!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_Dynamo_BonnyPasianotMalerba_2009_FeNi__MO_267721408934_005 Supported species : Fe Ni random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Fe (Configuration in file "config-F-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = -12.9527204138 Forces: 1 -5.87390506e+00 -4.84725585e+00 -8.96036533e+00 2 -9.51453674e+00 1.81155168e+01 -5.95879094e+00 3 9.44585509e+00 -8.06745996e+00 -1.11574291e+00 4 -6.44851547e+00 4.99687440e+00 2.42348448e+00 5 1.12301562e+01 -1.88081719e+01 1.99660501e+00 6 2.20036414e+00 1.52072897e+00 -2.88523802e+00 7 1.54555860e+00 -2.80440210e+01 -3.27455228e+01 8 -1.10151710e+01 -8.67682851e+00 -9.12130977e+00 9 -2.83012403e+00 -4.89971203e+00 -8.22294604e+00 10 -6.36218141e+00 8.28876657e+00 -1.44713702e+01 11 -1.92942690e+00 -7.84689202e+00 -5.03314927e-03 12 -5.78101278e+00 1.08945057e+01 1.76584798e+00 13 -1.40928840e+01 -1.23163327e+01 -3.86032105e+01 14 6.99241989e+00 1.16790911e+01 -8.64130727e+00 15 3.02632570e+01 -1.30592957e+01 1.62195601e+01 16 1.62651102e+00 2.22182786e+01 1.75475705e+01 17 -1.61418810e+01 -2.23089252e+00 -5.73057340e+00 18 1.58347484e+00 4.25906315e+00 2.13663463e+00 19 1.37563803e+01 -1.00153907e+01 1.04492599e+01 20 -5.48634883e+00 9.23914739e+00 3.89303267e+00 21 -1.12803138e+01 -9.97099066e+00 8.01851503e+00 22 2.00730216e+01 2.29261219e+01 2.27546703e+01 23 9.70757116e+00 -5.27105870e+00 5.26362630e+00 24 -8.39078337e+00 6.29691080e+00 3.76629101e+00 25 -8.58804679e+00 -6.52143865e+00 6.14567983e+00 26 1.43759993e+00 1.20868384e+01 -7.17963244e+00 27 2.19335344e+01 -3.65076645e+01 7.82346708e+00 28 -3.21540755e+01 2.72412503e+01 3.55139704e+00 29 -7.45086519e+00 2.08132718e+00 9.99799419e+00 30 5.71752038e+00 9.73752321e+00 5.72126280e+00 31 1.03391007e+01 -4.54757038e+00 6.76153366e+00 32 5.48774658e+00 1.00490313e+01 7.40461028e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Fe (Configuration in file "config-T-Fe.xyz") ----------------------------------------------------------------------------------------------------- Energy = 7.32803655941 Forces: 1 1.20281340e+00 -7.42646771e+00 -1.31413810e+00 2 -1.58620507e+01 1.86429131e+01 3.97769256e+00 3 1.17896065e+01 2.68014037e+00 8.13217188e-01 4 -1.96192665e+00 5.53292826e+00 3.72387334e-01 5 1.80651174e+01 -6.80894714e+00 3.30902903e+00 6 -3.99727337e+00 2.42998207e+01 2.87164285e+01 7 -2.46824939e+00 -2.36408366e+01 -3.34254799e+01 8 -1.03368843e+01 -8.95542604e+00 -9.55531976e+00 9 -6.27985893e+00 -1.60122148e+01 8.12513782e+00 10 -1.39880176e+01 -3.80356260e+00 -8.18048477e+00 11 -2.25701326e+00 -6.99172937e+00 -5.30659742e-01 12 2.18870513e+01 -6.76112835e-01 1.45809678e+01 13 -1.32908698e+01 -1.31735044e+01 -3.44283540e+01 14 -2.36500740e+01 1.26111254e+01 -2.48141576e+01 15 2.61350023e+01 -1.38834214e+01 1.60630535e+01 16 2.25371252e+00 1.87954690e+01 1.76660166e+01 17 2.16778772e+00 -1.41625737e+01 -2.97331119e+00 18 1.37931846e+00 3.96239033e+00 2.50938164e+00 19 1.70380302e+01 2.08602815e+00 8.01477423e+00 20 1.57800039e+01 2.40793977e+01 -3.10840894e+00 21 -1.13455703e+01 -5.94432481e+00 9.00502261e+00 22 3.01769121e+00 