Package evaluation of CrystalNets on Julia 1.13.0-DEV.1216 (bcb9a929e5*) started at 2025-09-28T16:11:26.141 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 9.82s ################################################################################ # Installation # Installing CrystalNets... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [7952bbbe] + CrystalNets v1.1.0 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 v1.1.0 [864edb3b] + DataStructures v0.19.1 [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 v1.3.3 [21216c6a] + Preferences v1.5.0 [92933f4c] + ProgressMeter v1.11.0 [ae029012] + Requires v1.3.1 [699a6c99] + SimpleTraits v0.9.5 [90137ffa] + StaticArrays v1.9.15 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [b718987f] + TextWrap v1.0.2 [0796e94c] + Tokenize v0.5.29 [1986cc42] + Unitful v1.25.0 [a7773ee8] + UnitfulAtomic v1.0.0 [78a364fa] + Chemfiles_jll v0.10.4+0 [ac4a9f1e] + spglib_jll v2.6.0+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 v8.16.0+0 [e37daf67] + LibGit2_jll v1.9.1+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.9.9 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.2+0 [efcefdf7] + PCRE2_jll v10.46.0+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 v1.67.1+0 [3f19e933] + p7zip_jll v17.6.0+0 Installation completed after 5.75s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 339.45s ################################################################################ # Testing # Testing CrystalNets Status `/tmp/jl_zVgqAu/Project.toml` [861a8166] Combinatorics v1.0.3 [7952bbbe] CrystalNets v1.1.0 [86223c79] Graphs v1.13.1 [18c5b727] PeriodicGraphs v0.10.4 [90137ffa] StaticArrays v1.9.15 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_zVgqAu/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 v1.1.0 [864edb3b] DataStructures v0.19.1 [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 v1.3.3 [21216c6a] Preferences v1.5.0 [92933f4c] ProgressMeter v1.11.0 [ae029012] Requires v1.3.1 [699a6c99] SimpleTraits v0.9.5 [90137ffa] StaticArrays v1.9.15 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [b718987f] TextWrap v1.0.2 [0796e94c] Tokenize v0.5.29 [1986cc42] Unitful v1.25.0 [a7773ee8] UnitfulAtomic v1.0.0 [78a364fa] Chemfiles_jll v0.10.4+0 [ac4a9f1e] spglib_jll v2.6.0+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 v8.16.0+0 [e37daf67] LibGit2_jll v1.9.1+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2025.9.9 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.5.2+0 [efcefdf7] PCRE2_jll v10.46.0+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 v1.67.1+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 16m48.7s [ 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 1.3s [ 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 9m23.6s [ 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 53.2s Test Summary: | Pass Broken Total Time Executable | 29 1 30 9.2s 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. --trace-compile is enabled during profile collection. ====================================================================================== cmd: /opt/julia/bin/julia 27 running 1 of 1 signal (10): User defined signal 1 uv_run at /workspace/srcdir/libuv/src/unix/core.c:434 ijl_process_events at /source/src/jl_uv.c:397 process_events at ./libuv.jl:133 [inlined] wait at ./task.jl:1188 yield at ./task.jl:1042 translation_to_direct_map at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/minimization.jl:677 find_first_valid_translation_unstable at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/minimization.jl:809 minimize_unstable at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/minimization.jl:287 [inlined] minimize at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/minimization.jl:274 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/query.jl:34 unknown function (ip: 0x7f382059fc92) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/query.jl:153 