Different results between torch.cdist and cdist

Hi all,

I am new to pytorch and I meet a problem that the result I got from cdist and torch.cdist is different. Part of the result in torch.cdist gives zeros but not in cdist, the rest part of the results are consistent between cdist and torch.cdist, why is this happened? following are part of the result:

cdist:

array([ 34.04802046, 31.41677035, 28.85756783, 26.39138085,
24.0468448 , 21.86313122, 19.89327195, 18.20681275,
16.88886593, 16.03058185, 15.70749236, 15.95214964,
16.73967861, 17.99896113, 19.63945935, 21.57438587,
23.73183279, 26.05658553, 28.507743 , 31.05538879,
33.67763256, 36.35833738, 39.08547631, 41.84997277,
44.64488753, 47.46484746, 50.3056409 , 53.16392826,
56.03703266, 58.92278669, 61.8194189 , 64.72546883,
67.63972263, 33.33915467, 30.64710421, 28.01768652,
25.47030663, 23.03220098, 20.74193925, 18.65405601,
16.84397719, 15.4099101 , 14.46413119, 14.10520659,
14.37715601, 15.2462578 , 16.61908959, 18.38314175,
20.43735948, 22.70311486, 25.12323996, 27.65724043,
30.27653728, 32.96080205, 35.69538112, 38.46954634,
41.27531656, 44.10666071, 46.95895315, 49.82859664,
52.71275752, 55.609177 , 58.5160348 , 61.43184915,
64.35540267, 67.28568655, 32.88967575, 30.15752863,
27.4813081 , 24.87906865, 22.37663555, 20.01148622,
17.83831109, 15.93584338, 14.411692 , 13.39561973,
13.00724375, 13.30165974, 14.23656959, 15.69795132,
17.55481237, 19.69561371, 22.03776216, 24.52363601,
27.1137324 , 29.78087048, 32.50609187, 35.27593756,
38.08067138, 40.91311885, 43.76789984, 46.64091356,
49.52898727, 52.42963229, 55.34087191, 58.26111796,
61.18908095, 64.1237038 , 67.06411224, 32.71027832,
29.96177682, 27.26634981, 24.64142029, 22.1121088 ,
19.71525088, 17.50533859, 15.56221839, 13.99744273,
12.94890594, 12.5467098 , 12.85168038, 13.81707098,
15.31852514, 17.21635775, 19.39455429, 21.76911799,
24.28250934, 26.89583651, 29.58262638, 32.32456567,
35.10873549, 37.92583643, 40.76904256, 43.633251 ,
46.51458217, 49.41004065, 52.31728088, 55.23444252,
58.16003269, 61.09284053, 64.0318743 , 66.97631438,
32.80539353, 30.06558842, 27.38038292, 24.76754188,
22.25257047, 19.87266098, 17.68243242, 15.76116043,
14.21829596, 13.18733111, 12.79263318, 13.09187632,
14.04076164, 15.52059114, 17.39639362, 19.5545461 ,
21.91177845, 24.41048539, 27.01143385, 29.68776382,
32.42081249, 35.19736985, 38.00790189, 40.84539592,
43.70460079, 46.58151878, 49.47305988, 52.37680226,
55.29082363, 58.21358037, 61.14381981, 64.08051547,
67.02281869, 33.17266016, 30.46590133, 27.81936206,
25.25198344, 22.79053377, 20.47325551, 18.3548346 ,
16.51198701, 15.04631107, 14.076123 , 13.70704201,
13.98673523, 14.87866003, 16.28251474, 18.07943716,
20.16461777, 22.45790666, 24.9018741 , 27.45631249,
30.09310315, 32.7923866 , 35.53992658, 38.32534596,
41.14095168, 43.98094663, 46.84089483, 49.71735301,
52.60761306, 55.50951913, 58.4213358 , 61.34165174,
64.26930838, 67.20334636, 33.8032087 , 31.15128698,
28.56831186, 26.074781 , 23.69894441, 21.47989125,
19.47129913, 17.74478097, 16.38972281, 15.50383099,
