Package evaluation to test CrystalNets on Julia 1.14.0-DEV.2058 (afc71c255e*) started at 2026-04-19T16:40:43.366 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.72s ################################################################################ # Installation # Installing CrystalNets... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [7952bbbe] + CrystalNets v1.2.0 Updating `~/.julia/environments/v1.14/Manifest.toml` [c7e460c6] + ArgParse v1.2.0 [ec485272] + ArnoldiMethod v0.4.0 [a963bdd2] + AtomsBase v0.5.2 [46823bd8] + Chemfiles v0.10.43 [7952bbbe] + CrystalNets v1.2.0 [864edb3b] + DataStructures v0.19.4 [ffbed154] + DocStringExtensions v0.9.5 [86223c79] + Graphs v1.14.0 [d25df0c9] + Inflate v0.1.5 [692b3bcd] + JLLWrappers v1.7.1 [1914dd2f] + MacroTools v0.5.16 [bac558e1] + OrderedCollections v1.8.1 [f305370e] + PeriodicGraphEmbeddings v1.0.2 [72a2d4b8] + PeriodicGraphEquilibriumPlacement v0.2.3 [18c5b727] + PeriodicGraphs v1.0.1 [7b2266bf] + PeriodicTable v1.2.1 [aea7be01] + PrecompileTools v1.3.3 [21216c6a] + Preferences v1.5.2 [92933f4c] + ProgressMeter v1.11.0 [ae029012] + Requires v1.3.1 [699a6c99] + SimpleTraits v0.9.5 [90137ffa] + StaticArrays v1.9.18 [1e83bf80] + StaticArraysCore v1.4.4 [10745b16] + Statistics v1.11.1 [b718987f] + TextWrap v1.0.2 [0796e94c] + Tokenize v0.5.29 [1986cc42] + Unitful v1.28.0 [a7773ee8] + UnitfulAtomic v1.0.0 [78a364fa] + Chemfiles_jll v0.10.4+0 [ac4a9f1e] + spglib_jll v2.7.0+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 v1.13.0 [b27032c2] + LibCURL v1.0.0 [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 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.14.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v1.0.0 [9e88b42a] + Serialization v1.11.0 [6462fe0b] + Sockets v1.11.0 [2f01184e] + SparseArrays v1.13.0 [f489334b] + StyledStrings v1.13.0 [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 v8.19.0+0 [e37daf67] + LibGit2_jll v1.9.2+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2026.3.19 [4536629a] + OpenBLAS_jll v0.3.30+0 [458c3c95] + OpenSSL_jll v3.5.6+0 [efcefdf7] + PCRE2_jll v10.47.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.68.1+0 [3f19e933] + p7zip_jll v17.8.0+0 Installation completed after 5.75s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 2.3 s ✓ Chemfiles_jll 2.2 s ✓ spglib_jll 8.3 s ✓ AtomsBase 77.4 s ✓ PeriodicGraphs 7.5 s ✓ Chemfiles 98.7 s ✓ PeriodicGraphEmbeddings 24.5 s ✓ PeriodicGraphEquilibriumPlacement 319.7 s ✓ CrystalNets 8 dependencies successfully precompiled in 542 seconds. 59 already precompiled. Precompilation completed after 565.58s ################################################################################ # Testing # Testing CrystalNets Status `/tmp/jl_xUPrCC/Project.toml` [861a8166] Combinatorics v1.1.0 [7952bbbe] CrystalNets v1.2.0 [86223c79] Graphs v1.14.0 [18c5b727] PeriodicGraphs v1.0.1 [90137ffa] StaticArrays v1.9.18 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_xUPrCC/Manifest.toml` [c7e460c6] ArgParse v1.2.0 [ec485272] ArnoldiMethod v0.4.0 [a963bdd2] AtomsBase v0.5.2 [46823bd8] Chemfiles v0.10.43 [861a8166] Combinatorics v1.1.0 [7952bbbe] CrystalNets v1.2.0 [864edb3b] DataStructures v0.19.4 [ffbed154] DocStringExtensions v0.9.5 [86223c79] Graphs v1.14.0 [d25df0c9] Inflate v0.1.5 [692b3bcd] JLLWrappers v1.7.1 [1914dd2f] MacroTools v0.5.16 [bac558e1] OrderedCollections v1.8.1 [f305370e] PeriodicGraphEmbeddings v1.0.2 [72a2d4b8] PeriodicGraphEquilibriumPlacement v0.2.3 [18c5b727] PeriodicGraphs v1.0.1 [7b2266bf] PeriodicTable v1.2.1 [aea7be01] PrecompileTools v1.3.3 [21216c6a] Preferences v1.5.2 [92933f4c] ProgressMeter v1.11.0 [ae029012] Requires v1.3.1 [699a6c99] SimpleTraits v0.9.5 [90137ffa] StaticArrays v1.9.18 [1e83bf80] StaticArraysCore v1.4.4 [10745b16] Statistics v1.11.1 [b718987f] TextWrap v1.0.2 [0796e94c] Tokenize v0.5.29 [1986cc42] Unitful v1.28.0 [a7773ee8] UnitfulAtomic v1.0.0 [78a364fa] Chemfiles_jll v0.10.4+0 [ac4a9f1e] spglib_jll v2.7.0+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 v1.13.0 [b27032c2] LibCURL v1.0.0 [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 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.14.0 [de0858da] Printf v1.11.0 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v1.0.0 [9e88b42a] Serialization v1.11.0 [6462fe0b] Sockets v1.11.0 [2f01184e] SparseArrays v1.13.0 [f489334b] StyledStrings v1.13.0 [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 v8.19.0+0 [e37daf67] LibGit2_jll v1.9.2+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2026.3.19 [4536629a] OpenBLAS_jll v0.3.30+0 [458c3c95] OpenSSL_jll v3.5.6+0 [efcefdf7] PCRE2_jll v10.47.0+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.2+0 [3161d3a3] Zstd_jll v1.5.7+1 [8e850b90] libblastrampoline_jll v5.15.0+0 [8e850ede] nghttp2_jll v1.68.1+0 [3f19e933] p7zip_jll v17.8.0+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 | 73 3 76 17m42.6s [ 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: 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 | 4 4 0.7s [ 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 | 17494 17494 9m31.9s [ 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 54.1s Test Summary: | Pass Broken Total Time Executable | 29 1 30 8.8s 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 ...................................... ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== .. cmd: /opt/julia/bin/julia 37 running 1 of 1 signal (10): User defined signal 1 unknown function (ip: 0x7a4b3ff0aafb) at /lib/x86_64-linux-gnu/libc.so.6 memmove at ./cmem.jl:28:22 [inlined] unsafe_copyto! at ./genericmemory.jl:139:43 [inlined] _growend_internal! at ./array.jl:1208:84 _growend! at ./array.jl:1228:53 [inlined] _push! at ./array.jl:1371:2 [inlined] push! at ./array.jl:1368:21 [inlined] _neighborhood at /home/pkgeval/.julia/packages/PeriodicGraphs/kX3ve/src/algorithms/neighborhood.jl:107:187 coordination_sequence at /home/pkgeval/.julia/packages/PeriodicGraphs/kX3ve/src/algorithms/neighborhood.jl:148:6 #partition_by_coordination_sequence##2 at ./none (unknown line) [inlined] iterate at ./generator.jl:48:23 [inlined] collect at ./array.jl:828:52 partition_by_coordination_sequence at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/topology.jl:192:50 .partition_by_coordination_sequence at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/topology.jl:189:3 [inlined] find_candidates at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/topology.jl:283:44 topological_key at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/topology.jl:661:20 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:63:5 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:56:206 unknown function (ip: 0x7a4b197b8443) at (unknown file) ...._jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:153:242 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:87:5 [inlined] #topological_genome#224 at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:90:10 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:90:4 unknown function (ip: 0x7a4ae35e99fc) at (unknown file) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 ..jl_apply at /source/src/julia.h:2327:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:243:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:693:13 eval_body at /source/src/interpreter.c:550:21 eval_body at /source/src/interpreter.c:558:21 eval_body at /source/src/interpreter.c:558:21 eval_body at /source/src/interpreter.c:558:21 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884:21 .ijl_eval_thunk at /source/src/toplevel.c:768:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 .. 