!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Exp6_KongChakrabarty_1973_ArNe__MO_946046425752_002 Supported species : Ar Ne random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ar (Configuration in file "config-F-Ar.xyz") ----------------------------------------------------------------------------------------------------- Energy = 800.874790411 Forces: 1 -2.08364110e+01 -4.43898033e+01 -4.52015846e+01 2 -5.71093501e+01 7.90066691e+01 -5.83570678e+01 3 7.39446713e+00 -5.79181595e+01 -1.20269547e+01 4 -3.51616193e+01 3.00536543e+01 1.91054813e+01 5 6.91909869e+01 -1.12297506e+02 -1.49967866e+01 6 2.58971798e+01 3.29855764e+00 -4.13714539e+01 7 2.34303513e+01 -1.51813027e+02 -1.39768334e+02 8 -1.10345886e+02 -1.08773936e+02 1.44912416e+01 9 -7.08842495e+01 -1.17226122e+01 -7.37624846e+01 10 -3.58369993e+01 1.04418495e+02 -9.93849029e+01 11 -2.88664731e+01 -7.32324418e+01 6.92591998e+01 12 -4.44088356e+01 8.97086342e+01 -4.74640899e+01 13 -1.83979545e+01 -2.54535655e+01 -2.12153285e+02 14 3.64592888e+01 3.82509988e+01 -2.00096443e+01 15 2.18934379e+02 5.39095126e+01 6.22879778e+01 16 4.51472613e+01 1.31357130e+02 7.68131329e+01 17 -7.37164748e+01 -4.42804560e+01 -1.96652175e+01 18 2.95927835e+01 5.84720740e+01 8.41399214e+00 19 2.38853005e+01 -6.14272928e+01 3.99943436e+01 20 -3.21004444e+01 3.43439461e+01 3.94404971e+01 21 -5.77112140e+01 -4.73415734e+01 3.96807422e+01 22 9.50966273e+01 1.18654353e+02 1.09317009e+02 23 2.08927707e+01 -1.14043927e+01 4.07336479e+01 24 1.90513534e+01 1.39191503e+01 2.73813372e+01 25 -3.80482463e+01 -7.51935101e+01 5.21725513e+01 26 -2.79091557e+01 9.12789950e+01 -4.21817058e+01 27 6.96732298e+01 -1.63182700e+02 5.72592344e+01 28 -1.45843234e+02 1.26742699e+02 2.68284852e+01 29 -3.68680389e+01 -5.75083501e+01 1.92624801e+01 30 4.19194256e+01 7.27395005e+01 -3.66829019e+01 31 6.69338571e+01 -7.07265246e+01 8.31454294e+01 32 4.05453251e+01 7.05114819e+01 7.74396308e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ar (Configuration in file "config-T-Ar.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1417.1886873 Forces: 1 1.12441244e+02 -1.07054115e+02 3.49804243e+01 2 -2.30455147e+02 5.97192321e+01 2.20549748e+02 3 8.06651344e+00 1.05503641e+01 -7.85503938e+00 4 7.14344469e+01 4.98290493e+01 -1.17440390e+01 5 1.16507553e+02 -2.57144791e+01 7.36226929e+00 6 -1.37566097e+02 1.62523186e+02 1.04437147e+02 7 -2.49904923e+01 -1.46712252e+02 -1.37599330e+02 8 -1.12816241e+02 -1.08353163e+02 1.59141832e+01 9 -1.20102318e+02 -8.08055472e+01 9.17133301e+01 10 -8.27769079e+01 2.05777906e+01 -5.13130473e+01 11 -2.85695878e+01 -7.42514351e+01 7.26871812e+01 12 -9.40999887e+00 4.86100081e+01 -4.79781517e+01 13 -1.48601350e+01 -3.59915035e+01 -1.77288033e+02 14 -1.80283272e+01 1.59603097e+01 -2.37933475e+01 15 1.82091180e+02 6.36102659e+01 6.16923808e+01 16 5.44978779e+01 9.40251790e+01 8.15747211e+01 17 4.99021621e+01 -8.21725568e+01 -1.73830482e+01 18 3.27712306e+01 5.94108504e+01 7.94104249e+00 19 2.41054336e+01 7.93142558e+00 2.88673711e+01 20 1.30398798e+02 1.54848593e+02 -3.13652803e+01 21 -6.27073703e+01 -3.96804129e+00 3.90405880e+01 22 -2.71966734e+01 1.83609574e+02 