15.1695266 , 15.42272023, 16.23594965, 17.53145239,
19.21191258, 21.18592332, 23.37924525, 25.73586739,
28.21490089, 30.78678928, 33.43010853, 36.12918374,
38.87240255, 41.65104371, 44.45846605, 47.28954393,
50.14027052, 53.00747579, 55.88862363, 58.78166392,
61.6849234 , 64.59702421, 67.51682234, 34.68268236,
32.10349229, 29.60371563, 27.20525209, 24.93735156,
22.83894185, 20.96098821, 19.36772544, 18.13434726,
17.33782894, 17.03954443, 17.26533626, 17.99548827,
19.17246358, 20.72025873, 22.56268786, 24.63372983,
26.88059537, 29.26281205, 31.74992805, 34.3191447 ,
36.95334159, 39.6395663 , 42.36792394, 45.13077376,
47.92215044, 50.73734585, 53.57260518, 56.42490397,
59.29178316, 62.17122575, 65.06156372, 67.96140696,
35.79273659, 33.29963595, 30.89678812, 28.60694458,
26.45946031, 24.49181091, 22.75070468, 21.2917901 ,
20.17637449, 19.46360319, 19.19837522, 19.39905598,
20.05166165, 21.11432918, 22.52910692, 24.23440572,
26.17350153, 28.29837353, 30.57030759, 32.95890575,
35.44058732, 37.9971182 , 40.61436634, 43.28131832,
45.98932786, 48.73155076, 51.50252228, 54.29784124,
57.11393284, 59.94786974, 62.79723599, 65.66002292,
68.53454875, 37.1126869 , 34.71451125, 32.41670947,
30.24216948, 28.21940072, 26.38333449, 24.77551413,
23.4429491 , 22.43474146, 21.79594885, 21.55943292,
21.73832813, 22.3226493 , 23.28189068, 24.57218337,
26.14455885, 27.9514529 , 29.95045043, 32.10568864,
34.38780314, 36.77317999, 39.24299337, 41.78227244,
44.37909477, 47.0239281 , 49.70910959, 52.42844016,
55.17687106, 57.95026196, 60.74519424, 63.55882618,
66.38878028, 69.23305503, 38.62101845, 36.32256637,
34.13318898, 32.07522957, 30.17558804, 28.46597751,
26.9825432 , 25.76438238, 24.85053644, 24.27539748,
24.06326422, 24.22367533, 24.74938804, 25.61792284,
26.79596485, 28.24481358, 29.92516092, 31.80033047,
33.83794881, 36.01045045, 38.29488613, 40.67239931,
43.12759937, 45.64795274, 48.22324492, 50.8451287 ,
53.50675541, 56.20247892, 58.92762 , 61.67827949,
64.45119023, 67.24359958, 70.05317585, 40.29658302,
38.09934861, 36.01813608, 34.07421149, 32.29237759,
30.7008699 , 29.33068656, 28.21409109, 27.38212369,
26.86124457, 26.66968732, 26.81451069, 27.29035994,
28.08041145, 29.15913698, 30.49591827, 32.05849019,
33.81556675, 35.7384711 , 37.80190575, 39.98411985,
42.2667198 , 44.63430703, 47.07406001, 49.57532539,
52.12924947, 54.72846071, 57.36680376, 60.03912004,
62.74106867, 65.46898089, 68.21974216, 70.99069645,
42.11942711, 40.0223925 , 38.04651973, 36.21164765,
34.54025459, 33.05714672, 31.78868841, 30.76144459,
30.00020391, 29.5255482 , 29.35138427, 29.48303784,
29.91647176, 30.63888125, 31.63047274, 32.86689167,
34.32168891, 35.96837627, 37.78187202, 39.73934594,
41.82058557, 44.00803494, 46.28663847, 48.6435881 ,
51.06803721, 53.55081873, 56.08418626, 58.66158633,
61.277463 , 63.92709312, 66.60644861, 69.31208234,
72.04103358, 44.0712795 , 42.07164649, 40.19663171,
38.46446363, 36.89526696, 35.51065314, 34.33296154,
33.38409816, 32.68399871, 32.24886872, 32.08948886,
32.20995277, 32.60715902, 33.27119747, 34.18652283,
35.33361154, 36.69073271, 38.23552835, 39.94623124,
