Open njzjz opened 1 year ago
TiborGY
commented
1 year ago PSIO error 12 means write error: https://github.com/psi4/psi4/blob/58efb602ee9fdf3d774a3a6f073dbf47f2ac249b/psi4/src/psi4/libpsio/config.h#L55
Unfortunately your environment does not seem to give you the rest of the error message, so we dont actually know why a write has failed. Are you sure you have enough free disk space for the temporary files?
njzjz
commented
1 year ago The disk space for the temporary file is about 245 GB. I don't know exactly how much space it requires.
Could this kind of error raise a Python exception? I use try...except to mark failed points, and core dumped can not be caught within the Python script.
loriab
commented
1 year ago The input file would be needed to see if it can be reproduced.
njzjz
commented
1 year ago Thanks. Below is the code to call psi4. I have omitted the code for reading data and processing and storing data.
import psi4
import numpy as np
# Actually, data is read from the file
data = {
"atom_names": ["C", "H", "N", "O"],
"atom_types": np.array([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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3, 3, 3, 3]),
"coords": np.array([[[-3.9865585648, -1.8582760752, 0.0587669877], [0.7980528366, 0.9905034199, -3.8757579839], [0.0178106787, -3.8114712569, -1.287341706], [0.1736042014, 2.8676674012, -2.6686480772], [1.5168871292, -3.4840112517, -1.2165490831], [5.9928177782, -1.0263175637, -0.727870595], [3.017388062, -3.0468838322, 0.725796647], [-1.1257063419, 2.2024569872, -2.1982624119], [3.7523959141, -2.0176820993, -0.1459387132], [2.6259054243, -0.1622076966, 1.1085321105], [2.049646823, 1.0182428923, 0.6838607968], [1.4062565931, 2.114871008, 1.4772425059], [-0.2523568246, -4.016672408, 1.0999647374], [2.3255033754, 3.3522821937, 1.6200106665], [3.7046766018, 2.9848831541, 2.1651825241], [1.1735625484, -4.5811334275, 0.9540162067], [2.4315347043, 4.0937068732, 0.2851573364], [3.2575655511, 5.3716076028, 0.3706631766], [6.7031283129, 1.0016787128, 0.6498103659], [5.2035205069, -1.8267984714, 0.310962209], [-0.8282256535, -1.9486626369, -0.0358093116], [-0.4674373308, 0.2364862053, -3.4484642696], [7.1610170448, -0.2486147189, -0.1207126491], [-6.5341397454, -0.0411486966, 1.763398572], [-7.0404010675, -0.1062099769, -0.5364760195], [-1.0082892403, 0.037578979, -1.0747103581], [-6.0424831429, 0.8949890937, 2.8738572621], [-3.9739485022, 1.6408470604, 2.0051764222], [-6.6202866638, 0.5125099574, -1.8747825793], [-2.4878029945, 1.6996757336, 2.3582928852], [-1.4969461675, -0.143208941, 1.1102807713], [-4.1119885595, -1.0217653672, -0.7882992237], [-4.2973010873, -0.0415607786, -1.847178749], [5.6555819166, -2.8072201692, 0.4649965987], [5.201041384, -1.3183226287, 1.275497881], [-6.4356133459, 1.9033044571, 2.6781390688], [-7.5986205227, -0.2620689834, 1.9372581796], [6.3682326149, -1.7072084584, -1.4948520646], [5.3206432155, -0.3239359453, -1.229189328], [7.7228189317, -0.8981040693, 0.5527825706], [-4.3826738861, 2.6590816954, 1.9262780172], [5.9839080242, 0.7189536547, 1.4232364458], [7.5670658959, 1.4471289795, 1.1506060496], [5.2715598856, 1.6911175648, -0.6410698838], [6.7401534369, 2.3783433323, -0.8548688716], [-0.2650650476, -0.8249766121, -3.3167075961], [-0.9582567982, -4.838510552, 1.2653010477], [1.6552489511, -4.6724884576, 1.9281749784], [-0.3212780436, -3.315804755, 1.9333902078], [-1.9737534209, 2.3488013352, 1.6496947171], [1.157489124, -5.5644038395, 