32 / 36 ......eval at ./boot.jl:517:3 include_string at ./loading.jl:3110:145 _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 _include at ./loading.jl:3170:45 include at ./Base.jl:327:3 IncludeInto at ./Base.jl:328:4 jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:243:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:693:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884:21 ijl_eval_thunk at /source/src/toplevel.c:768:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:517:3 exec_options at ./client.jl:318:410 _start at ./client.jl:593:36 jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] true_main at /source/src/jlapi.c:971:29 jl_repl_entrypoint at /source/src/jlapi.c:1138:15 main at /source/cli/loader_exe.c:58:15 unknown function (ip: 0x7a4b3fddf249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ 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/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007a4b255fc010 Total snapshots: 62. Utilization: 100% ╎62 @Base/client.jl:593 _start() ╎ 62 @Base/client.jl:318 exec_options(opts::Base.JLOptions) ╎ 62 @Base/boot.jl:517 eval(m::Module, e::Any) ╎ 62 @Base/Base.jl:328 (::Base.IncludeInto)(fname::String) ╎ 62 @Base/Base.jl:327 include(mapexpr::Function, mod::Module, _path::Str… ╎ 62 @Base/loading.jl:3170 _include(mapexpr::Function, mod::Module, _pat… ╎ ╎ 62 @Base/loading.jl:3110 include_string(mapexpr::typeof(identity), mo… ╎ ╎ 62 @Base/boot.jl:517 eval(m::Module, e::Any) ╎ ╎ 62 @CrystalNets/…uery.jl:90 topological_genome(g::PeriodicGraph2D) ╎ ╎ 62 @CrystalNets/…uery.jl:90 #topological_genome#224 ╎ ╎ 62 @CrystalNets/…ery.jl:87 topological_genome ╎ ╎ ╎ 62 @CrystalNets/…ery.jl:153 topological_genome(group::Underlying… ╎ ╎ ╎ 62 @CrystalNets/…ery.jl:34 topological_genome(net::CrystalNet2D… ╎ ╎ ╎ 62 @CrystalNets/…on.jl:274 getproperty(x::CrystalNets.Options,… ╎ ╎ ╎ 62 @CrystalNets/…n.jl:287 minimize_unstable ╎ ╎ ╎ 62 @CrystalNets/…n.jl:809 find_first_valid_translation_unsta… ╎ ╎ ╎ ╎ 42 @CrystalNets/…n.jl:677 translation_to_direct_map(shrunk_… 1╎ ╎ ╎ ╎ 1 @Base/task.jl:1067 yield() ╎ ╎ ╎ ╎ 4 @Base/task.jl:1069 yield() ╎ ╎ ╎ ╎ 1 @Base/task.jl:959 enq_work(t::Task) 1╎ ╎ ╎ ╎ 1 @Base/task.jl:255 threadid ╎ ╎ ╎ ╎ 3 @Base/task.jl:976 enq_work(t::Task) 1╎ ╎ ╎ ╎ 1 @Base/task.jl:906 push!(W::Base.IntrusiveLinkedListSy… ╎ ╎ ╎ ╎ 1 @Base/task.jl:909 push!(W::Base.IntrusiveLinkedListSy… ╎ ╎ ╎ ╎ 1 @Base/…cks-mt.jl:106 push!(q::Base.IntrusiveLinkedLi… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…motion.jl:637 getproperty(x::Base.IntrusiveL… ╎ ╎ ╎ ╎ 1 @Base/task.jl:952 workqueue_for(tid::Int64) ╎ ╎ ╎ ╎ 1 @Base/lock.jl:863 getindex(once::OncePerThread{Base.… ╎ ╎ ╎ ╎ ╎ 1 @Base/…rators.jl:320 getindex(A::AtomicMemory{Base.… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 checkbounds(A::AtomicMemory{Ba… 1╎ ╎ ╎ ╎ 1 @Base/task.jl:1070 yield() ╎ ╎ ╎ ╎ 36 @Base/task.jl:1071 yield() ╎ ╎ ╎ ╎ 1 @Base/task.jl:1229 wait() 1╎ ╎ ╎ ╎ 1 @Base/task.jl:1260 record_running_time!(t::Task) ╎ ╎ ╎ ╎ 31 @Base/task.jl:1233 wait() 31╎ ╎ ╎ ╎ 31 @Base/libuv.jl:133 record_running_time!(t::Task) ╎ ╎ ╎ ╎ 3 @Base/task.jl:1237 wait() 1╎ ╎ ╎ ╎ 1 @Base/task.jl:1207 trypoptask(W::Base.IntrusiveLinked… 1╎ ╎ ╎ ╎ 2 @Base/task.jl:1209 trypoptask(W::Base.IntrusiveLinked… ╎ ╎ ╎ ╎ 1 @Base/task.jl:933 popfirst!(W::Base.IntrusiveLinkedL… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…d_list.jl:85 popfirst!