Package evaluation of CrystalNets on Julia 1.13.0-DEV.421 (07dbfc665a*) started at 2025-04-23T20:08:21.170 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.67s ################################################################################ # Installation # Installing CrystalNets... Resolving package versions... Updating `~/.julia/environments/v1.13/Project.toml` [7952bbbe] + CrystalNets v1.0.1 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 v4.16.0 [7952bbbe] + CrystalNets v1.0.1 [864edb3b] + DataStructures v0.18.22 [ffbed154] + DocStringExtensions v0.9.4 [86223c79] + Graphs v1.12.1 [d25df0c9] + Inflate v0.1.5 [692b3bcd] + JLLWrappers v1.7.0 [1914dd2f] + MacroTools v0.5.16 [bac558e1] + OrderedCollections v1.8.0 [f305370e] + PeriodicGraphEmbeddings v0.3.3 [72a2d4b8] + PeriodicGraphEquilibriumPlacement v0.2.2 [18c5b727] + PeriodicGraphs v0.10.3 [7b2266bf] + PeriodicTable v1.2.1 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [92933f4c] + ProgressMeter v1.10.4 [ae029012] + Requires v1.3.1 [699a6c99] + SimpleTraits v0.9.4 [90137ffa] + StaticArrays v1.9.13 [1e83bf80] + StaticArraysCore v1.4.3 [10745b16] + Statistics v1.11.1 [b718987f] + TextWrap v1.0.2 [0796e94c] + Tokenize v0.5.29 [1986cc42] + Unitful v1.22.0 [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 v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.12.0 [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 v1.12.0 [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 v8.12.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2024.12.31 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.0.16+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Installation completed after 4.21s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 365.96s ################################################################################ # Testing # Testing CrystalNets Status `/tmp/jl_zT9aPH/Project.toml` [861a8166] Combinatorics v1.0.2 [7952bbbe] CrystalNets v1.0.1 [86223c79] Graphs v1.12.1 [18c5b727] PeriodicGraphs v0.10.3 [90137ffa] StaticArrays v1.9.13 [9a3f8284] Random v1.11.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_zT9aPH/Manifest.toml` [c7e460c6] ArgParse v1.2.0 [ec485272] ArnoldiMethod v0.4.0 [a963bdd2] AtomsBase v0.5.1 [46823bd8] Chemfiles v0.10.42 [861a8166] Combinatorics v1.0.2 [34da2185] Compat v4.16.0 [7952bbbe] CrystalNets v1.0.1 [864edb3b] DataStructures v0.18.22 [ffbed154] DocStringExtensions v0.9.4 [86223c79] Graphs v1.12.1 [d25df0c9] Inflate v0.1.5 [692b3bcd] JLLWrappers v1.7.0 [1914dd2f] MacroTools v0.5.16 [bac558e1] OrderedCollections v1.8.0 [f305370e] PeriodicGraphEmbeddings v0.3.3 [72a2d4b8] PeriodicGraphEquilibriumPlacement v0.2.2 [18c5b727] PeriodicGraphs v0.10.3 [7b2266bf] PeriodicTable v1.2.1 [aea7be01] PrecompileTools v1.3.2 [21216c6a] Preferences v1.4.3 [92933f4c] ProgressMeter v1.10.4 [ae029012] Requires v1.3.1 [699a6c99] SimpleTraits v0.9.4 [90137ffa] StaticArrays v1.9.13 [1e83bf80] StaticArraysCore v1.4.3 [10745b16] Statistics v1.11.1 [b718987f] TextWrap v1.0.2 [0796e94c] Tokenize v0.5.29 [1986cc42] Unitful