Code

MPI support for SGP construction#14

Code

Open

YuuuXie wants to merge 245 commits intomastermir-group/flare_pp:masterfrom mpi_distmatmir-group/flare_pp:mpi_distmatCopy head branch name to clipboard

+6,818-1,132

Commits

Commits on Apr 15, 2021

• add distmatrix into cmkae

  YuuuXie

  committed
  eec1c26

  Copy full SHA for eec1c26

Commits on Apr 16, 2021

• add parallel sgp

  YuuuXie

  committed
  6c483b8

  Copy full SHA for 6c483b8

• create matrix

  YuuuXie

  committed
  ee139d4

  Copy full SHA for ee139d4

• distribute training strucs

  YuuuXie

  committed
  9e94754

  Copy full SHA for 9e94754

• add test for ParallelSGP

  YuuuXie

  committed
  e03ec9f

  Copy full SHA for e03ec9f

• link to MPI

  YuuuXie

  committed
  55150e5

  Copy full SHA for 55150e5

Commits on Apr 17, 2021

• compile successfully with distmatrix

  YuuuXie

  committed
  a0bdd55

  Copy full SHA for a0bdd55

Commits on Apr 19, 2021

• add cholesky

  YuuuXie

  committed
  b84fb74

  Copy full SHA for b84fb74

Commits on Apr 20, 2021

• done matrix operation

  YuuuXie

  committed
  5d685c3

  Copy full SHA for 5d685c3

Commits on Apr 21, 2021

• adds brackets to constrain the scope of DistMatrix

  YuuuXie

  committed
  c0352fc

  Copy full SHA for c0352fc

Commits on Apr 24, 2021

• default blocking & distribute training set

  YuuuXie

  committed
  b26acf7

  Copy full SHA for b26acf7

Commits on Apr 25, 2021

• fixed u_size, solve segmentation fault

  YuuuXie

  committed
  c93b4d8

  Copy full SHA for c93b4d8

• add write_map & unit test

  YuuuXie

  committed
  6e0efad

  Copy full SHA for 6e0efad

• add openmp to compute_map_coef

  YuuuXie

  committed
  22532a6

  Copy full SHA for 22532a6

Commits on Apr 27, 2021

• debugging

  YuuuXie

  committed
  53df035

  Copy full SHA for 53df035

• Kuu & Kuu_inv match with SparseGP

  YuuuXie

  committed
  4c97acc

  Copy full SHA for 4c97acc

Commits on Apr 28, 2021

• fix: Kuf matches SparseGP

  YuuuXie

  committed
  25a05bc

  Copy full SHA for 25a05bc

Commits on May 3, 2021

• parallel_sgp matches sparse_gp in prediction of efs and var

  YuuuXie

  committed
  31b3276

  Copy full SHA for 31b3276

Commits on May 4, 2021

• fix mpibcast in test_parallel_sgp

  YuuuXie

  committed
  f91829e

  Copy full SHA for f91829e

• match Kuu and y with mpirun

  YuuuXie

  committed
  82a4a40

  Copy full SHA for 82a4a40

• fix b vector matching

  YuuuXie

  committed
  8edcace

  Copy full SHA for 8edcace

• fix Kuf match

  YuuuXie

  committed
  741448d

  Copy full SHA for 741448d

Commits on May 5, 2021

• change kuu to be built by rank 0

  YuuuXie

  committed
  bc06f2d

  Copy full SHA for bc06f2d

Commits on May 6, 2021

• efs & uncertainty match with mpirun

  YuuuXie

  committed
  39ddf67

  Copy full SHA for 39ddf67

• add python binding with mpi4py

  YuuuXie

  committed
  5776522

  Copy full SHA for 5776522

• remove debugging prints

  YuuuXie

  committed
  4261583

  Copy full SHA for 4261583

Commits on May 7, 2021

• add mpi timing file

  YuuuXie

  committed
  e364465

  Copy full SHA for e364465

• remove pybind of ParallelSGP due to distmat sharing issue

  YuuuXie

  committed
  fbdfbaa

  Copy full SHA for fbdfbaa

Commits on May 13, 2021

• fix timing

  YuuuXie

  committed
  2e5f998

  Copy full SHA for 2e5f998

• add timestamps

  YuuuXie

  committed
  499dc0c

  Copy full SHA for 499dc0c

• try computing a subset of descriptors in structure

  YuuuXie

  committed
  c4575cd

  Copy full SHA for c4575cd

• add reader for xyz file

  YuuuXie

  committed
  40152db

  Copy full SHA for 40152db

• Revert "try computing a subset of descriptors in structure"

