encore.cluster segmentation error

[Pippetta87]

Hi,

I want to cluster structures of trajectory using nucleicbackbone atoms positions but I get segmentation error. I've installed MDAnalysis using micromamba; the python code is:

fom MDAnalysis import Universe
import mdaencore as encore
ens1 = Universe("md.tpr","md.trr")
print(ens1.trajectory)
cluster_collection = encore.cluster(ens1,select='nucleicbackbone')

trajectory file is around 40Gb.
Below there is dmesg error which seems related (python error at end):

[871113.538133] Adding 134217724k swap on /swapfile. Priority:-2 extents:1096 across:314589184k SS
[872375.898687] signal: alloca_detect_c[1274766] overflowed sigaltstack
[872376.486926] signal: alloca_instrume[1275185] overflowed sigaltstack
[872376.718996] signal: alloca_instrume[1275368] overflowed sigaltstack
[872379.167676] signal: alloca_overflow[1278076] overflowed sigaltstack
[872380.065836] signal: alloca_safe_acc[1279909] overflowed sigaltstack
[872380.243977] signal: alloca_safe_acc[1280317] overflowed sigaltstack
[872380.474999] signal: alloca_safe_acc[1280812] overflowed sigaltstack
[872380.938115] signal: alloca_underflo[1281895] overflowed sigaltstack
[872381.744294] signal: asan-interface-[1283048] overflowed sigaltstack
[872382.173054] signal: asan-interface-[1283531] overflowed sigaltstack
[872382.921563] signal: asan-stack-smal[1284387] overflowed sigaltstack
[872383.328486] signal: bitfield-1.exe[1284863] overflowed sigaltstack
[872383.673606] signal: bitfield-1.exe[1285321] overflowed sigaltstack
[872384.433848] signal: bitfield-2.exe[1286171] overflowed sigaltstack
[872384.720389] signal: bitfield-2.exe[1286502] overflowed sigaltstack
[872384.925006] signal: bitfield-2.exe[1286735] overflowed sigaltstack
[872385.757716] signal: bitfield-3.exe[1287696] overflowed sigaltstack
[872386.327283] signal: bitfield-4.exe[1288338] overflowed sigaltstack
[872387.372626] signal: bitfield-5.exe[1289400] overflowed sigaltstack
[872388.111489] signal: clone-test-1.ex[1290106] overflowed sigaltstack
[872388.421354] signal: clone-test-1.ex[1292785] overflowed sigaltstack
[872389.346746] signal: global-overflow[1293694] overflowed sigaltstack
[872389.821267] signal: global-overflow[1294137] overflowed sigaltstack
[872390.070456] signal: halt_on_error-1[1294422] overflowed sigaltstack
[872390.333333] signal: halt_on_error-1[1294705] overflowed sigaltstack
[872391.061390] signal: halt_on_error-1[1295700] overflowed sigaltstack
[872391.191104] signal: halt_on_error-2[1295944] overflowed sigaltstack
[872392.426391] signal: heap-overflow-1[1297279] overflowed sigaltstack
[872396.750326] signal: null-deref-1.ex[1302116] overflowed sigaltstack
[872397.174763] signal: pointer-compare[1302565] overflowed sigaltstack
[872397.899024] signal: pointer-compare[1303402] overflowed sigaltstack
[872398.162049] signal: pointer-compare[1303645] overflowed sigaltstack
[872398.305217] signal: pointer-compare[1303821] overflowed sigaltstack
[872398.442883] signal: pointer-compare[1303982] overflowed sigaltstack
[872399.185015] signal: pointer-compare[1304889] overflowed sigaltstack
[872399.536340] signal: pointer-compare[1305274] overflowed sigaltstack
[872400.823378] signal: pointer-subtrac[1306736] overflowed sigaltstack
[872401.125514] signal: pointer-subtrac[1307067] overflowed sigaltstack
[872401.657519] signal: pointer-subtrac[1308970] overflowed sigaltstack
[872402.635862] signal: pointer-subtrac[1310014] overflowed sigaltstack
[872406.227644] signal: pr59063-2.exe[1313862] overflowed sigaltstack
[872406.544951] signal: pr61530.exe[1314223] overflowed sigaltstack
[872407.394549] signal: pr62089.exe[1315234] overflowed sigaltstack
[872407.995135] signal: pr62089.exe[1315905] overflowed sigaltstack
[872408.967140] signal: pr63888.exe[1316912] overflowed sigaltstack
[872409.112458] signal: pr63888.exe[1317063] overflowed sigaltstack
[872409.314635] signal: pr63888.exe[1317309] overflowed sigaltstack
[872409.612631] signal: pr63888.exe[1317623] overflowed sigaltstack
[872409.902557] signal: fstack_protecto[1317948] overflowed sigaltstack
[872410.205051] signal: pr70712.exe[1318271] overflowed sigaltstack
[872411.635066] get_sigframe: 2 callbacks suppressed
[872411.635070] signal: pr71480.exe[1319702] overflowed sigaltstack
