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(#134)\n\n* Refactor solve step to handle full-rank basis\r\n\r\n* Make ULV code use similar id_row() func to Ma's implementation\r\n\r\n* Handle BLR2 case\r\n\r\n* Remove unnecessary if check\r\n\r\n* Extend ULV nodependency to LDL nodependency\r\n\r\n* Use same vector x as SymmH2_ULV_SC22 for better result comparison\r\n\r\n* Removed unused methods\r\n\r\n* Update LDL implementation to H2-Eigen example file\r\n\r\n* Construct basis in advance before factorization\r\n\r\n* Added slicing the spectrum of H2-matrix using H2-LDL without trailing dependency\r\n\r\n* Simplify var names for easier debug\r\n\r\n* Added H2-Eig based on LDL without dependency that actually computes the fill-ins\r\n\r\n* Added test codes for ELSES matrices\r\n\r\n* Measure basis construction time\r\n\r\n* Use centroid instead of midpoint as cluster center\r\n\r\n* Remove unnecessary check\r\n\r\n* Fix missing change\r\n\r\n* Refactor get_skeleton and bugfix\r\n\r\n* Make one example file for both ELSES and synthetic matrices that is capable of printing output in CSV\r\n\r\n* Single example file for Eigen Synthetic matrix and ELSES matrix input\r\n\r\n* Added working example of H2-LDL without dependency that actually computes the fill-ins\r\n\r\n* Update h2-eig example files using h2-ldl without dependency that computes fill-in\r\n\r\n* Refactor example files for easier use in experiments\r\n\r\n* Added flag to skip dense eigenvalue computation\r\n\r\n* Also output ldl_min_rank of shifted matrix with largest ldl_max_rank\r\n\r\n* Update ldl min and max rank before exiting in case of singular shifted matrix\r\n\r\n* Use matrix norm as starting interval for slicing the spectrum of ELSES matrices\r\n\r\n* Allow example file to use SVD+ID+QR or ID+QR low-rank approximation\r\n\r\n* Added new set of eigenvalues to be computed\r\n\r\n* Allow full-rank basis on slicing the spectrum based on H2-LDL with trailing dependencies\r\n\r\n* Output starting interval\r\n\r\n* Default to CSV output\r\n\r\n* Added pragma omp to applicable places\r\n\r\n* Remove print command\r\n\r\n* Optimize inertia function\r\n\r\n* Temporarily remove omp pragmas\r\n\r\n* Dynamic fontsize on visualization based on block size\r\n\r\n* Use near and far neighbors list to iterate along inadmissible/admissible blocks within a level\r\n\r\n* Fixed bug where shift is not used when computing fill-in\r\n\r\n* Concat sample of nearfield blocks instead of its gram matrix when forming basis\r\n\r\n* Added pragma omp to applicable places\r\n\r\n* Minor refactor\r\n\r\n* Use cell farfield to obtain low-rank part of a block row\r\n\r\n* Use matrix norm as default starting interval for small matrices\r\n\r\n* Added pre-optimized example file for comparison purpose if necessary\r\n\r\n* Read bisection starting interval as input\r\n\r\n* Added slicing the spectrum with dense LDL\r\n\r\n* Added extra check to Matrix scale functions\r\n\r\n* Use midpoint as center of cells\r\n\r\n* Added ELSES bodies ordering based on Hilbert space filling curve\r\n\r\n* Optimize H2-LDL with dependency code\r\n\r\n* Handle full-rank cluster bases\r\n\r\n* Remove print statement\r\n\r\n* Refine interactions\r\n\r\n* Added refine interactions to LDL example file\r\n\r\n* Added PAPI Profiler\r\n\r\n* Added TODO comment\r\n\r\n* Temporarily remove solve step in generalized LDL example file\r\n\r\n* Use PAPI profiler with -O3 flag\r\n\r\n* Fixed wrong CSV header\r\n\r\n* Undo refine interactions\r\n\r\n* Added PAPI_FP_OPS output to H2-Eigen example file\r\n\r\n* Added construct min and max rank on the leaf level as output\r\n\r\n* Add cell's level information within space-filling curve-based partitioning\r\n\r\n* Output sparsity constants\r\n\r\n* Fix output\r\n\r\n* Changed admissibility to