  Show description for 2dd01ff
  YuuuXie

  committed
  2dd01ff

  Copy full SHA for 2dd01ff

Commits on May 14, 2021

• finish xyz reader

  YuuuXie

  committed
  c29925d

  Copy full SHA for c29925d

• try using distmat for global sparse descriptors

  YuuuXie

  committed
  a7d9908

  Copy full SHA for a7d9908

• add scripts & unit test

  YuuuXie

  committed
  a710a54

  Copy full SHA for a710a54

• add n_envs_by_type

  YuuuXie

  committed
  7bcb5a3

  Copy full SHA for 7bcb5a3

Commits on May 15, 2021

• distribute training set

  YuuuXie

  committed
  157858c

  Copy full SHA for 157858c

Commits on May 17, 2021

• distributing training data, pass unit test

  YuuuXie

  committed
  9537479

  Copy full SHA for 9537479

• rm debug flag & fix timing

  YuuuXie

  committed
  b555728

  Copy full SHA for b555728

Commits on May 18, 2021

• add print flag

  YuuuXie

  committed
  b5a2b0e

  Copy full SHA for b5a2b0e

Commits on May 19, 2021

• read extxyz format

  YuuuXie

  committed
  eb3ad8a

  Copy full SHA for eb3ad8a

Commits on May 22, 2021

• compilation succeed with utils

  YuuuXie

  committed
  cc0b79d

  Copy full SHA for cc0b79d

Commits on May 23, 2021

• fix utils unit test

  YuuuXie

  committed
  14e8e6a

  Copy full SHA for 14e8e6a

Commits on May 24, 2021

• add lock to 'get' and 'set' for multi-node

  YuuuXie

  committed
  65ff02c

  Copy full SHA for 65ff02c

Commits on May 25, 2021

• cp xyz file in cmake

  YuuuXie

  committed
  e9b0326

  Copy full SHA for e9b0326

• change to allgather

  YuuuXie

  committed
  1db0963

  Copy full SHA for 1db0963

• add a multinode test script

  YuuuXie

  committed
  a0af135

  Copy full SHA for a0af135

• fix par_sgp write_coef

  YuuuXie

  committed
  7c3e4c1

  Copy full SHA for 7c3e4c1

Commits on May 26, 2021

• change the input to vector of structures

  YuuuXie

  committed
  d13eae3

  Copy full SHA for d13eae3

Commits on May 28, 2021

• change sparse ind type

  YuuuXie

  committed
  2fffeba

  Copy full SHA for 2fffeba

Commits on Jun 4, 2021

• fix mysterious mpi bad request issue

  YuuuXie

  committed
  8c570d5

  Copy full SHA for 8c570d5

• add script for mpi executable

  YuuuXie

  committed
  28a9d81

  Copy full SHA for 28a9d81

Commits on Jun 9, 2021

• add docs for python api

  YuuuXie

  committed
  3499df2

  Copy full SHA for 3499df2

• add parallsgp doc

  YuuuXie

  committed
  209c223

  Copy full SHA for 209c223

Commits on Jun 10, 2021

• add docs

  YuuuXie

  committed
  2ed8cbd

  Copy full SHA for 2ed8cbd

Commits on Jun 13, 2021

• fix map omp

  YuuuXie

  committed
  0bbbd51

  Copy full SHA for 0bbbd51

• build matrix using local array

  YuuuXie

  committed
  9d04329

  Copy full SHA for 9d04329

• Merge branch 'mpi_distmat' of github.com:mir-group/flare_pp into mpi_distmat

  YuuuXie

  committed
  6c55fc4

  Copy full SHA for 6c55fc4

• fix varmap omp

  YuuuXie

  committed
  42078df

  Copy full SHA for 42078df

