!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 and Daniel S. Karls ----------------------------------------------------------------------------------------------------- Results for KIM Model : QUIP_GAP_Xu_2003_Pt__MO_370837021112_000 Supported species : Pt random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Pt (Configuration in file "config-F-Pt.xyz") ----------------------------------------------------------------------------------------------------- Energy = 143.24928549717941 Forces: 1 -9.91697335e+00 -1.24351976e+01 -1.39459157e+01 2 -4.76805864e+00 2.47840476e+00 -1.74046961e+01 3 3.47156508e+00 -1.93728777e+01 -4.77805065e+00 4 -1.45987043e+01 6.67266949e+00 5.69057785e+00 5 -2.70060291e+00 -2.18308523e+01 -1.16059146e+01 6 1.47719695e+01 6.27601037e+00 -1.68884338e+01 7 1.78793554e+01 -2.39126428e+01 -7.70571756e+00 8 -4.67828637e+00 -8.29104378e+00 -6.37204077e+00 9 -1.60801822e+01 -7.87745167e+00 -2.45729625e+01 10 -3.55697275e+00 3.02819188e+01 -2.44301560e+01 11 -1.13119538e+01 -1.41475459e+01 8.10711555e+00 12 -1.98536349e+01 1.92984922e+01 5.11741953e+00 13 5.27206627e+00 -1.06355301e+01 -3.66294880e+01 14 1.33851961e+01 1.65230897e+01 -1.31914193e+01 15 3.29683116e+01 -9.39732319e+00 9.69430710e-03 16 6.54278827e+00 3.48751019e+01 7.08531730e+00 17 -2.00839527e+01 -1.05304212e+01 -4.50806049e+00 18 -1.07685810e+01 7.34218880e+00 7.06869217e+00 19 4.17430963e+00 -1.90398874e+01 1.24653990e+01 20 -1.11374553e+01 8.56714977e+00 1.24480311e+01 21 -8.04065546e+00 -2.30945711e+01 5.88769076e+00 22 2.56908892e+01 1.44172109e+01 8.53386689e+00 23 1.10561187e+01 -5.69820834e+00 1.52287476e+01 24 2.73473258e+00 8.32199900e+00 1.73755031e+01 25 -2.19505153e+01 -1.16834012e+01 -3.25034959e+00 26 -5.35050638e+00 2.84973666e+01 -5.66111278e+00 27 4.02483430e+00 -1.76537905e+01 2.11259176e+01 28 -1.80610523e+01 1.80556259e+01 1.23679955e+01 29 -2.09267648e+00 -1.05682104e+01 9.95594118e+00 30 1.68911740e+01 1.85037511e+01 5.75362815e-01 31 2.00893743e+01 -9.86349894e+00 1.95647780e+01 32 5.99807915e+00 1.59214748e+01 2.23362675e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Pt (Configuration in file "config-T-Pt.xyz") ----------------------------------------------------------------------------------------------------- Energy = 143.24928549717941 Forces: 1 -9.91697335e+00 -1.24351976e+01 -1.39459157e+01 2 -4.76805864e+00 2.47840476e+00 -1.74046961e+01 3 3.47156508e+00 -1.93728777e+01 -4.77805065e+00 4 -1.45987043e+01 6.67266949e+00 5.69057785e+00 5 -2.70060291e+00 -2.18308523e+01 -1.16059146e+01 6 1.47719695e+01 6.27601037e+00 -1.68884338e+01 7 1.78793554e+01 -2.39126428e+01 -7.70571756e+00 8 -4.67828637e+00 -8.29104378e+00 -6.37204077e+00 9 -1.60801822e+01 -7.87745167e+00 -2.45729625e+01 10 -3.55697275e+00 3.02819188e+01 -2.44301560e+01 11 -1.13119538e+01 -1.41475459e+01 8.10711555e+00 12 -1.98536349e+01 1.92984922e+01 5.11741953e+00 13 5.27206627e+00 -1.06355301e+01 -3.66294880e+01 14 1.33851961e+01 1.65230897e+01 -1.31914193e+01 15 3.29683116e+01 -9.39732319e+00 9.69430710e-03 16 6.54278827e+00 3.48751019e+01 7.08531730e+00 17 -2.00839527e+01 -1.05304212e+01 -4.50806049e+00 18 -1.07685810e+01 