v1.22.0 [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 v1.12.0 [56ddb016] Logging v1.11.0 [d6f4376e] Markdown v1.11.0 [a63ad114] Mmap v1.11.0 [ca575930] NetworkOptions v1.3.0 [44cfe95a] Pkg v1.12.0 [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 v1.12.0 [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 v8.12.1+1 [e37daf67] LibGit2_jll v1.9.0+0 [29816b5a] LibSSH2_jll v1.11.3+1 [14a3606d] MozillaCACerts_jll v2024.12.31 [4536629a] OpenBLAS_jll v0.3.29+0 [458c3c95] OpenSSL_jll v3.0.16+0 [bea87d4a] SuiteSparse_jll v7.10.1+0 [83775a58] Zlib_jll v1.3.1+2 [8e850b90] libblastrampoline_jll v5.12.0+0 [8e850ede] nghttp2_jll v1.65.0+0 [3f19e933] p7zip_jll v17.5.0+2 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 16m46.5s [ 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 | 17492 17492 6m46.1s [ 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 51.3s Test Summary: | Pass Broken Total Time Executable | 29 1 30 9.9s 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 33 running 1 of 2 signal (10): User defined signal 1 __madvise at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) jl_gc_free_page at /source/src/gc-pages.c:199 gc_free_pages at /source/src/gc-stock.c:1319 gc_sweep_pool at /source/src/gc-stock.c:1451 [inlined] _jl_gc_collect at /source/src/gc-stock.c:3187 ijl_gc_collect at /source/src/gc-stock.c:3459 maybe_collect at /source/src/gc-stock.c:349 [inlined] jl_gc_small_alloc_inner at /source/src/gc-stock.c:725 ijl_gc_small_alloc at /source/src/gc-stock.c:774 Array at ./boot.jl:648 [inlined] BitArray at ./bitarray.jl:37 [inlined] BitArray at ./bitarray.jl:71 [inlined] falses at ./bitarray.jl:405 [inlined] falses at ./bitarray.jl:403 [inlined] translation_to_direct_map at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/minimization.jl:705 find_first_valid_translation_unstable at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/minimization.jl:805 minimize_unstable at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/minimization.jl:287 [inlined] minimize at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/minimization.jl:274 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/query.jl:34 unknown function (ip: 0x789924bdc2c2) at (unknown file) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/query.jl:153 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/query.jl:87 [inlined] #topological_genome#220 at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/query.jl:90 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/query.jl:90 [inlined] macro expansion at /home/pkgeval/.julia/packages/CrystalNets/0shPu/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: 0x7899178bc992) at (unknown file) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) unknown function (ip: 0x78994a55df14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:520 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30085.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 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 2 signal (10): User defined signal 1 unknown function (ip: 0x701c6ddfef14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:520 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30085.