Commits on Jun 14, 2021

• add docs to utils

  YuuuXie

  committed
  07cbda5

  Copy full SHA for 07cbda5

Commits on Jun 29, 2021

• add single atom energy to mpi_build

  YuuuXie

  committed
  104f2c3

  Copy full SHA for 104f2c3

Commits on Jul 5, 2021

• Merge https://github.com/mir-group/flare_pp into mpi_distmat

  YuuuXie

  committed
  79f0fdb

  Copy full SHA for 79f0fdb

• Merge branch 'mpi_distmat' of github.com:mir-group/flare_pp into mpi_distmat

  YuuuXie

  committed
  c3a9f15

  Copy full SHA for c3a9f15

• Merge github.com:mir-group/flare_pp into mpi_distmat

  YuuuXie

  committed
  62e30fe

  Copy full SHA for 62e30fe

• Merge branch 'mpi_distmat' of github.com:mir-group/flare_pp into mpi_distmat

  YuuuXie

  committed
  ef4664f

  Copy full SHA for ef4664f

Commits on Jul 13, 2021

• change file name b3 -> bk

  YuuuXie

  committed
  dcb8975

  Copy full SHA for dcb8975

• change class name B3 -> Bk

  YuuuXie

  committed
  12c8f40

  Copy full SHA for 12c8f40

• add body in descriptor_settings

  YuuuXie

  committed
  d844f4e

  Copy full SHA for d844f4e

• add indices module

  YuuuXie

  committed
  0e3c714

  Copy full SHA for 0e3c714

• add K to compute_Bk

  YuuuXie

  committed
  0088bd6

  Copy full SHA for 0088bd6

• nu replaces loops

  YuuuXie

  committed
  bd3c9c1

  Copy full SHA for bd3c9c1

• change to fwd & bwd

  YuuuXie

  committed
  e9e87d8

  Copy full SHA for e9e87d8

• add test to match bk and b3

  YuuuXie

  committed
  69514ef

  Copy full SHA for 69514ef

• add b3 for test

  YuuuXie

  committed
  9c1d73e

  Copy full SHA for 9c1d73e

• add K2

  YuuuXie

  committed
  e739328

  Copy full SHA for e739328

Commits on Jul 14, 2021

• change wigner3j to coeffs

  YuuuXie

  committed
  8b24c50

  Copy full SHA for 8b24c50

• compiled b2

  YuuuXie

  committed
  34befc8

  Copy full SHA for 34befc8

Commits on Jul 15, 2021

• try debuggin b2

  YuuuXie

  committed
  6a5f4cf

  Copy full SHA for 6a5f4cf

• add b1 & pass test

  YuuuXie

  committed
  4de2ab4

  Copy full SHA for 4de2ab4

Commits on Jul 16, 2021

• fix b2

  YuuuXie

  committed
  1e6fd28

  Copy full SHA for 1e6fd28

• add indices for add_training_structure

  YuuuXie

  committed
  97deba5

  Copy full SHA for 97deba5

Commits on Jul 17, 2021

• fix small bug

  YuuuXie

  committed
  d0f7811

  Copy full SHA for d0f7811

• add test

  YuuuXie

  committed
  a70eaa6

  Copy full SHA for a70eaa6

• add atomic indices for training structures, likelihood

  YuuuXie

  committed
  01e957b

  Copy full SHA for 01e957b

• use TYPED_TEST

  YuuuXie

  committed
  66a64f6

  Copy full SHA for 66a64f6

• inherit StructureTest

  YuuuXie

  committed
  ddfb3dc

  Copy full SHA for ddfb3dc

Commits on Jul 18, 2021

• add parametrized gtest

  YuuuXie

  committed
  55d917f

  Copy full SHA for 55d917f

• Merge branch 'train_struc_indices' into Bk_desc

  YuuuXie

  committed
  b22733b

  Copy full SHA for b22733b

• add multiplt kernel test

