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* CarpetLib: resolve conflict between collective communication and mem<T>Erik Schnetter2005-04-11
| | | | darcs-hash:20050411203309-891bb-5b74d6135f6cd6995f1eed6cc74dd2f29c42f8a8.gz
* CarpetLib: change the default for CarpetLib::use_waitall from "no" to "yes"Thomas Radke2005-04-11
| | | | | | | | Using CarpetLib::use_waitall = "yes" seems to improve Carpet performance both for the standard and for the collective buffers communication scheme. So I made it the default. darcs-hash:20050411173355-776a0-a1046bde7c4ccb4eebc00765b4264701b012c8d8.gz
* Carpet/CarpetLib: deactivate CarpetLib::minimise_outstanding_communicationsThomas Radke2005-04-11
| | | | | | | | | | | | | | The code to minimise the number of outstanding communication requests is superseded by the collective buffers communication code. Therefore the corresponding parameter has been deactivated (but not removed in order to keep backwards compatibility with older checkpoints). It is marked as deprecated in the param.ccl file and should not be used anymore (use CarpetLib::use_collective_communication_buffers instead). A level-2 warning of that meaning is printed at startup if the parameter is still set in a user's parfile. darcs-hash:20050411155524-776a0-ed9919869cc1f2821ab8b2fa23b4abea203b72ed.gz
* CarpetLib: remove erroneous assert statements in the collective buffers ↵Thomas Radke2005-04-11
| | | | | | communication code darcs-hash:20050411141439-776a0-98125bb76dcb733d3649cd50f9a27e4e7c9d2d6d.gz
* CarpetLib: some optimisations for the collective buffers communication schemeThomas Radke2005-04-11
| | | | | | | | | | | | | | | | | | | | | | | | | | | * Receive operations are posted earlier now (don't wait until send buffers are filled). * A send operation is posted as soon as its send buffer is full (don't wait until all send buffers have been filled). * MPI_Irsend() is used instead of MPI_Isend() This probably doesn't make a difference with most MPI implementations. * Use MPI_Waitsome() to allow for overlapping of communication and computation to some extent: data from already finished receive operations can be copied back while active receive operations are still going on. MPI_Waitsome() is now called (instead of MPI_Waitall()) to wait for (one or more) posted receive operations to finish. The receive buffers for those operations are then flagged as ready for data copying. The drawback of this overlapping communication/computation scheme is that the comm_state loop may be iterated more often now. My benchmarks on up to 16 processors showed no performance win compared to using MPI_Waitall() (in fact, the performance decreased). Maybe it performs better on larger numbers of processors when there is more potential for network congestion. The feature can be turned on/off by setting CarpetLib::use_waitall to yes/no. For now I recommend using CarpetLib::use_waitall = "yes" (which is not the default setting). darcs-hash:20050411122235-776a0-e4f4179f46fce120572231b19cacb69c940f7b82.gz
* CarpetLib: bugfix for collective buffers communicationThomas Radke2005-04-11
| | | | | | | | | | | | Collective buffers were accidentally used (eg. by CarpetIOHDF5 or CarpetIOASCII) even if CarpetLib::use_collective_communication_buffers was set to "no". Now this parameter is evaluated in the comm_state constructor (together with the variable type given) and the result stored in a flag comm_state::uses__collective_communication_buffers. This flag is then used later in comm_state::step() to decide about communication paths. darcs-hash:20050411100916-776a0-aef034c4a23dac96f515cf831d15c8b7e2ce2f9d.gz
* CarpetLib: Resolve conflict after introducing mem<T> classErik Schnetter2005-04-10
| | | | | | | | Resolve the conflict that exists between the patches that introduce the mem<T> class conflicts and the option CarpetLib::use_collective_communication_buffers. darcs-hash:20050410175106-891bb-a66f3783fd8c897d65ed07f55b812e346b406baa.gz
* CarpetLib: Introduce new class mem<T> for memory managementErik Schnetter2005-03-05