use cell's diameter\r\n\r\n* Added random_uniform_grid geometries\r\n\r\n* Changed output order for readability\r\n\r\n* Remove randomized SVD and fix QR\r\n\r\n* Rename function to be more descriptive\r\n\r\n* Added admissibility condition variants\r\n\r\n* Output memory usage\r\n\r\n* Added flag to turn off memory calculation\r\n\r\n* Ensure ELSES bodies are sorted based on hilbert indices on the same level\r\n\r\n* Add memory consumption in Dense LDL Slicing example\r\n\r\n* Move header print statement to the beginning\r\n\r\n* Trim directory name from ELSES geom name in output\r\n\r\n* Fix csp calculation\r\n\r\n* Allow using ELSES geometry with laplace kernel\r\n\r\n* Enable solve step\r\n\r\n* Allow fixed rank LRA compression\r\n\r\n* LDL factorize until minimum level that has admissible block\r\n\r\n* Output more csp\r\n\r\n* Refactor cardinal recursive bisection\r\n\r\n* Update H2-Eigen's LDL factorization\r\n\r\n* Hilbert index sort with cuboid bounding box\r\n\r\n* Allow switch between square and rectangular initial bounding box for hilbert partitioning\r\n\r\n* Use SVD that does not compute V when it's not necessary\r\n\r\n* Remove unused example file\r\n\r\n* Removed warning message\r\n\r\n* Remove rq step when using QR factorization to update cluster basis\r\n\r\n* Always sort ELSES geometry with a single fullerene as hilbert/morton leaf box regardless of leaf_size\r\n\r\n* Remove unused matrix creation\r\n\r\n* Sort atom within fullerene using cardinal recursive bisection\r\n\r\n* Added timer from FRANK to show computation breakdown\r\n\r\n* Optimize fill-in concatenation\r\n\r\n* Update LDL with dependency example files\r\n\r\n* Added H2-LDL with basis update strategy of MiaoMiaoMa2019's paper\r\n\r\n* Put identity dummy bases during H2-construction\r\n\r\n* Added MiaoMiaoMa_2019 paper fill-in recompression scheme\r\n\r\n* Added H2-Bisection based on H2-LDL with Ma2019 fill-in recompression\r\n\r\n* Better timer usage with macro\r\n\r\n* Parallelize fill-in computations\r\n\r\n* Parallelize parts of construction\r\n\r\n* Reflect OMP optimizations\r\n\r\n* Added scheduler implementation\r\n\r\n* Optimized scheduler with non-blocking communications\r\n\r\n* Added parallel H2-Slicing the spectrumg\r\n\r\n* Improve accuracy of task splitting\r\n\r\n* Reuse computed inertia to compute other eigenvalues within local computation\r\n\r\n* Added missing outputs\r\n\r\n* Added single-node LAPACK dsyev example file\r\n\r\n* Added LAPACK dsyevx wrapper\r\n\r\n* Added compute selected eigenvalues with LAPACK dsyevx example file\r\n\r\n* Renamed Master-Slave H2-Bisection code\r\n\r\n* Added non master-slave parallel slicing the spectrum\r\n\r\n* Minor bug fix\r\n\r\n* Fix typo\r\n\r\n* Fix starting index bug\r\n\r\n* Added dense eigenvalue solver memory consumption\r\n\r\n* fixes to mpi scaling\r\n\r\n* Added ScaLAPACK PDSYEVX routine\r\n\r\n* Fix Cmake files\r\n\r\n* Refactor example cmakelist\r\n\r\n* Enable/disable JSON\r\n\r\n* Remove unused vars\r\n\r\n* Added ScaLAPACK pdsyev example file\r\n\r\n* small optimization to master process\r\n\r\n* Added local interval debug message\r\n\r\n* Remove unused log\r\n\r\n* H2-Eigen executables with plain makefile\r\n\r\n* Proper handling of make.inc\r\n\r\n* Use plain for loop for backward compatibility with older version of OpenMP\r\n\r\n* Update makefile inc\r\n\r\n* Backward compatitiblity with older OpenMP in parallel H2-Bisection code\r\n\r\n* Added debug output option\r\n\r\n* Fix compilation of parallel eigen source files\r\n\r\n* Remove lambda capture initializer\r\n\r\n* Unify csv header\r\n\r\n* Temporary disable common particle, cell, and domain classes\r\n\r\n* init H2 eigen stuff\r\n\r\n* working with elses file FORTRAN wrapper\r\n\r\n* stuff\r\n\r\n* generate geometry from within