Open GUANGZChen opened 1 year ago
Sideboard
commented
1 year ago It looks like your calculation did not finish. Was it killed by the queuing system?
(When you want to quote raw text on Github issues, you should use three backticks ` above and below the quoted text, so it's not parsed as markdown.)
GUANGZChen
commented
1 year ago Hi, After rewriting the inputs, I set up the MPI gap_fit run. However, it was stopped and here is the output messages. Could some help out with this? Thank you so much in advance.
libAtoms::Hello World: 2023-07-05 15:24:01 libAtoms::Hello World: git version https://github.com/libAtoms/QUIP.git,v0.9.14-dirty libAtoms::Hello World: QUIP_ARCH linux_x86_64_gfortran_openmpi+openmp libAtoms::Hello World: compiled on Jul 5 2023 at 06:44:18 libAtoms::Hello World: MPI parallelisation with 48 processes libAtoms::Hello World: OpenMP parallelisation with 1 threads WARNING: libAtoms::Hello World: environment variable OMP_STACKSIZE not set explicitly. The default value - system and compiler dependent - may be too small for some applications. libAtoms::Hello World: MPI run with the same seed on each process libAtoms::Hello World: Random Seed = -1633787871 libAtoms::Hello World: global verbosity = 0
Calls to system_timer will do nothing by default
MPI hostnames :: arc-c009 MPI host refs :: 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 MPI my_host : 0 MPI hostname : arc-c009
================================ Input parameters ==============================
config_file = atoms_filename = //MANDATORY// at_file = CN_train_dataset.xyz gap = "distance_2b n_sparse=15 theta_uniform=1.0 sparse_method=FILE sparse_file=1.input covariance_type=ard_se cutoff=4.5 delta=2.0 add_species=F:distance_2b n_sparse=15 theta_uniform=1.0 sparse_method=FILE sparse_file=2.input covariance_type=ard_se cutoff=4.5 delta=2.0 add_species=F:distance_2b n_sparse=15 theta_uniform=1.0 sparse_method=FILE sparse_file=3.input covariance_type=ard_se cutoff=4.5 delta=2.0 add_species=F:angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=FILE sparse_file=4.input covariance_type=ard_se cutoff=2.5 delta=0.05 add_species=F:angle_3b n_sparse=0 theta_uniform=1.0 sparse_method=FILE sparse_file=5.input covariance_type=ard_se cutoff=2.5 delta=0.05 add_species=F:angle_3b n_sparse=0 theta_uniform=1.0 sparse_method=FILE sparse_file=6.input covariance_type=ard_se cutoff=2.5 delta=0.05 add_species=F:angle_3b n_sparse=0 theta_uniform=1.0 sparse_method=FILE sparse_file=7.input covariance_type=ard_se cutoff=2.5 delta=0.05 add_species=F:angle_3b n_sparse=0 theta_uniform=1.0 sparse_method=FILE sparse_file=8.input covariance_type=ard_se cutoff=2.5 delta=0.05 add_species=F:angle_3b n_sparse=0 theta_uniform=1.0 sparse_method=FILE sparse_file=9.input covariance_type=ard_se cutoff=2.5 delta=0.05 add_species=F:soap n_max=12 l_max=4 atom_sigma=0.5 zeta=4.0 cutoff=4.5 cutoff_transition_width=1.0 central_weight=1.0 n_sparse=45 delta=0.2 covariance_type=dot_product sparse_method=FILE sparse_file=10.input radial_decay=-0.5 add_species=F soap_exponent=1:soap n_max=12 l_max=4 atom_sigma=0.5 zeta=4.0 cutoff=4.5 cutoff_transition_width=1.0 central_weight=1.0 n_sparse=45 delta=0.2 covariance_type=dot_product sparse_method=FILE sparse_file=11.input radial_decay=-0.5 add_species=F soap_exponent=1" e0 = C:-148.6822264562:N:-271.4749770587 local_property0 = 0.0 e0_offset = 0.0 e0_method = isolated default_kernel_regularisation = //MANDATORY// default_sigma = "0.001 0.01 0.05 0.0" default_kernel_regularisation_local_property = 0.001 default_local_property_sigma = 0.001 sparse_jitter = 1.0e-8 hessian_displacement = 1.0e-2 hessian_delta = 1.0e-2 baseline_param_filename = quip_params.xml core_param_file = quip_params.xml baseline_ip_args = core_ip_args = energy_parameter_name = energy local_property_parameter_name = local_property force_parameter_name = force virial_parameter_name = virial stress_parameter_name = stress hessian_parameter_name = hessian config_type_parameter_name = config_type kernel_regularisation_parameter_name = sigma