| | | | | | | | | | | | | | | | | | | Introduce a new class mem<T> for memory management. Memory management has become sufficiently complicated to move into its own class. The class mem<T> features: 1. Allocating nelem items of type T 2. Managing contiguous regions of memory for several data<T> objects for vector groups 3. Allowing a pointer to a memory region to be passed in, which is used instead of allocating memory through new 4. Reference counting, so that the mem<T> object only goes away once the last using data<T> object does not need it any more. This makes it unnecessary to delete the first data<T> objects for a grid function group last. darcs-hash:20050305174647-891bb-e1f53adca34e5a668af96c662845cca0f259f8e6.gz
* CarpetLib: omit the name for the unused dummy function argument in ↵Thomas Radke2005-04-06
| | | | | | dist::datatype() to get rid of g++ compiler warnings darcs-hash:20050406145726-776a0-16ef8cd6d00ca41fcd3662b93bffe649476ff31f.gz
* CarpetLib: make fill_bbox_arrays() a static non-template function in data.cctradke2005-03-16
| | | | darcs-hash:20050316130144-3fd61-1f95c63b76c29de63f212546b5e4fa226afe7299.gz
* CarpetLib, Carpet: implement and use collective communication buffersThomas Radke2005-03-30
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | Collective buffers are used to gather all components' data on a processor before it gets send off to other processors in one go. This minimizes the number of outstanding MPI communications down to O(N-1) and thus improves overall efficiency as benchmarks show. Each processor allocates a pair of single send/recv buffers to communicate with all other processors. For this the class (actually, the struct) comm_state was extended by 3 more states: state_get_buffer_sizes: accumulates the sizes for the send/recv buffers state_fill_send_buffers: gathers all the data into the send buffers state_empty_recv_buffers: copies the data from the recv buffer back into the processor's components Send/recv buffers are exchanged during state_fill_send_buffers and state_empty_recv_buffers. The constructor for a comm_state struct now takes an argument <datatype> which denotes the CCTK datatype to use for the attached collective buffers. If a negative value is passed here then it falls back to using the old send/recv/wait communication scheme. The datatype argument has a default value of -1 to maintain backwards compatibility to existing code (which therefore will keep using the old scheme). The new communication scheme is chosen by setting the parameter CarpetLib::use_collective_communication_buffers to "yes". It defaults to "no" meaning that the old send/recv/wait scheme is still used. So far all the comm_state objects in the higher-level routines in thorn Carpet (restriction/prolongation, regridding, synchronization) have been enabled to use collective communication buffers. Other thorns (CarpetInterp, CarpetIO*, CarpetSlab) will follow in separate commits. darcs-hash:20050330152811-776a0-51f426887fea099d1a67b42bd79e4f786979ba91.gz
* CarpetLib: remove unused send_listvect argument in copycat() and intercat()Thomas Radke2005-03-23
| | | | darcs-hash:20050323191002-776a0-4a40d844dee2a66e8802669d960709e3488216c4.gz
* CarpetLib: Do not check invariant of bboxset classErik Schnetter2005-03-21
| | | | | | | | | Checking the invariant of the bboxset class is probably O(N^3) in the number of bboxes, possibly worse. It is a very slow operation when there are many components in a simulation, especially with AMR, and possibly also when running on many processors. darcs-hash:20050321020814-891bb-c5eb1cde6f3ac064e39a362b19bd20e15d03bc24.gz
* CarpetLib: Correct misleading commentErik Schnetter2005-03-21
| | | | darcs-hash:20050321020511-891bb-2775aab7e620a3c8da997c10cefcf5ac53124509.gz
* move block of duplicated assert() statements in ↵Thomas Radke2005-03-16
| | | | | | {copy,interpolate}_from_{recv,send,wait}() further up into {copy,interpolate}_from() so that the code is shared darcs-hash:20050316132044-776a0-525aa7485c2718a9717b6f253553982524872727.gz
* Carpet/CarpetLib: minimise the number of outstanding communication requeststradke2005-03-11
