Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:11:43) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_LiuOhotnickyAdams_1997_AlMg__MO_559870613549_000 Supported species : Al Mg random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Al (Configuration in file "config-F-Al.xyz") ----------------------------------------------------------------------------------------------------- Energy = -65.7517400283 Forces: 1 -1.33221294e+00 -1.12663460e+00 -2.13581863e+00 2 -1.09610679e+00 2.22087960e+00 -9.47033463e-01 3 1.81004205e+00 -8.19700331e-01 2.01114771e+00 4 -9.95294587e-01 1.49324390e+00 1.62027735e+00 5 1.11273039e+00 -2.36791910e+00 5.13056012e-02 6 6.37807492e-01 1.39643460e+00 -7.09774256e-01 7 1.57208331e+00 -5.85946643e+00 -5.46435026e+00 8 -3.97342221e+00 -2.54510958e+00 -7.50107444e-01 9 -1.94258969e+00 -1.97505004e+00 -2.94490234e+00 10 -1.05821519e+00 3.53532250e+00 -3.92371089e+00 11 -6.04628994e-01 -2.82508920e+00 3.78066131e+00 12 -7.90968976e-01 1.90314789e+00 1.14101160e+00 13 -1.39172744e+00 -3.19193068e+00 -7.79516228e+00 14 7.08625863e-01 1.39903013e+00 -5.52537139e-01 15 7.24772578e+00 -9.60847933e-01 2.40507482e+00 16 1.72851012e+00 5.54742656e+00 3.03645935e+00 17 -1.62524334e+00 -1.10777064e+00 -1.90400839e+00 18 7.28852601e-01 2.71441847e+00 -2.67300270e+00 19 1.25337601e+00 -2.35417862e+00 2.04277848e+00 20 -4.52451021e-01 1.72205960e+00 9.84886604e-01 21 -2.98747534e+00 -2.12465180e+00 5.37860508e-01 22 2.76572372e+00 5.30267435e+00 4.28831255e+00 23 6.78560872e-01 -2.48409857e-01 8.10667342e-01 24 2.22648074e-01 1.78926011e+00 1.52178597e+00 25 -1.78244520e+00 -1.81845811e+00 2.52863411e-01 26 -1.83269400e+00 3.45475880e+00 -2.13197692e+00 27 2.70360195e+00 -7.13104409e+00 1.56572760e+00 28 -4.05846915e+00 3.82822139e+00 4.57761932e-01 29 -2.45278576e+00 -2.34806203e+00 1.35817932e+00 30 9.70125602e-01 2.97586420e+00 -9.58335354e-01 31 2.70327565e+00 -3.12768509e+00 2.66338270e+00 32 1.53304115e+00 2.64926602e+00 2.36057591e+00 MONOATOMIC STRUCTURE (pbc=False)-- Species = Mg (Configuration in file "config-F-Mg.xyz") ----------------------------------------------------------------------------------------------------- Energy = -14.8890742954 Forces: 1 -1.38729737e+00 -1.82126091e+00 -1.74206904e+00 2 1.78264831e+00 -1.34802731e+00 -4.27890646e+00 3 5.51777745e-01 -2.04450340e+00 4.07356930e-01 4 -3.87503828e+00 5.09264156e-01 2.23624281e+00 5 -8.46801596e-01 -1.33509731e+00 -1.74224715e+00 6 1.92499317e+00 5.82106139e-01 -2.53336206e+00 7 1.85815011e+00 -1.89968044e+00 3.12804044e-01 8 7.64341040e-01 -2.97899467e+00 4.50842953e-01 9 -1.94064483e+00 6.10544043e-01 -1.47233486e+00 10 -7.66122106e-01 2.10586024e+00 -1.31560804e+00 11 -2.68665866e+00 3.47443795e+00 -9.35368039e-02 12 -1.18715202e+00 8.30011031e-01 3.02009593e-01 13 7.81575134e-01 -1.18948737e+00 -4.42026535e+00 14 1.87956092e+00 1.42322304e+00 -1.95269740e+00 15 3.53409588e+00 2.49891646e-01 1.52792378e+00 16 -1.06468366e+00 2.94387926e+00 1.77338969e+00 17 -1.11980364e+00 -6.51715484e-01 2.24005436e-02 18 5.03920652e-01 -2.68540527e+00 6.27163173e-01 19 1.39922511e-02 -2.11825707e+00 1.02982322e+00 20 -2.82127800e+00 -1.36074716e+00 2.23313385e+00 21 -1.70334637e+00 -2.49012215e+00 6.78934045e-01 22 2.72587061e+00 1.30440531e+00 -3.87241450e-01 23 6.81655581e-01 -8.95447057e-01 8.79147341e-01 24 9.48073054e-01 8.50582745e-01 1.99141904e+00 25 -3.37417354e+00 1.18144203e+00 -1.50847030e+00 26 8.04639804e-01 2.20377027e+00 -2.23362121e-01 27 8.56237134e-01 6.88711349e-01 2.16525483e+00 28 -6.11042199e-01 5.97063342e-01 7.13503396e-01 29 1.19431825e+00 9.19989242e-01 2.28939510e+00 30 1.36911792e+00 1.93399880e+00 -9.44775962e-01 31 8.96495172e-01 -1.23462842e+00 1.86146458e+00 32 3.12579507e-01 1.64419343e+00 1.11266811e+00 MIXED STRUCTURE (pbc=False)-- Species = Al Mg (Configuration in file "config-F-AlMg.xyz") ----------------------------------------------------------------------------------------------------- Energy = -50.4619811946 Forces: 1 -1.02146627e+00 -9.14765117e-01 -4.59055384e-01 2 1.24217376e+00 1.34700395e+00 -1.39847220e+00 3 4.31151825e-01 -1.42585930e+00 9.37082184e-01 4 -8.62919748e-01 2.56409705e-01 1.53510311e+00 5 5.17573079e-01 7.11512913e-02 4.08800504e-01 6 -6.90975894e-01 3.80686065e-01 3.01542446e-01 7 -1.64162391e-01 -9.41779030e-01 -1.14489873e+00 8 6.82483211e-01 1.04087418e+00 4.17046006e-01 9 -3.17260012e-01 4.90040079e-01 -5.67023792e-01 10 -1.49381562e+00 1.87593120e+00 -2.75471104e+00 11 -7.74290340e-01 -2.96924393e+00 1.71256623e+00 12 -5.11829072e-01 1.27459542e+00 -1.00490303e+00 13 1.82995899e-01 -1.99521350e+00 -1.27186846e+00 14 4.94365380e-01 6.75563968e-01 -1.01840572e-01 15 2.51856111e-01 -4.69259948e-01 1.07024171e+00 16 2.10178104e+00 1.69828912e+00 8.97102828e-01 17 -1.41116016e-01 5.38684348e-02 -7.70575235e-01 18 -8.99689142e-01 -3.57778397e-01 -1.61375574e+00 19 -7.72675785e-01 -1.80834807e+00 6.10114582e-01 20 -1.55131988e+00 -4.78386849e-01 4.09660463e-01 21 -9.71745373e-01 -1.85014488e+00 -3.95512531e-01 22 9.76881052e-01 2.41570736e+00 8.88992468e-01 23 -1.58781537e-01 4.06876602e-01 2.14953096e-01 24 1.86675210e+00 1.93131543e+00 6.55739129e-01 25 -3.96343721e-01 -1.36945018e+00 5.85141985e-01 26 -1.26337698e+00 2.07996081e+00 1.75703343e-01 27 1.88391127e+00 5.78616735e-01 8.40026027e-01 28 -3.64284302e-01 5.01509034e-01 8.00033160e-02 29 2.86757233e+00 -1.08523560e+00 2.46793851e-01 30 -7.25218810e-01 -6.88735360e-01 6.20193171e-02 31 -8.68610130e-01 -1.76232226e-02 -6.52633386e-01 32 4.50383967e-01 -7.06576001e-01 8.66174980e-02 ================================================================================ VALGRIND OUTPUT ================================================================================ ==1376== Memcheck, a memory error detector ==1376== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==1376== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==1376== Command: python runner2.py EAM_Dynamo_LiuOhotnickyAdams_1997_AlMg__MO_559870613549_000 ==1376== ==1376== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==1376== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==1376== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==1376== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==1376== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==1376== by 0x4010732: call_init (dl-init.c:72) ==1376== by 0x4010732: _dl_init (dl-init.c:119) ==1376== by 0x40151FE: dl_open_worker (dl-open.c:522) ==1376== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==1376== by 0x40147C9: _dl_open (dl-open.c:605) ==1376== by 0x544CF95: dlopen_doit (dlopen.c:66) ==1376== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==1376== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==1376== by 0x544D734: _dlerror_run (dlerror.c:162) ==1376== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==1376== ==1376== ==1376== HEAP SUMMARY: ==1376== in use at exit: 7,114,355 bytes in 4,269 blocks ==1376== total heap usage: 190,536 allocs, 186,267 frees, 90,772,516 bytes allocated ==1376== ==1376== LEAK SUMMARY: ==1376== definitely lost: 0 bytes in 0 blocks ==1376== indirectly lost: 0 bytes in 0 blocks ==1376== possibly lost: 182,135 bytes in 111 blocks ==1376== still reachable: 6,932,220 bytes in 4,158 blocks ==1376== suppressed: 0 bytes in 0 blocks ==1376== Rerun with --leak-check=full to see details of leaked memory ==1376== ==1376== For counts of detected and suppressed errors, rerun with: -v ==1376== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2566 from 172) ================================================================================ 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. === Verification check vc-memory-leak end (2018-12-15 06:12:19) ===