Package evaluation of CrystalNets on Julia 1.13.0-DEV.1022 (6a783956c1*) started at 2025-08-24T15:39:17.896 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.92s ################################################################################ # Installation # Installing CrystalNets... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [7952bbbe] + CrystalNets v1.0.2 Updating `~/.julia/environments/v1.13/Manifest.toml` [c7e460c6] + ArgParse v1.2.0 [ec485272] + ArnoldiMethod v0.4.0 [a963bdd2] + AtomsBase v0.5.1 [46823bd8] + Chemfiles v0.10.43 [7952bbbe] + CrystalNets v1.0.2 [864edb3b] + DataStructures v0.19.0 [ffbed154] + DocStringExtensions v0.9.5 [86223c79] + Graphs v1.13.1 [d25df0c9] + Inflate v0.1.5 [692b3bcd] + JLLWrappers v1.7.1 [1914dd2f] + MacroTools v0.5.16 [bac558e1] + OrderedCollections v1.8.1 [f305370e] + PeriodicGraphEmbeddings v0.3.3 [72a2d4b8] + PeriodicGraphEquilibriumPlacement v0.2.2 [18c5b727] + PeriodicGraphs v0.10.4 [7b2266bf] + PeriodicTable v1.2.1 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.5.0 [92933f4c] + ProgressMeter v1.10.4 [ae029012] + Requires v1.3.1 [699a6c99] + SimpleTraits v0.9.5 [90137ffa] + StaticArrays v1.9.14 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [b718987f] + TextWrap v1.0.2 [0796e94c] + Tokenize v0.5.29 [1986cc42] + Unitful v1.24.0 [a7773ee8] + UnitfulAtomic v1.0.0 [78a364fa] + Chemfiles_jll v0.10.4+0 [ac4a9f1e] + spglib_jll v2.4.0+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [8ba89e20] + Distributed v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.13.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [1a1011a3] + SharedArrays v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.11.0 [fa267f1f] + TOML v1.0.3 [a4e569a6] + Tar v1.10.0 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.15.0+1 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.8.12 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.2+0 [efcefdf7] + PCRE2_jll v10.45.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.66.0+0 [3f19e933] + p7zip_jll v17.6.0+0 Installation completed after 4.56s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 357.4s ################################################################################ # Testing # Testing CrystalNets Status `/tmp/jl_OLreDg/Project.toml` [861a8166] Combinatorics v1.0.3 [7952bbbe] CrystalNets v1.0.2 [86223c79] Graphs v1.13.1 [18c5b727] PeriodicGraphs v0.10.4 [90137ffa] StaticArrays v1.9.14 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_OLreDg/Manifest.toml` [c7e460c6] ArgParse v1.2.0 [ec485272] ArnoldiMethod v0.4.0 [a963bdd2] AtomsBase v0.5.1 [46823bd8] Chemfiles v0.10.43 [861a8166] Combinatorics v1.0.3 [7952bbbe] CrystalNets v1.0.2 [864edb3b] DataStructures v0.19.0 [ffbed154] DocStringExtensions v0.9.5 [86223c79] Graphs v1.13.1 [d25df0c9] Inflate v0.1.5 [692b3bcd] JLLWrappers v1.7.1 [1914dd2f] MacroTools v0.5.16 [bac558e1] OrderedCollections v1.8.1 [f305370e] PeriodicGraphEmbeddings v0.3.3 [72a2d4b8] PeriodicGraphEquilibriumPlacement v0.2.2 [18c5b727] PeriodicGraphs v0.10.4 [7b2266bf] PeriodicTable v1.2.1 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.5.0 [92933f4c] ProgressMeter v1.10.4 [ae029012] Requires v1.3.1 [699a6c99] SimpleTraits v0.9.5 [90137ffa] StaticArrays v1.9.14 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [b718987f] TextWrap v1.0.2 [0796e94c] Tokenize v0.5.29 [1986cc42] Unitful v1.24.0 [a7773ee8] UnitfulAtomic v1.0.0 [78a364fa] Chemfiles_jll v0.10.4+0 [ac4a9f1e] spglib_jll v2.4.0+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [8ba89e20] Distributed v1.11.0 [f43a241f] Downloads v1.7.0 [7b1f6079] FileWatching v1.11.0 [b77e0a4c] InteractiveUtils v1.11.0 [ac6e5ff7] JuliaSyntaxHighlighting v1.12.0 [b27032c2] LibCURL v0.6.4 [76f85450] LibGit2 v1.11.0 [8f399da3] Libdl v1.11.0 [37e2e46d] LinearAlgebra v1.13.