions can be made depending on the next input character . attached to each transition is an action of some kind . what the action actually does in the model itself is not directly defined . rather , each specific xml parser ( or preparser ) will have a different set of actions , and may have different implementations of those actions . as discussed above , the technology is not limited to xml parsing , and may be readily applied to other problems having a similar character . for example , actions may create dom objects , manipulate data structures , etc . in the present model , however , actions are abstract . note that xml is not regular , thus cannot be formally recognized by a dfa . in practice , however , most xml parsers are based on some state machine , and use structures like stacks to handle non - regular aspects . where q is a set of states , σ is an alphabet of possible input characters , a is a set of actions , t is a transition function , and q 0 is the start state . the special action ν is a no - op action . the transition function maps from the current state and input character to a new state and an action : as the machine executes , it enters a sequence of states . as it makes transitions , it also encounters a sequence of actions . in fig1 , an xml fragment is shown , and the corresponding execution for the xml processing automaton is shown in fig1 . since each chunk must be processed in parallel , before the previous chunk has been completely processed , the true state before the first input character is unknown . suppose a thread has now been assigned an xml chunk , starting with the character “ b ”. in the xml string shown in fig1 , initially the true automaton state could be 6 , 1 , or 7 . when the automaton encounters the first “ r ” character , it will move from state 1 to state 3 , and perform the start action . the transition from state 0 to state 2 , for example , is taken on the & gt ; character , and has the end action . one approach to processing this data would be to use some kind of searching in the area near the beginning of each chunk , to attempt to unambiguously determine the grammatical state of the beginning of the chunk . for example , an algorithm could backtrack from the beginning of the chunk to find a & lt ; character , indicating the beginning of a tag . unfortunately , the “& lt ;” character is also valid within a comment ( or a cdata section ), where it does not indicate the beginning of a tag . it could be assumed that this is unlikely , and proceed as if the first “& lt ;” before the start of the chunk does in fact indicate the beginning of a tag . eventually , after all preceding chunks have been parsed , the state at the beginning of the chunk would be positively determined . if this determination is that the beginning of the chunk is actually within a comment , the chunk would then require reprocessing with the true initial state . this would be expensive with respect to the goal of speeding processing , but since the “& lt ;” character is presumably not commonly within a comment , the cost would not be incurred very often . such techniques are essentially a form of speculative execution . the dfa state at the beginning of a chunk is unknown at the start of execution , but certain assumptions can be made . if the assumptions are wrong , a performance penalty is incurred . but if the assumption is usually correct , then the average performance may be improved . this form of speculative processing could be implemented as suggested , by adding code to search , backtrack , etc . it would be complex and error - prone , however . another approach which may be simpler to implement , is to simply assume that the true state at the beginning of a chunk is the most commonly occurring state , and begin execution in that state . for example , given the automaton in fig1 , if expected documents mostly contain character content , the true initial state for a chunk is likely to be state 0 . the automaton is then executed as far as possible . if an error is encountered , then either the assumption was incorrect , or the input is invalid . in either case , the thread must then wait for all preceding chunks to be processed , before reprocessing the chunk in the definitively true state . if no error was encountered , then the thread also waits for all preceding chunks to be completed . however , as long as the preceding chunk finishes in the state assumed for the beginning of this chunk , then no reprocessing is needed . as long as the assumption is usually correct , average performance will be improved . the above approach amounts to taking a single guess at the initial state , processing the chunk , then waiting for the preceding thread to pass the positively determined state . if the guessed state was wrong , then the thread must reprocess the chunk using the correct initial state . thus , wrong guesses can result in sequential execution . this speculative processing technique can be used in conjunction with the meta - dfa described below . the meta - dfa construction transforms the original dfa to a meta - dfa whose transition function runs multiple instances of the original dfa in parallel via sub - dfas . for each state q of the original dfa , the meta - dfa includes a complete copy of the dfa as a sub - dfa which begins execution in state q at the beginning of the chunk . the meta - dfa thus theoretically