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) 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:454 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30085.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 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()`. â”” @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 Overhead â•Ž [+additional indent] Count File:Line Function ========================================================= Thread 1 (interactive) Task 0x000078993d1744c0 Total snapshots: 169. Utilization: 0% â•Ž169 @Base/task.jl:1150 wait_forever() 168â•Ž 169 @Base/task.jl:1216 wait() Thread 2 (default) Task 0x00007898a9cf8c40 Total snapshots: 169. Utilization: 100% â•Ž169 @Base/…dingconstructs.jl:177 (::Base.Threads.var"#threading_run##0#thre… â•Ž 169 @Base/…ingconstructs.jl:243 #49 â•Ž 169 @Base/…ingconstructs.jl:276 (::var"#49#50"{var"#51#52"{Int64, Int64, … â•Ž 169 …hPu/test/runtests.jl:539 macro expansion â•Ž 169 @CrystalNets/…query.jl:90 topological_genome â•Ž 169 @CrystalNets/…query.jl:90 #topological_genome#220 â•Ž â•Ž 169 @CrystalNets/…query.jl:87 topological_genome â•Ž â•Ž 169 @CrystalNets/…uery.jl:153 topological_genome(group::UnderlyingNe… â•Ž â•Ž 169 @CrystalNets/…uery.jl:34 topological_genome(net::CrystalNet2D{R… â•Ž â•Ž 169 @CrystalNets/…ion.jl:274 minimize â•Ž â•Ž 169 @CrystalNets/…ion.jl:287 minimize_unstable 2â•Ž â•Ž â•Ž 169 @CrystalNets/…on.jl:805 find_first_valid_translation_unstabl… 1â•Ž â•Ž â•Ž 1 @Base/boot.jl:0 translation_to_direct_map(shrunk_pvmap::Vec… 1â•Ž â•Ž â•Ž 1 @CrystalNets/…on.jl:0 translation_to_direct_map(shrunk_pvma… â•Ž â•Ž â•Ž 100 @CrystalNets/…on.jl:673 translation_to_direct_map(shrunk_pv… 1â•Ž â•Ž â•Ž 1 @Base/task.jl:1194 wait() â•Ž â•Ž â•Ž 12 @Base/task.jl:1053 yield() â•Ž â•Ž â•Ž 1 @Base/task.jl:963 enq_work(t::Task) â•Ž â•Ž â•Ž 1 @Base/task.jl:258 threadpool 1â•Ž â•Ž â•Ž â•Ž 1 @Base/…nstructs.jl:68 _tpid_to_sym â•Ž â•Ž â•Ž 1 @Base/task.jl:964 enq_work(t::Task) 1â•Ž â•Ž â•Ž 1 @Base/…nstructs.jl:137 threadpoolsize 1â•Ž â•Ž â•Ž 9 @Base/task.jl:969 enq_work(t::Task) 1â•Ž â•Ž â•Ž 1 @Base/task.jl:867 push!(W::Base.IntrusiveLinkedListSynch… â•Ž â•Ž â•Ž 1 @Base/task.jl:868 push!(W::Base.IntrusiveLinkedListSynch… â•Ž â•Ž â•Ž â•Ž 1 @Base/locks-mt.jl:43 lock(l::Base.Threads.SpinLock) â•Ž â•Ž â•Ž â•Ž 1 @Base/locks-mt.jl:56 trylock 1â•Ž â•Ž â•Ž â•Ž 1 @Base/…motion.jl:632 == 1â•Ž â•Ž â•Ž 1 @Base/task.jl:869 push!(W::Base.IntrusiveLinkedListSynch… â•Ž â•Ž â•Ž 2 @Base/task.jl:870 push!(W::Base.IntrusiveLinkedListSynch… â•Ž â•Ž â•Ž â•Ž 1 @Base/…ked_list.jl:0 push! 1â•Ž â•Ž â•Ž â•Ž 1 @Base/…ompiler.jl:58 setproperty! â•Ž â•Ž â•Ž â•Ž 1 @Base/…ked_list.jl:55 push! 1â•Ž â•Ž â•Ž â•Ž 1 @Base/…ompiler.jl:54 getproperty â•Ž â•Ž â•Ž 1 @Base/task.jl:872 push!