| | | | | | | | | | | | | | | | | | | | | | | This patch greatly reduces the number of outstanding MPI_Isend/MPI_Irecv communication requests by moving the loop over comm_states (recv,send,wait) from the outermost to the innermost. This resolves problems with certain MPI implementations (specifically LAM, MPICH-NCSA, and Mvapich over Infiniband) which potentially resulted in some communication buffer overflow and caused the Cactus application to abort or hang forever. Preliminary benchmarks with BSSN_MoL show that the patch does not have a negative impact on myrinet clusters (measured to 64 processors). It even improves the Carpet performance on GigE clusters (measured up to 16 processors). The order of the communication loops is controlled by the boolean parameter CarpetRegrid::minimise_outstanding_communications which defaults to "no" (preserving the old behaviour). darcs-hash:20050311160040-3fd61-04d40ac79ef218252f9364a8d18796e9b270d295.gz
* CarpetLib: Use MPI_STATUS_IGNOREErik Schnetter2005-03-03
| | | | darcs-hash:20050303170559-891bb-836694ccb8375a1f09cfaeda646e4430e3e5bd07.gz
* CarpetLib: Small cleanups to vector group storage handlingErik Schnetter2005-03-03
| | | | darcs-hash:20050303101420-891bb-6c23d70652146f074a392970443190966c909d10.gz
* CarpetLib: Whitespace changesErik Schnetter2005-03-03
| | | | darcs-hash:20050303101349-891bb-251f1432b873c898f73e0315ed63a7764f8714e8.gz
* CarpetLib: Specialise some vect template members to remove compiler warningsErik Schnetter2005-02-09
| | | | darcs-hash:20050209223915-891bb-4c4001d07890086e95de8d5a91deffc66c32e469.gz
* CarpetLib: Specialise some vect template members to remove compiler warningsErik Schnetter2005-02-09
| | | | darcs-hash:20050209222027-891bb-e8501dfa40575303af1338c1d2d4528d08ea273c.gz
* Reverse iterator orderIan Hawke2005-02-09
| | | | | | | Reverse the order that variables are destroyed when refinement levels are removed. This ensures that vector GFs are treated correctly. darcs-hash:20050209173129-58c7f-c2507b49252fe45782dd06803201ef1cff74f889.gz
* CarpetLib: Use dist::rank() instead of MPI_Comm_rank()Erik Schnetter2005-02-01
| | | | darcs-hash:20050201231956-891bb-8c892504000762557eb01b8b6ef48d8f0b815e06.gz
* CarpetLib: Whitespace changeErik Schnetter2005-02-01
| | | | darcs-hash:20050201231759-891bb-db87543a706110d2cd819a7f38c1e67cf27e16a3.gz
* global: Change the way in which the grid hierarchy is storedErik Schnetter2005-02-01
| | | | | | | | | | | | | | | | | | | | Change the way in which the grid hierarchy is stored. The new hierarchy is map mglevel reflevel component timelevel i.e., mglevel moved from the bottom to almost the top. This is because mglevel used to be a true multigrid level, but is now meant to be a convergence level. Do not allocate all storage all the time. Allow storage to be switched on an off per refinement level (and for a single mglevel, which prompted the change above). Handle storage management with CCTK_{In,De}creaseGroupStorage instead of CCTK_{En,Dis}ableGroupStorage. darcs-hash:20050201225827-891bb-eae3b6bd092ae8d6b5e49be84c6f09f0e882933e.gz
* CarpetLib: Add missing #include <cassert>Erik Schnetter2005-01-12
| | | | darcs-hash:20050112093608-891bb-925d83a354f44638d28d3871d3e67a3ac5343fa6.gz
* CarpetLib: Restructure lightweight communication buffersErik Schnetter2005-01-03
| | | | | | | Restructure the lightweight communication buffers. Use lightweight communication buffers for interpolation as well. darcs-hash:20050103200712-891bb-7e42816d3b8d667916084e3f32527c8f35327d7f.gz
* CarpetLib: Rename data::interpolate_in_time to ↵Erik Schnetter2005-01-03
| | | | | | data::try_without_time_interpolation darcs-hash:20050103135332-891bb-e92a19212dfbadde889fda0760232f5b7749aac3.gz
* CarpetLib: Clean up some warning messagesErik Schnetter2005-01-03
| | | | darcs-hash:20050103135305-891bb-8813921b6e0e2988e9afd0be90c3d7ff092cee1e.gz
* CarpetLib: Add lightweight communication buffers (untested)Erik Schnetter2005-01-02
| | | | | | | | | | | Lightweight communication buffers use essentially only a vector<T> instead of a data<T> to transfer data between processors. This should reduce the computational overhead. Set the parameter "use_lightweight_buffers" to use this feature. This feature is completely untested. darcs-hash:20050102173524-891bb-6a3999cbd63e367c8520c175c8078374d294eaa8.gz
* CarpetLib: Add more checks to dh classErik Schnetter2005-01-02
| | | | darcs-hash:20050102173453-891bb-833515dd47ce1469ebe319718ab169e5eb82c6c4.gz
* CarpetLib: Move class commstate into its own fileErik Schnetter2005-01-01
| | | | darcs-hash:20050101193846-891bb-7bb505d29a25b04c0d23e792eea7ff404d1f4200.gz
* CarpetLib: Rename some variables to avoid shadowing class membersErik Schnetter2005-01-01
