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Update Sundials to include arkode - #3453

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WardBrian merged 4 commits into
developfrom
vendor-arkode
Oct 14, 2026
Merged

WardBrian merged 4 commits into
developfrom
vendor-arkode

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@SteveBronder

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Summary

This breaks up #3357 into two PRs. This PR just does the vendoring to add arkode from sundials and another PR will do the stan math changes to remove the use of boosts ode solvers

Tests

Update of a dependency so no new tests.

Release notes

Updates sundials dependency to add arkode

Checklist

  • Copyright holder: Andrew Johnson and Simons Foundation

    The copyright holder is typically you or your assignee, such as a university or company. By submitting this pull request, the copyright holder is agreeing to the license the submitted work under the following licenses:
    - Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
    - Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

  • the basic tests are passing

    • unit tests pass (to run, use: ./runTests.py test/unit)
    • header checks pass, (make test-headers)
    • dependencies checks pass, (make test-math-dependencies)
    • docs build, (make doxygen)
    • code passes the built in C++ standards checks (make cpplint)
  • the code is written in idiomatic C++ and changes are documented in the doxygen

  • the new changes are tested

Stop pruning */arkode when upgrading sundials so ARKODE is vendored
alongside CVODES, IDAS and KINSOL. ARKODE's XBraid interface is still
pruned, as it requires an external XBraid installation.
Adds the ARKODE sources produced by lib/upgrade-sundials.sh. No files
are modified by hand; src/arkode/xbraid is pruned by the script.
The generated header guards its deprecation block with `#if 0`, which
trips readability-avoid-unconditional-preprocessor-if.
Compile the vendored ARKODE sources into libsundials_arkode.a, add it to
SUNDIALS_TARGETS and clean-sundials, and make *arkode*.hpp headers depend
on the sundials targets so they are built before anything includes them.
@SteveBronder SteveBronder added the dependencies Pull requests that update a dependency file label Oct 13, 2026
@SteveBronder SteveBronder self-assigned this Oct 13, 2026
@SteveBronder
SteveBronder added this pull request to stack #3455 October 13, 2026 16:54
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Name Old Result New Result Ratio Performance change( 1 - new / old )
stat_comp_benchmarks/benchmarks/gp_regr/gp_regr.stan 0.23 0.22 1.0 0.44% faster
stat_comp_benchmarks/benchmarks/gp_regr/gen_gp_data.stan 0.06 0.06 1.0 0.41% faster
stat_comp_benchmarks/benchmarks/low_dim_corr_gauss/low_dim_corr_gauss.stan 0.02 0.02 0.96 -4.18% slower
stat_comp_benchmarks/benchmarks/arma/arma.stan 0.61 0.61 1.0 0.48% faster
stat_comp_benchmarks/benchmarks/arK/arK.stan 3.18 3.18 1.0 0.23% faster
stat_comp_benchmarks/benchmarks/pkpd/one_comp_mm_elim_abs.stan 43.2 42.84 1.01 0.85% faster
stat_comp_benchmarks/benchmarks/pkpd/sim_one_comp_mm_elim_abs.stan 0.57 0.58 0.99 -0.8% slower
stat_comp_benchmarks/benchmarks/gp_pois_regr/gp_pois_regr.stan 4.49 4.43 1.01 1.36% faster
stat_comp_benchmarks/benchmarks/low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 20.95 20.94 1.0 0.05% faster
stat_comp_benchmarks/benchmarks/garch/garch.stan 0.89 0.89 1.0 0.42% faster
stat_comp_benchmarks/benchmarks/eight_schools/eight_schools.stan 0.11 0.11 1.02 1.53% faster
stat_comp_benchmarks/benchmarks/irt_2pl/irt_2pl.stan 8.37 8.24 1.02 1.48% faster
stat_comp_benchmarks/benchmarks/low_dim_gauss_mix/low_dim_gauss_mix.stan 6.42 6.34 1.01 1.29% faster
stat_comp_benchmarks/benchmarks/sir/sir.stan 169.93 169.09 1.0 0.49% faster
performance.compilation 372.99 398.19 0.94 -6.76% slower
Mean result: 0.998670721000148