sigma_parameter_name = sigma force_mask_parameter_name = force_mask local_property_mask_parameter_name = local_property_mask parameter_name_prefix = config_type_kernel_regularisation = config_type_sigma = Liquid:0.050:0.5:0.5:0.0:Liquid_Interface:0.050:0.5:0.5:0.0:Amorphous_Bulk:0.005:0.2:0.2:0.0:Amorphous_Surfaces:0.005:0.2:0.2:0.0:Surfaces:0.002:0.1:0.2:0.0:Dimer:0.002:0.1:0.2:0.0:Fullerenes:0.002:0.1:0.2:0.0:Defects:0.001:0.01:0.05:0.0:Crystalline_Bulk:0.001:0.01:0.05:0.0:Nanotubes:0.001:0.01:0.05:0.0:Graphite:0.001:0.01:0.05:0.0:Diamond:0.001:0.01:0.05:0.0:Graphene:0.001:0.01:0.05:0.0:Graphite_Layer_Sep:0.001:0.01:0.05:0.0:Single_Atom:0.0001:0.001:0.05:0.0 kernel_regularisation_is_per_atom = T sigma_per_atom = T do_copy_atoms_file = T do_copy_at_file = F sparse_separate_file = T sparse_use_actual_gpcov = F gap_file = gap_new.xml gp_file = gap.xml verbosity = NORMAL rnd_seed = -1 openmp_chunk_size = 10000 do_ip_timing = F template_file = template.xyz sparsify_only_no_fit = F dryrun = F condition_number_norm = linear_system_dump_file = mpi_blocksize_rows = 0 mpi_blocksize_cols = 100 mpi_print_all = F export_covariance = F
======================================== ======================================
============== Gaussian Approximation Potentials - Database fitting ============
MPI_ABORT was invoked on rank 47 in communicator MPI_COMM_WORLD with errorcode 1.
gabor1
commented
1 year ago In the latest version we don't require this two-step fitting. can I close this?
Hi GAP developers, I am currently trying MPI gap fitting on an HPC system. I successfully finished the installation part.
For using part, I followed the instruction as follows,
I simply add sparsify_only_no_fit=T at the end of my original code which is attached below.
gap_fit at_file=CN_train_dataset.xyz e0={C:-148.6822264562:N:-271.4749770587} gap={distance_2b n_sparse=15 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=4.5 delta=2.0:angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05:soap n_max=12 l_max=4 atom_sigma=0.5 zeta=4.0 cutoff=4.5 cutoff_transition_width=1.0 central_weight=1.0 n_sparse=10000 delta=0.2 covariance_type=dot_product sparse_method=cur_points radial_decay=-0.5} default_sigma={0.001 0.01 0.05 0.0} config_type_sigma={Liquid:0.050:0.5:0.5:0.0:Liquid_Interface:0.050:0.5:0.5:0.0:Amorphous_Bulk:0.005:0.2:0.2:0.0:Amorphous_Surfaces:0.005:0.2:0.2:0.0:Surfaces:0.002:0.1:0.2:0.0:Dimer:0.002:0.1:0. :0.0:Fullerenes:0.002:0.1:0.2:0.0:Defects:0.001:0.01:0.05:0.0:Crystalline_Bulk:0.001:0.01:0.05:0.0:Nanotubes:0.001:0.01:0.05:0.0:Graphite:0.001:0.01:0.05:0.0:Diamond:0.001:0.01:0.05:0.0:Graphene:0.001:0.01:0.05:0.0:Graphite_Layer_Sep:0.001:0.01:0.05:0.0:Single_Atom:0.0001:0.001:0.05:0.0} energy_parameter_name=energy force_parameter_name=force sparse_jitter=1.0e-8 do_copy_at_file=F openmp_chunk_size=10000 gp_file=gap.xml sparsify_only_no_fit=T| tee out
Also, the output of this code is as follows: libAtoms::Hello World: 2023-06-29 00:41:14 libAtoms::Hello World: git version https://github.com/libAtoms/QUIP,v0.9.12-dirty libAtoms::Hello World: QUIP_ARCH linux_x86_64_gfortran_openmp libAtoms::Hello World: compiled on Jan 15 2023 at 16:26:45 libAtoms::Hello World: OpenMP parallelisation with 1 threads WARNING: libAtoms::Hello World: environment variable OMP_STACKSIZE not set explicitly. The default value - system and compiler dependent - may be too small for some applications. libAtoms::Hello World: Random Seed = 2474568 libAtoms::Hello World: global verbosity = 0
Calls to system_timer will do nothing by default
================================ Input parameters ==============================