Hatrix\r\n\r\n* update args to use elses arguments\r\n\r\n* fixing file outputs using ELSES binaries\r\n\r\n* update elses matrix from config xml files\r\n\r\n* temp fix of linking error\r\n\r\n* update H2 construction\r\natrix\r\n\r\n* updating functions for ELSES\r\n\r\n* fix compile issues on lab server for DTD\r\n\r\n* change run script\r\n\r\n* add special type for scalapack matrix\r\n\r\n* distributed matvec routine\r\n\r\n* fix index in block nrows and ncols\r\n\r\n* update omp for loops\r\n\r\n* update elses matrix file\r\n\r\n* obtain more elses matrices\r\n\r\n* update elses 30720 matrix size\r\n\r\n* start with generation of tree with elses geometry\r\n\r\n* start with building a tree list\r\n\r\n* update cell partitioning logic\r\n\r\n* benchmarking molecule center generation\r\n\r\n* use ELSES matrix generation in the construction scheme\r\n\r\n* generate ELSES matrix of arbitrary size\r\n\r\n* fail compile upon error\r\n\r\n* add to generate AY\r\n\r\n* writing SVD update\r\n\r\n* partially working scalapack stuff\r\n\r\n* use simple lapack and mpi calls for distributed compression\r\n\r\n* use plain MPI for obtaining S blocks\r\n\r\n* update BLR2 weak construction with elses\r\n\r\n* update elses matrix generation for fugaku\r\n\r\n* update fugaku script\r\n\r\n* Sort molecules using an out of place merge sort.\r\nSetup sort keys using a hilbert index.\r\n\r\nsorting particles to build the tree\r\n\r\nadd child parameters to the Cell class\r\n\r\nchange leaf size for the molecule interaction\r\n\r\nworking tree partitioning\r\n\r\nadd functions for hilbert index calculation\r\n\r\nget hilbert key for cells\r\n\r\nfixing generation of cells\r\n\r\nremove unnecesssary print statements\r\n\r\n* Generate admissibility condition from molecule dataset. Still too many\r\nCsp blocks per row.\r\n\r\ngenerate hilbert key and level IDs for leaf nodes\r\n\r\nupdate electron and molecule sorting:\r\n:\r\n\r\nsort electrons within the molecule\r\n\r\nbuild bottom up binary tree\r\n\r\nupdate geometry admis condition\r\n\r\nupdate cell index\r\n\r\n* hilbert index update\r\n\r\n* remove old particle sorting code\r\n\r\n* porting cell partition to the synthetic geometry\r\n\r\n* port Domain functions to work with synthentic 1D geometry\r\n\r\n* reassign a parent cell\r\n\r\n* update 2D grid generation code\r\n\r\n* Csp working fine for 2D uniform grid\r\n\r\n* sector sort function scaffold\r\n\r\n* dist compression of BLR2 matrix\r\n\r\n* dist matvec begin\r\n\r\n* move to alllreduce for skeleton blocks\r\n\r\n* use all gather for S block computation\r\n\r\n* update skeleton block generation\r\n\r\n* calculate distributed norm\r\n\r\n* accurate matvec with more processes\r\n\r\n* fugaku nodes\r\n\r\n* dont make\r\n\r\n* Distributed construction of BLR2 matrix without generation of the whole matrix.\r\n\r\nhilbert index update\r\n\r\nremove old particle sorting code\r\n\r\nporting cell partition to the synthetic geometry\r\n\r\nport Domain functions to work with synthentic 1D geometry\r\n\r\nreassign a parent cell\r\n\r\nupdate 2D grid generation code\r\n\r\nCsp working fine for 2D uniform grid\r\n\r\nsector sort function scaffold\r\n\r\ndist compression of BLR2 matrix\r\n\r\ndist matvec begin\r\n\r\nmove to alllreduce for skeleton blocks\r\n\r\nuse all gather for S block computation\r\n\r\nupdate skeleton block generation\r\n\r\ncalculate distributed norm\r\n\r\naccurate matvec with more processes\r\n\r\nfugaku nodes\r\n\r\ndont make\r\n\r\nupdate compile for fugaku\r\n\r\n* Working LDLT factorization with BLR2 matrix weak admissiblity for the laplace kernel. Starting with writing a scaffold for the parsec JDF.