!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!! !!!!! !!!!! 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_MendelevAckland_2007v3_Zr__MO_004835508849_000 Supported species : Zr random seed = 13 lattice constant (orig) = 3.000 perturbation amplitude = 0.300 number unit cells per side = 2 ----------------------------------------------------------------------------------------------------- MONOATOMIC STRUCTURE (pbc=False)-- Species = Zr (Configuration in file "config-F-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 593.566456656 Forces: 1 -3.58473807e+01 -3.98030341e+01 -4.69479105e+01 2 -1.97718448e+01 2.38112976e+01 -6.05019583e+01 3 -6.26610568e+00 -5.57182289e+01 3.05685769e+01 4 -5.15663484e+01 1.39343113e+01 1.03987248e+01 5 3.59506348e+01 -6.40789744e+01 -3.93282863e+01 6 2.89523942e+01 6.55712239e+00 -4.03258000e+01 7 3.85531745e+01 -9.30627985e+01 -5.53867716e+01 8 -3.54494046e+01 -5.46742435e+01 -1.45603411e+01 9 -4.43489117e+01 -5.06386525e+00 -5.65586484e+01 10 -2.77256079e+01 8.05658632e+01 -6.96605745e+01 11 -3.61218442e+01 -3.25114246e+01 2.47380345e+00 12 -5.20161910e+01 6.83463700e+01 -1.92032009e+01 13 1.65951504e+01 -2.80728556e+01 -1.30497780e+02 14 3.50894976e+01 3.86095841e+01 -3.13290883e+01 15 1.24988117e+02 -4.79772662e+00 -2.02645325e+01 16 2.29973578e+01 1.16372758e+02 2.86044814e+01 17 -6.48154871e+01 -4.70793637e+01 -2.49782296e+01 18 2.82992778e+01 1.46617850e+01 4.07853005e+00 19 2.43903672e+01 -5.65609040e+01 4.53343319e+01 20 -3.86389217e+01 2.97763434e+01 4.95113570e+01 21 -3.77869148e+01 -6.37632032e+01 1.48029207e+01 22 8.70258612e+01 4.54134843e+01 5.28745485e+01 23 4.19185108e+01 -2.48413183e+01 3.67676753e+01 24 -1.43813066e+01 2.33038512e+01 4.20429585e+01 25 -7.03260865e+01 -2.79437540e+01 3.62985951e+01 26 -1.14397552e+01 8.14027634e+01 -8.41919423e+00 27 2.07059278e+01 -8.09470127e+01 5.77678011e+01 28 -7.74837669e+01 6.39246212e+01 3.16638623e+01 29 -2.58366984e+01 -1.97877030e+01 3.30689911e+01 30 5.39683583e+01 6.52570294e+01 2.58944169e+00 31 6.56799684e+01 -2.73449935e+01 7.61843379e+01 32 2.47079777e+01 5.41142197e+01 6.29313785e+01 MONOATOMIC STRUCTURE (pbc=True)-- Species = Zr (Configuration in file "config-T-Zr.xyz") ----------------------------------------------------------------------------------------------------- Energy = 2431.31014729 Forces: 1 7.50198742e+01 -5.84389498e+01 1.21751574e+01 2 -3.08854901e+01 5.70680719e+01 5.71301443e+00 3 -8.69039855e-01 4.24753465e+01 5.93742820e+01 4 4.27987876e+01 4.98525235e+01 6.95669940e+00 5 5.96658474e+01 5.01078544e+00 -1.18293709e+01 6 -9.01074836e+01 1.08144371e+02 5.59739255e+01 7 -2.87406936e+01 -6.64483456e+01 -4.98006431e+01 8 -6.44701348e+01 -4.27631613e+01 2.79929509e+00 9 -6.08371187e+01 -6.42008934e+01 3.26684234e+01 10 -3.78909090e+01 1.01549616e+01 -3.29638526e+01 11 -2.21198875e+01 -6.19715056e+01 2.34534770e+01 12 -3.07243300e+00 2.09218243e+01 -1.63680266e+01 13 1.98386188e+01 -6.66774690e+01 -9.75293775e+01 14 -2.43046112e+01 -1.12491889e+00 -3.39141237e+01 15 7.92323136e+01 -1.55498230e+01 -1.72948695e+01 16 3.30353189e+01 5.75226172e+01 5.56292511e+01 17 2.63584439e+01 -3.73031872e+01 -3.06143779e+01 18 6.15544356e+01 4.08411812e+01 -6.28574354e+00 19 4.26750734e+01 1.50965120e+01 1.27329447e+01 20 4.48236664e+01 1.16283718e+02 -8.24098688e+00 21 -5.63535681e+01 4.34062093e+00 1.69337120e+01 22 1.03745971e+00 1.05863019e+02 6.18771058e+01 23 -5.93919125e+01 -8.95519193e+01 -6.88924377e+01 24 -1.89287440e+00 5.87172963e+01 -5.48477696e+01 25 -2.22370642e+01 -6.46642635e+01 3.86239137e+01 26 2.63534558e+00 1.35648289e+01 -2.79073795e+01 27 6.22211828e+01 -1.17371582e+02 -3.92959139e+01 28 -8.07216110e+01 4.07906404e+01 -1.19997777e+01 29 -4.74400848e+01 -4.52927379e+01 3.25512080e+01 30 -1.09416714e+01 1.20762074e+01 2.56610589e+01 31 3.92685701e+01 -5.07825678e+01 5.97380483e+01 32 5.21116497e+01 2.34167981e+01 4.92313397e+00 ================================================================================ VALGRIND OUTPUT ================================================================================ ==2103== Memcheck, a memory error detector ==2103== Copyright (C) 2002-2017, and GNU GPL'd, by Julian Seward et al. ==2103== Using Valgrind-3.13.0 and LibVEX; rerun with -h for copyright info ==2103== Command: python runner2.py EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000 ==2103== ==2103== Syscall param sched_getaffinity(mask) points to unaddressable byte(s) ==2103== at 0x4F3FF2F: sched_getaffinity@@GLIBC_2.3.4 (sched_getaffinity.c:36) ==2103== by 0x705438B: get_num_procs (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2103== by 0x705447C: blas_get_cpu_number (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2103== by 0x6E2C077: gotoblas_init (in /usr/local/lib/python2.7/dist-packages/numpy/.libs/libopenblasp-r0-8dca6697.3.0.dev.so) ==2103== by 0x4010732: call_init (dl-init.c:72) ==2103== by 0x4010732: _dl_init (dl-init.c:119) ==2103== by 0x40151FE: dl_open_worker (dl-open.c:522) ==2103== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2103== by 0x40147C9: _dl_open (dl-open.c:605) ==2103== by 0x544CF95: dlopen_doit (dlopen.c:66) ==2103== by 0x4FA32DE: _dl_catch_exception (dl-error-skeleton.c:196) ==2103== by 0x4FA336E: _dl_catch_error (dl-error-skeleton.c:215) ==2103== by 0x544D734: _dlerror_run (dlerror.c:162) ==2103== Address 0x0 is not stack'd, malloc'd or (recently) free'd ==2103== ==2103== ==2103== HEAP SUMMARY: ==2103== in use at exit: 10,115,869 bytes in 3,961 blocks ==2103== total heap usage: 118,702 allocs, 114,741 frees, 64,317,399 bytes allocated ==2103== ==2103== LEAK SUMMARY: ==2103== definitely lost: 0 bytes in 0 blocks ==2103== indirectly lost: 0 bytes in 0 blocks ==2103== possibly lost: 182,191 bytes in 111 blocks ==2103== still reachable: 9,933,678 bytes in 3,850 blocks ==2103== suppressed: 0 bytes in 0 blocks ==2103== Rerun with --leak-check=full to see details of leaked memory ==2103== ==2103== For counts of detected and suppressed errors, rerun with: -v ==2103== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 2501 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.