config_file = atoms_filename = //MANDATORY// at_file = CN_train_dataset.xyz gap = "distance_2b n_sparse=15 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=4.5 delta=2.0:angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05:soap n_max=12 l_max=4 atom_sigma=0.5 zeta=4.0 cutoff=4.5 cutoff_transition_width=1.0 central_weight=1.0 n_sparse=10000 delta=0.2 covariance_type=dot_product sparse_method=cur_points radial_decay=-0.5" e0 = C:-148.6822264562:N:-271.4749770587 local_property0 = 0.0 e0_offset = 0.0 e0_method = isolated default_kernel_regularisation = //MANDATORY// default_sigma = "0.001 0.01 0.05 0.0" default_kernel_regularisation_local_property = 0.001 default_local_property_sigma = 0.001 sparse_jitter = 1.0e-8 hessian_displacement = 1.0e-2 hessian_delta = 1.0e-2 baseline_param_filename = quip_params.xml core_param_file = quip_params.xml baseline_ip_args = core_ip_args = energy_parameter_name = energy local_property_parameter_name = local_property force_parameter_name = force virial_parameter_name = virial stress_parameter_name = stress hessian_parameter_name = hessian config_type_parameter_name = config_type kernel_regularisation_parameter_name = sigma sigma_parameter_name = sigma force_mask_parameter_name = force_mask parameter_name_prefix = config_type_kernel_regularisation = config_type_sigma = Liquid:0.050:0.5:0.5:0.0:Liquid_Interface:0.050:0.5:0.5:0.0:Amorphous_Bulk:0.005:0.2:0.2:0.0:Amorphous_Surfaces:0.005:0.2:0.2:0.0:Surfaces:0.002:0.1:0.2:0.0:Dimer:0.002:0.1:0.2:0.0:Fullerenes:0.002:0.1:0.2:0.0:Defects:0.001:0.01:0.05:0.0:Crystalline_Bulk:0.001:0.01:0.05:0.0:Nanotubes:0.001:0.01:0.05:0.0:Graphite:0.001:0.01:0.05:0.0:Diamond:0.001:0.01:0.05:0.0:Graphene:0.001:0.01:0.05:0.0:Graphite_Layer_Sep:0.001:0.01:0.05:0.0:Single_Atom:0.0001:0.001:0.05:0.0 kernel_regularisation_is_per_atom = T sigma_per_atom = T do_copy_atoms_file = T do_copy_at_file = F sparse_separate_file = T sparse_use_actual_gpcov = F gap_file = gap_new.xml gp_file = gap.xml verbosity = NORMAL rnd_seed = -1 openmp_chunk_size = 10000 do_ip_timing = F template_file = template.xyz sparsify_only_no_fit = T dryrun = F condition_number_norm = linear_system_dump_file = mpi_blocksize_rows = 0 mpi_blocksize_cols = 100 mpi_print_all = F
======================================== ======================================
WARNING: sparsify_only_no_fit == T: force, virial, hessian, stress parameters are ignored.
============== Gaussian Approximation Potentials - Database fitting ============
Initial parsing of command line arguments finished. Found 3 GAPs. Descriptors have been parsed XYZ file read Old GAP: {distance_2b n_sparse=15 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=4.5 delta=2.0} New GAP: {distance_2b n_sparse=15 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=4.5 delta=2.0 Z1=6 Z2=6} New GAP: {distance_2b n_sparse=15 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=4.5 delta=2.0 Z1=6 Z2=7} New GAP: {distance_2b n_sparse=15 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=4.5 delta=2.0 Z1=7 Z2=7} Old GAP: {angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05} New GAP: {angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=6 Z1=6 Z2=6} New GAP: {angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=6 Z1=6 Z2=7} New GAP: {angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=6 Z1=7 Z2=7} New GAP: {angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=7 Z1=6 Z2=6} New GAP: {angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=7 Z1=6 Z2=7} New GAP: {angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=7 Z1=7 Z2=7} Old GAP: {soap n_max=12 l_max=4 atom_sigma=0.5 zeta=4.0 cutoff=4.5 cutoff_transition_width=1.0 central_weight=1.0 n_sparse=10000 delta=0.2 covariance_type=dot_product sparse_method=cur_points radial_decay=-0.5} New GAP: {soap n_max=12 l_max=4 atom_sigma=0.5 zeta=4.0 cutoff=4.5 cutoff_transition_width=1.0 central_weight=1.0 n_sparse=10000 delta=0.2 covariance_type=dot_product sparse_method=cur_points radial_decay=-0.5 n_species=2 Z=6 species_Z={6 7 }} New GAP: {soap n_max=12 l_max=4 atom_sigma=0.5 zeta=4.0 cutoff=4.5 cutoff_transition_width=1.0 central_weight=1.0 n_sparse=10000 delta=0.2 covariance_type=dot_product sparse_method=cur_points radial_decay=-0.5 n_species=2 Z=7 species_Z={6 7 }} Sparse points and target errors per pre-defined types of configurations Liquid 0.50000000000000003E-001 0.50000000000000000E+000 0.50000000000000000E+000 