\r\n\r\nstart with inertia function\r\n\r\nadd a final dense block in the H2 matrix for the final factoirzation\r\n\r\nadding m_begin and m_end\r\n\r\nuse macro for disabling elses geometry for macos\r\n\r\nstart writing scalapack function\r\n\r\nuse 2D grid for scalapack with eigen value solver\r\n\r\nfactorize without parsec scaffold\r\n\r\nporting mth eigen value function from ridwan\r\n\r\nadd compute eigen value code to the main functino\r\n\r\nporting no parsec code for a single process run\r\n\r\nadd no parsec factorization in a different file\r\n\r\nfixing LDL factorization\r\n\r\nupdating singular value calculation\r\n\r\nupdate noparsec factorization\r\n\r\nstart writing JDF flows\r\n\r\nstarting with building C interfaces for the JDF\r\n\r\nupdate ptg interfaces\r\n\r\ncompiling PTG scaffold\r\n\r\naccurately obtain eigenvalue\r\n\r\nupdate ptg interfaeces\r\n\r\n* Working JDF scaffolds and pointers to data within the generated H2 matrix.\r\n\r\nwriting parsec scaffolds for accessing data from the DAG\r\n\r\nmake neighbour lists for near and far interactions\r\n\r\nupdate matrix map and data map\r\n\r\npass the H2 matrix level into the JDF\r\n\r\n* Working for weak BLR2 LDL but without the final LDL dense factorization.\r\n\r\nadding JDF task for generation of complements\r\n\r\nPTG flows for BLR2 weak work for shared memory. Working on fixing distributed memory kth eigenvalue computation.\r\n\r\nworking flow but has some strange error for empty list\r\n\r\nbasic make complement task is working\r\n\r\nupdate complement multiplication CORE function\r\n\r\nadd function for diagonal factorization\r\n\r\nstart building the merge task\r\n\r\nmake a separate data collection for non leaf dense blocks\r\n\r\nadd more functions for searching for index and reversing index calculation\r\n\r\nworking JDF for S blocks merging\r\n\r\nwrote flows for admissible blocks\r\n\r\nflows work for 4 block matrix.\r\n\r\nflow works with a single row of the merge matrix\r\n\r\nflow works with a single row of the merge matrix\r\n\r\nworking flows until merge step\r\n\r\ncopy functions for merge task\r\n\r\ntasks for performing final left and right solve\r\n\r\ncall destruct functions for parsec\r\n\r\nbasic working LDLT JDF flow\r\n\r\nadd matmul full task\r\n\r\nadd matmul full task\r\n\r\nmaking the final factorization work without any dependence on the level wise factorization\r\n\r\nworking final lu without chainging of sub graphs\r\n\r\nflows for inducing order between parts of the TRSM and GEMM\r\n\r\nGEMM flows\r\n\r\nGEMM flows\r\n\r\nuse mutex for locking unodered_map update\r\n\r\nconnect merge step with the final factorization\r\n\r\nclear previous maps\r\n\r\nclear previous maps\r\n\r\nadd new arena type for leaf bases\r\n\r\nworking with PTG for weak admis BLR\r\n\r\nupdate vpid with mpi rank calculation\r\n\r\nin the process of debugging multi process PTG\r\n\r\nstart with HSS matrix distributed compression\r\n\r\nuse type_local and delete data carefully\r\n\r\nfixing memeory issue\r\n\r\nworks if you don't delete the arena\r\n\r\nseems to be workign with the use of type_remote for sender and type_local for receiver\r\n\r\nworking until the merge_blocks task\r\n\r\nfinal LDL kind of works\r\n\r\nfinal LDL kind of works\r\n\r\nmerge blocks with 2 processes\r\n\r\nenabling TRSM with LDL\r\n\r\nworking without final LDL factorization\r\n\r\n* Update compilation for flowcx.\r\n\r\nupdate code for compilation with flocx\r\n\r\nupdate flowcx\r\n\r\n* update main file\r\n\r\n* use many threads in parsec\r\n\r\n* all gather timings\r\n\r\n* Start generation of transfer matrices.\r\n\r\ntimers for various functions\r\n\r\nfix final block generation\r\n\r\nstart with generation of transfer matrices\r\n\r\naccumulate blocks for the transfer matrix generation\r\n\r\ngenerating transfer matrix updates\r\n\r\n* Remove useless examples, change header file names and remove CUDA files.