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.13.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization v1.11.0 [1a1011a3] SharedArrays v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.11.0 [fa267f1f] TOML v1.0.3 [a4e569a6] Tar v1.10.0 [8dfed614] Test v1.11.0 [cf7118a7] UUIDs v1.11.0 [4ec0a83e] Unicode v1.11.0 [e66e0078] CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] LibCURL_jll v8.15.0+1 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.8.12 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.2+0 [efcefdf7] PCRE2_jll v10.45.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.13.1+0 [8e850ede] nghttp2_jll v1.66.0+0 [3f19e933] p7zip_jll v17.6.0+0 Testing Running tests... The following warning about altering performance, the two messages on warning toggling and the three error statements are expected. [ Warning: Warnings may critically alter performance for this operation and were turned off. [ Info: Use CrystalNets.toggle_warning(false) or the --no-warn option to remove this warning [ Info: Use the force_warn option to force printing warnings [ Error: Very suspicious connectivity found for MIL-100. [ Error: Atom ?, used in a bond, has either zero or multiple placements in CIF file MIL-101. This invalidates all bonds from the file, which will thus be discarded. [ Error: Atom ?, used in a bond, has either zero or multiple placements in CIF file MIL-53. This invalidates all bonds from the file, which will thus be discarded. The following warning about symmetry and the three warnings about 0-dimensional structures are expected. [ Warning: Missing _symmetry_equiv_pos_as_xyz and _space_group_symop_operation_xyz fields, will rely on other symmetry indications. [ Warning: Detected 192 structures of dimension 0 in NOTT-112, possibly complex solvent residues. They will be ignored for topology computation. [ Warning: Detected 40 structures of dimension 0 in FOWWAR, possibly complex solvent residues. They will be ignored for topology computation. [ Warning: Detected 2 structures of dimension 0 in CALFIG, possibly complex solvent residues. They will be ignored for topology computation. The following @error about carbon cycle disorder is expected. [ Info: Initial pass found C with invalid number of bonds. [ Error: Found what looks like a disordered carbon ring for CIZPOS: use of disordered input is not advised, please double-check the detected topology or provide a clean input. [ Info: Initial pass found O and C with invalid number of bonds. Test Summary: | Pass Broken Total Time MOF examples | 74 3 77 17m06.1s [ Warning: Guessing bonds with custom algorithm (from Chemfiles and VMD). This may take a while for big structures and may be inexact. [ Info: To avoid guessing bonds, use a file format that contains the bonds. [ Warning: Detected 6 structures of dimension 0 in Clathrate_hydrate, possibly complex solvent residues. They will be ignored for topology computation. [ Warning: Guessing bonds with custom algorithm (from Chemfiles and VMD). This may take a while for big structures and may be inexact. [ Info: To avoid guessing bonds, use a file format that contains the bonds. [ Warning: Detected 6 structures of dimension 0 in