(W::Base.IntrusiveLinkedListSynch… â•Ž â•Ž â•Ž â•Ž 1 @Base/locks-mt.jl:68 unlock 1â•Ž â•Ž â•Ž â•Ž 1 @Base/gcutils.jl:160 enable_finalizers 1â•Ž â•Ž â•Ž 1 @Base/task.jl:916 workqueue_for(tid::Int64) 1â•Ž â•Ž â•Ž 1 @Base/task.jl:917 workqueue_for(tid::Int64) 1â•Ž â•Ž â•Ž 1 @Base/task.jl:976 enq_work(t::Task) 1â•Ž â•Ž â•Ž 1 @Base/task.jl:1054 yield() 3â•Ž â•Ž â•Ž 86 @Base/task.jl:1055 yield() â•Ž â•Ž â•Ž 76 @Base/task.jl:1201 wait() 75â•Ž â•Ž â•Ž 76 @Base/libuv.jl:125 process_events â•Ž â•Ž â•Ž 2 @Base/task.jl:1206 wait() 1â•Ž â•Ž â•Ž 1 @Base/task.jl:916 workqueue_for(tid::Int64) 1â•Ž â•Ž â•Ž 1 @Base/task.jl:917 workqueue_for(tid::Int64) â•Ž â•Ž â•Ž 2 @Base/task.jl:1207 wait() â•Ž â•Ž â•Ž 2 @Base/task.jl:1177 trypoptask(W::Base.IntrusiveLinkedLis… 1â•Ž â•Ž â•Ž â•Ž 1 @Base/task.jl:893 popfirst!(W::Base.IntrusiveLinkedList… â•Ž â•Ž â•Ž â•Ž 1 @Base/task.jl:894 popfirst!(W::Base.IntrusiveLinkedList… â•Ž â•Ž â•Ž â•Ž 1 @Base/locks-mt.jl:43 lock(l::Base.Threads.SpinLock) â•Ž â┌ 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()`. â”” @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362 •Ž â•Ž â•Ž 1 @Base/locks-mt.jl:56 trylock 1â•Ž â•Ž â•Ž â•Ž 1 @Base/…motion.jl:632 == 1â•Ž â•Ž â•Ž 3 @Base/task.jl:1225 wait() 1â•Ž â•Ž â•Ž 1 @Base/task.jl:1113 try_yieldto(undo::typeof(Base.ensure_… 1â•Ž â•Ž â•Ž 1 @Base/task.jl:1114 try_yieldto(undo::typeof(Base.ensure_… â•Ž â•Ž â•Ž 2 @CrystalNets/…on.jl:675 translation_to_direct_map(shrunk_pv… 2â•Ž â•Ž â•Ž 2 @Base/…sentials.jl:952 getindex â•Ž â•Ž â•Ž 1 @CrystalNets/…on.jl:677 translation_to_direct_map(shrunk_pv… 1â•Ž â•Ž â•Ž 1 @Base/…sentials.jl:953 getindex â•Ž â•Ž â•Ž 1 @CrystalNets/…on.jl:678 translation_to_direct_map(shrunk_pv… â•Ž â•Ž â•Ž 1 @CrystalNets/…ty.jl:81 getindex 1â•Ž â•Ž â•Ž 1 @Base/…sentials.jl:953 getindex â•Ž â•Ž â•Ž 2 @CrystalNets/…on.jl:682 translation_to_direct_map(shrunk_pv… â•Ž â•Ž â•Ž 2 @CrystalNets/…n.jl:593 backtrack_to!(vmapprogress::Vector{… 1â•Ž â•Ž â•Ž 1 @Base/array.jl:0 attribute_next_available_modify!(vmappro… â•Ž â•Ž â•Ž 1 @CrystalNets/…n.jl:558 attribute_next_available_modify!(v… 1â•Ž â•Ž â•Ž 1 @CrystalNets/…n.jl:538 find_necessary_image â•Ž â•Ž â•Ž 1 @CrystalNets/…on.jl:687 translation_to_direct_map(shrunk_pv… â•Ž â•Ž â•Ž 1 @Graphs/…c/core.jl:132 degree â•Ž â•Ž â•Ž 1 @Graphs/…c/core.jl:100 outdegree â•Ž â•Ž â•Ž 1 @PeriodicGraphs/…l:58 outneighbors 1â•Ž â•Ž â•Ž â•Ž 1 @Base/…entials.jl:953 getindex â•Ž â•Ž â•Ž 29 @CrystalNets/…on.jl:695 translation_to_direct_map(shrunk_pv… â•Ž â•Ž â•Ž 2 @Base/array.jl:790 collect(itr::Base.Generator{Vector{Peri… â•Ž â•Ž â•Ž 1 @Base/generator.jl:45 iterate â•Ž â•Ž â•Ž 1 @Base/array.jl:901 iterate â•Ž â•Ž â•Ž â•Ž 1 @Base/array.jl:901 iterate 1â•Ž â•Ž â•Ž â•Ž 1 @Base/…entials.jl:953 getindex â•Ž â•Ž â•Ž 1 @Base/generator.jl:48 iterate â•Ž â•Ž â•Ž 1 @CrystalNets/…n.jl:697 #translation_to_direct_map##0 1â•Ž â•Ž â•Ž â•Ž 1 @Base/…entials.jl:953 getindex â•Ž â•Ž â•Ž 20 @Base/array.jl:795 collect(itr::Base.Generator{Vector{Peri… â•Ž â•Ž â•Ž 20 @Base/array.jl:670 _array_for â•Ž â•Ž â•Ž 20 @Base/…actarray.jl:871 similar â•Ž â•Ž â•Ž â•Ž 20 @Base/…ctarray.jl:872 similar â•Ž â•Ž â•Ž â•Ž 20 @Base/boot.jl:660 Array â•Ž â•Ž â•Ž â•Ž 15 @Base/boot.jl:647 Array 15â•Ž â•Ž â•Ž â•Ž 15 @Base/boot.jl:588 GenericMemory 5â•Ž â•Ž â•Ž â•Ž 5 @Base/boot.jl:648 Array â•Ž â•Ž â•Ž 6 @Base/array.jl:800 collect(itr::Base.Generator{Vector{Peri… â•Ž â•Ž â•Ž 6 @Base/array.jl:826 collect_to_with_first! 