!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! VERIFICATION CHECK: vc-memory-leak !!!!! !!!!! !!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Description: Check that the model has no memory leaks. This is tested using the Valgrind memory debugging tool (http://valgrind.org) by performing a series of energy and force calculations on a randomly distorted face-centered cubic (FCC) cube base structure for both non-periodic and periodic boundary conditions. Separate configurations are tested for each species supported by the model, as well as one containing a random distribution of all species. Configurations used for testing are provided as auxiliary files. Author: Ellad Tadmor ----------------------------------------------------------------------------------------------------- Results for KIM Model : EAM_IMD_BrommerGaehlerMihalkovic_2007_CaCd__MO_145183423516_003 Supported species : Ca Cd random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ca (Configuration in file "config-F-Ca.xyz") ----------------------------------------------------------------------------------------------------- Energy = 676.083662694 Forces: 1 -5.62353553e+02 -4.88264577e+02 -5.52565526e+02 2 1.16488287e+02 3.14053048e+01 -8.84569174e+02 3 2.51325629e+02 -7.06782570e+02 1.06584785e+01 4 -7.45524445e+02 -1.93276079e+01 4.49454385e+02 5 -1.81645247e+02 -9.38719562e+02 -7.20783821e+02 6 7.24706618e+02 2.64149742e+02 -8.62586936e+02 7 7.43015349e+02 -7.64910214e+02 2.90039560e+02 8 -4.26205761e+02 -2.12943543e+02 1.16327312e+02 9 -6.39882887e+02 -5.50370335e+01 -1.13836083e+03 10 2.69476336e+02 1.17980560e+03 -8.40908905e+02 11 -2.53651143e+02 -6.61084349e+02 2.31848236e+02 12 -1.13810673e+03 9.27996325e+02 8.73576448e+01 13 3.53792265e+02 -2.83505022e+02 -1.09850478e+03 14 6.86019829e+02 7.60771513e+02 -4.99275567e+02 15 1.08987312e+03 -2.84321806e+02 -1.75541881e+02 16 -1.35024008e+02 1.13295229e+03 -1.01761489e+02 17 -1.21267594e+03 -6.60889580e+02 -3.67690990e+02 18 2.76996845e+02 5.10842849e+02 -4.86180431e+02 19 2.93202112e+02 -1.17733687e+03 5.88034909e+02 20 -8.58824984e+02 5.42269996e+02 8.55741496e+02 21 -2.90710090e+02 -1.01981526e+03 2.10029404e+02 22 1.08083236e+03 3.24782233e+02 1.98852445e+02 23 3.88389683e+02 -2.48967003e+02 6.37290556e+02 24 4.37253454e+02 1.68742862e+02 7.63208992e+02 25 -9.83108126e+02 -5.90649025e+02 -1.43384212e+02 26 -9.62161065e+01 1.25653707e+03 -3.75160012e+02 27 -1.26963368e+02 -2.99385257e+02 1.04804411e+03 28 -7.00782853e+02 5.53461244e+02 8.32135290e+02 29 -3.76316779e+01 -5.81428155e+02 2.84898200e+02 30 6.91820868e+02 9.62603513e+02 -4.15812447e+01 31 7.77016970e+02 -4.31918663e+02 6.22230495e+02 32 2.09097189e+02 8.08965561e+02 1.06270428e+03 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ca (Configuration in file "config-T-Ca.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1072.77817911 Forces: 1 3.66385285e+02 -7.88488790e-01 7.13285680e+01 2 3.01743939e+02 1.55467782e+02 1.06568949e+02 3 1.08559536e+02 8.01388194e+02 2.44208032e+02 4 5.13798949e+02 2.27540586e+02 2.11950093e+02 5 4.91575208e+00 -1.04831955e+02 -2.51258274e+02 6 -7.03135551e+01 6.03530138e+02 -3.18549626e+02 7 -3.95863100e+02 -5.32385930e+02 4.17267743e+02 8 -4.58555164e+02 -2.21413833e+02 1.07324246e+02 9 -3.49679784e+02 -4.16080294e+02 -3.59495453e+02 10 2.66178847e+02 6.02186789e+02 3.59930953e+01 11 -2.64896960e+02 -6.59219478e+02 2.36404653e+02 12 -4.42418996e+02 1.61148560e+02 