Clathrate_hydrate, possibly complex solvent residues. They will be ignored for topology computation. [ Warning: Missing _symmetry_equiv_pos_as_xyz and _space_group_symop_operation_xyz fields, will rely on other symmetry indications. [ Warning: Guessing bonds with custom algorithm (from Chemfiles and VMD). This may take a while for big structures and may be inexact. [ Info: To avoid guessing bonds, use a file format that contains the bonds. Test Summary: | Pass Total Time Other kinds of structures | 3 3 1.1s [ Info: Checking that all known topologies are recognized (this can take a few minutes). [ Info: Use multiple threads to reduce this time Test Summary: | Pass Total Time Archive | 17492 17492 6m49.5s [ Info: Testing pcu [ Info: Testing afy, AFY [ Info: Testing apc, APC [ Info: Testing bam [ Info: Testing bcf [ Info: Testing cdp [ Info: Testing cnd [ Info: Testing ecb [ Info: Testing fiv [ Info: Testing ftd [ Info: Testing ftj [ Info: Testing ins [ Info: Testing kgt [ Info: Testing mot [ Info: Testing moz [ Info: Testing muh [ Info: Testing pbz [ Info: Testing qom [ Info: Testing sig [ Info: Testing sma [ Info: Testing sod-f [ Info: Testing sod-h [ Info: Testing utj [ Info: Testing utp [ Info: Testing nts [ Info: Testing lth [ Info: Testing cys [ Info: Testing llw-z [ Info: Testing nts Test Summary: | Pass Total Time Module | 31 31 53.7s Test Summary: | Pass Broken Total Time Executable | 29 1 30 9.0s 1 / 36 .................................................................................................... 2 / 36 .................................................................................................... 3 / 36 .................................................................................................... 4 / 36 .................................................................................................... 5 / 36 .................................................................................................... 6 / 36 .................................................................................................... 7 / 36 .................................................................................................... 8 / 36 .................................................................................................... 9 / 36 .................................................................................................... 10 / 36 .................................................................................................... 11 / 36 .................................................................................................... 12 / 36 .................................................................................................... 13 / 36 .................................................................................................... 14 / 36 .................................................................................................... 15 / 36 .................................................................................................... 16 / 36 .................................................................................................... 17 / 36 .................................................................................................... 18 / 36 .................................................. 19 / 36 .................................................. 20 / 36 .................................................. 21 / 36 .................................................. 