41.80247782, 43.78576155, 45.87961068, 48.06957913,
50.34312465, 52.68942932, 55.09919894, 57.56446374,
60.07839252, 62.635126 , 65.22963108, 67.85757535,
70.51522031, 73.19933098, 46.13576935, 44.22957128,
42.44997924, 40.81355779, 39.33817816, 38.04258171,
36.94568696, 36.06562833, 35.41857293, 35.01743952,
34.87071597, 34.98160365, 35.34767823, 35.96114734,
36.80964384, 37.87737638, 39.14640984, 40.59787144,
42.21294739, 43.97361356, 45.86310555, 47.86616982,
49.96915023, 52.15996297, 54.42800289, 56.76401378,
59.15994441, 61.60880444, 64.10452828, 66.64185102,
69.21619803, 71.82358827, 74.46055059, 48.29845495,
46.4810339 , 44.7909843 , 43.24324266, 41.85359958,
40.63827703, 39.61332253, 38.79382791, 38.1930209 ,
37.82132477, 37.68551936, 37.78814802, 38.12728541,
38.69671375, 39.48647131, 40.48366558, 41.67340807,
43.03973399, 44.56640511, 46.23754131, 48.03806811,
49.95399633, 51.97256499, 54.08228244, 56.27289788,
58.53532948, 60.86156882, 63.24457543, 65.67817052,
68.15693541, 70.67611765, 73.23154627, 75.81955638,
50.5467337 , 48.81309301, 47.20660771, 45.74067744,
44.42921713, 43.28626915, 42.3254871 , 41.55950698,
40.99924856, 40.65321813, 40.52690348, 40.62235429,
40.93801937, 41.46887015, 42.206788 , 43.14114875,
44.25951284, 45.54832861, 46.99357404, 48.58129026,
50.29798728, 52.13092448, 54.06828135, 56.09924073,
58.21400667, 60.40377748, 62.6606902 , 64.97774894,
67.34874624, 69.76818316, 72.23119232, 74.73346577,
77.27118911, 52.8696872 , 51.21473993, 49.68596731,
48.29535288, 47.05514713, 45.97752313, 45.07414331,
44.3556553 , 43.83115238, 43.50765083, 43.38964672,
43.47881329, 43.77388453, 44.27074348, 44.9627011 ,
45.84092334, 46.89494657, 48.11321831, 49.48360878,
50.99385551, 52.63192056, 54.38625583, 56.24598284,
58.20099954, 60.24202942, 62.36062757, 64.54915672,
66.80074397, 69.10922628, 71.46909065, 73.87541323,
76.32379997, 78.81033057, 55.25789863, 53.6766348 ,
52.21998549, 50.89865074, 49.72341912, 48.70486804,
47.85300338, 47.17685549, 46.68405998, 46.3804616 ,
46.26978474, 46.35341133, 46.63029598, 47.09703032,
47.74804737, 48.57593838, 49.57184232, 50.72586434,
52.02748384, 53.4659222 , 55.03045156, 56.7106371 ,
58.49651376, 60.3787039 , 62.34848551, 64.39782145,
66.51935936, 68.70641114, 70.95291885, 73.25341258,
75.60296434, 77.99714084, 80.43195721, 57.70326592,
56.19085922, 54.80108048, 53.54347937, 52.42756856,
51.46256608, 50.65709693, 50.01886875, 49.55434383,
49.26843568, 49.16426056, 49.24297187, 49.50369724,
49.9435862 , 50.55796242, 51.34056219, 52.28383199,
53.37925486, 54.61767673, 55.98960951, 57.485495 ,
59.09592116, 60.81178882, 62.6244315 , 64.52569397,
66.50797655, 68.5642524 , 70.68806454, 72.87350843,
75.1152048 , 77.4082667 , 79.7482634 , 82.13118335,
60.1988242 , 58.75069529, 57.42290448, 56.22397816,
55.16231941, 54.24598828, 53.48245512, 52.87833931,
52.43915073, 52.16905492, 52.07068324, 52.14500758,
52.39129295, 52.80713341, 53.38856714, 54.13025829,
55.02572694, 56.0676055 , 57.24790082, 58.55824374,
59.99011312, 61.53502608, 63.18469115, 64.93112472,