[872411.971333] signal: pr79944.exe[1320108] overflowed sigaltstack
[872412.969089] signal: pr80308.exe[1321125] overflowed sigaltstack
[872413.542118] signal: pr80308.exe[1321733] overflowed sigaltstack
[872413.862716] signal: pr81697.exe[1322081] overflowed sigaltstack
[872414.321498] signal: pr81697.exe[1322619] overflowed sigaltstack
[872414.514560] signal: pr81697.exe[1322850] overflowed sigaltstack
[872415.805795] signal: sanity-check-pu[1324376] overflowed sigaltstack
[872416.230376] signal: sanity-check-pu[1324818] overflowed sigaltstack
[872419.001564] signal: sleep-before-dy[1327968] overflowed sigaltstack
[872420.446881] signal: strip-path-pref[1329473] overflowed sigaltstack
[872420.739849] signal: strlen-overflow[1329784] overflowed sigaltstack
[872421.974004] signal: strncpy-overflo[1331081] overflowed sigaltstack
[872423.748145] signal: use-after-free-[1333453] overflowed sigaltstack
[872424.513132] signal: use-after-free-[1334489] overflowed sigaltstack
[872424.707204] signal: use-after-free-[1334755] overflowed sigaltstack
[872425.136071] signal: use-after-retur[1335324] overflowed sigaltstack
[872426.289126] signal: sse2_hw_availab[1336707] overflowed sigaltstack
[872426.576432] signal: deep-stack-uaf-[1337061] overflowed sigaltstack
[872427.622204] signal: deep-stack-uaf-[1338258] overflowed sigaltstack
[872427.900773] signal: deep-tail-call-[1338647] overflowed sigaltstack
[872428.966269] signal: deep-thread-sta[1340045] overflowed sigaltstack
[872429.482452] signal: deep-thread-sta[1340705] overflowed sigaltstack
[872430.101293] signal: default-options[1341502] overflowed sigaltstack
[872430.990111] signal: function-argume[1342566] overflowed sigaltstack
[872432.505405] signal: function-argume[1344528] overflowed sigaltstack
[872433.335258] signal: function-argume[1345498] overflowed sigaltstack
[872433.532673] signal: function-argume[1345700] overflowed sigaltstack
[872434.447775] signal: interception-fa[1346549] overflowed sigaltstack
[872434.768478] signal: interception-ma[1346862] overflowed sigaltstack
[872434.921386] signal: interception-ma[1347019] overflowed sigaltstack
[872435.215220] signal: interception-ma[1347365] overflowed sigaltstack
[872435.416950] signal: interception-ma[1347613] overflowed sigaltstack
[872435.900735] signal: interception-te[1348070] overflowed sigaltstack
[872436.082455] signal: interception-te[1348205] overflowed sigaltstack
[872436.240288] signal: interception-te[1348308] overflowed sigaltstack
[872438.579484] signal: pr55617.exe[1350678] overflowed sigaltstack
[872438.784120] signal: pr55617.exe[1353323] overflowed sigaltstack
[872440.462426] signal: pr77396-2.exe[1355395] overflowed sigaltstack
[872441.831107] signal: pr77396.exe[1357127] overflowed sigaltstack
[872443.105236] signal: pr81021.exe[1358862] overflowed sigaltstack
[872445.028621] signal: pr81021.exe[1361244] overflowed sigaltstack
[872445.788989] signal: pr85081.exe[1362238] overflowed sigaltstack
[872445.986933] signal: pr85081.exe[1362526] overflowed sigaltstack
[872446.754750] signal: pr85774.exe[1363598] overflowed sigaltstack
[872447.215094] signal: pr85774.exe[1364077] overflowed sigaltstack
[872449.090474] signal: pr90570.exe[1366712] overflowed sigaltstack
[872449.287740] signal: pr90570.exe[1366843] overflowed sigaltstack
[872449.605478] signal: pr90570.exe[1367067] overflowed sigaltstack
[872450.202328] signal: pr97414.exe[1367556] overflowed sigaltstack
[872452.677086] signal: use-after-scope[1369076] overflowed sigaltstack
[872452.983347] signal: use-after-scope[1369225] overflowed sigaltstack
[872454.065605] signal: use-after-scope[1369852] overflowed sigaltstack
[872455.361949] signal: use-after-scope[1370704] overflowed sigaltstack
[872455.768585] signal: use-after-scope[1371069] overflowed sigaltstack
[872456.032210] signal: use-after-scope[1371221] overflowed sigaltstack
[872456.404071] signal: use-after-scope[1371421] overflowed sigaltstack
[872456.683199] signal: use-after-scope[1371559] overflowed sigaltstack
[872457.619073] signal: use-after-scope[1372203] overflowed sigaltstack
[872461.347056] signal: use-after-scope[1374802] overflowed sigaltstack
[872462.771453] signal: use-after-scope[1375842] overflowed sigaltstack
[872463.788140] signal: use-after-scope[1376715] overflowed sigaltstack
