Model Extended KIM ID = === Verification check vc-memory-leak start (2018-12-15 06:26:39) === !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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 : Morse_Shifted_Jelinek_1972_Ar__MO_831902330215_002 Supported species : Ar random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Ar (Configuration in file "config-F-Ar.xyz") ----------------------------------------------------------------------------------------------------- Energy = 291.541646905 Forces: 1 -8.14552759e+00 -1.33114115e+01 -1.39139152e+01 2 -1.13109152e+01 1.73391678e+01 -1.82273577e+01 3 -1.66233907e+00 -1.92763258e+01 -1.83296873e+00 4 -1.14611243e+01 8.31674351e+00 7.34173150e+00 5 1.68345861e+01 -2.81750463e+01 -7.57822199e+00 6 8.41729359e+00 1.08174552e+00 -1.24864344e+01 7 1.12187240e+01 -3.84072819e+01 -3.25918682e+01 8 -1.06862364e+01 -1.29369752e+01 -6.23133272e+00 9 -1.51174492e+01 -1.91072387e+01 -3.40204903e+01 10 -1.49217345e+00 2.97162018e+01 -2.96432057e+01 11 -1.01839487e+01 -1.82717504e+01 1.57349843e+01 12 -2.16973574e+01 2.55545262e+01 1.83578245e+01 13 -5.06592689e+00 -1.44082475e+01 -5.51565498e+01 14 1.32117998e+01 1.57009146e+01 -1.23903714e+01 15 4.77042804e+01 -1.22994146e+01 6.61960486e+00 16 3.80733326e+00 4.07036411e+01 1.61087298e+01 17 -1.82024800e+01 -9.48696530e+00 -5.71502608e+00 18 -8.57287697e+00 1.09231164e+01 7.70671549e+00 19 4.65467375e+00 -1.79022605e+01 1.18227835e+01 20 -9.38357025e+00 9.81353656e+00 1.10736264e+01 21 -1.11202333e+01 -2.09111419e+01 9.91986308e+00 22 2.86173995e+01 2.74603031e+01 2.42781501e+01 23 9.00500752e+00 -4.88567550e+00 1.30052079e+01 24 3.75005904e+00 6.66220046e+00 1.33498017e+01 25 -1.82424006e+01 -8.66832592e+00 -7.21741561e+00 26 -7.92958252e+00 2.87581763e+01 -1.24621138e+01 27 1.50110849e+01 -3.91810682e+01 2.10668276e+01 28 -3.55774766e+01 3.16450691e+01 1.13564403e+01 29 -7.98680547e+00 -1.23883991e+01 1.12562052e+01 30 1.68082115e+01 2.35476327e+01 1.14898716e+01 31 2.25236931e+01 -8.54352427e+00 1.63353386e+01 32 1.22742774e+01 2.09380776e+01 2.26435653e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Ar (Configuration in file "config-T-Ar.xyz") ----------------------------------------------------------------------------------------------------- Energy = 501.284653116 Forces: 1 2.34690500e+01 -1.60183756e+01 5.75763127e+00 2 -3.83944094e+01 2.00465859e+01 2.92366912e+01 3 -4.05528141e+00 1.28991532e+00 1.32370657e+00 4 1.86718080e+01 1.58118329e+01 4.70773336e-01 5 2.75429907e+01 -4.51845266e+00 2.08036957e+00 6 -2.92920393e+01 3.34554314e+01 1.52421091e+01 7 -5.78760091e+00 -3.08767842e+01 -3.24888244e+01 8 -1.19762688e+01 -1.26917862e+01 -5.65507794e+00 9 -2.36404490e+01 -3.67906208e+01 8.10991349e+00 10 -1.18278221e+01 6.70613994e+00 -1.38638124e+01 11 -9.96717790e+00 -1.89354710e+01 1.71943267e+01 12 1.49561174e+01 7.97638020e+00 3.57243743e+01 13 -4.18319530e+00 -1.79790194e+01 -4.26990005e+01 14 -2.74789931e+01 9.93669554e+00 -2.24743541e+01 15 3.63679869e+01 -1.21548708e+01 7.91191399e+00 16 6.72925195e+00 2.63317179e+01 1.78576259e+01 17 1.57569689e+01 -1.85997488e+01 -6.65608301e+00 18 -8.23945492e+00 1.14787511e+01 7.41873425e+00 19 4.88193207e+00 3.98366689e+00 5.32877446e+00 20 2.69220046e+01 3.57823906e+01 -1.02457550e+01 21 -1.15966004e+01 -6.27155820e+00 1.10240139e+01 22 -4.20618358e+00 4.31718669e+01 2.95347586e+01 23 -2.94876192e+01 -3.70826643e+01 -1.65356216e+01 24 3.27048715e+01 1.20179819e+01 -3.64329389e+01 25 -5.36340901e+00 -1.29690645e+01 -6.46412354e+00 26 -5.69776233e+00 6.86695066e+00 -1.59805984e+01 27 3.05312621e+01 -4.15065480e+01 -1.28178783e+01 28 -3.58710486e+01 3.17234991e+01 -1.03333955e+01 29 -8.16964538e+00 -1.28879046e+01 1.11905202e+01 30 4.19902147e+00 9.28875296e+00 1.30979954e+01 31 1.46012085e+01 -1.06244109e+01 9.32689143e+00 32 1.79004866e+01 1.40387206e+01 4.81634009e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==2097== Memcheck, a memory error detector ==2097== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2097== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==2097== Command: python runner2.py Morse_Shifted_Jelinek_1972_Ar__MO_831902330215_002 ==2097== ==2097== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==2097== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==2097== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2097== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2097== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2097== by 0x4010732: call_init (dl-init.c:72) ==2097== by 0x4010732: _dl_init (dl-init.c:119) ==2097== by 0x40151FE: dl_open_worker (dl-open.c:522) ==2097== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2097== by 0x40147C9: _dl_open (dl-open.c:605) ==2097== by 0x544CF95: dlopen_doit (dlopen.c:66) ==2097== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2097== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==2097== by 0x544D734: _dlerror_run (dlerror.c:162) ==2097== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==2097== ==2097== ==2097== HEAP SUMMARY: ==2097== in use at exit: 4,606,172 bytes in 3,908 blocks ==2097== total heap usage: 119,207 allocs, 115,299 frees, 58,511,944 bytes allocated ==2097== ==2097== LEAK SUMMARY: ==2097== definitely lost: 0 bytes in 0 blocks ==2097== indirectly lost: 0 bytes in 0 blocks ==2097== possibly lost: 182,191 bytes in 111 blocks ==2097== still reachable: 4,423,981 bytes in 3,797 blocks ==2097== suppressed: 0 bytes in 0 blocks ==2097== Rerun with --leak-check=full to see details of leaked memory ==2097== ==2097== For counts of detected and suppressed errors, rerun with: -v ==2097== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2511 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. === Verification check vc-memory-leak end (2018-12-15 06:27:05) ===