  YuuuXie

  committed
  6e050ef

  Copy full SHA for 6e050ef

Commits on Jul 19, 2021

• add b1 for test

  YuuuXie

  committed
  28bb292

  Copy full SHA for 28bb292

• fix unit tests

  YuuuXie

  committed
  62b275c

  Copy full SHA for 62b275c

Commits on Jul 20, 2021

• allow mapping for multiple descriptors/kernels

  YuuuXie

  committed
  7cb6910

  Copy full SHA for 7cb6910

• update python interface for multiple kernels

  YuuuXie

  committed
  68bc8a7

  Copy full SHA for 68bc8a7

• write multiple descriptors to coef file

  YuuuXie

  committed
  ee8dca8

  Copy full SHA for ee8dca8

Commits on Jul 21, 2021

• add multiple cutoffs

  YuuuXie

  committed
  062c8f8

  Copy full SHA for 062c8f8

Commits on Jul 22, 2021

• add compute_likelihood_gradient_stable

  YuuuXie

  committed
  0c2f516

  Copy full SHA for 0c2f516

• add noise_one

  YuuuXie

  committed
  b115eff

  Copy full SHA for b115eff

• add Kuu_grad Kuf_grad

  YuuuXie

  committed
  9c4649b

  Copy full SHA for 9c4649b

Commits on Jul 23, 2021

• match datafit_grad

  YuuuXie

  committed
  a5b870c

  Copy full SHA for a5b870c

• match complexity_grad

  YuuuXie

  committed
  0836838

  Copy full SHA for 0836838

• fix multiple kernel grad

  YuuuXie

  committed
  1b33dfa

  Copy full SHA for 1b33dfa

• datafit grad over noise

  YuuuXie

  committed
  8530df8

  Copy full SHA for 8530df8

• complexity grad over noise

  YuuuXie

  committed
  43de96c

  Copy full SHA for 43de96c

• add pybinding to compute_grad_stable

  YuuuXie

  committed
  9b4862e

  Copy full SHA for 9b4862e

Commits on Jul 25, 2021

• add KnK

  YuuuXie

  committed
  a9247e2

  Copy full SHA for a9247e2

• add KnK

  YuuuXie

  committed
  fd86f80

  Copy full SHA for fd86f80

Commits on Jul 26, 2021

• add precompute KnK

  YuuuXie

  committed
  81286d1

  Copy full SHA for 81286d1

• rm diag

  YuuuXie

  committed
  6e815b6

  Copy full SHA for 6e815b6

Commits on Jul 27, 2021

• rm Kuu_grad Kuf_grad for speedup

  YuuuXie

  committed
  84a1962

  Copy full SHA for 84a1962

• change train() for precomputed kern matr

  YuuuXie

  committed
  2ffd3ca

  Copy full SHA for 2ffd3ca

Commits on Jul 29, 2021

• rm noise_vec loop in compute_likelihood_gradient

  YuuuXie

  committed
  e0b8856

  Copy full SHA for e0b8856

• call child Kuf_grad Kuu_grad

  YuuuXie

  committed
  292ef88

  Copy full SHA for 292ef88

Commits on Jul 30, 2021

• remove comments

  YuuuXie

  committed
  eb67338

  Copy full SHA for eb67338

Commits on Jul 31, 2021

• change test parameters

  YuuuXie

  committed
  92a0949

  Copy full SHA for 92a0949

• fix bug: KnK

  YuuuXie

  committed
  781f2bc

  Copy full SHA for 781f2bc

• change noise_vector in set_hyp

  YuuuXie

  committed
  49d8a6c

  Copy full SHA for 49d8a6c

• add test match like_grad_stable & like_grad

  YuuuXie

  committed
  c65d329

  Copy full SHA for c65d329

• fix kernels[i]->Kuu_grad & Kuf_grad

  YuuuXie

  committed
  3682ac8