(q::Base.IntrusiveLink… 1╎ ╎ ╎ ╎ 1 @Base/task.jl:1249 wait() ╎ ╎ ╎ ╎ 1 @CrystalNets/…n.jl:691 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 1 @Graphs/…/core.jl:160 degree ╎ ╎ ╎ ╎ 1 @Graphs/…/core.jl:118 outdegree ╎ ╎ ╎ ╎ 1 @PeriodicGraphs/…:58 outneighbors 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:1040 getindex ╎ ╎ ╎ ╎ 6 @CrystalNets/…n.jl:699 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 2 @Base/array.jl:828 collect(itr::Base.Generator{Vector{P… ╎ ╎ ╎ ╎ 1 @Base/…nerator.jl:45 iterate(::Base.Generator{Vector{P… ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:1242 iterate(A::Vector{PeriodicVerte… ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:1242 iterate(A::Vector{PeriodicVert… ╎ ╎ ╎ ╎ ╎ 1 @Base/…array.jl:1250 _iterate_abstractarray(A::Vect… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:1040 getindex(A::Vector{PeriodicVe… ╎ ╎ ╎ ╎ 1 @Base/…nerator.jl:48 iterate(::Base.Generator{Vector{P… ╎ ╎ ╎ ╎ 1 @CrystalNets/…jl:701 iterate(A::Vector{PeriodicVertex… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:1040 iterate(A::Vector{PeriodicVert… ╎ ╎ ╎ ╎ 1 @Base/array.jl:833 collect(itr::Base.Generator{Vector{P… ╎ ╎ ╎ ╎ 1 @Base/array.jl:701 iterate(::Base.Generator{Vector{Per… ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:872 iterate(A::Vector{PeriodicVertex… ╎ ╎ ╎ ╎ 1 @Base/array.jl:409 iterate(A::Vector{PeriodicVertex2… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:873 _iterate_abstractarray(A::Vect… ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:735 checkbounds(::Type{Bool}, A::Vec… ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:727 Array ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:714 Array 1╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:654 GenericMemory ╎ ╎ ╎ ╎ 3 @Base/array.jl:838 collect(itr::Base.Generator{Vector{P… ╎ ╎ ╎ ╎ 3 @Base/array.jl:864 iterate(::Base.Generator{Vector{Per… ╎ ╎ ╎ ╎ 3 @Base/array.jl:909 iterate(A::Vector{PeriodicVertex2D… ╎ ╎ ╎ ╎ 3 @Base/…erator.jl:48 iterate(A::Vector{PeriodicVertex… ╎ ╎ ╎ ╎ ╎ 1 @CrystalNets/…jl:702 _iterate_abstractarray(A::Vect… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:1039 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:391 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:387 checkbounds ╎ ╎ ╎ ╎ ╎ 2 @CrystalNets/…jl:703 _iterate_abstractarray(A::Vect… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:1039 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:391 checkbounds ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:387 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:1040 getindex ╎ ╎ ╎ ╎ 5 @CrystalNets/…n.jl:707 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 5 @Base/sort.jl:1734 iterate(A::Vector{UnitRange{Int64}}) ╎ ╎ ╎ ╎ 5 @Base/sort.jl:1741 #sort!#24 ╎ ╎ ╎ ╎ 5 @Base/sort.jl:1594 _sort! ╎ ╎ ╎ ╎ 5 @Base/sort.jl:561 _sort! ╎ ╎ ╎ ╎ ╎ 5 @Base/sort.jl:686 _sort! ╎ ╎ ╎ ╎ ╎ 5 @Base/sort.jl:747 _sort! ╎ ╎ ╎ ╎ ╎ 5 @Base/sort.jl:800 _sort!(v::Vector{PeriodicVertex… 1╎ ╎ ╎ ╎ ╎ 1 @Base/sort.jl:0 _sort!(v::Vector{PeriodicVertex2… 1╎ ╎ ╎ ╎ ╎ 1 @Base/sort.jl:837 _sort!(v::Vector{PeriodicVerte… ╎ ╎ ╎ ╎ ╎ 1 @Base/sort.jl:842 _sort!(v::Vector{PeriodicVerte… ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:1039 -(x::Int64, y::Int64) 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:391 checkbounds ╎ ╎ ╎ ╎ ╎ 1 @Base/sort.jl:844 _sort!(v::Vector{PeriodicVerte… ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:1039 getindex(A::Vector{Periodic… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:391 checkbounds(A::Vector{Perio… 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…als.jl:387 checkbounds(::Type{Bool}, A… ╎ ╎ ╎ ╎ ╎ 1 @Base/sort.jl:845 _sort!