1â•Ž â•Ž â•Ž 1 @Base/array.jl:0 collect_to! â•Ž â•Ž â•Ž 4 @Base/array.jl:848 collect_to! â•Ž â•Ž â•Ž â•Ž 1 @Base/generator.jl:45 iterate 1â•Ž â•Ž â•Ž â•Ž 1 @Base/array.jl:0 iterate â•Ž â•Ž â•Ž â•Ž 3 @Base/generator.jl:48 iterate â•Ž â•Ž â•Ž â•Ž 1 @CrystalNets/….jl:697 #translation_to_direct_map##0 1â•Ž â•Ž â•Ž â•Ž 1 @Base/…ntials.jl:952 getindex â•Ž â•Ž â•Ž â•Ž 1 @CrystalNets/….jl:698 #translation_to_direct_map##0 1â•Ž â•Ž â•Ž â•Ž 1 @Base/int.jl:87 + â•Ž â•Ž â•Ž â•Ž 1 @CrystalNets/….jl:699 #translation_to_direct_map##0 1â•Ž â•Ž â•Ž â•Ž 1 @Base/…ntials.jl:952 getindex â•Ž â•Ž â•Ž 1 @Base/array.jl:852 collect_to! â•Ž â•Ž â•Ž â•Ž 1 @Base/array.jl:986 setindex! 1â•Ž â•Ž â•Ž â•Ž 1 @Base/array.jl:991 _setindex! 1â•Ž â•Ž â•Ž 1 @Base/…sentials.jl:0 collect(itr::Base.Generator{Vector{Pe… â•Ž â•Ž â•Ž 5 @CrystalNets/…on.jl:703 translation_to_direct_map(shrunk_pv… â•Ž â•Ž â•Ž 5 @Base/sort.jl:1730 sort! â•Ž â•Ž â•Ž 5 @Base/sort.jl:1737 #sort!#23 â•Ž â•Ž â•Ž 5 @Base/sort.jl:1591 _sort! â•Ž â•Ž â•Ž â•Ž 5 @Base/sort.jl:561 _sort! â•Ž â•Ž â•Ž â•Ž 5 @Base/sort.jl:683 _sort! â•Ž â•Ž â•Ž â•Ž 5 @Base/sort.jl:744 _sort! â•Ž â•Ž â•Ž â•Ž 5 @Base/sort.jl:797 _sort!(v::Vector{PeriodicVertex2D}… 1â•Ž â•Ž â•Ž â•Ž 1 @Base/sort.jl:834 _sort!(v::Vector{PeriodicVertex2D… â•Ž â•Ž â•Ž â•Ž 1 @Base/sort.jl:836 _sort!(v::Vector{PeriodicVertex2D… 1â•Ž â•Ž â•Ž â•Ž â•Ž 1 @Base/int.jl:87 + â•Ž â•Ž â•Ž â•Ž 1 @Base/sort.jl:840 _sort!(v::Vector{PeriodicVertex2D… â•Ž â•Ž â•Ž â•Ž â•Ž 1 @Base/…ators.jl:425 > 1â•Ž â•Ž â•Ž â•Ž â•Ž 1 @Base/int.jl:83 < â•Ž â•Ž â•Ž â•Ž 1 @Base/sort.jl:842 _sort!(v::Vector{PeriodicVertex2D… â•Ž â•Ž â•Ž â•Ž â•Ž 1 @Base/…ering.jl:120 lt â•Ž â•Ž â•Ž â•Ž â•Ž 1 @Base/…ering.jl:118 lt â•Ž â•Ž â•Ž â•Ž â•Ž 1 @PeriodicGraphs/…:54 isless 1â•Ž â•Ž â•Ž â•Ž â•Ž 1 @PeriodicGraphs/…:51 cmp â•Ž â•Ž â•Ž â•Ž 1 @Base/sort.jl:845 _sort!(v::Vector{PeriodicVertex2D… â•Ž â•Ž â•Ž â•Ž â•Ž 1 @Base/array.jl:986 setindex! 1â•Ž â•Ž â•Ž â•Ž â•Ž 1 @Base/array.jl:991 _setindex! â•Ž â•Ž â•Ž 1 @CrystalNets/…on.jl:704 translation_to_direct_map(shrunk_pv… â•Ž â•Ž â•Ž 1 @Base/some.jl:158 macro expansion â•Ž â•Ž â•Ž 1 @Base/array.jl:2441 findfirst â•Ž â•Ž â•Ž 1 @Base/array.jl:2390 findnext 1â•Ž â•Ž â•Ž â•Ž 1 @Base/…entials.jl:952 getindex â•Ž â•Ž â•Ž 6 @CrystalNets/…on.jl:705 translation_to_direct_map(shrunk_pv… â•Ž â•Ž â•Ž 6 @Base/bitarray.jl:403 falses â•Ž â•Ž â•Ž 6 @Base/bitarray.jl:405 falses â•Ž â•Ž â•Ž 6 @Base/bitarray.jl:71 BitArray â•Ž â•Ž â•Ž â•Ž 6 @Base/bitarray.jl:37 BitArray â•Ž â•Ž â•Ž â•Ž 1 @Base/boot.jl:647 Array 1â•Ž â•Ž â•Ž â•Ž 1 @Base/boot.jl:588 GenericMemory 5â•Ž â•Ž â•Ž â•Ž 5 @Base/boot.jl:648 Array â•Ž â•Ž â•Ž 1 @CrystalNets/…on.jl:709 translation_to_direct_map(shrunk_pv… 1â•Ž â•Ž â•Ž 1 @Base/…sentials.jl:953 getindex 1â•Ž â•Ž â•Ž 3 @CrystalNets/…on.jl:711 translation_to_direct_map(shrunk_pv… â•Ž â•Ž â•Ž 2 @Base/bitarray.jl:682 getindex â•Ž â•Ž â•Ž 2 @Base/bitarray.jl:676 unsafe_bitgetindex 2â•Ž â•Ž â•Ž 2 @Base/…sentials.jl:953 getindex â•Ž â•Ž â•Ž 12 @CrystalNets/…on.jl:726 translation_to_direct_map(shrunk_pv… â•Ž â•Ž â•Ž 12 @Base/bitarray.jl:403 falses â•Ž â•Ž â•Ž 12 @Base/bitarray.jl:405 falses 2â•Ž â•Ž â•Ž 2 @Base/array.jl:0 fill!