22 / 36 .................................................. 23 / 36 .................................................. 24 / 36 .................................................. 25 / 36 .................................................. 26 / 36 .................................................. 27 / 36 .................................................. 28 / 36 .................................................. 29 / 36 .................................................. 30 / 36 .................................................. 31 / 36 .................................................. 32 / 36 ............................................ ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 27 running 1 of 1 signal (10): User defined signal 1 getindex at ./essentials.jl:967 [inlined] _sort! at ./sort.jl:839 _sort! at ./sort.jl:797 _sort! at ./sort.jl:744 [inlined] _sort! at ./sort.jl:683 [inlined] _sort! at ./sort.jl:561 [inlined] _sort! at ./sort.jl:1591 [inlined] #sort!#24 at ./sort.jl:1738 [inlined] sort! at ./sort.jl:1731 [inlined] translation_to_direct_map at /home/pkgeval/.julia/packages/CrystalNets/vvGQH/src/minimization.jl:703 find_first_valid_translation_unstable at /home/pkgeval/.julia/packages/CrystalNets/vvGQH/src/minimization.jl:805 minimize_unstable at /home/pkgeval/.julia/packages/CrystalNets/vvGQH/src/minimization.jl:287 [inlined] minimize at /home/pkgeval/.julia/packages/CrystalNets/vvGQH/src/minimization.jl:274 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/vvGQH/src/query.jl:34 unknown function (ip: 0x71dcb020fb82) at (unknown file) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/vvGQH/src/query.jl:153 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/vvGQH/src/query.jl:87 [inlined] #topological_genome#221 at /home/pkgeval/.julia/packages/CrystalNets/vvGQH/src/query.jl:90 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/vvGQH/src/query.jl:90 [inlined] macro expansion at /home/pkgeval/.julia/packages/CrystalNets/vvGQH/test/runtests.jl:539 [inlined] #51 at ./threadingconstructs.jl:276 #49 at ./threadingconstructs.jl:243 [inlined] #threading_run##0 at ./threadingconstructs.jl:177 unknown function (ip: 0x71dcad0fab32) at (unknown file) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 jl_apply at /source/src/julia.h:2378 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000071dc9aa5cd30 Total snapshots: 352. Utilization: 100% ╎350 @Base/…ingconstructs.jl:177 (::Base.Threads.var"#threading_run##0#thre… ╎ 350 @Base/…ingconstructs.jl:243 #49 ╎ 350 @Base/…ngconstructs.jl:276 (::var"#49#50"{var"#51#52"{Int64, Int64, … ╎ 350 …GQH/test/runtests.jl:539 macro expansion ╎ 350 @CrystalNets/…query.jl:90 topological_genome ╎ 350 @CrystalNets/…query.jl:90 #topological_genome#221 ╎ ╎ 350 @CrystalNets/…uery.jl:87 topological_genome ╎ ╎ 350 @CrystalNets/…ery.jl:153 topological_genome(group::UnderlyingNe… ╎ ╎ 350 @CrystalNets/…ery.jl:34 topological_genome(net::CrystalNet2D{R… ╎ ╎ 350 @CrystalNets/…ion.jl:274 minimize ╎ ╎ 350 @CrystalNets/…on.jl:287 minimize_unstable 2╎ ╎ ╎ 350 @CrystalNets/…on.jl:805 find_first_valid_translation_unstab… 1╎ ╎ ╎ 1 @CrystalNets/…n.jl:0 translation_to_direct_map(shrunk_pvma… 3╎ ╎ ╎ 235 @CrystalNets/…n.jl:673 translation_to_direct_map(shrunk_pv… 1╎ ╎ ╎ 1 @Base/task.jl:1038 yield() 7╎ ╎ ╎ 21 @Base/task.jl:1040 yield() ╎ ╎ ╎ 3 @Base/task.jl:950 enq_work(t::Task) ╎ ╎ ╎ 3 @Base/task.jl:258 threadpool 3╎ ╎ ╎ ╎ 3 @Base/…structs.jl:68 _tpid_to_sym ╎ ╎ ╎ 3 @Base/task.jl:951 enq_work(t::Task) 3╎ ╎ ╎ 3 @Base/…omotion.jl:637 == ╎ ╎ ╎ 8 @Base/task.jl:956 enq_work(t::Task) 1╎ ╎ ╎ 3 @Base/task.jl:876 push!