0.00000000000000000E+000 Liquid_Interface 0.50000000000000003E-001 0.50000000000000000E+000 0.50000000000000000E+000 0.00000000000000000E+000 Amorphous_Bulk 0.50000000000000001E-002 0.20000000000000001E+000 0.20000000000000001E+000 0.00000000000000000E+000 Amorphous_Surfaces 0.50000000000000001E-002 0.20000000000000001E+000 0.20000000000000001E+000 0.00000000000000000E+000 Surfaces 0.20000000000000000E-002 0.10000000000000001E+000 0.20000000000000001E+000 0.00000000000000000E+000 Dimer 0.20000000000000000E-002 0.10000000000000001E+000 0.20000000000000001E+000 0.00000000000000000E+000 Fullerenes 0.20000000000000000E-002 0.10000000000000001E+000 0.20000000000000001E+000 0.00000000000000000E+000 Defects 0.10000000000000000E-002 0.10000000000000000E-001 0.50000000000000003E-001 0.00000000000000000E+000 Crystalline_Bulk 0.10000000000000000E-002 0.10000000000000000E-001 0.50000000000000003E-001 0.00000000000000000E+000 Nanotubes 0.10000000000000000E-002 0.10000000000000000E-001 0.50000000000000003E-001 0.00000000000000000E+000 Graphite 0.10000000000000000E-002 0.10000000000000000E-001 0.50000000000000003E-001 0.00000000000000000E+000 Diamond 0.10000000000000000E-002 0.10000000000000000E-001 0.50000000000000003E-001 0.00000000000000000E+000 Graphene 0.10000000000000000E-002 0.10000000000000000E-001 0.50000000000000003E-001 0.00000000000000000E+000 Graphite_Layer_Sep 0.10000000000000000E-002 0.10000000000000000E-001 0.50000000000000003E-001 0.00000000000000000E+000 Single_Atom 0.10000000000000000E-003 0.10000000000000000E-002 0.50000000000000003E-001 0.00000000000000000E+000 default 0.10000000000000000E-002 0.10000000000000000E-001 0.50000000000000003E-001 0.00000000000000000E+000 Multispecies support added where requested
===================== Report on number of descriptors found ====================
Descriptor 1: distance_2b n_sparse=15 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=4.5 delta=2.0 Z1=6 Z2=6 Number of descriptors: 7382902 Number of partial derivatives of descriptors: 0
Descriptor 2: distance_2b n_sparse=15 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=4.5 delta=2.0 Z1=6 Z2=7 Number of descriptors: 44 Number of partial derivatives of descriptors: 0
Descriptor 3: distance_2b n_sparse=15 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=4.5 delta=2.0 Z1=7 Z2=7 Number of descriptors: 44 Number of partial derivatives of descriptors: 0
Descriptor 4: angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=6 Z1=6 Z2=6 Number of descriptors: 9039580 Number of partial derivatives of descriptors: 0
Descriptor 5: angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=6 Z1=6 Z2=7 Number of descriptors: 0 Number of partial derivatives of descriptors: 0
Descriptor 6: angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=6 Z1=7 Z2=7 Number of descriptors: 0 Number of partial derivatives of descriptors: 0
Descriptor 7: angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=7 Z1=6 Z2=6 Number of descriptors: 0 Number of partial derivatives of descriptors: 0
Descriptor 8: angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=7 Z1=6 Z2=7 Number of descriptors: 0 Number of partial derivatives of descriptors: 0
Descriptor 9: angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=7 Z1=7 Z2=7 Number of descriptors: 0 Number of partial derivatives of descriptors: 0
Descriptor 10: soap n_max=12 l_max=4 atom_sigma=0.5 zeta=4.0 cutoff=4.5 cutoff_transition_width=1.0 central_weight=1.0 n_sparse=10000 delta=0.2 covariance_type=dot_product sparse_method=cur_points radial_decay=-0.5 n_species=2 Z=6 species_Z={6 7 } Number of descriptors: 178167 Number of partial derivatives of descriptors: 0
Descriptor 11: soap n_max=12 l_max=4 atom_sigma=0.5 zeta=4.0 cutoff=4.5 cutoff_transition_width=1.0 central_weight=1.0 n_sparse=10000 delta=0.2 covariance_type=dot_product sparse_method=cur_points radial_decay=-0.5 n_species=2 Z=7 species_Z={6 7 } Number of descriptors: 79 Number of partial derivatives of descriptors: 0
======================================== ======================================