66.76673363, 68.68436854, 70.67735312, 72.73949412,
74.86507709, 77.04885158, 79.28600943, 81.57215856,
83.90329442, 62.73858439, 61.35043385, 60.08012563,
58.93528024, 57.92333743, 57.05136967, 56.32587809,
55.75258115, 55.33620936, 55.08032161, 54.98715841,
55.05754582, 55.29085923, 55.68505074, 56.23673744,
56.94134175, 57.7932709 , 58.78612016, 59.91288413,
61.1661626 , 62.53834991, 64.02180075, 65.60896839,
67.2925144 , 69.06539116, 70.92089973, 72.85272665,
74.85496338, 76.92211193, 79.04908011, 81.23116907,
83.46405567, 85.7437715 , 65.31739055, 63.98521134,
62.7682486 , 61.6733232 , 60.70703877, 59.87562374,
59.18476223, 58.63942225, 58.24369153, 58.00063246,
57.91216735, 57.97900386, 58.20060696, 58.57522013,
59.0999338 , 59.77079501, 60.58294891, 61.53080091,
62.60818814, 63.80854946, 65.12508538, 66.55090163,
68.07913241, 69.70304177, 71.41610318, 73.21205881,
75.08496066, 77.02919628, 79.03950178, 81.11096475,
83.23901948, 85.41943647, 87.64830796, 67.930796 ,
66.65087252, 65.48346791, 64.43469819, 63.51044082,
62.7162009 , 62.05697073, 61.53708945, 61.1601107 ,
60.92868702, 60.84447932, 60.9080982 , 61.11908203,
61.47591357, 61.9760737 , 62.6161279 , 63.39183887,
64.298297 , 65.33006015, 66.48129452, 67.74590971,
69.11768258, 70.59036624, 72.15778245, 73.81389659,
75.55287613, 77.36913373, 79.25735686, 81.21252599,
83.22992334, 85.30513409, 87.43404179, 89.61281954,
70.57495719, 69.34385585, 68.22254837, 67.21652972,
66.33104575, 65.5709798 , 64.9407357 , 64.44412243,
64.08424672, 63.8634202 , 63.78308711, 63.84377779,
64.04509134, 64.38570871, 64.86343537, 65.47527022,
66.21749597, 67.08578489, 68.07531341, 69.18087928,
70.3970157 , 71.71809801, 73.13843957, 74.65237508,
76.25433015, 77.93887752, 79.70078037, 81.53502409,
83.43683788, 85.40170769, 87.42538212, 89.50387254,
91.63344893, 73.24654339, 72.06109825, 70.98272778,
70.01637955, 69.166749 , 68.43818326, 67.83458329,
67.35930858, 67.01508945, 66.8039518 , 66.72715892,
66.78517425, 66.97764748, 67.30342505, 67.7605843 ,
68.34648892, 69.05786204, 69.89087259, 70.84122975,
71.90428078, 73.07510764, 74.34861881, 75.71963339,
77.18295565, 78.73343892, 80.36603864, 82.07585472,
83.85816412, 85.70844446, 87.62238991, 89.59592053,
91.62518615, 93.70656593, 75.94266032, 74.799956 ,
73.76163759, 72.83216969, 72.01576705, 71.31631276,
70.73727608, 70.28163337, 69.95179591, 69.74954848,
69.67600214, 69.73156413, 69.91592664, 70.2280753 ,
70.66631674, 71.22832361, 71.91119416, 72.71152321,
73.62548044, 74.64889237, 75.7773244 , 77.00615985,
78.33067354, 79.74609821, 81.24768268, 82.83074129,
84.49069454, 86.22310147, 88.02368425, 89.88834602,
91.81318267, 93.79448957, 95.82876414, 78.66078561,
77.55813919, 76.55723817, 75.6621205 , 74.87658005,
74.20409694, 73.64776822, 73.21024195, 72.89365739,
72.69959456, 72.6290356 , 72.68234018, 72.85923644,
73.15882788, 73.57961578, 74.11953603, 74.77600807,
75.54599357, 76.4260617 , 77.4124581 , 78.50117471,
79.68801787, 80.96867267, 82.33876193, 83.79389881,
85.32973245, 86.94198641, 88.62649019, 90.37920405,
92.19623792, 94.07386486, 96.00852989, 97.99685491]