(B::BitVector, x::Bool) â•Ž â•Ž â•Ž 10 @Base/bitarray.jl:71 BitArray â•Ž â•Ž â•Ž â•Ž 9 @Base/bitarray.jl:37 BitArray â•Ž â•Ž â•Ž â•Ž 3 @Base/boot.jl:647 Array 3â•Ž â•Ž â•Ž â•Ž 3 @Base/boot.jl:588 GenericMemory 5â•Ž â•Ž â•Ž â•Ž 6 @Base/boot.jl:648 Array 1â•Ž â•Ž â•Ž â•Ž 1 @Base/boot.jl:593 memoryref 1â•Ž â•Ž â•Ž â•Ž 1 @Base/bitarray.jl:39 BitArray â•Ž â•Ž â•Ž 1 @CrystalNets/…on.jl:751 translation_to_direct_map(shrunk_pv… â•Ž â•Ž â•Ž 1 @CrystalNets/…ty.jl:81 getindex 1â•Ž â•Ž â•Ž 1 @Base/…sentials.jl:953 getindex [1] signal 15: Terminated in expression starting at /PkgEval.jl/scripts/evaluate.jl:210 _jl_mutex_wait at /source/src/threading.c:970 _jl_mutex_lock at /source/src/threading.c:998 jl_mutex_lock at /source/src/julia_locks.h:65 [inlined] JL_UV_LOCK at /source/src/jl_uv.c:137 [inlined] ijl_iolock_begin at /source/src/jl_uv.c:147 [33] signal 15: Terminated in expression starting at /home/pkgeval/.julia/packages/CrystalNets/0shPu/test/runtests.jl:403 Overhead â•Ž [+additional indent] Count File:Line Function ========================================================= Thread 1 (interactive) Task 0x0000701c61993b20 Total snapshots: 217. Utilization: 0% â•Ž217 @Base/task.jl:1150 wait_forever() 216â•Ž 217 @Base/task.jl:1216 wait() Thread 2 (default) Task 0x0000701c63dfc100 Total snapshots: 217. Utilization: 0% â•Ž217 @Base/task.jl:1150 wait_forever() 216â•Ž 217 @Base/task.jl:1216 wait() == at ./promotion.jl:632 [inlined] unlock at ./locks-mt.jl:65 [inlined] popfirst! at ./task.jl:898 iolock_begin at ./libuv.jl:48 [inlined] uv_write at ./stream.jl:1086 unsafe_write at ./stream.jl:1154 unsafe_write at ./io.jl:803 [inlined] write at ./io.jl:837 unknown function (ip: 0x701c64513796) at (unknown file) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 macro expansion at ./lock.jl:376 [inlined] #handle_message#6 at ./logging/ConsoleLogger.jl:194 trypoptask at ./task.jl:1177 handle_message at ./logging/ConsoleLogger.jl:110 unknown function (ip: 0x701c6450e7ed) at (unknown file) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 apply_gr at ./reflection.jl:1278 _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 wait at ./task.jl:1207 jl_apply at /source/src/julia.h:2353 [inlined] jl_f_invokelatest at /source/src/builtins.c:854 yield at ./task.jl:1055 translation_to_direct_map at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/minimization.jl:673 find_first_valid_translation_unstable at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/minimization.jl:805 minimize_unstable at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/minimization.jl:287 [inlined] minimize at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/minimization.jl:274 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/query.jl:34 unknown