  Copy full SHA for 3682ac8

Commits on Aug 5, 2021

• preprocess training data

  YuuuXie

  committed
  f02c1d4

  Copy full SHA for f02c1d4

Commits on Aug 7, 2021

• fix compilation

  YuuuXie

  committed
  5bbeaf3

  Copy full SHA for 5bbeaf3

• add -lgfortran to allow compilation with downloaded scalapack

  YuuuXie

  committed
  651a66a

  Copy full SHA for 651a66a

• rm commented func

  YuuuXie

  committed
  299e126

  Copy full SHA for 299e126

• load_local loads struc of A's local part

  YuuuXie

  committed
  e7953bc

  Copy full SHA for e7953bc

• add A.set

  YuuuXie

  committed
  cd71bb9

  Copy full SHA for cd71bb9

• get back to the old adding scheme

  YuuuXie

  committed
  4786c7d

  Copy full SHA for 4786c7d

Commits on Aug 10, 2021

• as_dict supports multiple kernels/descs

  YuuuXie

  committed
  0942922

  Copy full SHA for 0942922

• add Bk to lammps

  YuuuXie

  committed
  09d7afe

  Copy full SHA for 09d7afe

• use original pair style

  YuuuXie

  committed
  a32f459

  Copy full SHA for a32f459

• add coeffs and indices

  YuuuXie

  committed
  06dbd59

  Copy full SHA for 06dbd59

• copy b1+b2 pair_style & add body K

  YuuuXie

  committed
  1db17b7

  Copy full SHA for 1db17b7

• replace descriptor_code with K

  YuuuXie

  committed
  e8c5513

  Copy full SHA for e8c5513

Commits on Aug 11, 2021

• done lammps file parsing

  YuuuXie

  committed
  ba9b7e2

  Copy full SHA for ba9b7e2

• write K to coeff file

  YuuuXie

  committed
  f81c4e5

  Copy full SHA for f81c4e5

• fix calling desc

  YuuuXie

  committed
  907b617

  Copy full SHA for 907b617

• rm neighbor loop in lmp descriptor

  YuuuXie

  committed
  c29b70f

  Copy full SHA for c29b70f

Commits on Aug 14, 2021

• add multiple kernels to local_unc

  YuuuXie

  committed
  a149ed1

  Copy full SHA for a149ed1

• Merge branch 'Bk' of github.com:mir-group/flare_pp into like_grad_stable

  YuuuXie

  committed
  d5f412f

  Copy full SHA for d5f412f

• fix local stds

  YuuuXie

  committed
  742b294

  Copy full SHA for 742b294

• Merge branch 'Bk' into like_grad_stable

  YuuuXie

  committed
  353dbb3

  Copy full SHA for 353dbb3

Commits on Aug 15, 2021

• separate kernel tests to debug

  YuuuXie

  committed
  897755c

  Copy full SHA for 897755c

• separate stree-energy kernel test & change b2_norm

  YuuuXie

  committed
  d56a9dc

  Copy full SHA for d56a9dc

• separate force stress kernels and fix unit test

  YuuuXie

  committed
  f62cf48

  Copy full SHA for f62cf48

• rm B2 binding, add Bk binding

  YuuuXie

  committed
  cd9f542

  Copy full SHA for cd9f542

• fix python test bugs except for lmp

  YuuuXie

  committed
  7874c4a

  Copy full SHA for 7874c4a

• Merge branch 'Bk' of github.com:mir-group/flare_pp into like_grad_stable

  YuuuXie

  committed
  e3ef23c

  Copy full SHA for e3ef23c

Commits on Aug 16, 2021

• pass compilation

  YuuuXie

  committed
  4a41f35

  Copy full SHA for 4a41f35

• pass b2 test (no variance)