(W::Base.IntrusiveLinkedListSync… 1╎ ╎ ╎ ╎ 1 @Base/…ompiler.jl:57 getproperty ╎ ╎ ╎ ╎ 1 @Base/locks-mt.jl:78 lock(l::Base.Threads.SpinLock) ╎ ╎ ╎ ╎ 1 @Base/locks-mt.jl:91 trylock 1╎ ╎ ╎ ╎ 1 @Base/…motion.jl:637 == 1╎ ╎ ╎ 1 @Base/task.jl:877 push!(W::Base.IntrusiveLinkedListSync… ╎ ╎ ╎ 3 @Base/task.jl:880 push!(W::Base.IntrusiveLinkedListSync… ╎ ╎ ╎ ╎ 1 @Base/locks-mt.jl:100 unlock 1╎ ╎ ╎ ╎ 1 @Base/…motion.jl:637 == ╎ ╎ ╎ ╎ 2 @Base/locks-mt.jl:103 unlock 2╎ ╎ ╎ ╎ 2 @Base/gcutils.jl:159 enable_finalizers 1╎ ╎ ╎ 1 @Base/task.jl:923 workqueue_for 3╎ ╎ ╎ 3 @Base/task.jl:1041 yield() 2╎ ╎ ╎ 207 @Base/task.jl:1042 yield() 1╎ ╎ ╎ 1 @Base/task.jl:0 trypoptask(W::Base.IntrusiveLinkedListSy… ╎ ╎ ╎ 2 @Base/task.jl:1184 wait() 2╎ ╎ ╎ 2 @Base/task.jl:1214 record_running_time! ╎ ╎ ╎ 173 @Base/task.jl:1188 wait() 172╎ ╎ ╎ 173 @Base/libuv.jl:133 process_events ╎ ╎ ╎ 6 @Base/task.jl:1191 wait() ╎ ╎ ╎ 3 @Base/task.jl:923 workqueue_for 1╎ ╎ ╎ ╎ 1 @Base/lock.jl:858 getindex(once::OncePerThread{Base.In… ╎ ╎ ╎ ╎ 1 @Base/lock.jl:861 getindex(once::OncePerThread{Base.In… 1╎ ╎ ╎ ╎ 1 @Base/…ompiler.jl:81 getproperty ╎ ╎ ╎ ╎ 1 @Base/lock.jl:940 getindex(once::OncePerThread{Base.In… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:398 getindex ╎ ╎ ╎ 3 @Base/…structs.jl:36 threadid ╎ ╎ ╎ ╎ 3 @Base/int.jl:1020 + 3╎ ╎ ╎ ╎ 3 @Base/int.jl:87 + ╎ ╎ ╎ 14 @Base/task.jl:1192 wait() 1╎ ╎ ╎ 1 @Base/task.jl:1162 trypoptask(W::Base.IntrusiveLinkedLi… ╎ ╎ ╎ 1 @Base/task.jl:1163 trypoptask(W::Base.IntrusiveLinkedLi… ╎ ╎ ╎ ╎ 1 @Base/task.jl:873 isempty 1╎ ╎ ╎ ╎ 1 @Base/…ompiler.jl:57 getproperty 1╎ ╎ ╎ 12 @Base/task.jl:1164 trypoptask(W::Base.IntrusiveLinkedLi… 1╎ ╎ ╎ ╎ 5 @Base/task.jl:902 popfirst!(W::Base.IntrusiveLinkedLis… ╎ ╎ ╎ ╎ 4 @Base/locks-mt.jl:78 lock(l::Base.Threads.SpinLock) ╎ ╎ ╎ ╎ 4 @Base/…cks-mt.jl:91 trylock 4╎ ╎ ╎ ╎ 4 @Base/…motion.jl:637 == 1╎ ╎ ╎ ╎ 2 @Base/task.jl:904 popfirst!(W::Base.IntrusiveLinkedLis… ╎ ╎ ╎ ╎ 1 @Base/…ed_list.jl:86 popfirst! ╎ ╎ ╎ ╎ 1 @Base/…d_list.jl:114 list_deletefirst! ╎ ╎ ╎ ╎ 1 @Base/task.jl:184 setproperty! 1╎ ╎ ╎ ╎ 1 @Base/…mpiler.jl:61 setproperty! ╎ ╎ ╎ ╎ 4 @Base/task.jl:906 popfirst!(W::Base.IntrusiveLinkedLis… ╎ ╎ ╎ ╎ 3 @Base/…cks-mt.jl:100 unlock 3╎ ╎ ╎ ╎ 3 @Base/…motion.jl:637 == ╎ ╎ ╎ ╎ 1 @Base/…cks-mt.jl:103 unlock 1╎ ╎ ╎ ╎ 1 @Base/gcutils.jl:159 enable_finalizers 1╎ ╎ ╎ 1 @Base/task.jl:1193 wait() 1╎ ╎ ╎ 8 @Base/task.jl:1203 wait() 1╎ ╎ ╎ 1 @Base/task.jl:1099 try_yieldto(undo::typeof(Base.ensure… 2╎ ╎ ╎ 2 @Base/task.jl:1100 try_yieldto(undo::typeof(Base.ensure… 4╎ ╎ ╎ 4 @Base/task.jl:1101 try_yieldto(undo::typeof(Base.ensure… ╎ ╎ ╎ 5 @CrystalNets/…n.jl:675 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 4 @Base/…sentials.jl:966 getindex 1╎ ╎ ╎ 4 @Base/…sentials.jl:387 checkbounds 3╎ ╎ ╎ 3 @Base/…entials.jl:383 checkbounds 1╎ ╎ ╎ 1 @Base/…sentials.jl:967 getindex ╎ ╎ ╎ 1 @CrystalNets/…n.jl:677 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 1 @Base/…sentials.jl:966 getindex ╎ ╎ ╎ 1 @Base/…sentials.jl:387 checkbounds 1╎ ╎ ╎ 1 @Base/…entials.jl:383 checkbounds ╎ ╎ ╎ 4 @CrystalNets/…n.jl:678 translation_to_direct_map(shrunk_pv… 1╎ ╎ ╎ 1 @Base/int.jl:86 - ╎ ╎ ╎ 3 @CrystalNets/…y.jl:81 getindex 3╎ ╎ ╎ 3 @Base/…sentials.jl:967 getindex ╎ ╎ ╎ 4 @CrystalNets/…n.jl:682 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 2 @CrystalNets/…n.jl:588 backtrack_to!(vmapprogress::Vector… ╎ ╎ ╎ 1 @Base/array.jl:995 setindex! 