Jenkins Console Log
Jenkins Build Stages
Commit hash: a827cdd3e0feedf2727b243d86681a6a8e0fd2ba

Machine information
Distributor ID:	Ubuntu
Description:	Ubuntu 20.04.3 LTS
Release:	20.04
Codename:	focal

CPU:

Architecture:                            x86_64
CPU op-mode(s):                          32-bit, 64-bit
Byte Order:                              Little Endian
Address sizes:                           43 bits physical, 48 bits virtual
CPU(s):                                  256
On-line CPU(s) list:                     0-255
Thread(s) per core:                      2
Core(s) per socket:                      64
Socket(s):                               2
NUMA node(s):                            2
Vendor ID:                               AuthenticAMD
CPU family:                              23
Model:                                   49
Model name:                              AMD EPYC 7742 64-Core Processor
Stepping:                                0
Frequency boost:                         enabled
CPU MHz:                                 1497.969
CPU max MHz:                             3416.0681
CPU min MHz:                             1500.0000
BogoMIPS:                                4491.56
Virtualization:                          AMD-V
L1d cache:                               4 MiB
L1i cache:                               4 MiB
L2 cache:                                64 MiB
L3 cache:                                512 MiB
NUMA node0 CPU(s):                       0-63,128-191
NUMA node1 CPU(s):                       64-127,192-255
Vulnerability Gather data sampling:      Not affected
Vulnerability Indirect target selection: Not affected
Vulnerability Itlb multihit:             Not affected
Vulnerability L1tf:                      Not affected
Vulnerability Mds:                       Not affected
Vulnerability Meltdown:                  Not affected
Vulnerability Mmio stale data:           Not affected
Vulnerability Old microcode:             Not affected
Vulnerability Reg file data sampling:    Not affected
Vulnerability Retbleed:                  Mitigation; untrained return thunk; SMT enabled with STIBP protection
Vulnerability Spec rstack overflow:      Mitigation; Safe RET
Vulnerability Spec store bypass:         Mitigation; Speculative Store Bypass disabled via prctl
Vulnerability Spectre v1:                Mitigation; usercopy/swapgs barriers and __user pointer sanitization
Vulnerability Spectre v2:                Mitigation; Retpolines; IBPB conditional; STIBP always-on; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected
Vulnerability Srbds:                     Not affected
Vulnerability Tsa:                       Not affected
Vulnerability Tsx async abort:           Not affected
Vulnerability Vmscape:                   Mitigation; IBPB before exit to userspace
Flags:                                   fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm constant_tsc rep_good nopl xtopology nonstop_tsc cpuid extd_apicid aperfmperf rapl pni pclmulqdq monitor ssse3 fma cx16 sse4_1 sse4_2 x2apic movbe popcnt aes xsave avx f16c rdrand lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs skinit wdt tce topoext perfctr_core perfctr_nb bpext perfctr_llc mwaitx cpb cat_l3 cdp_l3 hw_pstate ssbd mba ibrs ibpb stibp vmmcall fsgsbase bmi1 avx2 smep bmi2 cqm rdt_a rdseed adx smap clflushopt clwb sha_ni xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local clzero irperf xsaveerptr rdpru wbnoinvd amd_ppin arat npt lbrv svm_lock nrip_save tsc_scale vmcb_clean flushbyasid decodeassists pausefilter pfthreshold avic v_vmsave_vmload vgif v_spec_ctrl umip rdpid overflow_recov succor smca sev sev_es

G++:

g++ (Ubuntu 9.4.0-1ubuntu1~20.04) 9.4.0
Copyright (C) 2019 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Clang:

clang version 10.0.0-4ubuntu1 
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin

@WardBrian
WardBrian merged commit d12f488 into develop Oct 14, 2026
63 of 64 checks passed
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3 participants