  YuuuXie

  committed
  8c05ba7

  Copy full SHA for 8c05ba7

• add multiple kernels to python test

  YuuuXie

  committed
  2d97b6f

  Copy full SHA for 2d97b6f

Commits on Aug 17, 2021

• try using scatter for set

  YuuuXie

  committed
  b3f2c69

  Copy full SHA for b3f2c69

Commits on Aug 19, 2021

• update_db for multiple desc/kernels

  YuuuXie

  committed
  6dc8413

  Copy full SHA for 6dc8413

Commits on Sep 1, 2021

• add more scatter

  YuuuXie

  committed
  343f666

  Copy full SHA for 343f666

• test new scatter

  YuuuXie

  committed
  377cf9a

  Copy full SHA for 377cf9a

Commits on Sep 2, 2021

• A.collect works for collecting Kfu

  YuuuXie

  committed
  5130d67

  Copy full SHA for 5130d67

• done b.collect

  YuuuXie

  committed
  c18b2d7

  Copy full SHA for c18b2d7

Commits on Sep 3, 2021

• rm A.set & b.set

  YuuuXie

  committed
  ae2acab

  Copy full SHA for ae2acab

Commits on Sep 5, 2021

• fix mpi_construction exec

  YuuuXie

  committed
  d0b52e3

  Copy full SHA for d0b52e3

Commits on Sep 6, 2021

• change param in test

  YuuuXie

  committed
  08a885d

  Copy full SHA for 08a885d

• change to partial_forces

  YuuuXie

  committed
  ed990aa

  Copy full SHA for ed990aa

Commits on Sep 7, 2021

• fix bug dA=1 of Bk

  YuuuXie

  committed
  ce5487b

  Copy full SHA for ce5487b

• fix unit test for multiple kernels

  YuuuXie

  committed
  4d17b5f

  Copy full SHA for 4d17b5f

Commits on Sep 8, 2021

• compute_std passes compilation

  YuuuXie

  committed
  00dc29a

  Copy full SHA for 00dc29a

• change stds from vector_atom to array_atom

  YuuuXie

  committed
  424c0ab

  Copy full SHA for 424c0ab

Commits on Sep 9, 2021

• done lmp var unit test

  YuuuXie

  committed
  4fe6ef3

  Copy full SHA for 4fe6ef3

• Merge branch 'rewrite_b2lmp' of github.com:mir-group/flare_pp into Bk

  YuuuXie

  committed
  3bed77c

  Copy full SHA for 3bed77c

• Update version to 0.1.0

  Show description for 37fd533
  YuuuXie

  authored
  37fd533

  Copy full SHA for 37fd533

• Merge branch 'Bk' of github.com:mir-group/flare_pp into like_grad_stable

  YuuuXie

  committed
  62e02f9

  Copy full SHA for 62e02f9

• pass unit test

  YuuuXie

  committed
  6dfc15f

  Copy full SHA for 6dfc15f

Commits on Sep 12, 2021

• change u_size_single_kernel to a list

  YuuuXie

  committed
  3fefb22

  Copy full SHA for 3fefb22

• change n_clusters to a list for kernels

  YuuuXie

  committed
  a900ac7

  Copy full SHA for a900ac7

• change local_labels to vector

  YuuuXie

  committed
  1712667

  Copy full SHA for 1712667

• debugging multiple kernels