[872465.527528] signal: use-after-scope[1378318] overflowed sigaltstack
[872465.872907] signal: use-after-scope[1378636] overflowed sigaltstack
[872499.083466] process 'x86_64-pc-linux-gnu/libgomp/testsuite/pr52547.exe' started with executable stack
[872787.227723] signal: asan-stack-smal[1813216] overflowed sigaltstack
[872787.430247] signal: alloca_big_alig[1813413] overflowed sigaltstack
[872787.441205] signal: asan-stack-smal[1813438] overflowed sigaltstack
[872788.208664] signal: bitfield-1.exe[1814273] overflowed sigaltstack
[872788.319726] signal: bitfield-1.exe[1814432] overflowed sigaltstack
[872788.592488] signal: bitfield-1.exe[1814702] overflowed sigaltstack
[872788.647870] signal: alloca_detect_c[1814735] overflowed sigaltstack
[872789.220573] signal: halt_on_error-1[1815366] overflowed sigaltstack
[872789.348200] signal: halt_on_error-1[1815515] overflowed sigaltstack
[872789.402603] signal: bitfield-2.exe[1815569] overflowed sigaltstack
[872792.281443] get_sigframe: 16 callbacks suppressed
[872792.281448] signal: alloca_safe_acc[1819065] overflowed sigaltstack
[872792.305408] signal: memcmp-1.exe[1819101] overflowed sigaltstack
[872792.392203] signal: alloca_safe_acc[1819196] overflowed sigaltstack
[872792.906531] signal: clone-test-1.ex[1819639] overflowed sigaltstack
[872793.005564] signal: alloca_underflo[1819738] overflowed sigaltstack
[872793.721427] signal: global-overflow[1820468] overflowed sigaltstack
[872793.853771] signal: asan-interface-[1820609] overflowed sigaltstack
[872794.060542] signal: asan-interface-[1820853] overflowed sigaltstack
[872794.849849] signal: null-deref-1.ex[1821804] overflowed sigaltstack
[872794.967788] signal: pr63316.exe[1821934] overflowed sigaltstack
[872797.354697] get_sigframe: 15 callbacks suppressed
[872797.354700] signal: pr59063-1.exe[1824657] overflowed sigaltstack
[872797.387170] signal: pointer-compare[1824696] overflowed sigaltstack
[872797.435522] signal: pr70712.exe[1824758] overflowed sigaltstack
[872797.703675] signal: pr71480.exe[1825092] overflowed sigaltstack
[872797.866279] signal: pointer-subtrac[1825306] overflowed sigaltstack
[872798.156584] signal: pr59063-2.exe[1825605] overflowed sigaltstack
[872798.203178] signal: pointer-subtrac[1825650] overflowed sigaltstack
[872798.501823] signal: pr79944.exe[1825976] overflowed sigaltstack
[872798.859464] signal: pr59063-2.exe[1826356] overflowed sigaltstack
[872798.984595] signal: pr81697.exe[1826499] overflowed sigaltstack
[872802.415881] get_sigframe: 13 callbacks suppressed
[872802.415887] signal: stack-overflow-[1830052] overflowed sigaltstack
[872802.594831] signal: pr78541.exe[1830300] overflowed sigaltstack
[872802.833245] signal: pr80166.exe[1830581] overflowed sigaltstack
[872802.978635] signal: pr80166.exe[1830753] overflowed sigaltstack
[872803.039842] signal: stack-overflow-[1830819] overflowed sigaltstack
[872803.204146] signal: stack-overflow-[1831045] overflowed sigaltstack
[872803.333803] signal: strip-path-pref[1831218] overflowed sigaltstack
[872804.044883] signal: strlen-overflow[1832267] overflowed sigaltstack
[872804.264226] signal: strlen-overflow[1832501] overflowed sigaltstack
[872804.710318] signal: strncpy-overflo[1833033] overflowed sigaltstack
[872807.635582] get_sigframe: 20 callbacks suppressed
[872807.635585] signal: use-after-retur[1836740] overflowed sigaltstack
[872807.797717] signal: use-after-retur[1836963] overflowed sigaltstack
[872808.087402] signal: use-after-retur[1837327] overflowed sigaltstack
[872808.163512] signal: use-after-scope[1837413] overflowed sigaltstack
[872808.253952] signal: use-after-scope[1837545] overflowed sigaltstack
[872808.722792] signal: use-after-scope[1838057] overflowed sigaltstack
[872808.987478] signal: use-after-scope[1838371] overflowed sigaltstack
[872809.203781] signal: use-after-scope[1838590] overflowed sigaltstack
[872809.678699] signal: use-after-scope[1839013] overflowed sigaltstack
[872810.014162] signal: use-after-scope[1839349] overflowed sigaltstack
[873092.300617] show_signal: 2 callbacks suppressed
[873092.300620] traps: align-8.exe[2202350] trap invalid opcode ip:582eb0b9c152 sp:7ffdb5f435d8 error:0 in align-8.exe[1152,582eb0b9c000+1000]
[873092.408885] traps: align-8.exe[2202522] trap invalid opcode ip:638928cc7152 sp:7fff33cab658 error:0 in align-8.exe[1152,638928cc7000+1000]