3.63256210e+01 2.01052098e+01 23 -1.01671152e+01 -3.71819912e+01 -2.11412899e+01 24 -4.78095536e+00 8.04233149e+00 -1.09433064e+01 25 -5.08810049e+00 -7.14188061e+00 6.79271571e+00 26 2.80744798e+00 5.15350204e+00 -8.28690694e+00 27 2.64927822e+01 -3.69665910e+01 -5.93065145e-01 28 -3.52365470e+01 2.77099875e+01 -6.56478300e+00 29 -6.86167698e+00 2.53390521e+00 1.01121427e+01 30 1.00896886e+00 5.14933076e+00 8.72270593e+00 31 8.71360634e+00 -4.10879552e+00 5.27852324e+00 32 7.83324302e+00 9.27348869e+00 1.69525915e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Ni (Configuration in file "config-F-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = 28.8508610004 Forces: 1 -1.27116368e+01 -7.38567837e+00 -1.13602049e+01 2 4.72296689e+00 2.05446672e+01 -3.01769022e+01 3 8.10762578e+00 -2.98068673e+01 2.20451658e+01 4 -2.17307537e+01 9.78702460e+00 1.31513240e+01 5 4.33974581e+00 -1.39849717e+01 -1.54200891e+01 6 8.15819413e+00 1.91397875e+01 -2.01393346e+01 7 1.76441144e+01 -2.08209263e+01 -2.62475151e+00 8 1.55641643e+01 8.28975744e+00 6.58282283e+00 9 -1.38737035e+01 -6.93938436e+01 -5.84300702e+01 10 1.47523989e+01 9.87673764e+00 -1.15547642e+01 11 -3.18312157e+01 2.11627856e+01 -4.96300728e+01 12 -6.48474630e+00 6.68408239e+01 6.41788382e+01 13 -8.43475936e+00 -7.65812627e+00 -4.87264674e+00 14 9.73905355e+00 1.95280538e+01 -1.70722080e+01 15 3.13272747e+00 -1.85855019e+01 1.88652730e+01 16 -5.95771095e+00 5.68335873e+00 -3.02596294e+00 17 -1.29490149e+01 -5.84465191e+00 -7.45368807e+00 18 -2.52005904e+01 -4.81163802e+01 1.19488173e+01 19 9.56635576e+00 -3.24670202e+00 1.08463717e+01 20 -1.56763878e+01 -1.93525728e+01 1.96947803e+01 21 -3.37462265e+01 -2.39255107e+01 1.56454494e+01 22 3.20150856e+01 1.70055386e+01 -2.31796881e+01 23 7.25958213e+00 -1.58032285e+01 1.07898265e+01 24 -2.70850904e+01 8.51005845e+00 2.78839066e+01 25 -1.70224319e+01 4.95792277e+00 -2.12173226e+01 26 7.01353878e+00 8.34809894e+00 -4.06535280e-01 27 1.76890359e+01 1.31192793e+01 1.60332356e+01 28 -6.66697357e+00 8.45972744e+00 7.97324966e+00 29 6.86717690e+01 3.31147352e+01 2.65632380e+01 30 7.38524243e+00 4.72005049e+00 -3.12155046e+00 31 1.04768408e+01 3.23552551e+00 1.65413455e+00 32 -6.86719998e+00 1.60102813e+00 5.82935830e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ni (Configuration in file "config-T-Ni.xyz") ----------------------------------------------------------------------------------------------------- Energy = 57.4998303093 Forces: 1 1.78537175e+00 -8.51461295e+00 -8.65439019e+00 2 6.72713294e+00 1.83630716e+01 -2.29135871e+01 3 7.54994068e+00 -2.46405024e+01 2.02467955e+01 4 -1.20799165e+01 8.56590691e+00 1.67012009e+01 5 3.80532422e+00 -6.04537242e+00 -5.15978484e+00 6 -9.00011152e+00 3.79675301e+01 -2.91669195e+00 7 2.35657150e+01 -3.03388399e+00 -6.53181317e+00 8 1.57863559e+01 6.50224669e+00 5.30928381e+00 9 2.82284830e+01 -8.11352748e+01 -6.57621289e+01 10 1.54593411e+01 -4.82068782e+00 8.99740134e+00 11 -3.28026089e+01 2.19146601e+01 -4.99022415e+01 12 1.85148046e+01 6.86541374e+01 7.29584172e+01 13 -8.64995072e+00 -1.36223036e+01 1.00906577e+01 14 -2.48876263e+01 3.18610732e+01 -2.77727267e+01 15 -3.00717023e+01 -2.50130429e+01 3.32313929e+01 16 -1.59165585e+01 -1.69384774e+01 -1.06533097e+01 17 -1.61863388e+01 9.98283697e+00 -1.16791815e+01 18 -2.61958856e+01 -4.82146714e+01 1.28049284e+01 19 2.03449628e+01 1.88771256e+01 -2.11117542e+00 20 -1.40298800e+01 -2.08399428e+01 1.48923885e+01 21 -5.22881059e+01 1.27041385e+01 1.77594481e+01 22 2.97672331e+01 1.59640514e+01 -2.22556100e+01 23 1.30056754e+01 -9.66663496e+00 -1.01219183e+01 24 -2.56367082e+01 5.24936372e+00 2.24136463e+01 25 -2.37834031e+00 4.82464381e+00 -2.86377945e+01 26 1.16869952e+01 -5.27129211e+00 -4.73856523e+00 27 1.50574618e+01 5.96456209e+00 5.63217020e+00 28 -1.03571113e+01 -6.24770137e+00 1.21695640e+01 29 6.85489599e+01 3.32398152e+01 2.70538988e+01 30 2.26342711e+01 -2.47450342e+01 6.78725271e-01 31 -8.15540040e+00 1.95890882e+00 8.63925115e+00 32 -1.38317834e+01 -3.84463701e+00 -9.76825112e+00 MIXED STRUCTURE (pbc=False)-- Species = Fe Ni (Configuration in file "config-F-FeNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 1.20046688322 Forces: 1 -5.45581723e-01 -5.87216128e+00 -6.15917525e+00 2 -2.80469518e+01 3.13486441e+00 -5.88654770e+01 3 -1.18560046e+01 -2.16081318e+01 4.21191933e+00 4 -1.87407320e+01 -9.73206329e+00 1.04235820e+01 5 1.71471265e+00 -5.11403821e+00 -5.88515869e+00 6 3.04776986e+00 2.01073776e+00 -5.46029232e+00 7 1.49817585e+01 -1.64685376e+01 -2.23575336e+01 8 5.16845070e+01 6.06587319e+00 3.66868625e+01 9 -9.99449566e+00 -2.54571711e+00 -6.16167730e+00 10 8.98613102e+00 8.37246377e+00 -1.65149851e+01 11 1.22317297e+01 1.54953660e+01 1.18281814e+01 12 -4.56801814e+01 5.57972794e+00 -3.16390837e+01 13 -2.08743077e+01 -2.15974933e+01 -2.76823421e+00 14 2.56775300e+01 2.53229226e+01 -1.04575657e+01 15 6.81631784e+00 -1.13632437e+01 4.37482523e-01 16 -1.29776923e+01 4.62714343e+00 -8.37729450e+00 17 -1.27732056e+01 -4.23685142e+00 -8.83506695e+00 18 -1.47273292e+01 -1.12388373e+00 -1.71369717e+01 19 1.76303375e+01 -3.22277442e+01 1.66154740e+01 20 -1.75557752e+01 1.46766035e+01 9.41600301e+00 21 -2.68581141e+01 -1.31321835e+01 7.88801826e+00 22 9.64724625e+00 1.94507566e+01 6.64402726e+00 23 1.34807274e+01 -4.55922050e+00 1.14867933e+01 24 2.95451969e+00 4.17871142e+00 1.33733592e+01 25 -9.69875442e+00 -1.58741842e+00 7.57431937e+00 26 3.54060800e+01 6.11509756e+00 4.18885576e+01 27 9.01574951e+00 -1.05722260e+01 6.76397137e+00 28 -1.26199544e+01 1.18970123e+01 2.95160193e-01 29 1.16743911e+01 1.81959160e+01 -5.15542408e+00 30 1.32085509e+01 1.16655263e+01 1.73042115e+01 31 9.09616080e+00 -5.24418956e+00 9.37355814e-01 32 -4.30513967e+00 1.01963809e+01 1.99866147e+00 MIXED STRUCTURE (pbc=True)-- Species = Fe Ni (Configuration in file "config-T-FeNi.xyz") ----------------------------------------------------------------------------------------------------- Energy = 53.4874793885 Forces: 1 1.44736527e+01 -2.83990089e+01 4.56816030e+00 2 -2.80395245e+01 2.62050598e+00 -5.44774945e+01 3 -1.25167146e+01 8.30619028e+00 -6.76037924e+00 4 6.15317956e+00 -1.02374450e+01 2.37939951e+01 5 -4.58277752e+00 -1.61961840e+00 1.68918524e+01 6 -3.71526074e+01 1.05915396e+01 -7.77495663e+00 7 1.80392481e+01 4.54633857e+01 -6.96376508e+01 