1.28749589e+02 13 4.12047092e+02 -4.19991539e+02 -2.53826196e+02 14 -1.47230650e+02 2.04210939e+02 -1.65124838e+02 15 2.66594358e+02 -3.28453852e+02 -1.14569866e+02 16 3.59677307e+01 1.74472369e+02 -4.30532963e+01 17 -1.32915237e+02 -1.03260227e+02 -4.17821661e+02 18 2.71168690e+02 5.03141657e+02 -5.54854070e+02 19 2.73719147e+02 -2.34325081e+02 -3.52899580e+01 20 -2.32356162e+02 8.31014576e+02 -5.56522227e+01 21 -4.88641326e+02 -2.79976149e+02 1.39481750e+02 22 2.55627521e+02 4.61021557e+02 2.22970737e+02 23 -5.44859092e+02 -1.37324203e+02 1.49494429e+02 24 3.15054441e+02 4.58733386e+02 -1.81551716e+02 25 -1.73837130e+02 -7.95410759e+02 -1.85545262e+02 26 6.66758044e+01 1.43656385e+02 -2.70602740e+02 27 -6.75281647e+01 -5.05221971e+02 1.43965365e+02 28 -1.95887796e+02 2.55847853e+01 5.03200824e+02 29 -3.01317225e+01 -5.80218747e+02 2.88740676e+02 30 -2.18386287e+02 1.16854678e+02 3.89694638e+00 31 2.67257072e+02 -5.99365248e+02 1.60217160e+02 32 4.87806960e+02 4.48315377e+02 3.54323247e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Cd (Configuration in file "config-F-Cd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 473.952253303 Forces: 1 -5.71119101e+01 -8.26849973e+00 -4.23595352e+01 2 -1.72521683e+02 7.08381324e+01 -1.50952580e+02 3 -1.03823029e+02 -1.20425669e+02 1.17517620e+02 4 -7.29691725e+01 -3.44900019e+01 -1.93331636e+01 5 8.53636539e+01 -1.87238459e+02 -2.42063604e+02 6 1.54191372e+02 -9.74191577e+01 -1.25639704e+02 7 1.25331001e+02 -7.96591616e+01 4.47399430e+01 8 3.41319479e+01 9.61846989e+01 1.98130442e+02 9 -4.48908016e+01 -8.48644749e+01 -1.04380969e+02 10 6.88757709e+01 3.30748043e+01 -4.85589160e+01 11 3.13958452e+01 5.26424298e+01 -6.55505852e+01 12 -5.65721263e+01 9.15568231e+01 9.65558300e+01 13 -1.48594721e+02 1.43768153e+02 -1.26923155e+02 14 4.19819623e+01 6.90013320e+01 -3.28794927e+01 15 1.35178142e+02 6.88118866e+01 1.70397645e+02 16 -3.08607840e+01 2.66766942e+01 -6.60004058e+01 17 -5.02283088e+01 -5.97159308e+01 3.54276617e+01 18 -1.23446814e+02 -2.16161144e+01 -4.21486971e+01 19 -7.25983375e+01 -8.13103425e+01 1.18702782e+02 20 -4.35086824e+01 -7.44970971e+01 7.64849554e+01 21 7.71602126e+01 -9.23667377e+01 -4.56326083e+01 22 6.84766738e+01 6.64790280e+01 -1.25283454e+02 23 6.34496625e+01 -1.21670530e+02 1.16670836e+02 24 -3.14901425e+01 -9.71726122e+00 1.54175734e+02 25 -1.94272072e+02 -1.22697527e+02 -1.34503768e+02 26 1.37510772e+02 2.22875397e+02 -1.81649270e+02 27 7.10999934e+01 -1.24454191e+02 2.48923684e+02 28 -1.78448834e+02 2.04014047e+02 2.09441454e+02 29 1.72135583e+02 1.05723710e+02 -1.03021034e+02 30 9.54625730e+01 4.05161945e+01 -5.98047328e+01 31 4.87209722e+01 -2.33325910e+01 4.63179162e+01 32 -2.91287195e+01 5.15804161e+01 8.31991709e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cd (Configuration in file "config-T-Cd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 745.38403967 Forces: 1 -9.65484225e+00 1.91442889e+02 -1.40537919e+02 2 -2.05954981e+02 6.46125284e+01 -1.17698506e+02 3 -1.35748771e+02 2.50604696e-01 1.47524005e+02 4 1.22080297e+00 -4.66106899e+01 -4.80841160e+01 5 8.43646676e+01 -1.23999909e+02 -2.28138858e+02 6 1.69766138e+02 -9.15935655e+01 4.47566275e+01 7 5.11380750e+01 5.41545498e+01 7.47474941e+01 8 3.54625309e+01 9.60568981e+01 1.97080224e+02 9 1.15435879e+02 -1.09021124e+02 -2.01604060e+01 10 1.22643423e+02 -8.03318283e+01 4.37797091e+01 11 2.98143743e+01 5.41739960e+01 -6.69355295e+01 12 