pursues simultaneously all possible states at the beginning of the chunk . since the meta - dfa is also a dfa , the simultaneity is strictly conceptual , and can still be executed by a single core . as stated above , in the event that concurrent execution an evaluation of all possible states is not possible , it may be possible to estimate the most likely states , and evaluate those first or in a manner likely to produce an output soonest . if this estimate is correct , and this is recognized , further processing of incorrect state parallel tasks may be avoided . each state of the meta - dfa is an element from the cartesian product of the states of the original dfa . the start state of the meta - dfa is simply a vector where the first element is the first dfa state , the second element is the second dfa state , etc . the meta - dfa construct is now precisely defined . though the meta - dfa is also a dfa , for clarity , states of the meta - dfa are referred to as meta - states , and the actions of the meta - dfa as meta - actions . actions of the sub - dfa may be referred to as subactions when necessary . when not qualified with sub - or meta -, it is assumed herein that the meaning is clear from context . let n =| q |. then p is the cartesian product ( q ∪ δ ) n , a is the cartesian product ( a ∪ δ ) n . the start metastate p 0 =[ q 0 , . . . , q n - 1 ]. the transition function τ is defined as , for all cεσ : in other words , within the metastate vector , a sub - dfa goes from state q j 1 to q k 1 on character c , iff the original dfa also had t ( q j 1 , c )= q k 1 . the states of the original dfa are augmented with a special dead state , δ . this indicates in the metastate that the original dfa had no transition on this input character . once a sub - dfa enters the dead state , it can never exit , indicating that the sub - dfa encountered invalid input . fig2 shows a meta - dfa that has been constructed from the dfa in fig1 . as shown in fig2 , the process starts from the initial metastate vector [ 0 , 1 ], and considers every possible input character . this forms two new meta - states [ 1 , δ ] and [ δ , 0 ]. ( δ is the dead state and δ on any input will transition to itself .) the meta - dfa construction is continued on each new metastate . when the meta - dfa makes a transition , it also executes a meta - action . the meta - action is a vector of subactions , one for each sub - dfa . these subactions are the same as the original action that would have been taken by the original dfa . in the original dfa , the actions operated on some kind of whole parser state , such as the dom data structures that it might be constructing . note that use the word state is occasionally used herein in its more general sense , rather than to denote the state of an automaton . the meta - dfa , however , is pursuing multiple possibilities simultaneously or concurrently , and thus an instance of the meta - dfa must maintain multiple copies of this originally single state . therefore , each original action must now be executed as a subaction within a separate context , corresponding to each sub - dfa . furthermore , these actions may need to be modified to handle the fact that preceding actions may not have been executed because they were in a different chunk . each sub - dfa essentially begins execution on an empty parser state within its context . for example , an action to add an element to a parent cannot assume that the parent exists . this additional code logic could be complex in a full xml parser , but turned out to be relatively simple since the meta - dfa only needed to be applied to the much simpler preparser . if a sub - dfa enters the dead state , that means that its context and execution have died . a live context and execution thus correspond to a sub - dfa that is not in the dead state . as an example , fig3 shows one transition of a meta - dfa , which has two sub - dfas , sub - dfa , and sub - dfa . internally , the meta - dfa maintains separate executions for these two sub - dfas . when the meta - dfa makes a transition from metastate m2 to m3 on encountering the & gt ; character , sub - dfa , makes a transition from state 1 to 3 , and sub - dfa makes a transition from state 4 to 0 . the subactions are action_one , executed in context i , and action_two , executed in context j . the execution of a meta - dfa on a character sequence of length m , and its relationship to sub - dfas is shown in fig4 . seen from sub - dfas , the meta - dfa transitions from a vector of states to another vector of states . the transition function τ of the meta - dfa accepts an input character c j ( jε [ 0 , m − 1 ]) and transitions to another vector of states , with the destination state in each vector element determined by the original transition function t on the same input character c j . in the graph , q i k , l ( i k , l ε [ 0 , n − 1 ], kε [ 0 , n − 1 ], and lε [ 1 , m ] is the sub - dfa state , i k , l is an indexed variable , k is the index of the sub - dfa , l is the step number of the meta - dfa execution . after all the chunks are parsed by separate threads , each running an instance of the meta - dfa , the complete , true execution of the original dfa can be determined . since the thread for the first chunk can run the original dfa unambiguously in the start state , the ending state of the first chunk is definite . this ending state is then