!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_AcklandTichyVitek_1987v2_Cu__MO_762798677854_000 Supported species : Cu random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Cu (Configuration in file "config-F-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = -59.2387638363 Forces: 1 -4.02797770e-01 -1.45112483e+00 -1.18704229e+00 2 -2.54527065e-01 5.91567478e-01 -1.70721683e+00 3 1.30488260e+00 -3.19713588e+00 -2.40398019e+00 4 -2.22069426e+00 1.03335778e+00 4.80566220e-01 5 -1.74902882e-01 -2.55305533e+00 -8.01491769e-01 6 1.15955561e+00 1.13190338e+00 -1.32096354e+00 7 2.08279094e+00 -3.96799448e+00 -2.47385014e+00 8 -2.48097030e+00 -1.65451314e+00 -9.00722946e-01 9 -2.89091928e+00 -1.56077548e+00 -3.74376297e+00 10 6.83784581e-01 4.36525578e+00 -3.09398902e+00 11 -1.08801896e+00 -2.71258315e+00 1.58618640e+00 12 -2.62902236e+00 2.58789983e+00 1.45083480e+00 13 7.74103800e-01 -2.30092400e+00 -6.45857489e+00 14 1.72193988e+00 1.60985611e+00 -1.47772577e+00 15 6.30932482e+00 -2.04321883e+00 -1.56898527e+00 16 -1.19737457e+00 6.42459240e+00 1.09254444e+00 17 -4.25294068e+00 -1.83669388e+00 -4.00819123e-01 18 1.07471132e+00 3.36622641e+00 6.43834436e-01 19 1.14750694e+00 -2.40229741e+00 2.68941584e+00 20 -1.40668755e+00 1.64005055e+00 1.66517996e+00 21 -1.56957579e+00 -3.64486250e+00 9.50277566e-01 22 4.70921588e+00 2.39640295e+00 1.95413418e+00 23 1.82774548e+00 -9.25946559e-01 1.69358639e+00 24 -1.60616470e+00 1.54763024e+00 1.46013658e+00 25 -2.98784730e+00 -2.09686534e+00 -1.01643945e+00 26 3.19836519e-01 4.22413578e+00 -2.43038095e+00 27 1.03122000e+01 -1.38250837e+01 3.43324464e+00 28 -1.24454626e+01 1.24063281e+01 2.10047506e+00 29 -2.73472367e+00 -2.09762634e+00 3.08464211e+00 30 3.00295707e+00 4.05895616e+00 1.09088268e+00 31 2.97709729e+00 -1.67655599e+00 2.74077062e+00 32 9.34977000e-01 2.56309395e+00 2.86923325e+00 MONOATOMIC STRUCTURE (pbc=True)-- Species = Cu (Configuration in file "config-T-Cu.xyz") ----------------------------------------------------------------------------------------------------- Energy = -36.2794597559 Forces: 1 3.28973335e+00 -2.26118450e+00 1.27061680e+00 2 -9.51010231e-01 1.11424450e+00 1.31010220e+00 3 7.76276584e-01 1.09128966e-01 -2.29081126e+00 4 2.06807934e+00 2.49372587e+00 -6.56440904e-01 5 1.01730519e-01 -1.26219757e+00 5.96807832e-01 6 -2.04147191e+00 4.78546985e+00 1.87846346e+00 7 -1.60576804e+00 -2.68763209e+00 -2.44980913e+00 8 -2.56785286e+00 -1.90235983e+00 -6.75882428e-01 9 -3.81212548e+00 -3.78701555e+00 1.35694686e+00 10 5.45701853e-01 3.36287509e+00 -1.40494570e-01 11 -1.30383172e+00 -2.68689547e+00 1.76101651e+00 12 1.90136832e-01 9.73052219e-01 1.44716580e+00 13 1.01669187e+00 -2.72347844e+00 -4.05860236e+00 14 -6.72645847e-01 7.08333556e-01 -2.25407236e+00 15 3.70411901e+00 -2.01356078e+00 -1.62965209e+00 16 -9.66904873e-01 3.89747982e+00 1.34132414e+00 17 2.76372396e-01 -2.53678895e+00 -1.30904532e-01 18 1.44700190e+00 3.28084999e+00 7.82502220e-01 19 1.07813547e+00 8.84568977e-01 1.69263305e+00 20 2.58452430e+00 4.39289432e+00 -1.26214574e+00 21 -1.63208422e+00 -9.47906338e-01 1.73164043e+00 22 6.84195396e-01 4.22233089e+00 2.26314802e+00 23 -2.67071713e+00 -4.44268289e+00 -1.12128877e+00 24 -8.70299174e-01 2.40355423e+00 -2.64822847e+00 25 -1.72358450e-01 -2.89278241e+00 -6.72062435e-01 26 1.04408267e+00 -1.47595744e-01 -2.32378993e+00 27 1.14612465e+01 -1.44377193e+01 -1.64619723e+00 28 -1.32291286e+01 1.22962888e+01 -7.25938616e-01 29 -2.61391809e+00 -2.04074666e+00 3.10990262e+00 30 1.05335275e+00 1.95053070e+00 1.93001361e+00 31 1.72620885e+00 -1.83503224e+00 1.74610460e+00 32 2.06252705e+00 1.73025095e+00 4.67932649e-01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==28255== Memcheck, a memory error detector ==28255== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==28255== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==28255== Command: python runner2.py EAM_Dynamo_AcklandTichyVitek_1987v2_Cu__MO_762798677854_000 ==28255== ==28255== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==28255== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==28255== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==28255== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==28255== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==28255== by 0x4010732: call_init (dl-init.c:72) ==28255== by 0x4010732: _dl_init (dl-init.c:119) ==28255== by 0x40151FE: dl_open_worker (dl-open.c:522) ==28255== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==28255== by 0x40147C9: _dl_open (dl-open.c:605) ==28255== by 0x544CF95: dlopen_doit (dlopen.c:66) ==28255== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==28255== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==28255== by 0x544D734: _dlerror_run (dlerror.c:162) ==28255== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==28255== ==28255== ==28255== HEAP SUMMARY: ==28255== in use at exit: 9,927,801 bytes in 3,962 blocks ==28255== total heap usage: 112,903 allocs, 108,941 frees, 63,750,635 bytes allocated ==28255== ==28255== LEAK SUMMARY: ==28255== definitely lost: 0 bytes in 0 blocks ==28255== indirectly lost: 0 bytes in 0 blocks ==28255== possibly lost: 182,191 bytes in 111 blocks ==28255== still reachable: 9,745,610 bytes in 3,851 blocks ==28255== suppressed: 0 bytes in 0 blocks ==28255== Rerun with --leak-check=full to see details of leaked memory ==28255== ==28255== For counts of detected and suppressed errors, rerun with: -v ==28255== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2503 from 171) ================================================================================ 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.