========================= Memory Estimate (per process) ========================
Descriptors Descriptor 1 :: x 1 7382902 memory 59 MB Descriptor 1 :: xPrime 1 0 memory 0 B Descriptor 2 :: x 1 44 memory 352 B Descriptor 2 :: xPrime 1 0 memory 0 B Descriptor 3 :: x 1 44 memory 352 B Descriptor 3 :: xPrime 1 0 memory 0 B Descriptor 4 :: x 3 9039580 memory 216 MB Descriptor 4 :: xPrime 3 0 memory 0 B Descriptor 5 :: x 3 0 memory 0 B Descriptor 5 :: xPrime 3 0 memory 0 B Descriptor 6 :: x 3 0 memory 0 B Descriptor 6 :: xPrime 3 0 memory 0 B Descriptor 7 :: x 3 0 memory 0 B Descriptor 7 :: xPrime 3 0 memory 0 B Descriptor 8 :: x 3 0 memory 0 B Descriptor 8 :: xPrime 3 0 memory 0 B Descriptor 9 :: x 3 0 memory 0 B Descriptor 9 :: xPrime 3 0 memory 0 B Descriptor 10 :: x 1501 178167 memory 2139 MB Descriptor 10 :: xPrime 1501 0 memory 0 B Descriptor 11 :: x 1501 79 memory 948 KB Descriptor 11 :: xPrime 1501 0 memory 0 B Subtotal 2416 MB
Covariances yY 21245 2965 memory 503 MB 2 yy 21245 21245 memory 3610 MB A 21245 24210 memory 4114 MB 2 Subtotal 12 GB
Peak1 2920 MB Peak2 12 GB PEAK 12 GB
Free system memory 373 GB Total system memory 405 GB
======================================== ======================================
========== Report on number of target properties found in training XYZ: ========
Number of target energies (property name: energy) found: 2965 Number of target local_properties (property name: local_property) found: 0 Number of target forces (property name: //IGNORE//) found: 0 Number of target virials (property name: //IGNORE//) found: 0 Number of target Hessian eigenvalues (property name: //IGNORE//) found: 0
================================= End of report ================================
===== Report on per-configuration/per-atom sigma (error parameter) settings ====
Number of per-configuration setting of energy_sigma found: 0 Number of per-configuration setting of force_sigma found: 0 Number of per-configuration setting of virial_sigma found: 0 Number of per-configuration setting of hessian_sigma found: 0 Number of per-configuration setting of local_propery_sigma found:0 Number of per-atom setting of force_atom_sigma found: 0 Number of per-component setting of force_component_sigma found: 0 Number of per-component setting of virial_component_sigma found: 0
================================= End of report ================================
WARNING: gpCoordinates_sparsify: number of data points (0) less than the number of sparse points (200), number of sparse points changed to 0 WARNING: gpCoordinates_sparsify: affected descriptor : angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=6 Z1=6 Z2=7 WARNING: gpCoordinates_sparsify: number of data points (0) less than the number of sparse points (200), number of sparse points changed to 0 WARNING: gpCoordinates_sparsify: affected descriptor : angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=6 Z1=7 Z2=7 WARNING: gpCoordinates_sparsify: number of data points (0) less than the number of sparse points (200), number of sparse points changed to 0 WARNING: gpCoordinates_sparsify: affected descriptor : angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=7 Z1=6 Z2=6 WARNING: gpCoordinates_sparsify: number of data points (0) less than the number of sparse points (200), number of sparse points changed to 0 WARNING: gpCoordinates_sparsify: affected descriptor : angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=7 Z1=6 Z2=7 WARNING: gpCoordinates_sparsify: number of data points (0) less than the number of sparse points (200), number of sparse points changed to 0 WARNING: gpCoordinates_sparsify: affected descriptor : angle_3b n_sparse=200 theta_uniform=1.0 sparse_method=uniform covariance_type=ard_se cutoff=2.5 delta=0.05 Z=7 Z1=7 Z2=7 Started CUR decomposition
However, there was no .xml file generated as expected and only a .idx file was created. it would be appreciated if someone could help out with this and provide more details on the MPI running instruction.
Thank you so much in advance.