Package evaluation of CrystalNets on Julia 1.13.0-DEV.974 (7bbb213719*) started at 2025-08-12T15:54:58.096 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 10.04s ################################################################################ # 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 v0.10.42 [34da2185] + Compat v4.18.0 [7952bbbe] + CrystalNets v1.0.2 ⌅ [864edb3b] + DataStructures v0.18.22 [ffbed154] + DocStringExtensions v0.9.5 [86223c79] + Graphs v1.13.0 [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 v2025.7.15 [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 v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 4.63s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 352.84s ################################################################################ # Testing # Testing CrystalNets Status `/tmp/jl_p9HC1A/Project.toml` [861a8166] Combinatorics v1.0.3 [7952bbbe] CrystalNets v1.0.2 [86223c79] Graphs v1.13.0 [18c5b727] PeriodicGraphs v0.10.4 [90137ffa] StaticArrays v1.9.14 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_p9HC1A/Manifest.toml` [c7e460c6] ArgParse v1.2.0 [ec485272] ArnoldiMethod v0.4.0 [a963bdd2] AtomsBase v0.5.1 [46823bd8] Chemfiles v0.10.42 [861a8166] Combinatorics v1.0.3 [34da2185] Compat v4.18.0 [7952bbbe] CrystalNets v1.0.2 ⌅ [864edb3b] DataStructures v0.18.22 [ffbed154] DocStringExtensions v0.9.5 [86223c79] Graphs v1.13.0 [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 v2025.7.15 [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 v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. 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 16m40.2s [ 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 1.0s [ 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 6m42.4s [ 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 55.0s Test Summary: | Pass Broken Total Time Executable | 29 1 30 9.8s 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 .................................................. 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 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_process_events at /source/src/jl_uv.c:397 process_events at ./libuv.jl:133 [inlined] wait at ./task.jl:1180 yield at ./task.jl:1034 translation_to_direct_map at /home/pkgeval/.julia/packages/CrystalNets/vvGQH/src/minimization.jl:673 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: 0x730cc41d2fd2) at (unknown file) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 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: 0x730cc0d0c372) at (unknown file) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2375 [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 ============================================================== ====================================================================================== 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 ┌ 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 0x0000730c91539960 Total snapshots: 190. Utilization: 100% ╎190 @Base/…dingconstructs.jl:177 (::Base.Threads.var"#threading_run##0#thre… ╎ 190 @Base/…ingconstructs.jl:243 #49 ╎ 190 @Base/…ingconstructs.jl:276 (::var"#49#50"{var"#51#52"{Int64, Int64, … ╎ 190 …GQH/test/runtests.jl:539 macro expansion ╎ 190 @CrystalNets/…query.jl:90 topological_genome ╎ 190 @CrystalNets/…query.jl:90 #topological_genome#221 ╎ ╎ 190 @CrystalNets/…query.jl:87 topological_genome ╎ ╎ 190 @CrystalNets/…uery.jl:153 topological_genome(group::UnderlyingNe… ╎ ╎ 190 @CrystalNets/…uery.jl:34 topological_genome(net::CrystalNet2D{R… ╎ ╎ 190 @CrystalNets/…ion.jl:274 minimize ╎ ╎ 190 @CrystalNets/…ion.jl:287 minimize_unstable 1╎ ╎ ╎ 190 @CrystalNets/…on.jl:805 find_first_valid_translation_unstabl… ╎ ╎ ╎ 113 @CrystalNets/…on.jl:673 translation_to_direct_map(shrunk_pv… 3╎ ╎ ╎ 12 @Base/task.jl:1032 yield() 1╎ ╎ ╎ 9 @Base/task.jl:948 enq_work(t::Task) 3╎ ╎ ╎ 3 @Base/task.jl:869 push!(W::Base.IntrusiveLinkedListSynch… ╎ ╎ ╎ 4 @Base/task.jl:872 push!(W::Base.IntrusiveLinkedListSynch… ╎ ╎ ╎ ╎ 3 @Base/locks-mt.jl:100 unlock 3╎ ╎ ╎ ╎ 3 @Base/…omotion.jl:637 == ╎ ╎ ╎ ╎ 1 @Base/locks-mt.jl:103 unlock 1╎ ╎ ╎ ╎ 1 @Base/gcutils.jl:159 enable_finalizers ╎ ╎ ╎ 1 @Base/task.jl:915 workqueue_for 1╎ ╎ ╎ ╎ 1 @Base/lock.jl:858 getindex(once::OncePerThread{Base.Int… 2╎ ╎ ╎ 2 @Base/task.jl:1033 yield() 1╎ ╎ ╎ 99 @Base/task.jl:1034 yield() 1╎ ╎ ╎ 1 @Base/lock.jl:858 getindex(once::OncePerThread{Base.Intru… ╎ ╎ ╎ 1 @Base/task.jl:1176 wait() 1╎ ╎ ╎ 1 @Base/task.jl:1206 record_running_time! ╎ ╎ ╎ 83 @Base/task.jl:1180 wait() 83╎ ╎ ╎ 83 @Base/libuv.jl:133 process_events ╎ ╎ ╎ 5 @Base/task.jl:1183 wait() ╎ ╎ ╎ 2 @Base/task.jl:915 workqueue_for ╎ ╎ ╎ ╎ 2 @Base/lock.jl:863 getindex(once::OncePerThread{Base.Int… ╎ ╎ ╎ ╎ 1 @Base/…erators.jl:321 != 1╎ ╎ ╎ ╎ 1 @Base/…motion.jl:637 == ╎ ╎ ╎ ╎ 1 @Base/…erators.jl:425 > 1╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ 3 @Base/…nstructs.jl:36 threadid ╎ ╎ ╎ ╎ 3 @Base/int.jl:1020 + 3╎ ╎ ╎ ╎ 3 @Base/int.jl:87 + ╎ ╎ ╎ 5 @Base/task.jl:1184 wait() 1╎ ╎ ╎ 1 @Base/task.jl:0 trypoptask(W::Base.IntrusiveLinkedListSy… ╎ ╎ ╎ 4 @Base/task.jl:1156 trypoptask(W::Base.IntrusiveLinkedLis… ╎ ╎ ╎ ╎ 1 @Base/task.jl:894 popfirst!(W::Base.IntrusiveLinkedList… ╎ ╎ ╎ ╎ 1 @Base/locks-mt.jl:78 lock(l::Base.Threads.SpinLock) ╎ ╎ ╎ ╎ 1 @Base/locks-mt.jl:91 trylock 1╎ ╎ ╎ ╎ 1 @Base/…motion.jl:637 == 2╎ ╎ ╎ ╎ 2 @Base/task.jl:895 popfirst!(W::Base.IntrusiveLinkedList… ╎ ╎ ╎ ╎ 1 @Base/task.jl:896 popfirst!(W::Base.IntrusiveLinkedList… ╎ ╎ ╎ ╎ 1 @Base/…ed_list.jl:86 popfirst! ╎ ╎ ╎ ╎ 1 @Base/…ed_list.jl:96 list_deletefirst! 1╎ ╎ ╎ ╎ 1 @Base/…mpiler.jl:61 setproperty! 2╎ ╎ ╎ 3 @Base/task.jl:1195 wait() 1╎ ╎ ╎ 1 @Base/task.jl:1093 try_yieldto(undo::typeof(Base.ensure_… ╎ ╎ ╎ 2 @CrystalNets/…on.jl:675 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 1 @Base/…sentials.jl:966 getindex 1╎ ╎ ╎ 1 @Base/…sentials.jl:387 checkbounds 1╎ ╎ ╎ 1 @Base/…sentials.jl:967 getindex ╎ ╎ ╎ 1 @CrystalNets/…on.jl:676 translation_to_direct_map(shrunk_pv… 1╎ ╎ ╎ 1 @Base/int.jl:86 - ╎ ╎ ╎ 1 @CrystalNets/…on.jl:687 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 @Base/…entials.jl:966 getindex ╎ ╎ ╎ ╎ 1 @Base/…entials.jl:387 checkbounds ╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:383 checkbounds 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:11 length ╎ ╎ ╎ 1 @CrystalNets/…on.jl:688 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 1 @Base/operators.jl:321 != 1╎ ╎ ╎ 1 @Base/promotion.jl:637 == ╎ ╎ ╎ 27 @CrystalNets/…on.jl:695 translation_to_direct_map(shrunk_pv… 1╎ ╎ ╎ 1 @Base/…actarray.jl:0 collect(itr::Base.Generator{Vector{Pe… ╎ ╎ ╎ 3 @Base/array.jl:803 