[873092.511586] traps: align-8.exe[2202664] trap invalid opcode ip:63163f926152 sp:7fff1806b628 error:0 in align-8.exe[1152,63163f926000+1000]
[873092.616436] traps: align-8.exe[2202805] trap invalid opcode ip:56cc2e3fe152 sp:7ffe3e6826c8 error:0 in align-8.exe[1152,56cc2e3fe000+1000]
[873092.721912] traps: align-8.exe[2202942] trap invalid opcode ip:64f3ba810152 sp:7ffd02ea3118 error:0 in align-8.exe[1152,64f3ba810000+1000]
[873092.872573] traps: align-8.exe[2203122] trap invalid opcode ip:61cbaab1f152 sp:7ffcfef55048 error:0 in align-8.exe[1152,61cbaab1f000+1000]
[873097.559898] traps: nonnull-4.exe[2208144] trap invalid opcode ip:614229a35168 sp:7fff9d8e5880 error:0 in nonnull-4.exe[1168,614229a35000+1000]
[873097.693155] traps: nonnull-4.exe[2208246] trap invalid opcode ip:5f7a715f7215 sp:7ffdc9be1db8 error:0 in nonnull-4.exe[1215,5f7a715f7000+1000]
[873097.811678] traps: nonnull-4.exe[2208338] trap invalid opcode ip:5a1875d82052 sp:7fffa51745d8 error:0 in nonnull-4.exe[1052,5a1875d82000+1000]
[873097.921336] traps: nonnull-4.exe[2208449] trap invalid opcode ip:5b6e8e6a8052 sp:7ffd717a53a8 error:0 in nonnull-4.exe[1052,5b6e8e6a8000+1000]
[873097.955606] null-4.exe[2208468]: segfault at 0 ip 0000566784d49165 sp 00007fff0fa4b530 error 4 in null-4.exe[1165,566784d49000+1000] likely on CPU 21 (core 37, socket 0)
[873097.955620] Code: 89 e5 48 83 ec 10 48 c7 45 f8 00 00 00 00 48 83 7d f8 00 75 11 be 00 00 00 00 48 8d 3d 04 2f 00 00 e8 cf fe ff ff 48 8b 45 f8 0f 10 00 f2 0f 10 50 08 66 0f ef c9 66 0f 2e c1 7a 22 66 0f ef
[873098.031485] traps: nonnull-4.exe[2208550] trap invalid opcode ip:63b8dee65053 sp:7ffc3e212d48 error:0 in nonnull-4.exe[1053,63b8dee65000+1000]
[873098.128329] null-4.exe[2208610]: segfault at 8 ip 00005aa38ea8c152 sp 00007ffc37bcf680 error 4 in null-4.exe[1152,5aa38ea8c000+1000] likely on CPU 20 (core 36, socket 0)
[873098.128342] Code: c3 0f 1f 80 00 00 00 00 f3 0f 1e fa e9 77 ff ff ff 48 83 ec 08 be 00 00 00 00 48 8d 3d 17 2f 00 00 e8 e2 fe ff ff 66 0f ef c0 <66> 0f 2e 04 25 08 00 00 00 0f 9a c0 ba 01 00 00 00 0f 45 c2 84 c0
[873098.199077] traps: nonnull-4.exe[2208658] trap invalid opcode ip:5c95f4c560f0 sp:7fff5ed88378 error:0 in nonnull-4.exe[10f0,5c95f4c56000+1000]
[873098.263380] null-4.exe[2208712]: segfault at 8 ip 00005813a458c06b sp 00007ffc095249f0 error 4 in null-4.exe[106b,5813a458c000+1000] likely on CPU 8 (core 16, socket 0)
[873098.263389] Code: 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 48 83 ec 08 31 f6 48 8d 3d 03 30 00 00 e8 ce ff ff ff 66 0f ef c0 ba 01 00 00 00 <66> 0f 2e 04 25 08 00 00 00 0f 9a c0 0f 45 c2 84 c0 75 1e 66 0f 2e
[873098.358810] traps: nonnull-4.exe[2208806] trap invalid opcode ip:65314e6c90ae sp:7fffa5da1828 error:0 in nonnull-4.exe[10ae,65314e6c9000+1000]
[873102.625495] show_signal_msg: 54 callbacks suppressed
[873102.625498] null-8.exe[2212812]: segfault at 0 ip 00005ecaacf7214e sp 00007ffdb5699f50 error 4 in null-8.exe[114e,5ecaacf72000+1000] likely on CPU 6 (core 12, socket 0)
[873102.625505] Code: c3 0f 1f 00 c3 0f 1f 80 00 00 00 00 f3 0f 1e fa e9 77 ff ff ff 48 83 ec 08 be 00 00 00 00 48 8d 3d f7 2e 00 00 e8 e2 fe ff ff <8b> 04 25 00 00 00 00 48 83 c4 08 c3 00 00 f3 0f 1e fa 48 83 ec 08
[873102.818632] null-8.exe[2212974]: segfault at 0 ip 000057ab6210a062 sp 00007fff4c5ad360 error 4 in null-8.exe[1062,57ab6210a000+1000] likely on CPU 1 (core 0, socket 0)
[873102.818641] Code: 00 00 00 e9 e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 48 83 ec 08 31 f6 48 8d 3d e3 2f 00 00 e8 ce ff ff ff <8b> 04 25 00 00 00 00 48 83 c4 08 c3 66 90 f3 0f 1e fa 31 ed 49 89
[873102.970039] null-8.exe[2213102]: segfault at 0 ip 00005f6913d8c062 sp 00007ffdebcb87d0 error 4 in null-8.exe[1062,5f6913d8c000+1000] likely on CPU 5 (core 8, socket 0)
[873102.970049] Code: 00 00 00 e9 e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 48 83 ec 08 31 f6 48 8d 3d e3 2f 00 00 e8 ce ff ff ff <8b> 04 25 00 00 00 00 48 83 c4 08 c3 66 90 f3 0f 1e fa 31 ed 49 89
[873103.121357] null-8.exe[2213251]: segfault at 0 ip 00005a091e5f405f sp 00007ffd7a1bce10 error 4 in null-8.exe[105f,5a091e5f4000+1000] likely on CPU 5 (core 8, socket 0)
[873103.121366] Code: 00 68 00 00 00 00 e9 e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 50 31 f6 48 8d 3d e6 2f 00 00 e8 d1 ff ff ff <8b> 04 25 00 00 00 00 5a c3 0f 1f 84 00 00 00 00 00 f3 0f 1e fa 31
