IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed

[deleep225]

I am able to do the dpgen process in my laptop all the four iterations for methane molecule. But when I run it in the PBS nodes I am getting the above error during the second iteration. (1, 8).

[AnguseZhang]

Please provide necessary information including the version of software and installation way, input file, running commands, error log , etc., AS DETAILED AS POSSIBLE to help locate and reproduce your problem.

[deleep225]

Hi Zhang,
I used DeePMD-kit v2.0.3
dpgen Version: 0.10.3
I have installed deepmd through the conda cpu version.

here is the machine.json
{
"deepmd_version" : "2.0",
"train": [
{
"machine": {
"batch": "pbs",
"context_type": "LocalContext",
"work_path": "./tmp"
},
"resources": {
"numb_node": 1,
"numb_gpu": 0,
"partition": "all",
"time_limit": "120:0:0",
"task_per_node": 32,
"exclude_list": [],
"module_list": [],
"source_list": []
},
"command": "~/anaconda3/envs/deepmd/bin/dp"
}
],
"model_devi": [
{
"machine": {
"batch": "pbs",
"context_type": "LocalContext",
"work_path": "./tmp"
},
"resources": {
"numb_node": 1,
"numb_gpu": 0,
"partition": "all",
"time_limit": "120:0:0",
"task_per_node": 32,
"source_list": [
],
"module_list": [],
"exclude_list": [],
"envs": {
"GMX_DEEPMD_INPUT_JSON": "input.json"
}
},
"command": " /anaconda3/envs/deepmd/bin/lmp",
"group_size": 1
}
],
"fp": [
{
"machine": {
"batch": "pbs",
"context_type": "LocalContext",
"work_path": "./tmp"
},
"resources": {
"numb_node": 1,
"numb_gpu": 0,
"time_limit": "120:0:0",
"task_per_node": 32,
"partition": "cpu",
"exclude_list": [],
"source_list": [
],
"module_list": []
},
"command": "/softwares/q-e-qe-6.3/bin/pw.x < input",
"group_size": 20

param.json

"type_map": [
"H",
"C"
],
"mass_map": [
1,
12
],
"init_data_prefix": "./CH4.init.data/",
"init_data_sys": [
"02.md/sys-0004-0001/deepmd"
],
"init_batch_size": [
8
],
"sys_configs": [
[
"./CH4.init.data/01.scale_pert/sys-0004-0001/scale-1.000/00000*/POSCAR"
],
[
"./CH4.init.data/01.scale_pert/sys-0004-0001/scale-1.000/00001*/POSCAR"
]
],
"sys_batch_size": [
8,
8
],
"_comment": " that's all ",
"numb_models": 4,
"train_param": "input.json",
"default_training_param": {
"model": {
"type_map": [
"H",
"C"
],
"descriptor": {
"type": "se_a",
"sel": [
16,
4
],
"rcut_smth": 0.5,
"rcut": 5.00,
"neuron": [
10,
20,
40
],
"resnet_dt": false,
"axis_neuron": 12,
"seed": 1
},
"fitting_net": {
"neuron": [
120,
120,
120
],
"resnet_dt": true,
"seed": 1
}
},
"learning_rate": {
"type": "exp",
"start_lr": 0.001,
"decay_steps": 200
},
"loss": {
"start_pref_e": 0.02,
"limit_pref_e": 2,
"start_pref_f": 1000,
"limit_pref_f": 1,
"start_pref_v": 0.0,
"limit_pref_v": 0.0
},
"training": {
"stop_batch": 40000,
"disp_file": "lcurve.out",
"disp_freq": 1000,
"numb_test": 4,
"save_freq": 1000,
"save_ckpt": "model.ckpt",
"disp_training": true,
"time_training": true,
"profiling": false,
"profiling_file": "timeline.json",
"_comment": "that's all"
}
},
"model_devi_dt": 0.002,
"model_devi_skip": 0,
"model_devi_f_trust_lo": 0.012,
"model_devi_f_trust_hi": 0.10,
"model_devi_clean_traj": false,
"model_devi_jobs": [
{
"sys_idx": [
0
],
"temps": [
50
],
"press": [
1
],
"trj_freq": 10,
"nsteps": 1000,
"ensemble": "nvt",
"_idx": "00"
},
{
"sys_idx": [
1
],
"temps": [
50
],
"press": [
1
],
"trj_freq": 10,
"nsteps": 3000,
"ensemble": "nvt",
"_idx": "01"
}
],
"fp_style": "pwscf",
"shuffle_poscar": false,
"fp_task_max": 30,
"fp_task_min": 5,
"fp_pp_path": "./CH4.init.data/pp/",
"fp_pp_files": [
"H.tm.pbe.UPF", "C.tm.pbe.UPF"
],

"user_fp_params": {
"_comment": "pseudo_dir will be added automatically",
"control": {
"calculation": "scf",
"restart_mode": "from_scratch",
"outdir": "./OUT",
"tprnfor": true,
"tstress": true,
"disk_io": "none"
},
"_comment": "ibrav, nat and ntyp will be added automatically",
"system": {
"ecutwfc": 110,
"ts_vdw_econv_thr": 1e-8,
"nosym": true
},
"electrons": {
"conv_thr": 1e-8
},
"kspacing": 100
},
"_comment": " that's all "
}

[deleep225]

Error message

Traceback (most recent call last):
File "/home/reddy/.local/bin/dpgen", line 8, in
sys.exit(main())
File "/home/reddy/.local/lib/python3.9/site-packages/dpgen/main.py", line 175, in main
args.func(args)
File "/home/reddy/.local/lib/python3.9/site-packages/dpgen/generator/run.py", line 2997, in gen_run
run_iter (args.PARAM, args.MACHINE)
File "/home/reddy/.local/lib/python3.9/site-packages/dpgen/generator/run.py", line 2986, in run_iter
post_fp (ii, jdata)
File "/home/reddy/.local/lib/python3.9/site-packages/dpgen/generator/run.py", line 2867, in post_fp
post_fp_pwscf(iter_index, jdata)
File "/home/reddy/.local/lib/python3.9/site-packages/dpgen/generator/run.py", line 2608, in post_fp_pwscf
_sys = dpdata.LabeledSystem(oo, fmt = 'qe/pw/scf', type_map = jdata['type_map'])
File "/home/reddy/.local/lib/python3.9/site-packages/dpdata/system.py", line 883, in init
self.from_fmt(file_name, fmt, type_map=type_map, begin= begin, step=step, **kwargs)
File "/home/reddy/.local/lib/python3.9/site-packages/dpdata/system.py", line 120, in from_fmt
return self.from_fmt_obj(load_format(fmt), file_name, **kwargs)
File "/home/reddy/.local/lib/python3.9/site-packages/dpdata/system.py", line 890, in from_fmt_obj
data = fmtobj.from_labeled_system(file_name, **kwargs)
File "/home/reddy/.local/lib/python3.9/site-packages/dpdata/plugins/qe.py", line 42, in from_labeled_system
= dpdata.qe.scf.get_frame(file_name)
File "/home/reddy/.local/lib/python3.9/site-packages/dpdata/qe/scf.py", line 137, in get_frame
np.array(energy)[np.newaxis], force[np.newaxis, :, :], stress[np.newaxis, :, :]
IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed

[HuangJiameng]

According to the IndexError reported by dpdata, maybe there's something wrong with your data set. If the problem hasn't been solved, please provide your input files to help locate and reproduce the problem.

[njzjz]

Fixed by #572.