1╎ ╎ ╎ 1 @Base/array.jl:1000 _setindex! ╎ ╎ ╎ 1 @Base/…sentials.jl:966 getindex 1╎ ╎ ╎ 1 @Base/…entials.jl:387 checkbounds ╎ ╎ ╎ 2 @CrystalNets/…n.jl:593 backtrack_to!(vmapprogress::Vector… 1╎ ╎ ╎ 1 @Base/array.jl:0 attribute_next_available_modify!(vmappr… ╎ ╎ ╎ 1 @CrystalNets/…n.jl:556 attribute_next_available_modify!(… 1╎ ╎ ╎ 1 @Base/…entials.jl:967 getindex ╎ ╎ ╎ 1 @CrystalNets/…n.jl:688 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 1 @Graphs/…c/core.jl:160 degree ╎ ╎ ╎ 1 @Graphs/…c/core.jl:118 outdegree ╎ ╎ ╎ 1 @PeriodicGraphs/…l:58 outneighbors 1╎ ╎ ╎ ╎ 1 @Base/…entials.jl:967 getindex ╎ ╎ ╎ 36 @CrystalNets/…n.jl:695 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 5 @Base/array.jl:803 collect(itr::Base.Generator{Vector{Per… ╎ ╎ ╎ 2 @Base/generator.jl:45 iterate ╎ ╎ ╎ 2 @Base/…ctarray.jl:1241 iterate ╎ ╎ ╎ ╎ 2 @Base/…tarray.jl:1241 iterate ╎ ╎ ╎ ╎ 2 @Base/…tarray.jl:1249 _iterate 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ 3 @Base/generator.jl:48 iterate ╎ ╎ ╎ 1 @CrystalNets/….jl:696 #translation_to_direct_map##0 ╎ ╎ ╎ ╎ 1 @Base/…entials.jl:966 getindex 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:387 checkbounds ╎ ╎ ╎ 1 @CrystalNets/….jl:697 #translation_to_direct_map##0 1╎ ╎ ╎ ╎ 1 @Base/…entials.jl:967 getindex ╎ ╎ ╎ 1 @CrystalNets/….jl:699 #translation_to_direct_map##0 ╎ ╎ ╎ ╎ 1 @StaticArrays/…jl:16 - ╎ ╎ ╎ ╎ 1 @StaticArrays/…jl:39 map ╎ ╎ ╎ ╎ 1 @StaticArrays/…l:42 _map ╎ ╎ ╎ ╎ 1 @StaticArrays/…l:77 macro expansion 1╎ ╎ ╎ ╎ 1 @Base/int.jl:86 - ╎ ╎ ╎ 23 @Base/array.jl:808 collect(itr::Base.Generator{Vector{Per… ╎ ╎ ╎ 23 @Base/array.jl:676 _array_for ╎ ╎ ╎ 23 @Base/…ctarray.jl:872 similar ╎ ╎ ╎ ╎ 23 @Base/…ctarray.jl:873 similar ╎ ╎ ╎ ╎ 23 @Base/boot.jl:661 Array ╎ ╎ ╎ ╎ 16 @Base/boot.jl:648 Array 16╎ ╎ ╎ ╎ 16 @Base/boot.jl:588 GenericMemory 7╎ ╎ ╎ ╎ 7 @Base/boot.jl:649 Array ╎ ╎ ╎ 8 @Base/array.jl:813 collect(itr::Base.Generator{Vector{Per… ╎ ╎ ╎ 8 @Base/array.jl:839 collect_to_with_first! ╎ ╎ ╎ 7 @Base/array.jl:861 collect_to! ╎ ╎ ╎ ╎ 1 @Base/…nerator.jl:45 iterate ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:1241 iterate 1╎ ╎ ╎ ╎ 1 @Base/…ctarray.jl:0 _iterate ╎ ╎ ╎ ╎ 6 @Base/…nerator.jl:48 iterate ╎ ╎ ╎ ╎ 1 @CrystalNets/…jl:696 #translation_to_direct_map##0 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ ╎ 1 @CrystalNets/…jl:697 #translation_to_direct_map##0 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ ╎ 1 @CrystalNets/…jl:698 #translation_to_direct_map##0 1╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + ╎ ╎ ╎ ╎ 3 @CrystalNets/…jl:699 #translation_to_direct_map##0 ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:966 getindex ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:387 checkbounds 1╎ ╎ ╎ ╎ 1 @Base/…tials.jl:383 checkbounds 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ 1 @Base/array.jl:865 collect_to! ╎ ╎ ╎ ╎ 1 @Base/array.jl:995 setindex! 1╎ ╎ ╎ ╎ 1 @Base/array.jl:1000 _setindex! ╎ ╎ ╎ 13 @CrystalNets/…n.jl:703 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 13 @Base/sort.jl:1731 sort! ╎ ╎ ╎ 13 @Base/sort.jl:1738 #sort!#24 ╎ ╎ ╎ 13 @Base/sort.jl:1591 _sort! ╎ ╎ ╎ ╎ 13 @Base/sort.jl:561 _sort! ╎ ╎ ╎ ╎ 13 @Base/sort.jl:683 _sort! ╎ ╎ ╎ ╎ 13 @Base/sort.jl:744 _sort! ╎ ╎ ╎ ╎ 13 @Base/sort.jl:797 _sort!(v::Vector{PeriodicVertex2D… 3╎ ╎ ╎ ╎ 3 @Base/sort.jl:0 _sort!(v::Vector{PeriodicVertex2D}… 1╎ ╎ ╎ ╎ 1 @Base/sort.jl:834 _sort!(v::Vector{PeriodicVertex2… ╎ ╎ ╎ ╎ 3 @Base/sort.jl:839 _sort!(v::Vector{PeriodicVertex2… 3╎ ╎ ╎ ╎ ╎ 3 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ 1 @Base/sort.jl:841 _sort!