used to select the true execution of the second chunk . the ending state of the true execution of the second chunk is then used to select the true execution of the third chunk , and so on and so forth . based on this propagation of states , in some cases it is possible to estimate during evaluation of a chunk , what the end state will be , and this information used to control execution of subsequent meta - dfas . clearly , if the task is sufficiently complex such that earlier chunks are completely processed before later chunks commence processing , then the state vector - space which needs to be speculatively explored for the later chunks is correspondingly limited . the number of metastates is potentially very large , but most of the metastates are unreachable , and thus do not need to be actually generated . furthermore , the meta - dfa is used for preparsing only , which is quite small . the meta - dfa used in the example reported below had 611 states . this number has been found to be manageable . this is discussed in section 5 . 1 . the selected chunk size may be optimized based on an estimated complexity of the chunk , which may be derived from a history of analysis of documents of the same type , adaptive analysis of other chunks , or even a preliminary analysis of the chunk itself or the document as a whole . that is , the time for processing a chunk is not directly related to its length , though on a statistical basis this may be true . based on this determined or predicted complexity , an optimization may be performed to define a chunk size such that the number of parallel processes which must be run for each chunk , based on the number of possible starting states to be considered , the number of possible starting states from which no valid transition is possible , the number of resources available for parallel processing ( e . g ., processing cores ), and the possibility of avoiding non - productive processing based on false starting states if earlier results are available . thus , assuming that the goal is to obtain the preparsed results the fastest , and that there is no incremental cost for consumption of computing resources , then the optimum chunk size is the one which is small enough to allow a reasonable amount of parallelization of relatively low complexity tasks , to provide a speedup of processing , while being large enough to avoid an undue proliferation of non - productive tasks and a large post - processing task of addressing remnants . te meta - dfa construction was implemented as a program that takes an input file describing a dfa with transition actions , and output a source code fragment that could be used within a c ++ state machine to execute the meta - dfa . actions in the input file are output in the meta - dfa code fragment as macro invocations with a single parameter indicating the context . for example , a start action in the input dfa would be output as start ( 2 ) to indicate that the start action should be executed now within the context of sub - dfa 2 . thus , the computer readable program instructions are stored in a computer readable medium , such as a semiconductor or magnetic memory , and supplied to a processor to implement the method . in so doing , the apparatus assumes a special purpose . likewise , the algorithm implemented by the special purpose apparatus performs a transformation on the input , yields a qualitatively different form of information , though the original content is carried through . therefore , the processing results of the special purpose apparatus are similar or identical to a traditional system , while the internal operation is different and the output generated with shorter latency . the algorithm to generate the meta - dfa is similar to the subset construction algorithm to convert nfas to dfas . one difference , however , is that a set of states cannot be used , but rather a vector must be used . this is because separate execution contexts for each sub - dfa must be maintained . the initial state of the meta - dfa is [ 0 , 1 , 2 , . . . , n − 1 ]. a todo_list is maintained , which is initialized with only the initial state of the meta - dfa . on each step , the algorithm takes out the head element of the todo_list , and then for each possible input character , forms the next metastate according to the transition function definition above for t . then , if the next metastate is new , it is added to the end of the todo_list as new work to do . the process proceeds until the todo_list is empty . the pseudo code of the meta - dfa generation is given in algorithm 1 . since the original dfa is finite , the meta - dfa is clearly also finite . the construction algorithm is thus guaranteed to terminate . once the algorithm has terminated , the metastates can be enumerated and assigned a state number . execution of the meta - dfa is thus the same as a dfa . to visualize the meta - dfa construction process , a very simple dfa shown in fig1 is used as an example , and its generated meta - dfa is shown in fig2 . to apply the meta - dfa approach , the preparser is first modeled as a state machine as a dfa with actions on the transitions . because the skeleton only contains the beginning and ending of each element , the dfa for the preparser only needs to recognize enough to support this distinction . clearly , if the preparsing task were different , other attributes could be