| | | | darcs-hash:20050101191615-891bb-20b262ff1a4468d5e1c5ac8626a3ead0727c2da9.gz
* CarpetLib: Remove many this-> prefixes in class gfErik Schnetter2005-01-01
| | | | darcs-hash:20050101190036-891bb-cf588a05c760e0d465d2efc352defedae6ba4ce5.gz
* CarpetLib: Remove many this-> prefixes in class dataErik Schnetter2005-01-01
| | | | darcs-hash:20050101185718-891bb-143c84dacf00f458eed1b9c985900bbaf5e3b98b.gz
* CarpetLib: Correct errors in declaration of timestatErik Schnetter2005-01-01
| | | | darcs-hash:20050101185325-891bb-197dd6cea208ec8d17507e31d99c22f0161fa21b.gz
* global: Turn CarpetLib templates into classesErik Schnetter2005-01-01
| | | | | | | | | | | | | | | | | | | Turn most of the templates in CarpetLib, which used to have the form template<int D> class XXX into classes, i.e., into something like class XXX by setting D to the new global integer constant dim, which in turn is set to 3. The templates gf and data, which used to be of the form template<typename T, int D> class XXX are now of the form template<typename T> class XXX The templates vect, bbox, and bboxset remain templates. This change simplifies the code somewhat. darcs-hash:20050101182234-891bb-c3063528841f0d078b12cc506309ea27d8ce730d.gz
* CarpetLib: Move class timestat into its own fileErik Schnetter2005-01-01
| | | | darcs-hash:20050101171429-891bb-130630de8631b8f9bbe494e135662ffb089ecca0.gz
* CarpetLib: Output gh more elegantlyErik Schnetter2005-02-01
| | | | darcs-hash:20050201222816-891bb-3ac829f630cbb58de05bbc229f2de47b80d1434f.gz
* global: Replace "&&" and "||" by "and" and "or"Erik Schnetter2005-02-01
| | | | darcs-hash:20050201214347-891bb-286c20316478d9f1c8384f94764174cab5adb9e0.gz
* doc: Play with using doxygen for Fortran codeErik Schnetter2005-02-01
| | | | darcs-hash:20050201212131-891bb-df7215694d99c95de5b1e2fceba6c0aff56ef586.gz
* CarpetLib: Change checking of processor number in data classErik Schnetter2004-12-30
| | | | | | | | | | | | | Remove functions gdata::lives_on_this_processor() and gdata::this_processor_is(proc). Introduce dist::rank() and dist::size() instead. Re-introduce assert statement in data::proc(). Move declaration and definition of assignment operator near the constructor and destructor. darcs-hash:20041230191026-891bb-90eeb1be4c04753c165e13e7c1e65f06847180ca.gz
* CarpetLib: Instantiate vect and bbox for CCTK_REAL instead of doubleErik Schnetter2005-01-27
| | | | darcs-hash:20050127104948-891bb-214d1033924b4db7a215a624eb337f8a619ac82d.gz
* CarpetLib: Remove unused variables from Fortran codeErik Schnetter2005-01-01
| | | | darcs-hash:20050101191544-891bb-4f1f960cbe9c99a9cdc42c1ba590ecdc6eb75f5f.gz
* CarpetLib/src/defs.hh: no need to '#include <complex>'Thomas Radke2005-01-18
| | | | darcs-hash:20050118180403-776a0-eb91906a7335386c49a03ae70f5caaf20a5441c3.gz
* CarpetLib: Try harder to normalise bboxsetsErik Schnetter2005-01-04
| | | | | | | | Try harder to normalise bboxsets. This is slower, but also more successful at finding the smalles possible number of bboxes. This improves e.g. recombined HDF5 I/O. darcs-hash:20050104214651-891bb-b6e00cf25685c8111472315f5fcdc37518db3700.gz
* global: Remove $Header$ keywords from Carpet arrangementErik Schnetter2005-01-01
| | | | darcs-hash:20050101162121-891bb-ac9d070faecc19f91b4b57389d3507bfc6c6e5ee.gz
* CarpetLib: Collect more timing statisticsErik Schnetter2004-12-30
| | | | | | | | | | | | | Collect more timing statistics in the data class. Print these statistics to stdout when the Cactus parameter print_timestats is set. Create a timer class "timestat". This is a timer that can be started, stopped, and it prints the total time as well as some statistics. For memory allocation statistics, count the number of objects as well as the number of bytes. darcs-hash:20041230212136-891bb-c14edfa7d539ae9b135eee76afadaad51fd0b098.gz
* CarpetLib: Do not #include <complex>Erik Schnetter2004-12-30
| | | | darcs-hash:20041230191410-891bb-fba06c8c0054b5324a4164e79205b36c7e5bfc3c.gz
* CarpetLib: Make data class conform closer to C++ standardErik Schnetter2004-12-28
| | | | | | | | Add missing this-> prefixes Declare template specialisation before definigg it Rename some local variables to avoid name clashes darcs-hash:20041228183523-891bb-acc5a1a8c1f247512a38dba56ff5419d96280fa3.gz
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