!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : SW_MX2_WenShirodkarPlechac_2017_MoS__MO_201919462778_001 Supported species : Mo S random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Mo (Configuration in file "config-F-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 124.027969651 Forces: 1 -6.84899056e+00 -1.44045533e+01 -1.55321165e+01 2 -9.17015137e+00 1.19387599e+01 -1.24284661e+01 3 1.04840994e+01 -2.55289088e+01 -1.38158440e+01 4 -1.34853044e+01 1.13650656e+01 7.87106953e+00 5 5.06746090e+00 -2.30901624e+01 -4.80385639e+00 6 1.21690698e+01 7.00037031e+00 -1.23346848e+01 7 7.86948738e+00 -5.15524807e+01 -4.71197814e+01 8 -2.34249524e+01 -1.81586632e+01 -8.41949245e-01 9 -1.95529297e+01 -1.23436376e+01 -3.11934639e+01 10 -7.58463829e+00 3.43442278e+01 -3.45142875e+01 11 -6.56873372e+00 -2.66437532e+01 1.95175518e+01 12 -1.80991614e+01 2.50354952e+01 4.89406109e+00 13 -1.23792238e+01 -2.13449644e+01 -7.22742692e+01 14 1.39932179e+01 1.66254811e+01 -1.15620986e+01 15 6.40215987e+01 -6.76411247e+00 2.21192226e+01 16 7.71354214e+00 4.88382853e+01 2.59277405e+01 17 -2.35391010e+01 -1.13565725e+01 -6.95727141e+00 18 7.64997772e+00 2.35311182e+01 1.19363184e+01 19 7.97424189e+00 -1.96469202e+01 1.07819887e+01 20 -9.81909059e+00 1.44158368e+01 1.15613374e+01 21 -1.95161738e+01 -1.79305835e+01 1.22962620e+01 22 3.45926167e+01 4.38437587e+01 3.10963279e+01 23 7.49267318e+00 -4.08102240e+00 1.78032626e+01 24 4.47085735e+00 1.09331179e+01 9.61069948e+00 25 -1.64388617e+01 -1.43691466e+01 1.14586525e+01 26 -1.00058829e+01 3.10180224e+01 -1.62172974e+01 27 2.50321170e+01 -5.90584007e+01 1.72271976e+01 28 -4.99849455e+01 4.13687946e+01 7.64618729e+00 29 -1.50040579e+01 -2.14041058e+01 1.06447994e+01 30 1.52647043e+01 2.30358334e+01 -2.23561785e+00 31 2.33726134e+01 -1.86278876e+01 2.37270343e+01 32 1.42539212e+01 2.30117084e+01 2.57112911e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mo (Configuration in file "config-T-Mo.xyz") ----------------------------------------------------------------------------------------------------- Energy = 6.42793754824 Forces: 1 3.16571971e+01 -2.97738501e+01 7.59111409e+00 2 -7.06946610e+01 1.13229408e+01 8.34788651e+01 3 9.14208659e+00 -1.95770663e+00 -1.14749917e+01 4 2.15387251e+01 1.89276850e+01 -2.84452571e+00 5 1.55415306e+01 -1.50660840e+01 1.00481856e+01 6 -4.12009925e+01 6.48895686e+01 6.61740652e+01 7 -9.65751508e+00 -4.91084597e+01 -4.71946717e+01 8 -2.22642121e+01 -2.07186323e+01 -2.08614246e+00 9 -3.77936314e+01 -3.35430618e+01 2.42408050e+01 10 -1.68155883e+01 2.20677288e+01 -1.39497206e+01 11 -9.63135521e+00 -2.55011689e+01 1.88190030e+01 12 6.78406961e+00 9.49198505e+00 1.47515958e+01 13 -8.46473732e+00 -2.26798399e+01 -6.14764293e+01 14 -1.48928017e+01 8.69264684e+00 -2.22270083e+01 15 5.25462102e+01 -4.60881309e+00 2.12470437e+01 16 1.11118268e+01 3.95427977e+01 2.36656002e+01 17 1.67948117e+01 -2.69461770e+01 -4.88167567e+00 18 6.24208099e+00 2.09265829e+01 1.28849895e+01 19 7.01688720e+00 5.41197894e+00 6.21347624e+00 20 8.51550873e+01 6.88234288e+01 -1.15980716e+01 21 -1.96612117e+01 -2.25019663e+00 1.33920750e+01 22 -6.85712831e+00 6.31137799e+01 3.97474940e+01 23 -7.85175947e+01 -8.77708671e+01 -6.64549199e+01 24 6.56008316e+01 2.29974352e+01 -9.18279396e+01 25 -4.00242663e+00 -1.65444019e+01 1.24898012e+01 26 -8.35495897e+00 7.81725125e+00 -1.92022069e+01 27 4.49800922e+01 -5.88460552e+01 -2.46854311e+01 28 -5.35977920e+01 4.50436673e+01 -1.43913095e+01 29 -1.24504638e+01 -1.89063163e+01 1.35089237e+01 30 -8.12283381e-01 8.51484093e+00 2.98347251e+00 31 1.84119912e+01 -1.81583534e+01 1.81530615e+01 32 2.31459262e+01 1.47956656e+01 4.90547256e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = S (Configuration in file "config-F-S.xyz") ----------------------------------------------------------------------------------------------------- Energy = 145.891565174 Forces: 1 -3.03706376e+00 -2.31768135e+00 -1.94562467e+00 2 -2.09138535e+01 1.35584625e+01 -2.11167213e+01 3 -1.69147013e+01 -1.63577493e+01 8.08376719e+00 4 -1.19721164e+01 -3.18873962e+00 -1.74621151e+00 5 1.89658297e+01 -3.05709144e+01 -1.31086960e+01 6 7.16890534e+00 -1.23332570e+00 -9.68235672e+00 7 5.77120709e+00 -1.16318928e+01 -3.22693117e+00 8 1.05341585e+01 8.47041147e+00 9.01410980e+00 9 -4.78129213e+00 -2.37420112e+00 -4.75866672e+00 10 -6.36878678e+00 7.17757706e+00 -1.02536924e+01 11 -2.32993894e+00 4.40787415e+00 -2.79819583e-01 12 -5.10659272e+00 7.94668862e+00 -2.82467978e+00 13 4.81448623e+00 6.45626869e+00 -1.29160802e+01 14 4.64583108e+00 2.55323663e+00 -4.33221632e+00 15 1.11260203e+01 3.91982834e+00 -5.71356784e+00 16 5.70279523e+00 9.62338469e+00 2.63907806e+00 17 -1.32270768e+01 -1.02947370e+01 -9.21207884e+00 18 -1.16980294e+00 2.00262241e+01 -1.46217736e+01 19 4.08446984e+00 -2.38945648e+01 2.63296975e+01 20 -1.98788453e+01 1.37331540e+01 9.64095609e+00 21 1.28071813e+01 -2.43160834e+01 -3.41999956e+00 22 6.03830925e+00 1.60591594e+00 9.69245476e+00 23 8.24540693e+00 -7.07591019e+00 6.52404372e+00 24 4.78968066e+00 -1.35905245e+00 1.19498724e+01 25 -6.98502807e+00 -2.01879000e+00 4.65040706e+00 26 -5.95949178e+00 1.27713568e+01 8.58846320e-01 27 -3.03286762e+00 1.27713519e+01 9.51314282e+00 28 -1.92745581e+00 3.30826185e+00 4.29044930e+00 29 -1.66486148e+01 -2.53861665e+01 7.40459548e+00 30 2.97779249e+01 2.86085076e+01 4.98201867e-01 31 5.78925664e+00 1.22457694e+00 2.80673609e+00 32 -7.93422128e-03 3.85672725e+00 5.26275774e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = S (Configuration in file "config-T-S.xyz") ----------------------------------------------------------------------------------------------------- Energy = 260.247530293 Forces: 1 1.03599946e+01 2.36567034e+00 2.08765698e+00 2 -2.76359822e+01 1.37956253e+01 -3.20346230e-01 3 -1.66591216e+01 -1.22934858e+01 7.53702699e+00 4 1.20918860e+01 -1.14964661e+01 -1.16530415e+00 5 1.54370501e+01 -2.08318283e+01 -6.66627226e+00 6 -2.54861763e+00 -1.55604981e+00 -1.34579917e+00 7 -8.13872335e+00 2.05313106e+00 2.23205298e+00 8 1.07542869e+01 8.05189699e+00 9.32448152e+00 9 1.39706344e+01 2.56768511e+00 1.25938930e+01 10 -6.57075707e+00 1.96602266e+00 -6.78496496e+00 11 -2.28700520e+00 4.64324525e+00 -5.45272161e-01 12 1.05286143e+01 -2.39678798e+00 -4.44835868e+00 13 4.00686047e+00 1.86924223e+01 7.35569381e+00 14 3.38965347e+01 -1.07424546e+01 4.50977701e+01 15 -1.22730314e+01 