analyzed . furthermore , because the preparse is followed by a full parse , the preparse is allowed to accept ill - formed xml . such xml will be rejected later in the full parse . as a result , the dfa can be quite simple , and is shown in fig5 . the work in [ 6 ] showed that preparsing is an order - of - magnitude faster than full xml parsing . the xml preparser is responsible for finding the beginning and ending of each element , and consequently its dfa requires only two actions , start and end . the start action is used to signify the start of an element , while the end action signifies the end of an element . referring to fig5 , the start action occurs on the transition from state 1 to state 3 . the end action occurs on the transition from state 2 to state 0 , and from state 4 to state 0 . start create a new skeleton item with the start position set to the start of the element . push a reference to the item onto the stack . end edit the item on the top of the stack , filling end position of the represented element , and then pop the stack . the dfa is then represented as an input file to the meta - dfa generating program . the actions are specified simply as strings . the transformation outputs a c ++ code fragment , with the actions carried along as macro invocations . the corresponding context number is given as an argument to the action invocation , so that it can be used within the action definition to isolate the action within the true context . also , the resulting meta - dfa has 611 metastates . when preparsing a well - formed , complete xml document , the stack is always empty at the end of the document . furthermore , during preparsing of complete documents , the preparser uses the stack to keep track only of start - tags for which the corresponding end - tags has not yet been encountered . because an end - tag can never appear before its corresponding start - tag , the stack never contains items with end - tags for which the corresponding start - tag is missing . for data - parallel preparsing , however , each thread preparses in parallel on a chunk that may not be well - balanced , since the chunk divisions occur at arbitrary positions . the division will result in xml fragments with unbalanced start and end - tags . thus , after a chunk has been preparsed , the stack could contain references to items for which the end - tag , has not yet been encountered , or references to items for which the end - tag was encountered , but not the start - tag . the items in the stack are unpaired , because the corresponding start - or end - tag is in the preceding or following chunk , respectively . this non - empty stack is called the stack remnant . handling unpaired end - tags requires modifying the skeleton generation logic so that if an end - tag is encountered while the stack is empty , its corresponding start - tag is assumed to be in the preceding chunk . a new skeleton item is still created , but without the start position . because this logic is encapsulated in the actions , which are given in the generated meta - dfa code fragment as macro invocations , only the macro definitions corresponding to the actions need to be changed . since actions are executed within a separate context for each sub - dfa , each action must execute on the stack and skeleton for that context . the redefined actions are : start ( i ) create a new skeleton item with the start position set to the start of the element , and push a reference to the item onto the stack . all operations within context i . end ( i ) if the stack is empty , create a new skeleton item with the end position set to the end of the element , and push a reference to the item onto the stack . otherwise , check whether or not the top item on the stack has its element end position set . if set , create a new skeleton item with the end position set to the end of the element , and push a reference to the item onto the stack . if not set , edit the top element on the stack , filling in its element end position , then pop stack . all operations within context i . since chunks only contain a portion of the xml document , the skeleton resulting from the preparse of a single chunk is incomplete , and is known as a skeleton fragment . the references on the stack remnant also indicate that the referent items are also incomplete . the relationship between the skeleton fragment and the stack remnant is shown in fig6 . fig6 shows the relationship between an xml chunk , its skeleton fragment , and the stack remnant . the stack remnant contains references to items in the skeleton . on the right side , is shown the corresponding xml . arrows from the character location in the xml chunk point to the corresponding position information in the skeleton item . as can be seen , skeleton items which are missing either start or end position information correspond to unpaired xml tags . after using the meta - dfa to preparse a chunk , the results shown in fig7 are obtained . as you can see , some of the contexts will still be live . these contexts will have an associated skeleton fragment and stack remnant . the live context corresponding to the actual state at the beginning of the chunk will be the true context . each context is in an equivalence class , which is used to remove static duplicates . each context normally has a separate skeleton , but contexts within an equivalence class instead only have a