(v::Vector{PeriodicVertex2… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:966 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:387 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:383 checkbounds ╎ ╎ ╎ ╎ 1 @Base/sort.jl:845 _sort!(v::Vector{PeriodicVertex2… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:995 setindex! 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1000 _setindex! ╎ ╎ ╎ ╎ 3 @Base/sort.jl:848 _sort!(v::Vector{PeriodicVertex2… ╎ ╎ ╎ ╎ ╎ 3 @Base/array.jl:995 setindex! 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:0 _setindex! 1╎ ╎ ╎ ╎ ╎ 2 @Base/array.jl:999 _setindex! 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:383 checkbounds 1╎ ╎ ╎ ╎ 1 @Base/sort.jl:849 _sort!(v::Vector{PeriodicVertex2… ╎ ╎ ╎ 1 @CrystalNets/…n.jl:704 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 1 @Base/some.jl:157 macro expansion ╎ ╎ ╎ 1 @Base/array.jl:2465 findfirst ╎ ╎ ╎ 1 @Base/array.jl:2414 findnext ╎ ╎ ╎ ╎ 1 @Base/…entials.jl:966 getindex 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:387 checkbounds ╎ ╎ ╎ 21 @CrystalNets/…n.jl:705 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 21 @Base/bitarray.jl:403 falses ╎ ╎ ╎ 21 @Base/bitarray.jl:405 falses 1╎ ╎ ╎ 1 @Base/array.jl:0 fill!(B::BitVector, x::Bool) ╎ ╎ ╎ 19 @Base/bitarray.jl:71 BitArray 1╎ ╎ ╎ ╎ 1 @Base/bitarray.jl:32 BitArray ╎ ╎ ╎ ╎ 14 @Base/bitarray.jl:37 BitArray ╎ ╎ ╎ ╎ 5 @Base/boot.jl:648 Array 5╎ ╎ ╎ ╎ 5 @Base/boot.jl:588 GenericMemory 9╎ ╎ ╎ ╎ 9 @Base/boot.jl:649 Array 4╎ ╎ ╎ ╎ 4 @Base/bitarray.jl:39 BitArray ╎ ╎ ╎ 1 @Base/bitarray.jl:382 fill!(B::BitVector, x::Bool) ╎ ╎ ╎ ╎ 1 @Base/array.jl:335 fill! 1╎ ╎ ╎ ╎ 1 @Base/array.jl:0 _fill! ╎ ╎ ╎ 3 @CrystalNets/…n.jl:711 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 1 @Base/bitarray.jl:681 getindex ╎ ╎ ╎ 1 @Base/…actarray.jl:698 checkbounds ╎ ╎ ╎ 1 @Base/…ctarray.jl:688 checkbounds ╎ ╎ ╎ ╎ 1 @Base/…ctarray.jl:753 checkindex 1╎ ╎ ╎ ╎ 1 @Base/int.jl:521 < ╎ ╎ ╎ 2 @Base/bitarray.jl:682 getindex 1╎ ╎ ╎ 1 @Base/bitarray.jl:0 unsafe_bitgetindex ╎ ╎ ╎ 1 @Base/bitarray.jl:676 unsafe_bitgetindex 1╎ ╎ ╎ 1 @Base/…entials.jl:967 getindex ╎ ╎ ╎ 1 @CrystalNets/…n.jl:717 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 1 @Base/iterators.jl:197 iterate ╎ ╎ ╎ 1 @Base/…ctarray.jl:1241 iterate ╎ ╎ ╎ 1 @Base/…ctarray.jl:1249 _iterate 1╎ ╎ ╎ ╎ 1 @Base/…entials.jl:967 getindex ╎ ╎ ╎ 2 @CrystalNets/…n.jl:722 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 2 @CrystalNets/…n.jl:593 backtrack_to!(vmapprogress::Vector… 1╎ ╎ ╎ 1 @Base/array.jl:0 attribute_next_available_modify!(vmappr… ╎ ╎ ╎ 1 @CrystalNets/…n.jl:117 attribute_next_available_modify!(… ╎ ╎ ╎ 1 @Base/subarray.jl:222 view ╎ ╎ ╎ ╎ 1 @Base/range.jl:994 getindex 1╎ ╎ ╎ ╎ 1 @Base/int.jl:86 - ╎ ╎ ╎ 11 @CrystalNets/…n.jl:726 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 11 @Base/bitarray.jl:403 falses ╎ ╎ ╎ 11 @Base/bitarray.jl:405 falses 1╎ ╎ ╎ 1 @Base/array.jl:0 fill!(B::BitVector, x::Bool) ╎ ╎ ╎ 10 @Base/bitarray.jl:71 BitArray ╎ ╎ ╎ ╎ 9 @Base/bitarray.jl:37 BitArray ╎ ╎ ╎ ╎ 4 @Base/boot.jl:648 Array 4╎ ╎ ╎ ╎ 4 @Base/boot.jl:588 GenericMemory 5╎ ╎ ╎ ╎ 5 @Base/boot.jl:649 Array 1╎ ╎ ╎ ╎ 1 @Base/bitarray.jl:39 BitArray ╎ ╎ ╎ 1 @CrystalNets/…n.jl:732 translation_to_direct_map(shrunk_pv… 1╎ ╎ ╎ 1 @Base/…sentials.jl:967 getindex ╎ ╎ ╎ 2 @CrystalNets/…n.jl:738 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 2 @Base/bitarray.jl:682 getindex ╎ ╎ ╎ 2 @Base/bitarray.jl:676 unsafe_bitgetindex 2╎ ╎ ╎ 2 @Base/…entials.jl:967 getindex ╎ ╎ ╎ 1 @CrystalNets/…n.jl:739 translation_to_direct_map(shrunk_pv… 1╎ ╎ ╎ 1 @Base/…sentials.jl:967 getindex 1╎ ╎ ╎ 1 @CrystalNets/…n.jl:751 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 3 @CrystalNets/…n.jl:756 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 3 @CrystalNets/…n.jl:550 attribute_next_available! ╎ ╎ ╎ 1 @CrystalNets/…n.jl:560 attribute_next_available_modify!