  YuuuXie

  committed
  c621bae

  Copy full SHA for c621bae

Commits on Sep 13, 2021

• pass unit test with multiple kernels

  YuuuXie

  committed
  50a57ec

  Copy full SHA for 50a57ec

Commits on Sep 14, 2021

• solve conflict of merging like_grad_stable

  YuuuXie

  committed
  10ea653

  Copy full SHA for 10ea653

• fix conflict

  YuuuXie

  committed
  df05e4e

  Copy full SHA for df05e4e

• try adding compute_likelihood_grad

  YuuuXie

  committed
  c659be3

  Copy full SHA for c659be3

• rm finalize to pass unit test

  YuuuXie

  committed
  55f2e3b

  Copy full SHA for 55f2e3b

Commits on Sep 17, 2021

• add compute_KnK

  YuuuXie

  committed
  1a5eb3c

  Copy full SHA for 1a5eb3c

Commits on Sep 19, 2021

• add compute_dKnK

  YuuuXie

  committed
  b474d5d

  Copy full SHA for b474d5d

Commits on Sep 21, 2021

• fix conflict: change to list input for mapping

  YuuuXie

  committed
  4761988

  Copy full SHA for 4761988

• complete likelihood & grad calculation

  YuuuXie

  committed
  5bbdb9e

  Copy full SHA for 5bbdb9e

• mv finalize from source to script

  YuuuXie

  committed
  fb5e048

  Copy full SHA for fb5e048

• match dK_alpha

  YuuuXie

  committed
  5be8d35

  Copy full SHA for 5be8d35

Commits on Sep 23, 2021

• pass unit test with serial dKnK

  YuuuXie

  committed
  72af360

  Copy full SHA for 72af360

• compute_likelihood_grad pass unit test with mpirun

  YuuuXie

  committed
  6458838

  Copy full SHA for 6458838

• remove print flags

  YuuuXie

  committed
  3f544f6

  Copy full SHA for 3f544f6

• add timer

  YuuuXie

  committed
  5e9174b

  Copy full SHA for 5e9174b

• add timer

  YuuuXie

  committed
  0b0f8f6

  Copy full SHA for 0b0f8f6

• add initial value to .h

  YuuuXie

  committed
  23bc528

  Copy full SHA for 23bc528

• separate like_grad parts

  YuuuXie

  committed
  96ef772

  Copy full SHA for 96ef772

• merge methods & rm distmatrix from header

  YuuuXie

  committed
  3f00346

  Copy full SHA for 3f00346

• add ParallelSGP to pybind

  YuuuXie

  committed
  10f2f32

  Copy full SHA for 10f2f32

Commits on Sep 30, 2021

• fix name

  YuuuXie

  committed
  4699007

  Copy full SHA for 4699007

• add parallelsgp module

  YuuuXie

  committed
  ecd81f2

  Copy full SHA for ecd81f2

• try adding cppoptlib

  YuuuXie

  committed
  5c05c85

  Copy full SHA for 5c05c85

• rm cppoptlib

  YuuuXie

  committed
  b476030

  Copy full SHA for b476030

• add set_hyperparameters

  YuuuXie

  committed
  ac5dd1d

  Copy full SHA for ac5dd1d

• Merge branch 'mpi_distmat' of https://github.com/mir-group/flare_pp into mpi_distmat