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/query.jl:87 [inlined] #topological_genome#221 at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/query.jl:90 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/query.jl:90 unknown function (ip: 0x7f381fae540c) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:690 eval_body at /source/src/interpreter.c:550 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:793 jl_eval_toplevel_stmts at /source/src/toplevel.c:622 jl_toplevel_eval_flex at /source/src/toplevel.c:734 ijl_toplevel_eval at /source/src/toplevel.c:805 ijl_toplevel_eval_in at /source/src/toplevel.c:850 eval at ./boot.jl:489 include_string at ./loading.jl:2914 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:2974 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_24410.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:690 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:793 jl_eval_toplevel_stmts at /source/src/toplevel.c:622 jl_toplevel_eval_flex at /source/src/toplevel.c:734 ijl_toplevel_eval at /source/src/toplevel.c:805 ijl_toplevel_eval_in at /source/src/toplevel.c:850 eval at ./boot.jl:489 exec_options at ./client.jl:296 _start at ./client.jl:563 jfptr__start_51780.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7f387375d249) 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x00007f38597fc010 Total snapshots: 165. Utilization: 100% ╎165 @Base/client.jl:563 _start() ╎ 165 @Base/client.jl:296 exec_options(opts::Base.JLOptions) ╎ 165 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ 165 @Base/Base.jl:311 (::Base.IncludeInto)(fname::String) ╎ 165 @Base/Base.jl:310 include(mapexpr::Function, mod::Module, _path::St… ╎ 165 @Base/loading.jl:2974 _include(mapexpr::Function, mod::Module, _pa… ╎ ╎ 165 @Base/loading.jl:2914 include_string(mapexpr::typeof(identity), m… ╎ ╎ 165 @Base/boot.jl:489 eval(m::Module, e::Any) ╎ ╎ 165 @CrystalNets/…uery.jl:90 topological_genome(g::PeriodicGraph2D) ╎ ╎ 165 @CrystalNets/…ery.jl:90 #topological_genome#221 ╎ ╎ 165 @CrystalNets/…ery.jl:87 topological_genome ╎ ╎ ╎ 165 @CrystalNets/…ry.jl:153 topological_genome(group::Underlying… ╎ ╎ ╎ 165 @CrystalNets/…ry.jl:34 topological_genome(net::CrystalNet2D… ╎ ╎ ╎ 165 @CrystalNets/…n.jl:274 minimize ╎ ╎ ╎ 165 @CrystalNets/…n.jl:287 minimize_unstable 1╎ ╎ ╎ 165 @CrystalNets/…n.jl:809 find_first_valid_translation_unst… 2╎ ╎ ╎ ╎ 2 @CrystalNets/….jl:0 translation_to_direct_map(shrunk_pv… 2╎ ╎ ╎ ╎ 90 @CrystalNets/….jl:677 translation_to_direct_map(shrunk_… 3╎ ╎ ╎ ╎ 11 @Base/task.jl:1040 yield() 2╎ ╎ ╎ ╎ 7 @Base/task.jl:947 enq_work(t::Task) 1╎ ╎ ╎ ╎ 1 @Base/task.jl:876 push!(W::Base.IntrusiveLinkedListS… 1╎ ╎ ╎ ╎ 1 @Base/task.jl:877 push!(W::Base.IntrusiveLinkedListS… ╎ ╎ ╎ ╎ 1 @Base/task.jl:880 push!(W::Base.IntrusiveLinkedListS… ╎ ╎ ╎ ╎ 1 @Base/…cks-mt.jl:100 unlock 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == 1╎ ╎ ╎ ╎ 1 @Base/task.jl:882 push!(W::Base.IntrusiveLinkedListS… ╎ ╎ ╎ ╎ 1 @Base/task.jl:923 workqueue_for ╎ ╎ ╎ ╎ 1 @Base/lock.jl:863 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…ators.jl:320 != 1╎ ╎ ╎ ╎ ╎ 1 @Base/…otion.jl:637 == 1╎ ╎ ╎ ╎ 1 @Base/task.jl:963 enq_work(t::Task) 4╎ ╎ ╎ ╎ 77 @Base/task.jl:1042 yield() ╎ ╎ ╎ ╎ 61 @Base/task.jl:1188 wait() 61╎ ╎ ╎ ╎ 61 @Base/libuv.jl:133 process_events ╎ ╎ ╎ ╎ 3 @Base/task.jl:1191 wait() ╎ ╎ ╎ ╎ 1 @Base/task.jl:923 workqueue_for 1╎ ╎ ╎ ╎ 1 @Base/lock.jl:863 getindex ╎ ╎ ╎ ╎ 2 @Base/…tructs.jl:36 threadid ╎ ╎ ╎ ╎ 2 @Base/int.jl:1058 + 2╎ ╎ ╎ ╎ ╎ 2 @Base/int.jl:87 + ╎ ╎ ╎ ╎ 4 @Base/task.jl:1192 wait() 1╎ ╎ ╎ ╎ 1 @Base/task.jl:1163 trypoptask(W::Base.IntrusiveLinke… ╎ ╎ ╎ ╎ 3 @Base/task.jl:1164 trypoptask(W::Base.IntrusiveLinke… 1╎ ╎ ╎ ╎ 1 @Base/task.jl:902 popfirst!(W::Base.IntrusiveLinked… 1╎ ╎ ╎ ╎ 1 @Base/task.jl:903 popfirst!(W::Base.IntrusiveLinked… ╎ ╎ ╎ ╎ 1 @Base/task.jl:904 popfirst!