5.23872821e-01 -1.01978059e+02 1.89089654e+02 13 -1.51215019e+02 1.77183730e+02 -6.86311813e+01 14 -2.92871513e+01 7.04630080e+01 9.43591198e+00 15 6.13313813e+01 7.92435057e+01 1.94099300e+02 16 -3.42340191e+01 -1.86993254e+02 -7.14411211e+01 17 3.44278477e+01 -4.19841096e+01 4.87914329e+01 18 -1.24247584e+02 -2.29318218e+01 -3.99688838e+01 19 -5.60334853e+01 1.21408082e+02 9.41640617e+01 20 1.79703594e+02 -8.08705818e+01 1.30252004e+02 21 8.10309830e+00 1.05613058e+02 -2.08034679e+01 22 -1.20668738e+02 6.74696778e+01 -1.65905878e+02 23 3.72624837e+01 -1.70759618e+02 7.68416955e+01 24 -7.02728916e+01 -2.58424388e+01 -3.16623178e+01 25 -9.33422184e+01 -1.20751294e+02 -2.17710982e+02 26 1.35585781e+02 1.38052011e+02 -2.21396311e+02 27 8.14709880e+01 -1.59542022e+02 2.06578823e+02 28 -2.07141440e+02 1.73870303e+02 1.18289285e+02 29 1.73355769e+02 1.06912634e+02 -1.02035008e+02 30 1.28919634e+02 -6.87932162e+01 -6.57490906e+01 31 -1.84507491e+02 -1.16023082e+01 2.25253436e+00 32 -2.82217087e+01 -5.73016358e+01 4.91768132e+01 MIXED STRUCTURE (pbc=False)-- Species = Ca Cd (Configuration in file "config-F-CaCd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 484.584022313 Forces: 1 -2.05175939e+02 -2.81030880e+02 -2.56763448e+02 2 1.58127233e+02 -1.56163566e+02 -7.64675445e+02 3 1.02158935e+02 -5.77743349e+02 -4.11526322e+02 4 -8.30712700e+02 -2.28518224e+02 2.91744786e+01 5 2.46836343e+02 -1.75803717e+02 -1.53172559e+02 6 2.50030295e+02 -1.00212515e+02 -2.16175399e+02 7 1.31226351e+02 -1.75639278e+02 2.97521830e+00 8 -2.04791470e+02 -2.39701015e+02 -1.68215828e+02 9 -3.06663126e+02 1.21034522e+02 -2.20359390e+02 10 -1.28279079e+02 6.80374001e+02 -4.25920132e+02 11 4.20525057e+02 9.44233011e+01 -1.24578759e+01 12 -5.07138266e+02 2.85591659e+02 -1.37982758e+02 13 3.54075061e+02 2.67845568e+02 -4.62124072e+02 14 1.40224995e+02 1.97050183e+02 -1.18424941e+02 15 1.88139777e+02 -2.12139674e+02 -1.89548133e+02 16 -1.02232095e+02 3.01862122e+02 -2.77313603e+02 17 -4.87322376e+02 -1.91658376e+02 2.85416910e+02 18 1.72098511e+02 -1.86762405e+02 6.10887194e+01 19 -2.45264008e+02 -1.11027833e+02 5.61520466e+02 20 -3.52208636e+01 -1.84948474e+02 3.58730159e+02 21 4.11803584e+02 -4.12266087e+02 -3.25432652e+01 22 4.18796386e+02 -8.10302936e+01 1.84285117e+02 23 2.20548071e+02 -8.05319536e+01 9.37411692e+01 24 5.81380485e+01 2.46335724e+02 1.97368644e+02 25 -9.71147052e+02 1.00182629e+02 3.93624417e+02 26 1.45253528e+02 7.22314393e+02 1.60610132e+02 27 -2.46068876e+02 -1.39799565e+02 3.46185607e+02 28 -1.52449793e+02 1.25373385e+02 2.96715607e+02 29 1.02884398e+02 -3.43645092e+02 1.07309537e+02 30 6.95831901e+02 4.71488759e+02 2.67029823e+02 31 1.78459363e+02 -2.94414184e+01 1.99578496e+02 32 2.73078068e+01 2.94187472e+02 3.01848669e+02 MIXED STRUCTURE (pbc=True)-- Species = Ca Cd (Configuration in file "config-T-CaCd.xyz") ----------------------------------------------------------------------------------------------------- Energy = 771.313013314 Forces: 1 -1.31448977e+02 -2.59720493e+02 -1.47088550e+02 2 1.24006463e+02 9.12901019e+01 -2.97201670e+02 3 2.46557889e+02 4.30008573e+02 -4.60404151e+02 4 -2.38853255e+02 -1.24092475e+02 3.65101567e+02 5 5.03997920e+02 -5.16859022e+01 1.41350025e+02 6 -4.76999025e+02 -2.37501141e+02 -1.33486761e+02 7 -2.56056476e+02 -1.92993599e+02 -1.09480890e+02 8 -1.87685682e+02 -2.46978131e+02 -1.75274380e+02 9 -5.51932720e+01 2.06163107e+02 -5.77012928e+01 10 1.47783007e+00 -6.87866602e+01 -2.97064587e+01 11 4.08832763e+02 3.30078633e+01 -1.48418630e+01 12 -3.29270128e+02 -7.11033175e+01 -6.11011331e+02 13 3.86937954e+02 9.41235432e+01 -2.61382393e+01 14 6.30074080e+01 1.89653059e+02 -8.63889745e+01 15 5.97200713e+01 -1.91055301e+02 -2.89911085e+02 16 1.47265749e+02 -8.62748309e+01 -5.26455843e+02 17 -2.32071232e+02 1.06539933e+03 3.01569154e+02 18 1.69603246e+02 -1.88533532e+02 6.62829759e+01 19 4.11384641e+00 2.12048521e+02 -2.96928369e+02 20 1.07137586e+02 -2.28256488e+02 8.47554666e+01 21 5.19218482e+02 4.50726947e+02 2.93784838e+02 22 6.39998519e+01 -2.90508364e+02 1.63490217e+02 23 -1.15194248e+02 8.19658126e+01 2.73635185e+02 24 3.36996429e+00 2.38283929e+02 7.15405464e+01 25 -1.51216615e+02 -1.46173492e+02 4.30354632e+02 26 1.72294070e+02 -4.56363656e+02 2.54126521e+02 27 -3.15878179e+02 -8.01980356e+01 8.73193141e+01 28 -4.11396370e+02 -4.06475904e+02 3.90634817e+02 29 1.07599819e+02 -4.49540638e+02 1.25934410e+02 30 -2.87256502e+02 1.65273256e+02 1.10587614e+02 31 -5.44181725e+01 2.17148671e+02 2.30019396e+01 32 1.53797221e+02 3.01149251e+02 7.85506360e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==11567== Memcheck, a memory error detector ==11567== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==11567== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==11567== Command: python runner2.py EAM_IMD_BrommerGaehlerMihalkovic_2007_CaCd__MO_145183423516_003 ==11567== ==11567== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==11567== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==11567== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11567== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11567== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==11567== by 0x4010732: call_init (dl-init.c:72) ==11567== by 0x4010732: _dl_init (dl-init.c:119) ==11567== by 0x40151FE: dl_open_worker (dl-open.c:522) ==11567== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==11567== by 0x40147C9: _dl_open (dl-open.c:605) ==11567== by 0x544CF95: dlopen_doit (dlopen.c:66) ==11567== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==11567== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==11567== by 0x544D734: _dlerror_run (dlerror.c:162) ==11567== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==11567== ==11567== ==11567== HEAP SUMMARY: ==11567== in use at exit: 10,254,636 bytes in 4,200 blocks ==11567== total heap usage: 278,030 allocs, 273,830 frees, 111,393,928 bytes allocated ==11567== ==11567== LEAK SUMMARY: ==11567== definitely lost: 0 bytes in 0 blocks ==11567== indirectly lost: 0 bytes in 0 blocks ==11567== possibly lost: 182,735 bytes in 112 blocks ==11567== still reachable: 10,071,901 bytes in 4,088 blocks ==11567== suppressed: 0 bytes in 0 blocks ==11567== Rerun with --leak-check=full to see details of leaked memory ==11567== ==11567== For counts of detected and suppressed errors, rerun with: -v ==11567== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2531 from 170) ================================================================================ To pass this verification check the number of bytes that are "definitely lost" or "indirectly lost" must be zero. NOTE that Valgrind will typically report non-zero "possibly lost" bytes due to Python's internal memory allocation and garbage collection that it does not monitor. Full Valgrind output written to auxiliary file "valgrind.out" Grade: P Comment: No memory leak detected.