(v::Vector{PeriodicVerte… ╎ ╎ ╎ ╎ ╎ 1 @Base/…ring.jl:120 getindex(A::Vector{PeriodicV… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ring.jl:118 checkbounds(A::Vector{Perio… ╎ ╎ ╎ ╎ ╎ ╎ 1 @PeriodicGraphs/…:54 checkbounds(::Type{Bool}… ╎ ╎ ╎ ╎ ╎ ╎ 1 @PeriodicGraphs/…:51 length(a::Vector{Period… ╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…ber.jl:44 iszero 1╎ ╎ ╎ ╎ ╎ ╎ 1 @Base/…on.jl:637 == ╎ ╎ ╎ ╎ 1 @CrystalNets/…n.jl:708 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 1 @Base/some.jl:157 iterate(A::Vector{UnitRange{Int64}}) ╎ ╎ ╎ ╎ 1 @Base/array.jl:2523 iterate(A::Vector{UnitRange{Int64}… 1╎ ╎ ╎ ╎ 1 @Base/array.jl:0 _iterate_abstractarray(A::Vector{Uni… ╎ ╎ ╎ ╎ 2 @CrystalNets/…n.jl:709 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 2 @Base/bitarray.jl:393 broadcasted(::typeof(+), ::Int64,… ╎ ╎ ╎ ╎ 2 @Base/bitarray.jl:395 broadcasted(::Base.Broadcast.Def… ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:71 +(x::Int64, y::Int64) ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:37 BitArray ╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:714 Array 1╎ ╎ ╎ ╎ ╎ 1 @Base/boot.jl:654 GenericMemory ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:372 fill!(B::BitVector, x::Bool) ╎ ╎ ╎ ╎ 1 @Base/array.jl:359 fill!(A::Vector{UInt64}, x::Int64) 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:0 _fill!(A::Vector{UInt64}, x::UInt6… ╎ ╎ ╎ ╎ 2 @CrystalNets/…n.jl:721 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 2 @Base/…erators.jl:197 setindex!(A::Vector{Int64}, x::In… ╎ ╎ ╎ ╎ 2 @Base/…tarray.jl:1242 _setindex!(A::Vector{Int64}, x::… ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:1249 checkbounds(A::Vector{Int64}, I… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:387 checkbounds(::Type{Bool}, A::Ve… ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:1250 checkbounds(A::Vector{Int64}, I… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:1040 getindex ╎ ╎ ╎ ╎ 2 @CrystalNets/…n.jl:726 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:590 backtrack_to!(vmapprogress::Vecto… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:1040 (::Colon)(start::Int64, stop::In… ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:597 backtrack_to!(vmapprogress::Vecto… 1╎ ╎ ╎ ╎ 1 @Base/array.jl:0 attribute_next_available_modify!(vmap… ╎ ╎ ╎ ╎ 1 @CrystalNets/…n.jl:733 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 1 @Base/bitarray.jl:669 setindex!(A::Vector{Int64}, x::In… ╎ ╎ ╎ ╎ 1 @Base/bitarray.jl:663 _setindex!(A::Vector{Int64}, x::… ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:1039 getindex 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:391 checkbounds ====================================================================================== Information request received. A stacktrace will print followed by a 1.0 second profile. --trace-compile is enabled during profile collection. ====================================================================================== 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:457:34 wait at ./task.jl:1246:50 wait_forever at ./task.jl:1168:5 jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] start_task at /source/src/task.c:1275:19 unknown function (ip: (nil)) at (unknown file) ============================================================== Profile collected. A report will print at the next yield point. Disabling --trace-compile ============================================================== ┌ 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/v1.14/Profile/src/Profile.jl:1361 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x000079cccc080790 Total snapshots: 437. Utilization: 0% ╎437 @Base/task.jl:1168 wait_forever() 436╎ 437 @Base/task.jl:1246 wait() [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 