(… ╎ ╎ ╎ 1 @CrystalNets/…y.jl:81 getindex 1╎ ╎ ╎ ╎ 1 @Base/…entials.jl:967 getindex ╎ ╎ ╎ 1 @CrystalNets/…n.jl:565 attribute_next_available_modify!(… ╎ ╎ ╎ 1 @Base/subarray.jl:216 view ╎ ╎ ╎ ╎ 1 @Base/subarray.jl:249 unsafe_view ╎ ╎ ╎ ╎ 1 @Base/subarray.jl:28 SubArray 1╎ ╎ ╎ ╎ 1 @Base/…sional.jl:917 ensure_indexable ╎ ╎ ╎ 1 @CrystalNets/…n.jl:569 attribute_next_available_modify!(… ╎ ╎ ╎ 1 @Base/array.jl:1310 push! ╎ ╎ ╎ ╎ 1 @Base/array.jl:1313 _push! ╎ ╎ ╎ ╎ 1 @Base/array.jl:1176 _growend! 1╎ ╎ ╎ ╎ 1 @Base/int.jl:87 + ╎ ╎ ╎ 1 @CrystalNets/…n.jl:765 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 1 @Base/iterators.jl:197 iterate ╎ ╎ ╎ 1 @Base/…ctarray.jl:1241 iterate ╎ ╎ ╎ 1 @Base/…ctarray.jl:1249 _iterate 1╎ ╎ ╎ ╎ 1 @Base/…entials.jl:967 getindex ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile ====================================================================================== cmd: /opt/julia/bin/julia 1 running 0 of 1 signal (10): User defined signal 1 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1200 wait_forever at ./task.jl:1137 jfptr_wait_forever_58420.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 jl_apply at /source/src/julia.h:2378 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point ============================================================== ┌ Warning: There were no samples collected in one or more groups. │ This may be due to idle threads, or you may need to run your │ program longer (perhaps by running it multiple times), │ or adjust the delay between samples with `Profile.init()`. └ @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000709977d5d1e0 Total snapshots: 427. Utilization: 0% ╎427 @Base/task.jl:1137 wait_forever() 426╎ 427 @Base/task.jl:1200 wait() ...... 33 / 36 .................................................. 34 / 36 .................................................. 35 / 36 .................................................. 36 / 36 .................................................. Test Summary: | Pass Total Time Unstable nets | 35 35 13m02.6s [ Warning: Guessing bonds with custom algorithm (from Chemfiles and VMD). This may take a while for big structures and may be inexact. [ Info: To avoid guessing bonds, use a file format that contains the bonds. [ Warning: Guessing bonds with custom algorithm (from Chemfiles and VMD). This may take a while for big structures and may be inexact. [ Info: To avoid guessing bonds, use a file format that contains the bonds. Test Summary: | Pass Total Time Non-CIF Files | 3 3 0.8s [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404 uv_run at /workspace/srcdir/libuv/src/unix/core.c:430 ijl_task_get_next at /source/src/scheduler.c:457 wait at ./task.jl:1200 wait_forever at ./task.jl:1137 jfptr_wait_forever_58420.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4022 [inlined] ijl_apply_generic at /source/src/gf.c:4219 jl_apply at /source/src/julia.h:2378 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) Allocations: 19878848 (Pool: 19878331; Big: 517); GC: 18 Testing CrystalNets tests passed PkgEval terminated after 2724.32s: test duration exceeded the time limit