1.31391257e+02 23 -1.39229463e+02 -1.84649633e+02 -1.15037827e+02 24 2.00207386e+02 5.48355318e+01 -2.52746428e+02 25 -4.36156566e+00 -8.71845065e+01 4.86424943e+01 26 -2.04939474e+01 2.42931013e+01 -5.63626430e+01 27 1.37053977e+02 -1.67801188e+02 -6.72475589e+01 28 -1.44551161e+02 1.42617671e+02 -3.45289084e+01 29 -3.71557226e+01 -5.83301858e+01 1.91922874e+01 30 -1.44840986e+01 3.26137346e+01 -2.31618665e+01 31 4.99669929e+01 -7.69540376e+01 6.64573991e+01 32 6.03104589e+01 5.43767765e+01 2.29607229e+01 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ne (Configuration in file "config-F-Ne.xyz") ----------------------------------------------------------------------------------------------------- Energy = 90.4111854245 Forces: 1 -2.60740463e+00 -4.15273510e-01 -1.56599105e+00 2 -1.34157082e+01 5.36076388e+00 -1.51540358e+01 3 -1.97666698e+01 -1.42958321e+01 1.14201354e+01 4 -1.13000683e+00 2.14589291e-01 -1.49619698e+00 5 1.60212202e+01 -1.36277045e+01 -2.38504671e+01 6 1.06619187e+01 -1.00992274e+01 -6.03297078e+00 7 5.15007111e+00 -2.11032523e+00 3.15526569e+00 8 1.14123087e+01 1.49225451e+01 2.07933473e+01 9 -5.66117851e+00 -1.11605659e+01 -6.82180586e+00 10 1.35027878e+01 8.99268673e+00 -1.03594166e+01 11 -3.27830084e+00 2.08046132e-01 3.23771701e+00 12 -1.11423150e+01 4.74626079e+00 1.37207919e+01 13 -1.80732316e+01 1.20322140e+01 -1.87391225e+01 14 7.67304687e-01 1.19211372e+00 -5.17854893e-01 15 1.57994841e+01 2.14964715e+00 2.04141275e+01 16 5.28378726e+00 4.66475422e+00 -3.99375700e+00 17 -1.47783219e+00 -1.84093403e+00 -1.02842090e-01 18 -1.00143987e+01 -3.34873238e+00 -1.70062881e+00 19 -7.58058851e+00 -5.17022306e+00 1.02806485e+01 20 -2.90345198e+00 -4.66265871e+00 5.92269162e+00 21 1.09278785e+01 -5.00707085e+00 -6.63744091e+00 22 2.66889581e+00 5.27551054e+00 -8.09329356e+00 23 5.60513477e+00 -1.10052598e+01 7.49040884e+00 24 -4.84498381e+00 4.22538650e+00 5.23330329e+00 25 -1.93822476e+01 -2.54599663e+01 -1.83981326e+01 26 1.97728797e+01 1.75542469e+01 -2.47638061e+01 27 5.20511382e-01 -1.12428770e+01 1.79106642e+01 28 -1.75566669e+01 2.55747657e+01 3.40006676e+01 29 1.38598705e+01 5.67152338e+00 -8.56775954e+00 30 -2.26638756e+01 8.03344254e+01 -6.96048332e+01 31 2.83048894e+01 -8.03229443e+01 6.87800083e+01 32 1.23991795e+00 6.65011575e+00 4.04057822e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ne (Configuration in file "config-T-Ne.xyz") ----------------------------------------------------------------------------------------------------- Energy = 121.817190061 Forces: 1 -3.84906092e+00 2.40582156e+01 -1.18636407e+01 2 -1.45145577e+01 5.32495708e+00 -1.34602485e+01 3 -1.79880097e+01 -5.88933333e+00 1.57166082e+01 4 4.59424419e+00 8.10484095e-01 -6.12110487e+00 5 1.59768318e+01 -1.28780755e+01 -2.18484859e+01 6 1.48589514e+01 -7.06643442e+00 3.82076002e+00 7 -2.04126983e+00 9.72995087e-01 7.26239650e+00 8 1.14168595e+01 1.49219463e+01 2.07832089e+01 9 -2.08212606e+00 -1.35183394e+01 -5.04994218e+00 10 2.06792957e+01 -6.74871594e+00 -1.41616473e+01 11 -3.28771147e+00 2.08842107e-01 3.23117666e+00 12 -7.51692376e+00 -9.83345600e+00 2.57849023e+01 13 -1.80407738e+01 1.26171977e+01 -1.74119011e+01 14 -6.37795297e+00 1.44461968e+00 -1.08987476e+00 15 1.42077723e+01 2.41601600e+00 2.04788333e+01 16 6.07708792e+00 -2.90498304e+00 -6.50800860e+00 17 5.98523049e+00 -7.16781043e+00 -3.82507166e+00 18 -1.00137811e+01 -3.36572427e+00 -1.71208343e+00 19 -1.24915726e+01 8.73982591e+00 8.82726289e+00 20 5.10202135e+00 -2.39039446e+00 1.05699185e+01 21 1.08633012e+01 2.92991359e+00 -5.00927382e+00 22 -1.39754374e+01 9.72977906e+00 -8.09553308e+00 23 2.88517615e+00 -1.26772470e+01 6.87278224e+00 24 -8.93069126e+00 3.36809990e+00 -4.69559187e+00 25 -1.22755194e+01 -2.63736311e+01 -2.23978829e+01 26 1.93365457e+01 1.34637020e+01 -2.69050241e+01 27 7.52808338e-01 -1.14571832e+01 1.69341939e+01 28 -1.69543334e+01 2.21735436e+01 3.27504312e+01 29 1.38701523e+01 5.68028152e+00 -8.55297404e+00 30 -2.45465577e+01 7.90417836e+01 -7.00099431e+01 31 1.91998433e+01 -8.26175118e+01 6.86125267e+01 32 9.08015717e+00 -3.01336283e+00 7.07323056e+00 MIXED STRUCTURE (pbc=False)-- Species = Ar Ne (Configuration in file "config-F-ArNe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 316.770236148 Forces: 1 -1.30483186e+01 -6.42882409e+01 -5.64443004e+01 2 3.07864819e+01 -3.18472072e+01 -2.22336788e+01 3 8.68136240e+00 -5.42510991e+00 5.05258760e+00 4 -2.14677490e+01 3.86615663e+01 5.40762512e+01 5 -7.44248245e+01 -4.68067259e+01 -6.71145727e+00 6 8.95678419e+01 4.21919733e+01 -4.68034753e+01 7 4.52805562e+01 -1.09582905e+02 -3.54974021e+01 8 -6.75688998e+01 2.47165146e+01 -3.18664727e+01 9 -3.43835720e+01 2.02535399e+01 -1.29235028e+01 10 5.90660189e+00 1.25220387e+01 -2.69435260e+01 11 4.29646398e+01 -4.70950496e+01 1.11579058e+01 12 -5.92659221e+01 7.81008701e+01 -1.49118760e+01 13 -1.80582662e+01 -1.76761115e+01 -5.34410780e+01 14 5.18281942e+01 2.73601758e+01 -3.96376042e+01 15 4.04048116e+01 -1.56015091e+01 2.32939309e+01 16 -4.04898987e+01 4.98090419e+01 4.00106872e+01 17 -4.18117843e+00 -4.21588963e+00 9.71831102e-01 18 -6.29926786e+00 -2.78665851e+01 -2.97294124e+01 19 -1.91862061e+01 -1.04940075e+00 1.87420651e+01 20 -1.56648900e+00 2.19155068e-01 3.44108969e+00 21 -2.21347222e+01 -4.00407842e+01 -1.55749393e+01 22 6.54298424e+01 6.75052501e+01 7.61490952e+01 23 2.16228187e+01 -5.77957039e+00 2.26622378e+01 24 -2.14180500e+01 -3.73752793e+00 1.89843936e+01 25 -1.91945907e+01 -3.56034116e+01 2.02614760e+01 26 -4.49537933e+00 2.13460345e+01 7.14886891e-01 27 -1.91085249e+01 8.13819365e+00 2.53964902e+01 28 -3.72928425e+00 2.04519700e+01 2.42066741e+01 29 -4.47262487e+00 -2.64813932e+00 -2.78120834e+00 30 1.66817509e+01 1.49785820e+01 -3.05773539e+00 31 2.39315599e+01 1.09159099e+01 2.27731634e+01 32 1.14073067e+01 2.20933523e+01 3.06629033e+01 MIXED STRUCTURE (pbc=True)-- Species = Ar Ne (Configuration in file "config-T-ArNe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 596.708526122 Forces: 1 5.25304105e+01 -8.38375220e+01 -5.86209009e+01 2 3.99333291e+01 -3.44775717e+01 4.14841148e-01 3 8.38555487e+00 2.52550631e+01 -1.68001877e+01 4 3.28567441e+01 5.90351882e+01 4.72078926e+01 5 -7.67481842e+01 -4.39120477e+01 -1.04069760e+00 6 2.43900446e+01 6.28759592e+01 -2.16903264e+01 7 7.30481118e+00 -1.15546418e+02 -2.38631443e+01 8 -6.79922373e+01 2.47129685e+01 -3.18412963e+01 9 -1.96681942e+01 2.97379724e+01 6.61573622e+00 10 -5.10272975e+00 1.05841484e+01 -1.19628588e+01 11 4.29200486e+01 -4.71683474e+01 1.11860834e+01 12 -5.44463164e+01 5.54447319e+01 -1.35679277e+01 13 -1.42495120e+02 -3.44803062e+01 1.06805666e+02 14 5.65111490e+01 3.54189421e+01 -2.22114880e+01 15 3.20496170e+01 -1.40924817e+01 2.01360588e+01 16 -4.18254631e+01 4.05086565e+01 4.26790964e+01 17 2.84641715e+00 5.69100310e-01 1.50168344e+00 18 -6.29860622e+00 -2.78419785e+01 -2.99874025e+01 19 -2.48877244e+01 2.23576528e+01 3.34154715e+01 20 9.04007955e-01 -1.18030128e+01 -2.48478428e+01 21 4.73151105e+01 5.53675347e+01 -6.71188792e-01 22 3.05465594e+01 5.45197409e+01 8.97175388e+01 23 1.73969180e+01 -1.18538084e+01 9.82730566e-01 24 -2.55220274e+01 -8.69122645e+00 1.26181552e+00 25 6.43085145e+01 -8.65364594e+01 1.88829956e+00 26 -7.68125276e+01 -8.24950808e+01 -1.70634893e+01 27 -2.02054199e+01 1.34500366e+01 1.08405006e+01 28 8.83677083e+01 2.81978668e+01 9.79804332e+01 29 -5.01526778e+00 -2.90264220e+00 -2.92730268e+00 30 -1.19352789e+02 4.77265100e+01 -6.30496585e+01 31 1.32880141e+02 7.53694009e+00 -1.27041680e+02 32 4.92552166e+00 3.23398910e+01 -5.44645612e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==13012== Memcheck, a memory error detector ==13012== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==13012== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==13012== Command: python runner2.py Exp6_KongChakrabarty_1973_ArNe__MO_946046425752_002 ==13012== ==13012== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==13012== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==13012== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==13012== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==13012== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==13012== by 0x4010732: call_init (dl-init.c:72) ==13012== by 0x4010732: _dl_init (dl-init.c:119) ==13012== by 0x40151FE: dl_open_worker (dl-open.c:522) ==13012== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==13012== by 0x40147C9: _dl_open (dl-open.c:605) ==13012== by 0x544CF95: dlopen_doit (dlopen.c:66) ==13012== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==13012== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==13012== by 0x544D734: _dlerror_run (dlerror.c:162) ==13012== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==13012== ==13012== ==13012== HEAP SUMMARY: ==13012== in use at exit: 5,072,171 bytes in 4,099 blocks ==13012== total heap usage: 199,868 allocs, 195,769 frees, 74,969,429 bytes allocated ==13012== ==13012== LEAK SUMMARY: ==13012== definitely lost: 0 bytes in 0 blocks ==13012== indirectly lost: 0 bytes in 0 blocks ==13012== possibly lost: 182,735 bytes in 112 blocks ==13012== still reachable: 4,889,436 bytes in 3,987 blocks ==13012== suppressed: 0 bytes in 0 blocks ==13012== Rerun with --leak-check=full to see details of leaked memory ==13012== ==13012== For counts of detected and suppressed errors, rerun with: -v ==13012== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2527 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.