7.34218880e+00 7.06869217e+00 19 4.17430963e+00 -1.90398874e+01 1.24653990e+01 20 -1.11374553e+01 8.56714977e+00 1.24480311e+01 21 -8.04065546e+00 -2.30945711e+01 5.88769076e+00 22 2.56908892e+01 1.44172109e+01 8.53386689e+00 23 1.10561187e+01 -5.69820834e+00 1.52287476e+01 24 2.73473258e+00 8.32199900e+00 1.73755031e+01 25 -2.19505153e+01 -1.16834012e+01 -3.25034959e+00 26 -5.35050638e+00 2.84973666e+01 -5.66111278e+00 27 4.02483430e+00 -1.76537905e+01 2.11259176e+01 28 -1.80610523e+01 1.80556259e+01 1.23679955e+01 29 -2.09267648e+00 -1.05682104e+01 9.95594118e+00 30 1.68911740e+01 1.85037511e+01 5.75362815e-01 31 2.00893743e+01 -9.86349894e+00 1.95647780e+01 32 5.99807915e+00 1.59214748e+01 2.23362675e+01 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1295869== Memcheck, a memory error detector ==1295869== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1295869== Using Valgrind-3.15.0 and LibVEX; rerun with -h for copyright info ==1295869== Command: python runner2.py QUIP_GAP_Xu_2003_Pt__MO_370837021112_000 ==1295869== ==1295869== Conditional jump or move depends on uninitialised value(s) ==1295869== at 0x699E487: NpyIter_GetInnerFixedStrideArray (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==1295869== by 0x6A9ACFC: execute_ufunc_loop (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==1295869== by 0x6AA3E77: ufunc_generic_fastcall (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==1295869== by 0x5F40F0: ??? (in /usr/bin/python3.8) ==1295869== by 0x5F43B4: PyObject_CallFunctionObjArgs (in /usr/bin/python3.8) ==1295869== by 0x69B0AC5: array_add (in /usr/local/lib/python3.8/dist-packages/numpy/core/_multiarray_umath.cpython-38-x86_64-linux-gnu.so) ==1295869== by 0x50F78E: PyNumber_Add (in /usr/bin/python3.8) ==1295869== by 0x56BCD2: _PyEval_EvalFrameDefault (in /usr/bin/python3.8) ==1295869== by 0x5F6CE5: _PyFunction_Vectorcall (in /usr/bin/python3.8) ==1295869== by 0x56B618: _PyEval_EvalFrameDefault (in /usr/bin/python3.8) ==1295869== by 0x5697D9: _PyEval_EvalCodeWithName (in /usr/bin/python3.8) ==1295869== by 0x5F6EC2: _PyFunction_Vectorcall (in /usr/bin/python3.8) ==1295869== ==1295869== ==1295869== HEAP SUMMARY: ==1295869== in use at exit: 2,277,284 bytes in 1,712 blocks ==1295869== total heap usage: 2,007,699 allocs, 2,005,987 frees, 1,440,108,917 bytes allocated ==1295869== ==1295869== LEAK SUMMARY: ==1295869== definitely lost: 0 bytes in 0 blocks ==1295869== indirectly lost: 0 bytes in 0 blocks ==1295869== possibly lost: 188,754 bytes in 107 blocks ==1295869== still reachable: 2,088,498 bytes in 1,604 blocks ==1295869== of which reachable via heuristic: ==1295869== stdstring : 38 bytes in 1 blocks ==1295869== suppressed: 32 bytes in 1 blocks ==1295869== Rerun with --leak-check=full to see details of leaked memory ==1295869== ==1295869== Use --track-origins=yes to see where uninitialised values come from ==1295869== For lists of detected and suppressed errors, rerun with: -s ==1295869== ERROR SUMMARY: 7 errors from 1 contexts (suppressed: 7714 from 561) ================================================================================ 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.