single skeleton , which is referenced via a pointer . this can be seen in context 3 , for example . a similar situation exists for the stack . when all chunks have been preparsed , the true execution can be unambiguously determined . the execution of the first chunk is already fully determined , since the beginning of the first chunk must be the start of the document . the final state of the first chunk is thus used to select the correct context from the second chunk . the process continues until all the correct contexts are obtained . from this fully determined execution , the true stack remnants and skeleton fragments are extracted from the appropriate contexts . once the true context is obtained from each chunk , the skeletons are then merged , as shown in fig8 . the merging proceeds by matching the items referenced in the stack remnants , and updating items that match . a match here means that it is determined that a given item with a missing end - tag should be paired with an item with a missing start - tag . items 1 - 2 match , because the left - side item is missing the end position , while the right - side item is missing the start position . because item 3 does not match , the remaining items are copied to the merging stack on the left . a merging stack is maintained as the process proceeds . initially the merging stack is just the stack from the first chunk . as the process proceeds , stack remnant from each chunk ( from the true context ) is examined , starting from the top of the merging stack , and the bottom of the other , proceeding item by item , going down the stack on the merging stack and up the stack on the other . after merging the skeletons from all chunks , the merging stack must be empty , if the document is well - formed . to demonstrate that the technique can be applied to xml containing scientific data , molecular information from the protein data bank ( pdb ) [ 10 ] was used , which is generally representative of a broad class of xml used in scientific applications . fig9 shows the structure of the test xml document , named 1kzk . xml . the experiments were run on a sun e6500 with 30 400 mhz us - ii processors , running solaris 10 . every test is the average of ten runs , with a warm file cache . the programs are compiled by g ++ 4 . 0 with the option − o3 , and the libxml2 library was version 2 . 6 . 16 . the graphs shown in the figures used a file sized to 34 mb , but sizes up to 56 mb were tested , which did not produce any significant difference . below about 64 kb , per document parallel overheads start to dominate the code . the optimization of these smaller documents may be important for other applications . in theory the meta - dfa generation algorithm may lead to a state explosion . however , the input dfa is small , since it is used only for preparsing , and furthermore , during the meta - dfa generation , most of the metastates will transition to the dead metastate . the meta - dfas are generated for a variety of dfas designed for parsing xml , as shown in table 1 . the results also show that different dfas will result in different sizes of meta - dfas , and that the number of states in the resulting meta - dfa is not just a function of the number of states in the dfa . this is in part because most of the new created metastates will just have a transition to the dead metastate . thus , most metastates are unreachable , and never generated . the meta - dfa only needs to be generated once for a given xml parser , and is done entirely offline , and so does not affect actual xml parsing performance . in theory , a large number of meta - dfa states could result in overflow of the instruction cache and cause performance degradation , but this was not seen in practice . this is because most xml documents only require the meta - dfa to use a small number of the total possible metastates . the large majority of metastates are never used for most documents . intuitively , this is because most possible interpretations of an xml chunk are quickly invalidated as more and more of a chunk is processed . for example , encountering a & lt ; in a chunk means that what follows is almost certainly a start - or end - tag . fig1 shows the speedup of the parallel preparser relative to the non - parallel preparser . the results show that parallel preparsing can indeed take advantage of multiple processors , and scales well to 30 processors . the drop - off after 30 is because the machine only has 30 processors . the performance of the full pxp parsing was then tested . fig1 shows the total wall - clock time spent by full parsing with parallel preparsing compared to sequential preparsing . fig1 shows the corresponding speedup graph comparing pxp with parallel preparsing against pxp with sequential preparsing . the speedup is measured relative to the standalone version of libxml2 . this graph shows that parallel preparsing is crucial to maintaining the scalability of pxp . the speedup curve is near straight until all 30 processors in the test machine are exhausted . pxp with sequential preparsing shows much less performance gain as the number of threads increase , and only scales to a few processors before leveling - off . to further improve scalability to beyond 30 cores other issues may be considered . for example , while it was initially suspected that the sequential merge stage might be a bottleneck . however , merge