[873103.324462] null-8.exe[2213466]: segfault at 0 ip 00005f968a40f062 sp 00007ffda0665b30 error 4 in null-8.exe[1062,5f968a40f000+1000] likely on CPU 0 (core 0, socket 0)
[873103.324471] Code: 00 00 00 e9 e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 48 83 ec 08 31 f6 48 8d 3d e3 2f 00 00 e8 ce ff ff ff <8b> 04 25 00 00 00 00 48 83 c4 08 c3 66 90 f3 0f 1e fa 31 ed 49 89
[873103.541478] null-8.exe[2213670]: segfault at 0 ip 00005e240583f062 sp 00007ffc07c61720 error 4 in null-8.exe[1062,5e240583f000+1000] likely on CPU 2 (core 4, socket 0)
[873103.541488] Code: 00 00 00 e9 e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 48 83 ec 08 31 f6 48 8d 3d e3 2f 00 00 e8 ce ff ff ff <8b> 04 25 00 00 00 00 48 83 c4 08 c3 66 90 f3 0f 1e fa 31 ed 49 89
[873103.680940] null-9.exe[2213832]: segfault at 0 ip 0000607f68d1f165 sp 00007ffde1d01780 error 4 in null-9.exe[1165,607f68d1f000+1000] likely on CPU 16 (core 32, socket 0)
[873103.680953] Code: 89 e5 48 83 ec 10 48 c7 45 f8 00 00 00 00 48 83 7d f8 00 75 11 be 00 00 00 00 48 8d 3d e4 2e 00 00 e8 cf fe ff ff 48 8b 45 f8 <8b> 00 c9 c3 00 00 00 f3 0f 1e fa 48 83 ec 08 48 83 c4 08 c3 00 00
[873103.835629] null-9.exe[2214003]: segfault at 0 ip 0000572574d5714e sp 00007ffdda074c40 error 4 in null-9.exe[114e,572574d57000+1000] likely on CPU 16 (core 32, socket 0)
[873103.835643] Code: c3 0f 1f 00 c3 0f 1f 80 00 00 00 00 f3 0f 1e fa e9 77 ff ff ff 48 83 ec 08 be 00 00 00 00 48 8d 3d f7 2e 00 00 e8 e2 fe ff ff <8b> 04 25 00 00 00 00 48 83 c4 08 c3 00 00 f3 0f 1e fa 48 83 ec 08
[873103.925169] null-2.exe[2214088]: segfault at 0 ip 000064af67b0f166 sp 00007fff69c943a0 error 4 in null-2.exe[1166,64af67b0f000+1000] likely on CPU 11 (core 20, socket 0)
[873103.925178] Code: e5 53 48 83 ec 18 48 c7 45 e8 00 00 00 00 48 83 7d e8 00 75 11 be 00 00 00 00 48 8d 3d 03 2f 00 00 e8 ce fe ff ff 48 8b 45 e8 <48> 8b 18 48 85 db 75 11 be 00 00 00 00 48 8d 3d 06 2f 00 00 e8 b1
[873104.002018] null-9.exe[2214183]: segfault at 0 ip 000064fef8585062 sp 00007ffc840b0ae0 error 4 in null-9.exe[1062,64fef8585000+1000] likely on CPU 11 (core 20, socket 0)
[873104.002028] Code: 00 00 00 e9 e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 48 83 ec 08 31 f6 48 8d 3d e3 2f 00 00 e8 ce ff ff ff <8b> 04 25 00 00 00 00 48 83 c4 08 c3 66 90 f3 0f 1e fa 31 ed 49 89
[873282.926084] show_signal: 31 callbacks suppressed
[873282.926087] traps: cleanup-1.exe[2363334] general protection fault ip:724a4db69597 sp:7ffd73f5b1b8 error:0 in libc.so.6[168597,724a4da25000+171000]
[873283.057910] traps: cleanup-2.exe[2363454] general protection fault ip:796aedaf2597 sp:7ffe34a19c88 error:0 in libc.so.6[168597,796aed9ae000+171000]
[873496.547710] traps: align-8.exe[2487246] trap invalid opcode ip:56ae8f9dc152 sp:7ffe6d014138 error:0 in align-8.exe[1152,56ae8f9dc000+1000]
[873496.681295] traps: align-8.exe[2487342] trap invalid opcode ip:64c417465152 sp:7ffd8dbc78d8 error:0 in align-8.exe[1152,64c417465000+1000]
[873496.830466] traps: align-8.exe[2487432] trap invalid opcode ip:60196f5bb152 sp:7ffdfe47d058 error:0 in align-8.exe[1152,60196f5bb000+1000]
[873496.966886] traps: align-8.exe[2487516] trap invalid opcode ip:64ffa3d38152 sp:7ffd1955e568 error:0 in align-8.exe[1152,64ffa3d38000+1000]
[873497.093507] traps: align-8.exe[2487609] trap invalid opcode ip:55e46230d152 sp:7ffde29dc198 error:0 in align-8.exe[1152,55e46230d000+1000]
[873497.306079] traps: align-8.exe[2487706] trap invalid opcode ip:5ab77053c152 sp:7ffc43f78b08 error:0 in align-8.exe[1152,5ab77053c000+1000]
[873497.621255] traps: nonnull-4.exe[2487898] trap invalid opcode ip:618c54d8f168 sp:7fffe3136800 error:0 in nonnull-4.exe[1168,618c54d8f000+1000]
[873497.796133] traps: nonnull-4.exe[2487969] trap invalid opcode ip:57ad6af1b215 sp:7ffe691a2cc8 error:0 in nonnull-4.exe[1215,57ad6af1b000+1000]
[873497.939131] traps: nonnull-4.exe[2488046] trap invalid opcode ip:63280433a052 sp:7ffe1cdddbb8 error:0 in nonnull-4.exe[1052,63280433a000+1000]
[873498.076456] traps: nonnull-4.exe[2488139] trap invalid opcode ip:5df133323052 sp:7ffd3db00fc8 error:0 in nonnull-4.exe[1052,5df133323000+1000]
[873501.628193] show_signal_msg: 22 callbacks suppressed