  YuuuXie

  committed
  aca3e74

  Copy full SHA for aca3e74

• unify sgp and parsgp interface for training

  YuuuXie

  committed
  1c18cd6

  Copy full SHA for 1c18cd6

• fix small bugs

  YuuuXie

  committed
  b97af76

  Copy full SHA for b97af76

Commits on Oct 3, 2021

• optimization works in python

  YuuuXie

  committed
  d5102b7

  Copy full SHA for d5102b7

• mpi training in python works

  YuuuXie

  committed
  8d3dedb

  Copy full SHA for 8d3dedb

Commits on Oct 10, 2021

• fix sparse_ind bug

  YuuuXie

  committed
  542a4d1

  Copy full SHA for 542a4d1

Commits on Oct 12, 2021

• resolve compilation issue of '-fPIC' of scalapack static

  YuuuXie

  committed
  125bf28

  Copy full SHA for 125bf28

• add compilation instruction to README

  YuuuXie

  committed
  17b4d61

  Copy full SHA for 17b4d61

Commits on Oct 14, 2021

• fix dK_alpha bug

  YuuuXie

  committed
  78f2d1e

  Copy full SHA for 78f2d1e

• add update_db to parallel_sgp

  YuuuXie

  committed
  1824269

  Copy full SHA for 1824269

• fix a bug in initialization

  YuuuXie

  committed
  da3adaa

  Copy full SHA for da3adaa

• fix mpi_bcast of likelihood grad

  YuuuXie

  committed
  093aa1e

  Copy full SHA for 093aa1e

Commits on Oct 19, 2021

• add destructor & fix a bug of like_grad with multiple kernels

  YuuuXie

  committed
  b81f014

  Copy full SHA for b81f014

• rm debug flags

  YuuuXie

  committed
  dcaaf34

  Copy full SHA for dcaaf34

• rm unsupported class variables

  YuuuXie

  committed
  8dad80f

  Copy full SHA for 8dad80f

• fix a bug of local_noise in set_hyp

  YuuuXie

  committed
  98d8780

  Copy full SHA for 98d8780

• rm print flags

  YuuuXie

  committed
  48a59b7

  Copy full SHA for 48a59b7

Commits on Oct 20, 2021

• add destructors

  YuuuXie

  committed
  7a8151f

  Copy full SHA for 7a8151f

Commits on Oct 23, 2021

• add deepcopy to mean_efs to prevent memory accumulation

  YuuuXie

  committed
  b587629

  Copy full SHA for b587629

• solve conflict with master

  YuuuXie

  committed
  62936c0

  Copy full SHA for 62936c0

• change dir of parsgp test

  YuuuXie

  committed
  acf537e

  Copy full SHA for acf537e

Commits on Oct 27, 2021

• solve conflict with master

  YuuuXie

  committed
  995c27a

  Copy full SHA for 995c27a

• add back b2 to python binding

  YuuuXie

  committed
  f745867

  Copy full SHA for f745867

• add virtual to fix bugs

  YuuuXie

  committed
  f26e9e8

  Copy full SHA for f26e9e8

• fix bug in add_random_envs

  YuuuXie

  committed
  8896bae

  Copy full SHA for 8896bae

• add err handler & fence & barrier

  YuuuXie

  committed
  10161f1

  Copy full SHA for 10161f1

Commits on Nov 1, 2021

• able to update one frame when adding training data

  YuuuXie

  committed
  26c5ac2

  Copy full SHA for 26c5ac2

• add condition for finalize

  YuuuXie

  committed
  920da5b

  Copy full SHA for 920da5b

• add timing for likelihood_grad

  YuuuXie

  committed
  a65310a

  Copy full SHA for a65310a

• fix a bug of update training set

  YuuuXie

  committed
  d19e7ca

  Copy full SHA for d19e7ca

Commits on Nov 2, 2021

• add 'update' arg to 'build' in python

  YuuuXie

  committed
  31e59ba

  Copy full SHA for 31e59ba

• fix a small bug of KnK matrix size

  YuuuXie

  committed
  55a3ef8

  Copy full SHA for 55a3ef8

• add precompute_KnK to ParallelSGP

  YuuuXie

  committed
  cf6e675

  Copy full SHA for cf6e675

• pass test of parallel prediction

  YuuuXie

  committed
  e1c5d7c

  Copy full SHA for e1c5d7c

• merge master python tests

  YuuuXie

  committed
  6824005

  Copy full SHA for 6824005

• add python binding for predict functions

  YuuuXie

  committed
  3d04e27

  Copy full SHA for 3d04e27

Commits on Nov 3, 2021

• predict_on_structures now compute descriptorsw

  YuuuXie

  committed
  7cc895d

  Copy full SHA for 7cc895d

• predict_on_struc returns mean values

  YuuuXie

  committed
  8231365

  Copy full SHA for 8231365

• randomly set species

  YuuuXie

  committed
  7640208

  Copy full SHA for 7640208

Commits on Nov 4, 2021

• change 'specific' mode of sparse_gp to allow different atoms for different kernels

  YuuuXie

  committed
  3e48c4a

  Copy full SHA for 3e48c4a

• predict_on_structures returns structure list

  YuuuXie

  committed
  6ec2bc6

  Copy full SHA for 6ec2bc6

• add predict_on_structures to python unit test

  YuuuXie

  committed
  530f99b

  Copy full SHA for 530f99b

Commits on Nov 5, 2021

• add sparse desc by update

  YuuuXie

  committed
  ce4e7c8

  Copy full SHA for ce4e7c8

• update and pop training_structures when update one structure

  YuuuXie

  committed
  2ef1203

  Copy full SHA for 2ef1203

Commits on Nov 6, 2021

• replace computation of dKnK with the SparseGP::compute_dKnK

  YuuuXie

  committed
  0b4da78

  Copy full SHA for 0b4da78

• update gather/allgather interface

  YuuuXie

  committed
  95a1bdd

  Copy full SHA for 95a1bdd

• R is gathered from QR

  YuuuXie

  committed
  dd32f22

  Copy full SHA for dd32f22

• change Matrix into Eigen::Matrix

  YuuuXie

  committed
  fd140b7

  Copy full SHA for fd140b7