(W::Base.IntrusiveLinked… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…d_list.jl:85 popfirst! ╎ ╎ ╎ ╎ 5 @Base/task.jl:1203 wait() 4╎ ╎ ╎ ╎ 4 @Base/task.jl:1100 try_yieldto(undo::typeof(Base.ens… 1╎ ╎ ╎ ╎ 1 @Base/task.jl:1101 try_yieldto(undo::typeof(Base.ens… ╎ ╎ ╎ ╎ 3 @CrystalNets/….jl:679 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 3 @Base/…entials.jl:964 getindex 1╎ ╎ ╎ ╎ 3 @Base/…ntials.jl:385 checkbounds 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:381 checkbounds ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:681 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 1 @Base/…entials.jl:964 getindex ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:385 checkbounds 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:381 checkbounds ╎ ╎ ╎ ╎ 2 @CrystalNets/….jl:682 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 2 @CrystalNets/….jl:81 getindex ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:964 getindex 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:385 checkbounds 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:686 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:597 backtrack_to!(vmapprogress::Vect… ╎ ╎ ╎ ╎ 1 @CrystalNets/…jl:569 attribute_next_available_modify!… ╎ ╎ ╎ ╎ 1 @Base/array.jl:2490 findfirst 1╎ ╎ ╎ ╎ 1 @Base/array.jl:2440 findnext ╎ ╎ ╎ ╎ 27 @CrystalNets/….jl:699 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 2 @Base/array.jl:828 collect(itr::Base.Generator{Vector{… ╎ ╎ ╎ ╎ 1 @Base/…nerator.jl:45 iterate ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:1245 iterate ╎ ╎ ╎ ╎ 1 @Base/…array.jl:1245 iterate ╎ ╎ ╎ ╎ ╎ 1 @Base/…array.jl:1253 _iterate_abstractarray 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ 1 @Base/…nerator.jl:48 iterate ╎ ╎ ╎ ╎ 1 @CrystalNets/…jl:703 #translation_to_direct_map##0 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 22 @Base/array.jl:833 collect(itr::Base.Generator{Vector{… ╎ ╎ ╎ ╎ 22 @Base/array.jl:701 _array_for ╎ ╎ ╎ ╎ 22 @Base/…tarray.jl:876 similar ╎ ╎ ╎ ╎ 22 @Base/array.jl:409 similar ╎ ╎ ╎ ╎ ╎ 22 @Base/…array.jl:877 similar ╎ ╎ ╎ ╎ ╎ 22 @Base/boot.jl:669 Array ╎ ╎ ╎ ╎ ╎ 22 @Base/boot.jl:661 Array ╎ ╎ ╎ ╎ ╎ 18 @Base/boot.jl:648 Array 18╎ ╎ ╎ ╎ ╎ 18 @Base/boot.jl:588 GenericMemory 4╎ ╎ ╎ ╎ ╎ 4 @Base/boot.jl:649 Array ╎ ╎ ╎ ╎ 3 @Base/array.jl:838 collect(itr::Base.Generator{Vector{… ╎ ╎ ╎ ╎ 3 @Base/array.jl:864 collect_to_with_first! ╎ ╎ ╎ ╎ 2 @Base/array.jl:886 collect_to! ╎ ╎ ╎ ╎ 2 @Base/…erator.jl:48 iterate ╎ ╎ ╎ ╎ ╎ 1 @CrystalNets/…l:700 #translation_to_direct_map##0 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ ╎ 1 @CrystalNets/…l:703 #translation_to_direct_map##0 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ 1 @Base/array.jl:890 collect_to! ╎ ╎ ╎ ╎ 1 @Base/array.jl:1020 setindex! 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1024 _setindex! ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:708 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 1 @Base/some.jl:157 macro expansion ╎ ╎ ╎ ╎ 1 @Base/array.jl:2490 findfirst 1╎ ╎ ╎ ╎ 1 @Base/array.jl:0 findnext ╎ ╎ ╎ ╎ 9 @CrystalNets/….jl:709 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 9 @Base/bitarray.jl:398 falses ╎ ╎ ╎ ╎ 9 @Base/…tarray.jl:400 falses ╎ ╎ ╎ ╎ 7 @Base/…tarray.jl:71 BitArray ╎ ╎ ╎ ╎ 5 @Base/…tarray.jl:37 BitArray ╎ ╎ ╎ ╎ ╎ 2 @Base/boot.jl:648 Array 2╎ ╎ ╎ ╎ ╎ 2 @Base/boot.jl:588 GenericMemory 3╎ ╎ ╎ ╎ ╎ 3 @Base/boot.jl:649 Array 2╎ ╎ ╎ ╎ 2 @Base/…tarray.jl:39 BitArray 1╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:372 fill!(B::BitVector, x::Bool) ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:377 fill!(B::BitVector, x::Bool) ╎ ╎ ╎ ╎ 1 @Base/array.jl:359 fill! 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:0 _fill! ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:713 translation_to_direct_map(shrunk_… 1╎ ╎ ╎ ╎ 1 @Base/…entials.jl:965 getindex ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:714 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 1 @Base/…erators.jl:196 iterate ╎ ╎ ╎ ╎ 1 @Base/…rators.jl:197 iterate ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:1245 iterate ╎ ╎ ╎ ╎ 1 @Base/…array.jl:1245 iterate ╎ ╎ ╎ ╎ ╎ 1 @Base/…array.jl:1253 _iterate_abstractarray 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:965 getindex ╎ ╎ ╎ ╎ 2 @CrystalNets/….jl:715 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 2 @Base/bitarray.jl:677 getindex ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:669 unsafe_bitgetindex ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:121 get_chunks_id ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:114 _div64 ╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:580 >> 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:573 >> ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:671 unsafe_bitgetindex ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:964 getindex 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:385 checkbounds ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:721 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 1 @Base/…erators.jl:197 iterate ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:1245 iterate ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:1253 _iterate_abstractarray ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 4 @CrystalNets/….jl:726 translation_to_direct_map(shrunk_… 1╎ ╎ ╎ ╎ 1 @Base/array.jl:1524 resize!(a::Vector{Tuple{Int64, Pai… ╎ ╎ ╎ ╎ 3 @CrystalNets/…jl:597 backtrack_to!(vmapprogress::Vecto… ╎ ╎ ╎ ╎ 1 @CrystalNets/…jl:562 attribute_next_available_modify!… 1╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:0 find_necessary_image ╎ ╎ ╎ ╎ 1 @CrystalNets/…jl:578 attribute_next_available_modify!… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 1 @CrystalNets/…jl:582 attribute_next_available_modify!… 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 13 @CrystalNets/….jl:730 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 13 @Base/bitarray.jl:398 falses ╎ ╎ ╎ ╎ 13 @Base/…tarray.jl:400 falses ╎ ╎ ╎ ╎ 12 @Base/…tarray.jl:71 BitArray ╎ ╎ ╎ ╎ 9 @Base/…tarray.jl:37 BitArray ╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:648 Array 6╎ ╎ ╎ ╎ ╎ 6 @Base/boot.jl:588 GenericMemory 3╎ ╎ ╎ ╎ ╎ 3 @Base/boot.jl:649 Array 3╎ ╎ ╎ ╎ 3 @Base/…tarray.jl:39 BitArray ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:374 fill!(B::BitVector, x::Bool) ╎ ╎ ╎ ╎ 1 @Base/…array.jl:1256 isempty ╎ ╎ ╎ ╎ ╎ 1 @Base/…array.jl:103 length 1╎ ╎ ╎ ╎ ╎ 1 @Base/…piler.jl:57 getproperty ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:733 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 1 @Base/bitarray.jl:677 getindex ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:671 unsafe_bitgetindex ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:964 getindex 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:385 checkbounds ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:742 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 1 @Base/bitarray.jl:677 getindex ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:671 unsafe_bitgetindex 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:744 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 1 @Base/bitarray.jl:697 setindex! ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:684 unsafe_bitsetindex! ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:691 _unsafe_bitsetindex! 1╎ ╎ ╎ ╎ 1 @Base/int.jl:418 | ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:760 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:554 attribute_next_available! 1╎ ╎ ╎ ╎ 1 @CrystalNets/…jl:557 attribute_next_available_modify!