function (ip: 0x789924bdc2c2) at (unknown file) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/query.jl:153 topological_genome at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/query.jl:87 [inlined] #topological_genome#220 at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/query.jl:90 [inlined] topological_genome at /home/pkgeval/.julia/packages/CrystalNets/0shPu/src/query.jl:90 [inlined] macro expansion at /home/pkgeval/.julia/packages/CrystalNets/0shPu/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: 0x7899178bc992) at (unknown file) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 #invokelatest_gr#234 at ./reflection.jl:0 [inlined] invokelatest_gr at ./reflection.jl:1281 [inlined] #handle_message_nothrow#2 at ./logging/logging.jl:428 jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) unknown function (ip: 0x78994a55df14) at /lib/x86_64-linux-gnu/libc.so.6 pthread_cond_wait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line) uv_cond_wait at /workspace/srcdir/libuv/src/unix/thread.c:822 ijl_task_get_next at /source/src/scheduler.c:520 handle_message_nothrow at ./logging/logging.jl:425 _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_invoke at /source/src/gf.c:3505 tojlinvoke3008.1 at /opt/julia/share/julia/compiled/v1.13/Profile/nGhxz_X6ROR.so (unknown line) macro expansion at ./logging/logging.jl:355 [inlined] #warning_empty#40 at /source/usr/share/julia/stdlib/v1.13/Profile/src/Profile.jl:0 wait at ./task.jl:1216 warning_empty at /source/usr/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1360 [inlined] #print#5 at /source/usr/share/julia/stdlib/v1.13/Profile/src/Profile.jl:358 print at /source/usr/share/julia/stdlib/v1.13/Profile/src/Profile.jl:271 [inlined] print at /source/usr/share/julia/stdlib/v1.13/Profile/src/Profile.jl:271 [inlined] print at /source/usr/share/julia/stdlib/v1.13/Profile/src/Profile.jl:271 _peek_report at /source/usr/share/julia/stdlib/v1.13/Profile/src/Profile.jl:94 jfptr__peek_report_2847.1 at /opt/julia/share/julia/compiled/v1.13/Profile/nGhxz_X6ROR.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jl_apply at /source/src/julia.h:2353 [inlined] jl_f_invokelatest at /source/src/builtins.c:854 wait_forever at ./task.jl:1150 profile_printing_listener at ./Base.jl:331 jfptr_wait_forever_30085.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 2264471019 (Pool: 2264467805; Big: 3214); GC: 657 #start_profile_listener##0 at ./Base.jl:349 jfptr_YY.start_profile_listenerYY.YY.0_16198.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) 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:454 wait at ./task.jl:1216 wait_forever at ./task.jl:1150 jfptr_wait_forever_30085.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:3498 [inlined] ijl_apply_generic at /source/src/gf.c:3698 jl_apply at /source/src/julia.h:2353 [inlined] start_task at /source/src/task.c:1249 unknown function (ip: (nil)) at (unknown file) Allocations: 21338305 (Pool: 21337831; Big: 474); GC: 22 PkgEval terminated after 2730.08s: test duration exceeded the time limit