\r\n\r\nremove some useless examples about HSS matrices\r\n\r\nremove useless scripts and makefile stuff\r\n\r\nremove CUDA files\r\n\r\nchange .h files to .hpp and remove the Context classes\r\n\r\n* Rename example files based on new naming convention\r\n\r\n* Removed unnecessary file\r\n\r\n* Fix Hatrix header include statement in example files\r\n\r\n* Removed context function calls\r\n\r\n* Removed CUDA-related lines\r\n\r\n* Temporarily disable common Particle, Cell, and Domain class until proper merging step is taken\r\n\r\n* move H2 symmetric shared basis matrix to the Hatrix trunk\r\n\r\n* setup gather loops for transfer matrix\r\n\r\n* debugging JDF\r\n\r\n* working on a new technique that would take advantage of many processes\r\n\r\n* making an array of communicators and groups for transfer matrix generation\r\n\r\n* update type commit\r\n\r\n* updating sendcounts of MPI gatherv functions\r\n\r\n* make new communicators for each block\r\n\r\n* start writing gather code for MPI\r\n\r\n* implementing a new logic for transfer matrix generation\r\n\r\n* update transfer matrix generation from SVD\r\n\r\n* update block loop for transfer matrix\r\n\r\n* working with cmake in the apple accelerate framework\r\n\r\n* using variables to detect LAPACKE on macos\r\n\r\n* updating LAPACKE GSL and OPENMP on macos\r\n\r\n* remove Domain and Particle classes from BLR2 examples\r\n\r\n* start writing specificiation for BLR2 strong\r\n\r\n* porting the new interface to the strong BLR2 class\r\n\r\n* update CMAKE for Domain and other stuff\r\n\r\n* update openmp with cmake\r\n\r\n* Write construction for BLR2 and move matrix generator functions into Hatrix trunk.\r\n\r\nadd greens function to the example file\r\n\r\nadding functions for matrix generation into header files\r\n\r\ncompile basic dense block generation program\r\n\r\nupdate BLR2 strong construction\r\n\r\nadd matvec scaffold\r\n\r\nwriting matvec\r\n\r\nmatvec\r\n\r\nbasic BLR2 strong construction example\r\n\r\n* Blr2 weak con (#122)\r\n\r\n* add 1d laplace greens function\r\n\r\n* put a diagonal admissiblity function inside Hatrix trunk\r\n\r\n* weak admis BLR2\r\n\r\n* remove gsl dependency\r\n\r\n* H2 weak con 2lvl (#125)\r\n\r\n* Start porting H2 weak matrix generation from Hatrix library.\r\n\r\n* writing transfer matrix generation for HSS matrix\r\n\r\n* generate transfer matrix\r\n\r\n* writing matvec routine for HSS matrix\r\n\r\n* finish writing matvec verification\r\n\r\n* remove old code\r\n\r\n* HSS multi-level construction. (#126)\r\n\r\n* start updating H2 weak construction for multi level matrix\r\n\r\n* construction and verfication of HSS matrix with multiple levels is done\r\n\r\n* update dense LU 2x2 example (#127)\r\n\r\n* update dense QR example and use GSL numeric functions on macos (#128)\r\n\r\n* H2 matrix construction with strong admissibility (fixed rank) (#129)\r\n\r\n* remove old 2level H2 strong file\r\n\r\n* fixing the H2_strong_CON example\r\n\r\n* make basic scaffold for H2 matrix construction\r\n\r\n* update transfer matrix generation\r\n\r\n* construction error function\r\n\r\n* update SVD compresion with max rank and accuracy\r\n\r\n* fix dimensions for accuracy based factoirzation\r\n\r\n* fix conditional for generation of admissible blocks\r\n\r\n* update matrix-vector multiplication\r\n\r\n* add function that recreates the matrix for matrix construction error checking\r\n\r\n* add +3 to rank for avoiding catastrophic failure\r\n\r\n* fixing construction for large H2 matrix\r\n\r\n* cross check with code from ridwan\r\n\r\n* working with 1D laplace\r\n\r\n* working for strong admis\r\n\r\n* working H2 strong compression\r\n\r\n* update H2 compression code\r\n\r\n* Documentation for functions within Hatrix. 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