!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_SunMendelevBecker_2006_Mg__MO_848345414202_005 Supported species : Mg random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Mg (Configuration in file "config-F-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 94.0420722988 Forces: 1 -4.50790844e+00 -1.08738093e+01 -1.13292695e+01 2 -4.37319087e+00 6.91210414e+00 -9.47263151e+00 3 2.68111457e+00 -8.87335853e+00 -3.23958506e+00 4 -7.47595576e+00 8.79422172e+00 5.97455613e+00 5 5.63239959e+00 -1.30883817e+01 -1.88747699e+00 6 5.76409909e+00 -1.87383626e+00 -7.15961652e+00 7 3.36032396e+00 -1.80693488e+01 -1.52880318e+01 8 -1.35691526e+01 -1.41358252e+01 8.67645265e-01 9 -5.85296252e+00 -2.73800277e-01 -9.10301634e+00 10 -4.20640706e+00 9.86921198e+00 -1.17281132e+01 11 -3.02693936e+00 -6.91596053e+00 1.68733282e+00 12 -7.29697215e+00 8.59689877e+00 -1.13816638e+00 13 -3.16453467e+00 -1.81404657e-01 -2.53191254e+01 14 5.25705370e+00 5.03334231e+00 -3.48414741e+00 15 2.98787995e+01 8.24970100e+00 3.46412577e+00 16 3.73814782e+00 1.75533689e+01 8.10381192e+00 17 -8.92702107e+00 -3.03856789e+00 3.30767693e+00 18 1.39057133e+00 6.19678737e+00 1.72384281e-01 19 1.97085846e-01 -6.49456401e+00 7.77003671e+00 20 -4.08379641e+00 2.70894172e-01 3.35724699e+00 21 -2.46202306e+00 -8.69468101e+00 4.43243111e+00 22 1.36379931e+01 9.83590326e+00 1.24254185e+01 23 3.05562589e+00 -2.17511469e+00 4.68106111e+00 24 -3.30343800e-01 -4.42373966e-01 5.65103045e+00 25 -7.57106892e+00 -4.15293671e+00 6.17535923e+00 26 -2.63043158e+00 9.27128328e+00 -2.44222913e+00 27 6.85523782e+00 -1.53533221e+01 6.64590610e+00 28 -1.64421546e+01 1.38144938e+01 2.95870049e+00 29 -8.66637128e+00 -3.48768270e+00 2.55086108e+00 30 8.10153199e+00 9.47539502e+00 -1.57895694e+00 31 1.12661332e+01 -3.90841170e+00 1.38160037e+01 32 3.77111676e+00 8.15977444e+00 9.12877755e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Mg (Configuration in file "config-T-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = 280.292599669 Forces: 1 2.76265023e+00 -1.26555833e+01 -8.66394129e+00 2 -1.72714591e+01 6.13299537e+00 1.04845791e+01 3 7.72034702e+00 2.52810483e+00 -1.84186026e+00 4 1.04703815e+01 1.22723367e+01 1.22544316e+01 5 1.26480799e+01 -1.35783071e+00 1.85527218e+00 6 -1.02903868e+01 5.15834522e+00 -5.20891607e+00 7 -6.89337377e+00 -1.80417200e+01 -1.74708356e+01 8 -1.76509782e+01 -1.55784952e+01 2.88895024e+00 9 -1.02967552e+01 -5.88739030e+00 8.45264190e+00 10 -8.08085830e+00 7.39123775e-01 -5.62141926e+00 11 -2.85829909e+00 -9.82506793e+00 4.72768895e+00 12 -2.90611585e+00 -5.95771873e-01 1.98252346e+00 13 -2.06332806e+00 -1.97650576e+00 -2.09640981e+01 14 -3.97138781e+00 2.99298258e+00 -5.42848705e+00 15 2.53970397e+01 1.00096830e+01 5.17796060e+00 16 5.75861225e+00 1.32137559e+01 1.13812659e+01 17 5.81916500e+00 -7.45050370e+00 4.80468009e+00 18 2.55082367e+00 1.02830497e+01 -7.33662305e-01 19 1.10153324e+00 3.25931437e+00 5.06411856e+00 20 6.37759007e+00 5.69623913e+00 -7.22253552e+00 21 -5.09388374e+00 -1.56248680e+00 6.05773031e+00 22 4.67738789e-01 2.27121475e+01 1.55820297e+01 23 -8.78753878e+00 -8.92627696e+00 -6.80453022e-01 24 1.25810159e+01 2.75608538e+00 -1.72402108e+01 25 -9.11432147e-01 -6.80079154e+00 7.54948985e+00 26 -1.21747885e+00 -6.04585251e-01 -6.18843783e+00 27 1.53042718e+01 -2.02748533e+01 -1.14451698e+01 28 -1.90502444e+01 1.49751010e+01 -3.74354715e+00 29 -1.09837262e+01 -5.66088399e+00 3.13301505e+00 30 3.14355443e+00 3.02451213e+00 -8.89303347e-01 31 7.87856147e+00 -4.85282864e+00 1.00695779e+01 32 8.34588129e+00 6.29779881e+00 1.87692199e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==6609== Memcheck, a memory error detector ==6609== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==6609== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==6609== Command: python runner2.py EAM_Dynamo_SunMendelevBecker_2006_Mg__MO_848345414202_005 ==6609== ==6609== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==6609== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==6609== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6609== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6609== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==6609== by 0x4010732: call_init (dl-init.c:72) ==6609== by 0x4010732: _dl_init (dl-init.c:119) ==6609== by 0x40151FE: dl_open_worker (dl-open.c:522) ==6609== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==6609== by 0x40147C9: _dl_open (dl-open.c:605) ==6609== by 0x544CF95: dlopen_doit (dlopen.c:66) ==6609== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==6609== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==6609== by 0x544D734: _dlerror_run (dlerror.c:162) ==6609== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==6609== ==6609== ==6609== HEAP SUMMARY: ==6609== in use at exit: 10,107,685 bytes in 3,960 blocks ==6609== total heap usage: 118,510 allocs, 114,550 frees, 64,304,175 bytes allocated ==6609== ==6609== LEAK SUMMARY: ==6609== definitely lost: 0 bytes in 0 blocks ==6609== indirectly lost: 0 bytes in 0 blocks ==6609== possibly lost: 182,191 bytes in 111 blocks ==6609== still reachable: 9,925,494 bytes in 3,849 blocks ==6609== suppressed: 0 bytes in 0 blocks ==6609== Rerun with --leak-check=full to see details of leaked memory ==6609== ==6609== For counts of detected and suppressed errors, rerun with: -v ==6609== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2509 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.