torch.cdist:
tensor([ 34.0480, 31.4167, 28.8575, 26.3913, 24.0468, 21.8631, 19.8932,
18.2067, 16.8888, 16.0305, 15.7074, 15.9521, 16.7396, 17.9989,
19.6394, 21.5743, 23.7318, 26.0566, 28.5077, 31.0554, 33.6776,
36.3583, 39.0854, 41.8499, 44.6449, 47.4648, 50.3056, 53.1639,
56.0370, 58.9228, 61.8194, 64.7254, 67.6397, 33.3391, 30.6471,
28.0177, 25.4703, 23.0322, 20.7419, 18.6540, 16.8439, 15.4098,
14.4641, 14.1051, 14.3771, 15.2462, 16.6190, 18.3831, 20.4373,
22.7031, 25.1232, 27.6572, 30.2765, 32.9608, 35.6954, 38.4695,
41.2753, 44.1066, 46.9589, 49.8286, 52.7127, 55.6092, 58.5160,
61.4318, 64.3554, 67.2857, 32.8896, 30.1575, 27.4813, 24.8790,
22.3766, 20.0115, 17.8383, 15.9358, 14.4116, 13.3956, 13.0072,
13.3016, 14.2365, 15.6979, 17.5548, 19.6956, 22.0377, 24.5236,
27.1137, 29.7808, 32.5061, 35.2759, 38.0807, 40.9131, 43.7679,
46.6409, 49.5290, 52.4296, 55.3409, 58.2611, 61.1891, 64.1237,
67.0641, 32.7102, 29.9617, 27.2663, 24.6414, 22.1121, 19.7152,
17.5053, 15.5621, 13.9973, 12.9488, 12.5466, 12.8516, 13.8170,
15.3185, 17.2163, 19.3945, 21.7691, 24.2825, 26.8958, 29.5826,
32.3245, 35.1087, 37.9258, 40.7690, 43.6332, 46.5146, 49.4100,
52.3173, 55.2344, 58.1600, 61.0928, 64.0318, 66.9763, 32.8054,
30.0656, 27.3804, 24.7675, 22.2525, 19.8726, 17.6824, 15.7611,
14.2182, 13.1873, 12.7926, 13.0918, 14.0407, 15.5206, 17.3964,
19.5545, 21.9117, 24.4105, 27.0114, 29.6877, 32.4208, 35.1974,
38.0079, 40.8454, 43.7046, 46.5815, 49.4730, 52.3768, 55.2908,
58.2136, 61.1438, 64.0805, 67.0228, 33.1726, 30.4659, 27.8193,
25.2520, 22.7905, 20.4732, 18.3548, 16.5119, 15.0463, 14.0761,
13.7070, 13.9867, 14.8786, 16.2825, 18.0794, 20.1646, 22.4579,
24.9019, 27.4563, 30.0931, 32.7924, 35.5399, 38.3253, 41.1409,
43.9809, 46.8409, 49.7173, 52.6076, 55.5095, 58.4213, 61.3416,
64.2693, 67.2033, 33.8032, 31.1513, 28.5683, 26.0748, 23.6989,
21.4799, 19.4713, 17.7447, 16.3897, 15.5038, 15.1695, 15.4227,
16.2359, 17.5314, 19.2119, 21.1859, 23.3792, 25.7359, 28.2149,
30.7868, 33.4301, 36.1292, 38.8724, 41.6510, 44.4585, 47.2895,
50.1403, 53.0075, 55.8886, 58.7816, 61.6849, 64.5970, 67.5168,
34.6827, 32.1035, 29.6037, 27.2052, 24.9373, 22.8389, 20.9610,
19.3677, 18.1343, 17.3378, 17.0395, 17.2653, 17.9955, 19.1724,
20.7202, 22.5627, 24.6337, 26.8806, 29.2628, 31.7499, 34.3191,
36.9533, 39.6396, 42.3679, 45.1308, 47.9221, 50.7373, 53.5726,
56.4249, 59.2918, 62.1712, 65.0615, 67.9614, 35.7927, 33.2996,
30.8968, 28.6069, 26.4594, 24.4918, 22.7507, 21.2918, 20.1763,
19.4636, 19.1983, 19.3990, 20.0516, 21.1143, 22.5291, 24.2344,
26.1735, 28.2984, 30.5703, 32.9589, 35.4406, 37.9971, 40.6143,
43.2813, 45.9893, 48.7315, 51.5025, 54.2978, 57.1139, 59.9479,
62.7972, 65.6600, 68.5345, 37.1127, 34.7145, 32.4167, 30.2421,
28.2194, 26.3833, 24.7755, 23.4429, 22.4347, 21.7959, 21.5594,
21.7383, 22.3226, 23.2819, 24.5722, 26.1445, 27.9514, 29.9504,
32.1057, 34.3878, 36.7732, 39.2430, 41.7823, 44.3791, 47.0239,
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Could you describe how the other cdist call is used? I’m familiar with torch.cdist, but cdist should not be a tensor method so unsure how you are using it or where it’s defined.

basically for cdist I have two np.ndarray A and B, and I simply do:
cdist(A,B);

And then I convert A and B to pytorch.tensor using torch.from_numpy(), and I do:
torch.cdist(A_torch, B_torch)

Thanks!

I just solve the problem.

One more question, is there anyway I can avoid the “memory allocate problem” by using pytorch? The pytorch.cdist and other pytorch tensor really use a lot of memory.

Thanks!

cdist is not a built-in Python method so I still don’t know where it’s coming from:

cdist
NameError: name 'cdist' is not defined

You could try to reduce the tensor shapes to avoid running out of memory.