8 5.13894425e+01 4.91248643e+00 3.51603353e+01 9 -1.22761173e+01 5.52439233e+00 7.39065530e+00 10 7.92966026e+00 1.78527315e+01 2.73811498e+00 11 1.06099344e+01 1.55762221e+01 1.07849614e+01 12 -4.21047007e+01 -4.93195764e+00 -3.84772035e+01 13 -2.36874716e+01 -2.22171221e+01 4.52599601e+00 14 2.88081184e+01 2.62641130e+01 1.03987148e+00 15 -5.47464705e+00 -5.83896616e+00 -6.88501730e+00 16 -8.25186515e+00 -1.55202615e+01 -9.89080524e+00 17 -1.82309679e+01 2.46402824e+01 -1.92929567e-01 18 -1.52703909e+01 -1.82730511e+00 -1.60692638e+01 19 1.68787724e+01 -2.75632394e+01 1.65253515e+01 20 -1.27178722e+01 1.82838616e+01 -9.09613469e+00 21 -5.13450651e+01 2.27576282e+01 2.08884208e+01 22 2.54221056e+00 1.57286491e+01 6.03079829e+00 23 1.11370763e+01 2.48488730e+00 2.23710908e+00 24 5.91742569e+00 1.41932446e+01 1.25330137e+00 25 5.13173842e+00 -1.80350513e+00 1.74544619e+01 26 4.18605919e+01 -2.54650811e+01 4.76504115e+01 27 1.85578048e+01 -1.73056116e+01 -1.95854153e+01 28 -1.00569743e+01 2.42092875e+00 5.96758864e-01 29 1.21949432e+01 1.84365507e+01 -5.01489926e+00 30 3.12295289e+01 -7.89990569e+01 4.67509204e+01 31 9.48159242e+00 -9.79743814e+00 -1.00018254e+01 32 -1.06272241e+01 -4.53198251e+00 -1.24175007e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==30348== Memcheck, a memory error detector ==30348== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==30348== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==30348== Command: python runner2.py EAM_Dynamo_BonnyPasianotMalerba_2009_FeNi__MO_267721408934_005 ==30348== ==30348== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==30348== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==30348== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30348== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30348== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==30348== by 0x4010732: call_init (dl-init.c:72) ==30348== by 0x4010732: _dl_init (dl-init.c:119) ==30348== by 0x40151FE: dl_open_worker (dl-open.c:522) ==30348== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==30348== by 0x40147C9: _dl_open (dl-open.c:605) ==30348== by 0x544CF95: dlopen_doit (dlopen.c:66) ==30348== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==30348== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==30348== by 0x544D734: _dlerror_run (dlerror.c:162) ==30348== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==30348== ==30348== ==30348== HEAP SUMMARY: ==30348== in use at exit: 22,246,649 bytes in 4,273 blocks ==30348== total heap usage: 192,866 allocs, 188,593 frees, 93,858,090 bytes allocated ==30348== ==30348== LEAK SUMMARY: ==30348== definitely lost: 0 bytes in 0 blocks ==30348== indirectly lost: 0 bytes in 0 blocks ==30348== possibly lost: 182,735 bytes in 112 blocks ==30348== still reachable: 22,063,914 bytes in 4,161 blocks ==30348== suppressed: 0 bytes in 0 blocks ==30348== Rerun with --leak-check=full to see details of leaked memory ==30348== ==30348== For counts of detected and suppressed errors, rerun with: -v ==30348== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2522 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.