… ╎ ╎ ╎ ╎ 2 @CrystalNets/….jl:769 translation_to_direct_map(shrunk_… ╎ ╎ ╎ ╎ 2 @Base/…erators.jl:197 iterate ╎ ╎ ╎ ╎ 2 @Base/…tarray.jl:1245 iterate 1╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:1252 _iterate_abstractarray ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:1253 _iterate_abstractarray 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:965 getindex ====================================================================================== 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 wait at ./task.jl:1200 wait_forever at ./task.jl:1137 jfptr_wait_forever_72924.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] start_task at /source/src/task.c:1281 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/v1.13/Profile/src/Profile.jl:1362 Overhead ╎ [+additional indent] Count File:Line Function ========================================================= Thread 1 (default) Task 0x0000745295a043d0 Total snapshots: 413. Utilization: 0% ╎413 @Base/task.jl:1137 wait_forever() 412╎ 413 @Base/task.jl:1200 wait() [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 [27] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/test/runtests.jl:415 getindex at ./essentials.jl:965 [inlined] #translation_to_direct_map##0 at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/minimization.jl:700 [inlined] iterate at ./generator.jl:48 [inlined] collect_to! at ./array.jl:886 [inlined] collect_to_with_first! at ./array.jl:864 [inlined] collect at ./array.jl:838 translation_to_direct_map at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/minimization.jl:699 find_first_valid_translation_unstable at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/minimization.jl:809 minimize_unstable at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/minimization.jl:287 [inlined] minimize at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/minimization.jl:274 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/query.jl:34 unknown function (ip: 0x7f382059fc92) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/query.jl:153 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/query.jl:87 [inlined] #topological_genome#221 at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/query.jl:90 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/uzTYu/src/query.jl:90 unknown function (ip: 0x7f381fae540c) at (unknown file) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:690 eval_body at /source/src/interpreter.c:550 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 eval_body at /source/src/interpreter.c:558 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:793 jl_eval_toplevel_stmts at /source/src/toplevel.c:622 jl_toplevel_eval_flex at /source/src/toplevel.c:734 ijl_toplevel_eval at /source/src/toplevel.c:805 ijl_toplevel_eval_in at /source/src/toplevel.c:850 eval at ./boot.jl:489 include_string at ./loading.jl:2914 _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 _include at ./loading.jl:2974 include at ./Base.jl:310 IncludeInto at ./Base.jl:311 jfptr_IncludeInto_24410.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] do_call at /source/src/interpreter.c:123 eval_value at /source/src/interpreter.c:243 eval_stmt_value at /source/src/interpreter.c:194 [inlined] eval_body at /source/src/interpreter.c:690 jl_interpret_toplevel_thunk at /source/src/interpreter.c:899 jl_toplevel_eval_flex at /source/src/toplevel.c:793 jl_eval_toplevel_stmts at /source/src/toplevel.c:622 jl_toplevel_eval_flex at /source/src/toplevel.c:734 ijl_toplevel_eval at /source/src/toplevel.c:805 ijl_toplevel_eval_in at /source/src/toplevel.c:850 eval at ./boot.jl:489 exec_options at ./client.jl:296 _start at ./client.jl:563 jfptr__start_51780.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4116 [inlined] ijl_apply_generic at /source/src/gf.c:4313 jl_apply at /source/src/julia.h:2271 [inlined] true_main at /source/src/jlapi.c:971 jl_repl_entrypoint at /source/src/jlapi.c:1138 main at /source/cli/loader_exe.c:58 unknown function (ip: 0x7f387375d249) 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: 2699417307 (Pool: 2699413468; Big: 3839); GC: 658 PkgEval terminated after 2729.98s: test duration exceeded the time limit