[873501.628198] null-10.exe[2489370]: segfault at 0 ip 00005ceb4c376066 sp 00007ffcc9c4fa60 error 4 in null-10.exe[1066,5ceb4c376000+1000] likely on CPU 17 (core 33, socket 0)
[873501.628208] Code: e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 53 31 f6 48 8d 3d 06 30 00 00 e8 d1 ff ff ff 48 8d 05 1c 30 00 00 <48> 0f bf 14 25 00 00 00 00 48 8d 1c 50 48 85 db 74 0c b8 17 00 00
[873501.638508] null-5.exe[2489374]: segfault at 0 ip 000065008064f06b sp 00007ffecd575e80 error 4 in null-5.exe[106b,65008064f000+1000] likely on CPU 0 (core 0, socket 0)
[873501.638517] Code: 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 48 83 ec 08 31 f6 48 8d 3d 03 30 00 00 e8 ce ff ff ff 66 0f ef c0 ba 01 00 00 00 0f 10 0c 25 00 00 00 00 f3 0f 10 14 25 04 00 00 00 0f 2e c8 0f
[873501.793814] null-5.exe[2489429]: segfault at 0 ip 0000623fffab0064 sp 00007fff4dcf0530 error 4 in null-5.exe[1064,623fffab0000+1000] likely on CPU 18 (core 34, socket 0)
[873501.793827] Code: 00 e9 e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 51 31 f6 48 8d 3d 06 30 00 00 e8 d1 ff ff ff 0f 57 c0 b1 01 0f 10 14 25 00 00 00 00 f3 0f 10 0c 25 04 00 00 00 0f 2e d0 0f
[873501.823885] null-10.exe[2489439]: segfault at 0 ip 0000654d2f0a0066 sp 00007ffe23d83cf0 error 4 in null-10.exe[1066,654d2f0a0000+1000] likely on CPU 19 (core 35, socket 0)
[873501.823898] Code: e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 53 31 f6 48 8d 3d 06 30 00 00 e8 d1 ff ff ff 48 8d 05 1c 30 00 00 <48> 0f bf 14 25 00 00 00 00 48 8d 1c 50 48 85 db 74 0c b8 17 00 00
[873501.969285] null-10.exe[2489500]: segfault at 0 ip 00006412777a2066 sp 00007ffde7ed36c0 error 4 in null-10.exe[1066,6412777a2000+1000] likely on CPU 16 (core 32, socket 0)
[873501.969298] Code: e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 53 31 f6 48 8d 3d 06 30 00 00 48 8d 1d 21 30 00 00 e8 ca ff ff ff <48> 0f bf 04 25 00 00 00 00 48 01 c0 48 01 c3 75 0e 31 f6 48 8d 3d
[873502.019336] null-5.exe[2489515]: segfault at 0 ip 00005b660d13806b sp 00007ffcbfac9070 error 4 in null-5.exe[106b,5b660d138000+1000] likely on CPU 18 (core 34, socket 0)
[873502.019349] Code: 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 48 83 ec 08 31 f6 48 8d 3d 03 30 00 00 e8 ce ff ff ff 66 0f ef c0 ba 01 00 00 00 0f 10 0c 25 00 00 00 00 f3 0f 10 14 25 04 00 00 00 0f 2e c8 0f
[873502.185925] null-10.exe[2489596]: segfault at 0 ip 00005d037f224066 sp 00007ffc00144580 error 4 in null-10.exe[1066,5d037f224000+1000] likely on CPU 17 (core 33, socket 0)
[873502.185938] Code: e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 53 31 f6 48 8d 3d 06 30 00 00 e8 d1 ff ff ff 48 8d 05 1c 30 00 00 <48> 0f bf 14 25 00 00 00 00 48 8d 1c 50 48 85 db 74 0c b8 17 00 00
[873502.192648] null-5.exe[2489599]: segfault at 0 ip 000055e7a7a5e06b sp 00007ffcb4b39460 error 4 in null-5.exe[106b,55e7a7a5e000+1000] likely on CPU 6 (core 12, socket 0)
[873502.192657] Code: 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 48 83 ec 08 31 f6 48 8d 3d 03 30 00 00 e8 ce ff ff ff 66 0f ef c0 ba 01 00 00 00 0f 10 0c 25 00 00 00 00 f3 0f 10 14 25 04 00 00 00 0f 2e c8 0f
[873502.345060] null-6.exe[2489671]: segfault at 0 ip 00005a033aadb165 sp 00007fffe1d401c0 error 6 in null-6.exe[1165,5a033aadb000+1000] likely on CPU 19 (core 35, socket 0)
[873502.345073] Code: 89 e5 48 83 ec 10 48 c7 45 f8 00 00 00 00 48 83 7d f8 00 75 11 be 00 00 00 00 48 8d 3d 04 2f 00 00 e8 cf fe ff ff 48 8b 45 f8 <48> c7 00 2a 00 00 00 b8 00 00 00 00 c9 c3 00 f3 0f 1e fa 48 83 ec
[873502.378812] null-10.exe[2489686]: segfault at 0 ip 00005b8f47a06066 sp 00007fffbe072530 error 4 in null-10.exe[1066,5b8f47a06000+1000] likely on CPU 18 (core 34, socket 0)
[873502.378824] Code: e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 53 31 f6 48 8d 3d 06 30 00 00 e8 d1 ff ff ff 48 8d 05 1c 30 00 00 <48> 0f bf 14 25 00 00 00 00 48 8d 1c 50 48 85 db 74 0c b8 17 00 00
[873506.676180] show_signal_msg: 43 callbacks suppressed
[873506.676183] null-3.exe[2491795]: segfault at 0 ip 00005a4e6129b05f sp 00007fff42783a70 error 4 in null-3.exe[105f,5a4e6129b000+1000] likely on CPU 12 (core 24, socket 0)
[873506.676190] Code: 00 68 00 00 00 00 e9 e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 53 31 f6 48 8d 3d 26 30 00 00 e8 d1 ff ff ff <48> 8b 1c 25 00 00 00 00 48 85 db 74 04 8b 03 5b c3 31 f6 48 8d 3d