collect(itr::Base.Generator{Vector{Peri… ╎ ╎ ╎ 3 @Base/generator.jl:45 iterate ╎ ╎ ╎ 3 @Base/…ctarray.jl:1241 iterate ╎ ╎ ╎ ╎ 3 @Base/…ctarray.jl:1241 iterate 2╎ ╎ ╎ ╎ 2 @Base/…tarray.jl:1248 _iterate ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:1249 _iterate 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ 18 @Base/array.jl:808 collect(itr::Base.Generator{Vector{Peri… ╎ ╎ ╎ 18 @Base/array.jl:676 _array_for ╎ ╎ ╎ 18 @Base/…actarray.jl:872 similar ╎ ╎ ╎ ╎ 18 @Base/…ctarray.jl:873 similar ╎ ╎ ╎ ╎ 18 @Base/boot.jl:661 Array ╎ ╎ ╎ ╎ 14 @Base/boot.jl:648 Array 14╎ ╎ ╎ ╎ 14 @Base/boot.jl:588 GenericMemory 4╎ ╎ ╎ ╎ 4 @Base/boot.jl:649 Array ╎ ╎ ╎ 5 @Base/array.jl:813 collect(itr::Base.Generator{Vector{Peri… ╎ ╎ ╎ 5 @Base/array.jl:839 collect_to_with_first! ╎ ╎ ╎ 5 @Base/array.jl:861 collect_to! ╎ ╎ ╎ ╎ 2 @Base/generator.jl:45 iterate ╎ ╎ ╎ ╎ 2 @Base/…tarray.jl:1241 iterate 1╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:0 _iterate ╎ ╎ ╎ ╎ 1 @Base/…tarray.jl:1249 _iterate 1╎ ╎ ╎ ╎ 1 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ ╎ 3 @Base/generator.jl:48 iterate ╎ ╎ ╎ ╎ 1 @CrystalNets/….jl:698 #translation_to_direct_map##0 1╎ ╎ ╎ ╎ 1 @Base/int.jl:522 <= ╎ ╎ ╎ ╎ 2 @CrystalNets/….jl:699 #translation_to_direct_map##0 2╎ ╎ ╎ ╎ 2 @Base/…ntials.jl:967 getindex ╎ ╎ ╎ 8 @CrystalNets/…on.jl:703 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 8 @Base/sort.jl:1731 sort! ╎ ╎ ╎ 8 @Base/sort.jl:1738 #sort!#24 ╎ ╎ ╎ 8 @Base/sort.jl:1591 _sort! ╎ ╎ ╎ ╎ 8 @Base/sort.jl:561 _sort! ╎ ╎ ╎ ╎ 1 @Base/sort.jl:651 _sort! ╎ ╎ ╎ ╎ 1 @Base/sort.jl:490 _hi ╎ ╎ ╎ ╎ 1 @Base/…dtuple.jl:331 merge ╎ ╎ ╎ ╎ 1 @Base/…dtuple.jl:332 macro expansion 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tuple.jl:156 _new_NamedTuple ╎ ╎ ╎ ╎ 7 @Base/sort.jl:683 _sort! ╎ ╎ ╎ ╎ 7 @Base/sort.jl:744 _sort! 1╎ ╎ ╎ ╎ 7 @Base/sort.jl:797 _sort!(v::Vector{PeriodicVertex2D}… ╎ ╎ ╎ ╎ 1 @Base/sort.jl:839 _sort!(v::Vector{PeriodicVertex2D… 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ 2 @Base/sort.jl:841 _sort!(v::Vector{PeriodicVertex2D… ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:966 getindex ╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:387 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…ials.jl:383 checkbounds 1╎ ╎ ╎ ╎ ╎ 1 @Base/…tials.jl:967 getindex ╎ ╎ ╎ ╎ 1 @Base/sort.jl:842 _sort!(v::Vector{PeriodicVertex2D… ╎ ╎ ╎ ╎ ╎ 1 @Base/…ering.jl:120 lt ╎ ╎ ╎ ╎ ╎ 1 @CrystalNets/…l:703 #translation_to_direct_map##2 ╎ ╎ ╎ ╎ ╎ 1 @Base/…tors.jl:425 > 1╎ ╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ ╎ 1 @Base/sort.jl:848 _sort!(v::Vector{PeriodicVertex2D… ╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:995 setindex! 1╎ ╎ ╎ ╎ ╎ 1 @Base/array.jl:1000 _setindex! 1╎ ╎ ╎ ╎ 1 @Base/sort.jl:849 _sort!(v::Vector{PeriodicVertex2D… ╎ ╎ ╎ 1 @CrystalNets/…on.jl:704 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 1 @Base/some.jl:158 macro expansion ╎ ╎ ╎ 1 @Base/array.jl:2465 findfirst ╎ ╎ ╎ 1 @Base/array.jl:2412 findnext ╎ ╎ ╎ ╎ 1 @Base/…erators.jl:425 > 1╎ ╎ ╎ ╎ 1 @Base/int.jl:83 < ╎ ╎ ╎ 14 @CrystalNets/…on.jl:705 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 14 @Base/bitarray.jl:403 falses ╎ ╎ ╎ 14 @Base/bitarray.jl:405 falses ╎ ╎ ╎ 14 @Base/bitarray.jl:71 BitArray ╎ ╎ ╎ ╎ 11 @Base/bitarray.jl:37 BitArray ╎ ╎ ╎ ╎ 5 @Base/boot.jl:648 Array 5╎ ╎ ╎ ╎ 5 @Base/boot.jl:588 GenericMemory 5╎ ╎ ╎ ╎ 6 @Base/boot.jl:649 Array 3╎ ╎ ╎ ╎ 3 @Base/bitarray.jl:39 BitArray ╎ ╎ ╎ 1 @CrystalNets/…on.jl:711 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 1 @Base/bitarray.jl:682 getindex ╎ ╎ ╎ 1 @Base/bitarray.jl:676 unsafe_bitgetindex ╎ ╎ ╎ 1 @Base/…sentials.jl:966 getindex 1╎ ╎ ╎ ╎ 1 @Base/…entials.jl:387 checkbounds ╎ ╎ ╎ 2 @CrystalNets/…on.jl:722 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 2 @CrystalNets/…n.jl:593 backtrack_to!(vmapprogress::Vector{… ╎ ╎ ╎ 1 @CrystalNets/…n.jl:560 attribute_next_available_modify!(v… ╎ ╎ ╎ 1 @CrystalNets/…y.jl:81 getindex 1╎ ╎ ╎ ╎ 1 @Base/…entials.jl:967 getindex ╎ ╎ ╎ 1 @CrystalNets/…n.jl:574 attribute_next_available_modify!(v… 1╎ ╎ ╎ 1 @Base/…sentials.jl:967 getindex ╎ ╎ ╎ 15 @CrystalNets/…on.jl:726 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 15 @Base/bitarray.jl:403 falses 1╎ ╎ ╎ 15 @Base/bitarray.jl:405 falses 1╎ ╎ ╎ 1 @Base/array.jl:0 fill!(B::BitVector, x::Bool) ╎ ╎ ╎ 13 @Base/bitarray.jl:71 BitArray ╎ ╎ ╎ ╎ 12 @Base/bitarray.jl:37 BitArray ╎ ╎ ╎ ╎ 3 @Base/boot.jl:648 Array 3╎ ╎ ╎ ╎ 3 @Base/boot.jl:588 GenericMemory 9╎ ╎ ╎ ╎ 9 @Base/boot.jl:649 Array 1╎ ╎ ╎ ╎ 1 @Base/bitarray.jl:39 BitArray ╎ ╎ ╎ 1 @CrystalNets/…on.jl:729 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 1 @Base/bitarray.jl:682 getindex ╎ ╎ ╎ 1 @Base/bitarray.jl:676 unsafe_bitgetindex 1╎ ╎ ╎ 1 @Base/…sentials.jl:967 getindex ╎ ╎ ╎ 1 @CrystalNets/…on.jl:732 translation_to_direct_map(shrunk_pv… 1╎ ╎ ╎ 1 @Base/…sentials.jl:967 getindex ╎ ╎ ╎ 1 @CrystalNets/…on.jl:733 translation_to_direct_map(shrunk_pv… ╎ ╎ ╎ 1 @Base/…sentials.jl:966 getindex ╎ ╎ ╎ 1 @Base/…sentials.jl:387 checkbounds 1╎ ╎ ╎ 1 @Base/…sentials.jl:383 checkbounds wait at ./task.jl:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_70431.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2375 [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 0x00007e8c23b111e0 Total snapshots: 445. Utilization: 0% ╎445 @Base/task.jl:1129 wait_forever() 444╎ 445 @Base/task.jl:1192 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 wait at ./task.jl:1192 wait_forever at ./task.jl:1129 jfptr_wait_forever_70431.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2375 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) Allocations: 21307974 (Pool: 21307446; Big: 528); GC: 19 [27] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/CrystalNets/vvGQH/test/runtests.jl:403 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_process_events at /source/src/jl_uv.c:397 process_events at ./libuv.jl:133 [inlined] wait at ./task.jl:1180 yield at ./task.jl:1034 translation_to_direct_map at /home/pkgeval/.julia/packages/CrystalNets/vvGQH/src/minimization.jl:673 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: 0x730cc41d2fd2) at (unknown file) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 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: 0x730cc0d0c372) at (unknown file) _jl_invoke at /source/src/gf.c:4015 [inlined] ijl_apply_generic at /source/src/gf.c:4212 jl_apply at /source/src/julia.h:2375 [inlined] start_task at /source/src/task.c:1253 unknown function (ip: (nil)) at (unknown file) Allocations: 2505218177 (Pool: 2505214309; Big: 3868); GC: 652 PkgEval terminated after 2722.43s: test duration exceeded the time limit