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:457:34 wait at ./task.jl:1246:50 wait_forever at ./task.jl:1168:5 jfptr_wait_forever_0.1 at /opt/julia/lib/julia/sys.so (unknown line) [37] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/CrystalNets/gASyq/test/runtests.jl:415 _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] start_task at /source/src/task.c:1275:19 unknown function (ip: (nil)) at (unknown file) Allocations: 19872485 (Pool: 19871789; Big: 696); GC: 17 size at ./essentials.jl:12:2 [inlined] axes at ./abstractarray.jl:102:5 [inlined] LinearIndices at ./indices.jl:533:3 [inlined] keys at ./abstractarray.jl:170:2 [inlined] findnext at ./array.jl:2469:9 [inlined] findfirst at ./array.jl:2523:6 [inlined] macro expansion at ./some.jl:157:1 [inlined] translation_to_direct_map at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/minimization.jl:708:555 find_first_valid_translation_unstable at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/minimization.jl:809:124 minimize_unstable at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/minimization.jl:287:8 [inlined] minimize at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/minimization.jl:274:10 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:34:79 unknown function (ip: 0x7a4b197b8443) at (unknown file) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:153:242 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:87:5 [inlined] #topological_genome#224 at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:90:10 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/gASyq/src/query.jl:90:4 unknown function (ip: 0x7a4ae35e99fc) at (unknown file) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:243:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:693:13 eval_body at /source/src/interpreter.c:550:21 eval_body at /source/src/interpreter.c:558:21 eval_body at /source/src/interpreter.c:558:21 eval_body at /source/src/interpreter.c:558:21 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884:21 ijl_eval_thunk at /source/src/toplevel.c:768:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:517:3 include_string at ./loading.jl:3110:145 _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 _include at ./loading.jl:3170:45 include at ./Base.jl:327:3 IncludeInto at ./Base.jl:328:4 jfptr_IncludeInto_1.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] do_call at /source/src/interpreter.c:123:26 eval_value at /source/src/interpreter.c:243:16 eval_stmt_value at /source/src/interpreter.c:194:23 [inlined] eval_body at /source/src/interpreter.c:693:13 jl_interpret_toplevel_thunk at /source/src/interpreter.c:884:21 ijl_eval_thunk at /source/src/toplevel.c:768:18 jl_toplevel_eval_flex at /source/src/toplevel.c:712:26 jl_eval_toplevel_stmts at /source/src/toplevel.c:602:15 jl_toplevel_eval_flex at /source/src/toplevel.c:684:27 ijl_toplevel_eval at /source/src/toplevel.c:782:12 ijl_toplevel_eval_in at /source/src/toplevel.c:827:13 eval at ./boot.jl:517:3 exec_options at ./client.jl:318:410 _start at ./client.jl:593:36 jfptr__start_0.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4113:23 [inlined] ijl_apply_generic at /source/src/gf.c:4339:12 jl_apply at /source/src/julia.h:2327:12 [inlined] true_main at /source/src/jlapi.c:971:29 jl_repl_entrypoint at /source/src/jlapi.c:1138:15 main at /source/cli/loader_exe.c:58:15 unknown function (ip: 0x7a4b3fddf249) at /lib/x86_64-linux-gnu/libc.so.6 __libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S unknown function (ip: (nil)) at (unknown file) Allocations: 1553811940 (Pool: 1553807276; Big: 4664); GC: 540 PkgEval terminated after 2722.7s: test duration exceeded the time limit