[873506.782144] null-9.exe[2491857]: segfault at 0 ip 000065288870f062 sp 00007ffe06b7cc60 error 4 in null-9.exe[1062,65288870f000+1000] likely on CPU 4 (core 8, socket 0)
[873506.782153] Code: 00 00 00 e9 e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 48 83 ec 08 31 f6 48 8d 3d e3 2f 00 00 e8 ce ff ff ff <8b> 04 25 00 00 00 00 48 83 c4 08 c3 66 90 f3 0f 1e fa 31 ed 49 89
[873506.827487] null-3.exe[2491884]: segfault at 0 ip 00006144bd09a05f sp 00007ffed6563ae0 error 4 in null-3.exe[105f,6144bd09a000+1000] likely on CPU 0 (core 0, socket 0)
[873506.827496] Code: 00 68 00 00 00 00 e9 e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 53 31 f6 48 8d 3d 26 30 00 00 e8 d1 ff ff ff <48> 8b 1c 25 00 00 00 00 48 85 db 75 0e 31 f6 48 8d 3d eb 2f 00 00
[873507.019696] null-3.exe[2491987]: segfault at 0 ip 000060a5a89ea05f sp 00007ffd882aa880 error 4 in null-3.exe[105f,60a5a89ea000+1000] likely on CPU 16 (core 32, socket 0)
[873507.019709] Code: 00 68 00 00 00 00 e9 e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 53 31 f6 48 8d 3d 26 30 00 00 e8 d1 ff ff ff <48> 8b 1c 25 00 00 00 00 48 85 db 74 04 8b 03 5b c3 31 f6 48 8d 3d
[873507.212837] null-3.exe[2492075]: segfault at 0 ip 0000608da059e05f sp 00007ffe7beba910 error 4 in null-3.exe[105f,608da059e000+1000] likely on CPU 17 (core 33, socket 0)
[873507.212851] Code: 00 68 00 00 00 00 e9 e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 53 31 f6 48 8d 3d 26 30 00 00 e8 d1 ff ff ff <48> 8b 1c 25 00 00 00 00 48 85 db 74 04 8b 03 5b c3 31 f6 48 8d 3d
[873507.347173] null-4.exe[2492139]: segfault at 0 ip 00005b2ee7799165 sp 00007fff13b52d40 error 4 in null-4.exe[1165,5b2ee7799000+1000] likely on CPU 16 (core 32, socket 0)
[873507.347186] Code: 89 e5 48 83 ec 10 48 c7 45 f8 00 00 00 00 48 83 7d f8 00 75 11 be 00 00 00 00 48 8d 3d 04 2f 00 00 e8 cf fe ff ff 48 8b 45 f8 0f 10 00 f2 0f 10 50 08 66 0f ef c9 66 0f 2e c1 7a 22 66 0f ef
[873507.496052] null-4.exe[2492218]: segfault at 8 ip 00005e6f9e7d1152 sp 00007ffe772b69f0 error 4 in null-4.exe[1152,5e6f9e7d1000+1000] likely on CPU 17 (core 33, socket 0)
[873507.496067] Code: c3 0f 1f 80 00 00 00 00 f3 0f 1e fa e9 77 ff ff ff 48 83 ec 08 be 00 00 00 00 48 8d 3d 17 2f 00 00 e8 e2 fe ff ff 66 0f ef c0 <66> 0f 2e 04 25 08 00 00 00 0f 9a c0 ba 01 00 00 00 0f 45 c2 84 c0
[873507.689817] null-4.exe[2492299]: segfault at 8 ip 00005c470533b06b sp 00007ffc90d0e470 error 4 in null-4.exe[106b,5c470533b000+1000] likely on CPU 1 (core 0, socket 0)
[873507.689827] Code: 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 48 83 ec 08 31 f6 48 8d 3d 03 30 00 00 e8 ce ff ff ff 66 0f ef c0 ba 01 00 00 00 <66> 0f 2e 04 25 08 00 00 00 0f 9a c0 0f 45 c2 84 c0 75 1e 66 0f 2e
[873507.850425] null-4.exe[2492393]: segfault at 8 ip 00005f266814b06b sp 00007fffc5babd00 error 4 in null-4.exe[106b,5f266814b000+1000] likely on CPU 5 (core 8, socket 0)
[873507.850434] Code: 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 48 83 ec 08 31 f6 48 8d 3d 03 30 00 00 e8 ce ff ff ff 66 0f ef c0 ba 01 00 00 00 <66> 0f 2e 04 25 08 00 00 00 0f 9a c0 0f 45 c2 84 c0 75 1e 66 0f 2e
[873508.002765] null-4.exe[2492493]: segfault at 8 ip 00006239156a0064 sp 00007ffc63dfd2b0 error 4 in null-4.exe[1064,6239156a0000+1000] likely on CPU 3 (core 4, socket 0)
[873508.002775] Code: 00 e9 e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 51 31 f6 48 8d 3d 06 30 00 00 e8 d1 ff ff ff 0f 57 c0 b1 01 <66> 0f 2e 04 25 08 00 00 00 0f 9a c2 0f 45 d1 84 d2 75 16 66 0f 2e
[873512.583737] show_signal: 2 callbacks suppressed
[873512.583741] traps: overflow-add-4.[2505139] trap invalid opcode ip:5f24749ca145 sp:7ffc89fdff90 error:0 in overflow-add-4.exe[1145,5f24749ca000+1000]
[873512.714189] traps: overflow-add-4.[2505222] trap invalid opcode ip:6460c744614f sp:7ffdade75d28 error:0 in overflow-add-4.exe[114f,6460c7446000+1000]
[873512.864400] traps: overflow-add-4.[2505331] trap invalid opcode ip:5d743ec35063 sp:7fff66d0be28 error:0 in overflow-add-4.exe[1063,5d743ec35000+1000]
[873513.042992] traps: overflow-add-4.[2505442] trap invalid opcode ip:58488a100063 sp:7ffc3e450068 error:0 in overflow-add-4.exe[1063,58488a100000+1000]
[873513.170752] traps: overflow-add-4.[2505531] trap invalid opcode ip:63361333305c sp:7ffc6b663c78 error:0 in overflow-add-4.exe[105c,633613333000+1000]