1.01388994e+01 -7.46338626e+00 16 5.74143441e+00 2.41715738e+00 4.75786010e+00 17 -2.69689564e+00 -1.84282708e+00 -1.61987656e+01 18 -1.65212642e+00 2.04221602e+01 -1.49235885e+01 19 6.14590491e+00 -1.99932209e+01 1.64257982e+01 20 -1.34628722e+01 1.20792484e+01 2.54396568e+00 21 2.49118729e+01 4.45746276e+00 -4.73687335e+00 22 -1.42782711e+00 2.06721972e+00 1.05665510e+01 23 3.30785690e+00 9.36267970e+00 -8.84916959e-01 24 1.39599088e+01 -9.23813466e+00 -1.67860694e+01 25 4.88117231e+00 -1.55839252e+00 8.06657582e+00 26 -1.96794872e+01 -1.54631125e+01 -2.27074865e+00 27 -4.36845636e+00 1.38217170e+01 2.07078116e+00 28 1.64056927e+00 -1.07199071e+01 -2.58276131e-01 29 -1.64339617e+01 -2.56965061e+01 7.54063402e+00 30 1.97275378e+01 2.39763391e+01 3.75850960e+00 31 -1.28779737e+01 9.14750348e-01 -1.59345448e+01 32 -4.26492799e+01 -9.96415953e+00 -4.12257637e+01 MIXED STRUCTURE (pbc=False)-- Species = Mo S (Configuration in file "config-F-MoS.xyz") ----------------------------------------------------------------------------------------------------- Energy = 70.8280751985 Forces: 1 1.05681746e+00 -7.23690623e-02 -5.73988907e-02 2 -1.10099212e+01 5.89804475e+00 -1.69619145e+01 3 -1.21947316e+01 -9.91087912e+00 -5.73444583e+00 4 -1.55939044e+01 -1.37010294e+01 -2.53069081e+01 5 1.20710605e+01 -1.64568666e+01 -1.12153867e+01 6 6.82684825e+00 -1.14524209e+00 -1.07495886e+01 7 1.07787696e+01 -6.15388774e+00 -8.24045067e+00 8 -2.44117904e+01 -1.76634006e+01 -3.60049260e+01 9 -1.99955245e+01 -1.78181716e+01 -1.25067930e+01 10 1.05243271e+01 1.51076134e+01 -1.08794442e+01 11 -8.61371457e+00 1.15054870e+01 5.70434196e+00 12 -1.69936242e+01 1.61049783e+01 -5.23384115e+00 13 -1.75714116e+00 -1.11732849e+01 -2.34542380e+01 14 1.35211041e+01 1.31966806e+01 -1.18059067e+01 15 3.63645823e+01 -1.42950659e+01 6.44210865e+00 16 -1.69204517e+01 3.28008554e+01 6.89450212e+00 17 -1.81516871e+01 -2.83625078e+01 2.44625316e+00 18 2.54703133e+01 6.78928296e+00 -8.15608271e+00 19 -2.34753518e+01 -3.46268325e+01 8.85727102e+00 20 -2.48028486e+01 -7.19078292e+00 1.58377169e+01 21 3.16729481e+00 -1.20273963e+01 1.95651278e+01 22 4.44501320e+01 -1.25911344e+01 2.79311452e+01 23 1.91594654e+00 -4.63645262e+00 3.45394568e+00 24 2.82200230e+01 1.93794369e+01 8.13258894e+00 25 -7.99654036e+00 1.30414337e+01 9.67397025e+00 26 1.38528421e+01 1.00201351e+01 1.70966943e+01 27 9.72523231e+00 1.89643532e+01 1.81122028e+01 28 -3.79398635e+00 6.69551791e+00 4.37921397e+00 29 -3.00126104e+01 1.94930931e+01 1.13830600e+01 30 8.54291510e+00 9.58026637e+00 3.16056220e+00 31 1.24002831e+01 5.87948258e+00 1.24661323e+01 32 -3.16466303e+00 3.36864254e+00 4.77048769e+00 MIXED STRUCTURE (pbc=True)-- Species = Mo S (Configuration in file "config-T-MoS.xyz") ----------------------------------------------------------------------------------------------------- Energy = 377.08290124 Forces: 1 9.71012923e+00 1.30748601e+01 5.27424903e+00 2 -3.97307371e+01 2.33075607e+01 5.29410798e+01 3 -1.25334613e+01 1.35551443e+01 -4.70272067e+00 4 8.15619601e+00 -7.64514039e+00 -1.65071809e+01 5 4.07369759e+01 -2.03667325e+01 5.85895799e+01 6 -1.23166828e+01 2.64107597e-01 -9.35547337e+00 7 -5.58069138e+00 2.46516090e+01 -1.40116575e+01 