time turned out to be only 1 / 1000 of the wall clock time , even with 30 threads , and therefore could not account for the deviation from the ideal . further investigations on this issue suggests that load imbalance is the main cause . to obtain some experimental evidence , the speedup if the load were perfectly balanced was estimated by using the equation where s is the time required for parallel preparsing with one thread and t i is the time required by thread i during a parallel preparse with n threads . the effect of this equation is to give what the speedup would have been if the load had been perfectly balanced . the results are shown in fig1 on the line associated with “ speedup if the load is perfectly balanced ”. this line is much more close to the ideal when compared to the actual speedup line , and thus confirmed that the workload on each thread is different , and that some chunks will be more costly to preparse than others . if the deviation from ideal was caused by overhead , for example , the artificial load - balancing computation would not help so much . the reason why some chunks cost more is that there exists different number of contexts on different chunks . in fact , the number of contexts depends on the exact character position that the meta - dfa was started in . thus , some threads have to perform more work than others , causing them to slow down . if a chunk is likely to require more time - consuming processing , for example a complex table structure is noted during preparsing , then that chunk may be subdivided , leading to an earlier conclusion of preparsing processing for that subdivided chunk . note that by subdividing a chunk , the later portion of that chunk would require processing of its entire state vector space . assuming that all processing power is consumed in the evaluation , a decision is made whether to subdivide an earlier chunk and immediately commence evaluation , so that its end state can be obtained earlier , or commence ( or continue ) processing of another chunk in the queue or in process . various known optimization techniques may be applied to this problem . a data - parallel approach to parallel xml parsing is attractive and produces a significant speedup . by selecting arbitrary starting points within an xml data object or stream , the starting state of a chunk is not definitely known , and therefore the parallel processing proceeds to consider all or some of the possibilities , before the actual state is known with certainty . the approach of transforming the original dfa to a meta - dfa , addresses this challenge by tracking all possible executions via a metastate . operations in the original dfa are preserved by modeling them as actions , which are executed in the meta - dfa within separate contexts , thus maintaining the separation between different possibilities . the results show significant speedup when applied on the preparsing phase of the pxp . since each meta - dfa presumes a different starting state , it is possible to simplify each respective meta - dfa for its particular application , though a generic dfa may be used for each instance with a constrained presumed starting state . maintaining multiple possibilities incurs a cost , however , and therefore the present invention may be used in conjunction with other techniques which exploit various strategies to reduce this cost . there are some duplications that could be eliminated , for example . sophisticated work - stealing techniques using non - blocking synchronization may address load - imbalance issues . applying dfa state minimization algorithms to the dfa may also show promise in reducing code size [ 13 ]. another avenue of future work is to explore how the meta - dfa approach can be used for other types of xml processing , such as canonicalization [ 17 ]. many variations of the invention will occur to those skilled in the art . some variations include operating on data types other than xml , operating on asymmetric or adaptively allocated parallel processing systems , adaptive chunking of objects , using multi - processor systems ( e . g ., gpu - type parallel processing arrays ) to evaluate the same data with different presumptions , and statistical or biased selection of processing tasks based on likely high yield processing results and likely superfluous processing results . the pre - parsing system may be distributed over time and space , and , for example , may be embedded in a network appliance or network router which processes the object as it is being communicated . thus , the object and its preparsed skeleton may be delivered to a destination . all such variations are intended to be within the scope and spirit of the invention , which is limited only by the claims . the examples presented herein are not intended to limit the scope of the invention . it is understood that the present invention may be executed on a variety of computing platforms , both general and special purpose , implementing specific functionality as described herein . each of the following reference is incorporated herein by reference as if set forth in their entirety . g . m . amdahl . validity of the single - processor approach to achieving large scale computing capabilities . in proceedings of afips conference vol . 30 , pages 483 - 485 , atlantic city , n . j ., 1967 . afips press . 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