[873513.368865] traps: overflow-add-4.[2505652] trap invalid opcode ip:5ba2613f1063 sp:7ffd4fc93d48 error:0 in overflow-add-4.exe[1063,5ba2613f1000+1000]
[873513.558251] traps: overflow-add-4.[2505775] trap invalid opcode ip:5e245a572063 sp:7fffcc8cd898 error:0 in overflow-add-4.exe[1063,5e245a572000+1000]
[873515.104189] pr59667.exe[2506817]: segfault at 0 ip 00005665426c72c6 sp 00007ffc39bec8e0 error 6 in pr59667.exe[12c6,5665426c7000+1000] likely on CPU 2 (core 4, socket 0)
[873515.104197] Code: c8 00 74 0b 48 89 c2 83 e2 03 48 85 d2 74 0f 48 89 c6 48 8d 3d 4b 2e 00 00 e8 96 fd ff ff 48 8b 45 c8 f3 0f 10 05 96 0d 00 00 0f 11 00 b8 00 00 00 00 48 83 c4 48 5b 41 5c 41 5d 41 5e 41 5f
[873515.307344] pr59667.exe[2506953]: segfault at 0 ip 00005a65f52df14e sp 00007ffd6468adc0 error 6 in pr59667.exe[114e,5a65f52df000+1000] likely on CPU 22 (core 38, socket 0)
[873515.307357] Code: c3 0f 1f 00 c3 0f 1f 80 00 00 00 00 f3 0f 1e fa e9 77 ff ff ff 48 83 ec 08 be 00 00 00 00 48 8d 3d f7 2e 00 00 e8 e2 fe ff ff 04 25 00 00 00 00 00 00 80 3f b8 00 00 00 00 48 83 c4 08 c3 00
[873515.494979] pr59667.exe[2507054]: segfault at 0 ip 0000625c5f0cb064 sp 00007ffc703c9a80 error 6 in pr59667.exe[1064,625c5f0cb000+1000] likely on CPU 8 (core 16, socket 0)
[873515.494988] Code: 00 e9 e0 ff ff ff ff 25 7a 2f 00 00 66 90 00 00 00 00 00 00 00 00 48 83 ec 08 31 f6 48 8d 3d e3 2f 00 00 e8 ce ff ff ff 31 c0 04 25 00 00 00 00 00 00 80 3f 48 83 c4 08 c3 66 2e 0f 1f 84 00
[873526.520002] show_signal: 4 callbacks suppressed
[873526.520007] traps: null-5.exe[2514062] trap invalid opcode ip:60aaf666f129 sp:7ffc5ebeb038 error:0 in null-5.exe[1129,60aaf666f000+1000]
[873526.662402] traps: null-5.exe[2514154] trap invalid opcode ip:61fbf6cc3129 sp:7fff336587f8 error:0 in null-5.exe[1129,61fbf6cc3000+1000]
[873526.804541] traps: null-5.exe[2514242] trap invalid opcode ip:5c245745b129 sp:7fff392acb78 error:0 in null-5.exe[1129,5c245745b000+1000]
[873526.934832] traps: null-5.exe[2514356] trap invalid opcode ip:56783bb38129 sp:7ffc1b48d918 error:0 in null-5.exe[1129,56783bb38000+1000]
[873527.105319] traps: null-5.exe[2514474] trap invalid opcode ip:5f91796b7129 sp:7ffefe8d9498 error:0 in null-5.exe[1129,5f91796b7000+1000]
[873527.306442] traps: null-5.exe[2514605] trap invalid opcode ip:5ec4e4c2a129 sp:7fff7f2a9238 error:0 in null-5.exe[1129,5ec4e4c2a000+1000]
[1230618.319672] python[3198041]: segfault at 0 ip 0000708213e77f0b sp 00007ffc9aa82ed0 error 4 in affinityprop.cpython-311-x86_64-linux-gnu.so[1bf0b,708213e60000+1a000] likely on CPU 9 (core 16, socket 0)
[1230618.319683] Code: 11 41 0f af c8 4d 63 d6 41 f7 d7 45 01 e7 41 83 e7 03 41 89 cb 41 c1 eb 1f 44 01 d9 d1 f9 01 c1 48 63 c9 f3 45 0f 10 54 8d 00 46 0f 58 54 95 00 45 0f 2f d5 0f 86 1c 0a 00 00 41 0f 28 ed 45
[1230649.936840] systemd-journald[506]: Under memory pressure, flushing caches.
[1230655.952926] systemd-journald[506]: Under memory pressure, flushing caches.
[1248837.001967] Adding 268435452k swap on /swapfile. Priority:-2 extents:1108 across:478625792k SS
[1351221.374205] python[3445013]: segfault at 0 ip 000070d5480a9f0b sp 00007ffc914d93c0 error 4 in affinityprop.cpython-311-x86_64-linux-gnu.so[1bf0b,70d548092000+1a000] likely on CPU 9 (core 16, socket 0)
[1351221.374215] Code: 11 41 0f af c8 4d 63 d6 41 f7 d7 45 01 e7 41 83 e7 03 41 89 cb 41 c1 eb 1f 44 01 d9 d1 f9 01 c1 48 63 c9 f3 45 0f 10 54 8d 00 46 0f 58 54 95 00 45 0f 2f d5 0f 86 1c 0a 00 00 41 0f 28 ed 45

Need more RAM/bigger swap file?

Any suggestion?

Best regards

[orbeckst]

Can you make it work on a shorter trajectory or smaller system?

[Pippetta87]

yes it work on 20ns trajectory, using around 20Gb of ram; also entire trajectory file is 4Gb not 40 Gb as stated in original post.
Can larger swapfile temporarily solve the crash problem?
Currently I have 64 GB of ram and 256Gb of swap...

[orbeckst]

ENCORE loads trajectories into memory. Perhaps you can preprocess your trajectory so that it only contains the nucleicbackbone atoms

ens1 = mda.Universe("md.tpr","md.trr")
nbb = ens1.select_atoms("nucleicbackbone")
nbb.atoms.write("nucleicbackbone.trr", frames="all")
nbb.atoms.write("nucleicbackbone.gro")

and then use

ens1_nbb = mda.Universe("nucleicbackbone.gro", "nucleicbackbone.trr")

If you have a lot of solvent then this may reduce the memory footprint dramatically.