8 -2.85493926e+01 -2.00282080e+01 -3.89301898e+01 9 -8.58953838e-01 -2.92887019e+01 5.96234193e+00 10 9.19240399e-01 9.48795021e-01 5.71237197e+00 11 -1.22835908e+01 5.96440195e+00 1.44926817e+01 12 8.38620237e+00 -1.00329944e+01 -3.34682092e-02 13 -8.45486647e+00 -1.55871992e+01 6.99761678e-01 14 -2.14417910e+01 -5.42660877e-01 -4.01566769e+00 15 1.86217208e+01 -2.19008419e+01 4.94034078e+00 16 -1.98512171e+01 1.25547753e+01 5.09263793e+00 17 -6.31007366e+00 -1.06065153e+01 1.52730298e+01 18 2.54969623e+01 1.23627862e+01 -1.33537425e+01 19 -7.28804010e+01 -4.00052748e+01 -6.55206646e+01 20 -1.15788571e+01 7.33873633e-01 5.28912106e+00 21 -1.49598734e+01 8.27115202e+00 2.33656727e+01 22 1.89891299e+01 -2.25154346e+01 3.25686131e+01 23 -5.77077389e+00 9.07406263e+00 -8.48568954e+00 24 5.22124370e+01 3.76228010e+01 -4.57585065e+01 25 2.61823946e+01 1.96151678e+01 1.78442095e+01 26 1.42541154e+01 -8.38098326e+00 1.72153295e+01 27 1.90614286e+01 2.34667343e+01 -1.36125807e+01 28 1.81868042e+01 2.53085400e+00 -2.77131469e+01 29 -3.33741312e+01 2.03669884e+01 1.42497265e+01 30 7.32549463e+00 -1.66078699e+01 1.99149552e+01 31 2.33679255e+01 4.87803360e+00 -3.96502431e+00 32 1.48683379e+01 -9.73515063e+00 -3.34599891e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==2793== Memcheck, a memory error detector ==2793== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2793== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==2793== Command: python runner2.py SW_MX2_WenShirodkarPlechac_2017_MoS__MO_201919462778_001 ==2793== ==2793== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==2793== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==2793== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2793== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2793== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2793== by 0x4010732: call_init (dl-init.c:72) ==2793== by 0x4010732: _dl_init (dl-init.c:119) ==2793== by 0x40151FE: dl_open_worker (dl-open.c:522) ==2793== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2793== by 0x40147C9: _dl_open (dl-open.c:605) ==2793== by 0x544CF95: dlopen_doit (dlopen.c:66) ==2793== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2793== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==2793== by 0x544D734: _dlerror_run (dlerror.c:162) ==2793== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==2793== ==2793== ==2793== HEAP SUMMARY: ==2793== in use at exit: 4,689,081 bytes in 4,301 blocks ==2793== total heap usage: 192,984 allocs, 188,683 frees, 74,592,255 bytes allocated ==2793== ==2793== LEAK SUMMARY: ==2793== definitely lost: 0 bytes in 0 blocks ==2793== indirectly lost: 0 bytes in 0 blocks ==2793== possibly lost: 182,735 bytes in 112 blocks ==2793== still reachable: 4,506,346 bytes in 4,189 blocks ==2793== suppressed: 0 bytes in 0 blocks ==2793== Rerun with --leak-check=full to see details of leaked memory ==2793== ==2793== For counts of detected and suppressed errors, rerun with: -v ==2793== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2525 from 173) ================================================================================ 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.