0.4736865667], [1.6275273384, -2.4374739884, -1.5061238113], [-2.3642992505, 2.0857513251, 3.371584088], [-2.1504701352, -0.2655020749, 2.9919815006], [2.0884535097, -4.1168389228, -1.9076390582], [-1.9375728156, 2.4525666513, -2.8929217819], [0.9661878722, 2.6551256953, -1.938751508], [1.6022040792, 0.7841724731, -3.157160468], [0.0402096324, 3.9447647083, -2.7816946538], [-1.2467265935, 0.3780860721, -4.2084641204], [1.1057392299, 0.6873032458, -4.8782205076], [-4.102496078, 1.1336002767, 1.0432065929], [-1.3867786933, 2.5179094766, -1.1894915886], [4.3013076735, 5.1465739282, 0.5694956485], [3.7453584779, -2.3026160384, -1.2011059512], [-3.5436704242, -0.2263867341, -2.6214227607], [-4.1477441305, 0.9681629588, -1.4354234002], [-6.385367684, 1.5720686653, -1.6936358888], [-8.1293707449, -0.008364784, -0.4022235369], [-6.7835818427, -1.173938393, -0.5304731763], [-5.9690222981, -0.9837445356, 1.7942878858], [-6.4295543745, 0.5345655452, 3.830479889], [-0.1642482084, -4.8870667374, -1.3346361942], [-0.4246651863, -3.3287027858, -2.1574341496], [7.835478458, 0.065926779, -0.9217655086], [0.2801993817, 0.956672257, 2.7286499313], [1.7470023071, 1.3598969122, 3.3460428246], [-3.829442847, -2.5711178289, 0.8127942519], [4.203697503, 3.8694521886, 2.5508165156], [2.7646312712, -0.6072610943, 2.0709963606], [1.8229417322, 3.9989502928, 2.3471195754], [2.8732914, 3.4283145737, -0.4584330667], [1.4232745887, 4.3450459859, -0.0530997127], [4.329620552, 2.5614196883, 1.3839267312], [2.8817086248, 6.0173146394, 1.1617793827], [3.6252554546, 2.2719743014, 2.9830155292], [-7.4434855186, 0.4410405616, -2.5890974162], [3.2010845698, 5.9140326326, -0.5704640658], [0.5088426041, 2.4245642089, 0.9265473367], [6.0893550874, 2.0422571744, -0.1530407297], [-1.862134336, 0.4034738095, 2.2937204065], [-1.4138901004, 0.644406742, 0.0455352137], [-0.7095180298, -1.2632553768, -1.1676109686], [-0.6142721952, -3.2938004635, -0.1006904859], [1.97840289, -3.6814323378, 0.1492620683], [-0.9437197295, 0.7707072186, -2.1950994456], [3.0305830988, -0.7745567723, -0.0274639225], [2.1393686347, 1.0406513402, -0.6640047053], [2.7240826757, -0.0248994808, -1.0779442116], [0.9643448844, 1.7016817799, 2.7995701586], [-1.1897838302, -1.4434141329, 1.1398546593], [-4.6504826146, 0.9351211172, 3.0300907006], [0.5539503234, 2.3790185178, -3.9384263268], [-6.3763829627, 0.5740180369, 0.5055913646], [-5.5478006374, -0.1317291531, -2.5089137294], [3.352889237, -3.2422161861, 1.8787720858]]])
}
psi4.set_memory("8 GB")
psi4.set_num_threads(4)
types = np.array(data["atom_names"])[data["atom_types"]]
buff = ["0 1"]
for tt, cc in zip(types, data["coords"][0]):
buff.append(" ".join([tt] + [str(x) for x in cc]))
psi4.geometry("\n".join(buff))
G, wfn = psi4.gradient("WB97M-D3BJ/def2-TZVPPD", return_wfn=True)
energy = wfn.energy()
wfn.gradient().print_out()
gradient = np.array(G)
# post process energy and gradient
susilehtola
commented
8 months ago I bet this is because of the calls to exit() in libpsio, combined with the lack of flushing of the error messages to the output. I have replaced the calls to exit() in #3118, which should solve this issue.
I use psi4 v1.7 to perform gradient calculations under the WB97M-D3BJ/DEF2-TZVPPD level. Most structures work fine, but I get the following error in some structures without a clear error message.
I used conda to install psi4 in a new environment.
Below is the full log, which includes the geometry:
CPU information: