Use Perfect Forwarding in all functions that use `apply` family of functors by SteveBronder · Pull Request #3221 · stan-dev/math

SteveBronder · 2025-07-11T20:42:30Z

Summary

This fixes #3208 by using perfect forwarding for all functions that use our underlying apply family of functions for calling functions on containers and containers and containers. The issue was that the Holder class, when used in the apply functors, did not have enough type information to know which arguments it should take ownership of.

Consider the following function, where all types are passed in via constant reference.

template <typename T1, typename T2, require_any_container_t<T1, T2>* = nullptr>
inline auto gamma_p(const T1& a, const T2& b) {
  return apply_scalar_binary(
      [](const auto& c, const auto& d) { return gamma_p(c, d); }, a, b);
}

Calling this function with an Eigen expression that has a temporary in it would not give apply_scalar_binary and the Holder inside of apply_scalar_binary enough information to know that the Holder class should own any of the input arguments. As an example we can look at a simplified version of the code used in poisson_lccdf.hpp.

auto log_Pi = log(gamma_p(n_val + 1.0, lambda_val)));
double log_sum = sum(log_Pi);

gamma_p uses apply_scalar_binary and log uses apply_scalar_unary. We need to make sure the inputs and results of the gamma_p function do not fall out of scope by the time we go through log and then assign to log_Pi. Before this PR it would be possible for the expression n_val + 1.0 to fall out of scope as well as the result of gamma_p to go out of scope from log after log_Pi is assigned.

To combat this we now use perfect forwarding for all of the functions that use our internal apply family of functors. This should allow the Holder used internally by the apply functors to know which types need to be owned by it to make sure things do not fall out of scope.

Tests

There is no new tests for this. Since it is an isue on gcc I do wonder how we should test this in our CI/CD?

Side Effects

I'd like to think of some test we can write so that, in the future, developers do not accidentally write functions that use the apply family of functors that do not use perfect forwarding.

Release notes

Adds perfect forwarding to all functions that use the apply family of functors.

Checklist

Copyright holder: Steve Bronder

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

WardBrian · 2025-07-14T16:12:46Z

@SteveBronder anything I can do to help this over the line?

SteveBronder · 2025-07-14T19:29:42Z

Right now it is just making sure the tests pass. I think I got it so we should be good!

WardBrian

Gonna leave the proper review to @andrjohns, just two things that stood out

stan/math/prim/core/complex_base.hpp

Jenkinsfile

… and O2

WardBrian · 2025-07-15T13:50:28Z

Math pipeline looks good, upstream has some (I believe legitimate) failures. All seem to blame trigamma in some way or another


--- Compiling C++ code ---
clang++-6.0 -std=c++17 -D_REENTRANT -Wno-sign-compare -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2020.3/include    -O0 -I src -I stan/src -I stan/lib/rapidjson_1.1.0/ -I lib/CLI11-1.9.1/ -I stan/lib/stan_math/ -I stan/lib/stan_math/lib/eigen_3.4.0 -I stan/lib/stan_math/lib/boost_1.87.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials    -DBOOST_DISABLE_ASSERTS          -c -include-pch stan/src/stan/model/model_header.hpp.gch/model_header_4_2.hpp.gch -x c++ -o ../stanc3/test/integration/good/stanc_helper.o ../stanc3/test/integration/good/stanc_helper.hpp
In file included from ../stanc3/test/integration/good/int_overloads.hpp:1:
In file included from stan/src/stan/model/model_header.hpp:6:
In file included from /home/jenkins/workspace/Stan_Stan_downstream_tests/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
In file included from /home/jenkins/workspace/Stan_Stan_downstream_tests/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:11:
In file included from /home/jenkins/workspace/Stan_Stan_downstream_tests/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/rev/constraint.hpp:24:
In file included from /home/jenkins/workspace/Stan_Stan_downstream_tests/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/prim/constraint.hpp:4:
In file included from /home/jenkins/workspace/Stan_Stan_downstream_tests/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/prim/fun.hpp:335:
/home/jenkins/workspace/Stan_Stan_downstream_tests/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/prim/fun/trigamma.hpp:142:12: error: function 'trigamma<stan::math::var_value<double, void> &, nullptr>' with deduced return type cannot be used before it is defined
    return trigamma(std::forward<T>(x));
           ^
/home/jenkins/workspace/Stan_Stan_downstream_tests/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/rev/functor/apply_scalar_unary.hpp:34:15: note: in instantiation of function template specialization 'stan::math::trigamma_fun::fun<stan::math::var_value<double, void> &>' requested here
    return F::fun(std::forward<T2>(x));
              ^
/home/jenkins/workspace/Stan_Stan_downstream_tests/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/prim/fun/trigamma.hpp:159:47: note: in instantiation of function template specialization 'stan::math::apply_scalar_unary<stan::math::trigamma_fun, stan::math::var_value<double, void> &, void>::apply<stan::math::var_value<double, void> &>' requested here
  return apply_scalar_unary<trigamma_fun, T>::apply(std::forward<T>(x));
                                              ^
../stanc3/test/integration/good/int_overloads.hpp:521:44: note: in instantiation of function template specialization 'stan::math::trigamma<stan::math::var_value<double, void> &, nullptr>' requested here
      transformed_param_real = stan::math::trigamma(p_real);
                                           ^
../stanc3/test/integration/good/int_overloads.hpp:811:12: note: in instantiation of function template specialization 'int_overloads_model_namespace::int_overloads_model::log_prob_impl<false, false, Eigen::Matrix<stan::math::var_value<double, void>, -1, 1, 0, -1, 1>, Eigen::Matrix<int, -1, 1, 0, -1, 1>, nullptr, nullptr, nullptr>' requested here
    return log_prob_impl<propto__, jacobian__>(params_r, params_i, pstream);
           ^
/home/jenkins/workspace/Stan_Stan_downstream_tests/performance-tests-cmdstan/cmdstan/stan/src/stan/model/model_base_crtp.hpp:98:50: note: in instantiation of function template specialization 'int_overloads_model_namespace::int_overloads_model::log_prob<false, false, stan::math::var_value<double, void> >' requested here
    return static_cast<const M*>(this)->template log_prob<false, false>(theta,
                                                 ^
../stanc3/test/integration/good/int_overloads.hpp:129:3: note: in instantiation of member function 'stan::model::model_base_crtp<int_overloads_model_namespace::int_overloads_model>::log_prob' requested here
  ~int_overloads_model() {}
  ^
/home/jenkins/workspace/Stan_Stan_downstream_tests/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/prim/fun/trigamma.hpp:158:13: note: 'trigamma<stan::math::var_value<double, void> &, nullptr>' declared here
inline auto trigamma(T&& x) {
            ^
1 error generated.
make: [make/program:77: ../stanc3/test/integration/good/int_overloads.o] Error 1 (ignored)

SteveBronder · 2025-07-15T15:18:59Z

Yes I missed one requires in trigamma

…ypes

stan-buildbot · 2025-08-01T20:21:09Z

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
arma/arma.stan	0.31	0.3	1.03	3.31% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.01	0.01	1.1	9.1% faster
gp_regr/gen_gp_data.stan	0.02	0.02	1.05	4.77% faster
gp_regr/gp_regr.stan	0.09	0.09	1.04	3.39% faster
sir/sir.stan	68.28	68.45	1.0	-0.25% slower
irt_2pl/irt_2pl.stan	4.0	4.03	0.99	-0.57% slower
eight_schools/eight_schools.stan	0.06	0.05	1.05	4.5% faster
pkpd/sim_one_comp_mm_elim_abs.stan	0.24	0.24	1.0	0.31% faster
pkpd/one_comp_mm_elim_abs.stan	19.33	18.78	1.03	2.82% faster
garch/garch.stan	0.43	0.41	1.06	5.54% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan	2.82	2.57	1.1	8.89% faster
arK/arK.stan	1.86	1.71	1.09	8.02% faster
gp_pois_regr/gp_pois_regr.stan	2.85	2.81	1.02	1.56% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	8.52	8.38	1.02	1.63% faster
performance.compilation	174.93	178.41	0.98	-1.99% slower
Mean result: 1.0364710339049357

Jenkins Console Log
Blue Ocean
Commit hash: e775f450bb86eacc0a0443dbaf4a36bc3407e56f

Machine information

No LSB modules are available. 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: 46 bits physical, 48 bits virtual
CPU(s): 80
On-line CPU(s) list: 0-79
Thread(s) per core: 2
Core(s) per socket: 20
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 85
Model name: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Stepping: 4
CPU MHz: 2400.000
CPU max MHz: 3700.0000
CPU min MHz: 1000.0000
BogoMIPS: 4800.00
Virtualization: VT-x
L1d cache: 1.3 MiB
L1i cache: 1.3 MiB
L2 cache: 40 MiB
L3 cache: 55 MiB
NUMA node0 CPU(s): 0,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78
NUMA node1 CPU(s): 1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79
Vulnerability Gather data sampling: Mitigation; Microcode
Vulnerability Itlb multihit: KVM: Mitigation: VMX disabled
Vulnerability L1tf: Mitigation; PTE Inversion; VMX conditional cache flushes, SMT vulnerable
Vulnerability Mds: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Meltdown: Mitigation; PTI
Vulnerability Mmio stale data: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Reg file data sampling: Not affected
Vulnerability Retbleed: Mitigation; IBRS
Vulnerability Spec rstack overflow: Not affected
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; IBRS; IBPB conditional; STIBP conditional; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected
Vulnerability Srbds: Not affected
Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT vulnerable
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti intel_ppin ssbd mba ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts hwp hwp_act_window hwp_epp hwp_pkg_req pku ospke md_clear flush_l1d arch_capabilities

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 · 2025-08-05T19:41:29Z

I'm running the distribution tests on this branch with all the tests enabled + -O3 + ASan here. It is almost done, and so far looks good

stan-buildbot · 2025-08-06T06:14:38Z

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
arma/arma.stan	0.31	0.32	0.98	-2.35% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.01	0.01	1.1	8.92% faster
gp_regr/gen_gp_data.stan	0.02	0.02	1.05	4.47% faster
gp_regr/gp_regr.stan	0.09	0.09	1.06	5.73% faster
sir/sir.stan	67.69	68.55	0.99	-1.27% slower
irt_2pl/irt_2pl.stan	4.0	3.99	1.0	0.33% faster
eight_schools/eight_schools.stan	0.05	0.05	1.02	1.88% faster
pkpd/sim_one_comp_mm_elim_abs.stan	0.24	0.25	0.97	-3.09% slower
pkpd/one_comp_mm_elim_abs.stan	19.06	18.68	1.02	1.99% faster
garch/garch.stan	0.43	0.4	1.07	6.25% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan	2.67	2.56	1.04	4.13% faster
arK/arK.stan	1.75	1.72	1.02	1.85% faster
gp_pois_regr/gp_pois_regr.stan	2.8	2.71	1.03	3.15% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	8.51	8.39	1.01	1.36% faster
performance.compilation	177.97	178.78	1.0	-0.45% slower
Mean result: 1.0235379783466787

Jenkins Console Log
Blue Ocean
Commit hash: e775f450bb86eacc0a0443dbaf4a36bc3407e56f

Machine information

No LSB modules are available. 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: 46 bits physical, 48 bits virtual
CPU(s): 80
On-line CPU(s) list: 0-79
Thread(s) per core: 2
Core(s) per socket: 20
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 85
Model name: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Stepping: 4
CPU MHz: 2400.000
CPU max MHz: 3700.0000
CPU min MHz: 1000.0000
BogoMIPS: 4800.00
Virtualization: VT-x
L1d cache: 1.3 MiB
L1i cache: 1.3 MiB
L2 cache: 40 MiB
L3 cache: 55 MiB
NUMA node0 CPU(s): 0,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78
NUMA node1 CPU(s): 1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79
Vulnerability Gather data sampling: Mitigation; Microcode
Vulnerability Itlb multihit: KVM: Mitigation: VMX disabled
Vulnerability L1tf: Mitigation; PTE Inversion; VMX conditional cache flushes, SMT vulnerable
Vulnerability Mds: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Meltdown: Mitigation; PTI
Vulnerability Mmio stale data: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Reg file data sampling: Not affected
Vulnerability Retbleed: Mitigation; IBRS
Vulnerability Spec rstack overflow: Not affected
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; IBRS; IBPB conditional; STIBP conditional; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected
Vulnerability Srbds: Not affected
Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT vulnerable
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti intel_ppin ssbd mba ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts hwp hwp_act_window hwp_epp hwp_pkg_req pku ospke md_clear flush_l1d arch_capabilities

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 · 2025-08-06T18:19:35Z

Looks like that full run passed 👍🏻

@andrjohns are you able to review again? Thanks!

WardBrian

I went through all of @andrjohns comments to confirm they were addressed, and a few other small things stood out to me

stan/math/prim/functor/apply_scalar_ternary.hpp

stan/math/prim/functor/apply_scalar_binary.hpp

stan/math/rev/fun/logit.hpp

stan-buildbot · 2025-08-12T01:17:31Z

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
arma/arma.stan	0.3	0.31	0.99	-0.79% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.01	0.01	1.1	9.21% faster
gp_regr/gen_gp_data.stan	0.03	0.02	1.08	7.01% faster
gp_regr/gp_regr.stan	0.09	0.09	1.07	6.89% faster
sir/sir.stan	69.61	66.67	1.04	4.23% faster
irt_2pl/irt_2pl.stan	3.98	3.96	1.0	0.37% faster
eight_schools/eight_schools.stan	0.06	0.05	1.09	8.1% faster
pkpd/sim_one_comp_mm_elim_abs.stan	0.27	0.24	1.12	10.81% faster
pkpd/one_comp_mm_elim_abs.stan	18.91	18.46	1.02	2.39% faster
garch/garch.stan	0.45	0.4	1.12	10.51% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan	2.78	2.57	1.08	7.49% faster
arK/arK.stan	1.95	1.7	1.15	12.8% faster
gp_pois_regr/gp_pois_regr.stan	2.91	2.75	1.06	5.5% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	9.09	8.34	1.09	8.17% faster
performance.compilation	181.41	177.75	1.02	2.02% faster
Mean result: 1.0691770183654012

Jenkins Console Log
Blue Ocean
Commit hash: 792180447d143165290a7cf746790514fdd0d084

Machine information

No LSB modules are available. 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: 46 bits physical, 48 bits virtual
CPU(s): 80
On-line CPU(s) list: 0-79
Thread(s) per core: 2
Core(s) per socket: 20
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 85
Model name: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Stepping: 4
CPU MHz: 2400.000
CPU max MHz: 3700.0000
CPU min MHz: 1000.0000
BogoMIPS: 4800.00
Virtualization: VT-x
L1d cache: 1.3 MiB
L1i cache: 1.3 MiB
L2 cache: 40 MiB
L3 cache: 55 MiB
NUMA node0 CPU(s): 0,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78
NUMA node1 CPU(s): 1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79
Vulnerability Gather data sampling: Mitigation; Microcode
Vulnerability Itlb multihit: KVM: Mitigation: VMX disabled
Vulnerability L1tf: Mitigation; PTE Inversion; VMX conditional cache flushes, SMT vulnerable
Vulnerability Mds: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Meltdown: Mitigation; PTI
Vulnerability Mmio stale data: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Reg file data sampling: Not affected
Vulnerability Retbleed: Mitigation; IBRS
Vulnerability Spec rstack overflow: Not affected
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; IBRS; IBPB conditional; STIBP conditional; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected
Vulnerability Srbds: Not affected
Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT vulnerable
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti intel_ppin ssbd mba ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts hwp hwp_act_window hwp_epp hwp_pkg_req pku ospke md_clear flush_l1d arch_capabilities

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

Just gave this a once over and it looks good to me now. We can wait a couple days before merging if you want to give @andrjohns another chance to look

stan-buildbot · 2025-08-12T22:10:03Z

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
arma/arma.stan	0.32	0.3	1.07	6.67% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.01	0.01	1.13	11.19% faster
gp_regr/gen_gp_data.stan	0.02	0.02	1.05	4.49% faster
gp_regr/gp_regr.stan	0.09	0.09	1.04	4.18% faster
sir/sir.stan	70.79	67.14	1.05	5.16% faster
irt_2pl/irt_2pl.stan	4.25	4.02	1.06	5.47% faster
eight_schools/eight_schools.stan	0.06	0.05	1.06	5.98% faster
pkpd/sim_one_comp_mm_elim_abs.stan	0.27	0.24	1.11	9.94% faster
pkpd/one_comp_mm_elim_abs.stan	19.41	18.67	1.04	3.81% faster
garch/garch.stan	0.45	0.4	1.12	10.41% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan	2.77	2.55	1.09	8.04% faster
arK/arK.stan	1.91	1.71	1.12	10.55% faster
gp_pois_regr/gp_pois_regr.stan	2.84	2.72	1.04	4.24% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	8.88	8.35	1.06	5.97% faster
performance.compilation	177.67	179.98	0.99	-1.3% slower
Mean result: 1.068712301746707

Jenkins Console Log
Blue Ocean
Commit hash: a534e266df6d111101436ad27c8924a8af101e00

Machine information

No LSB modules are available. 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: 46 bits physical, 48 bits virtual
CPU(s): 80
On-line CPU(s) list: 0-79
Thread(s) per core: 2
Core(s) per socket: 20
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 85
Model name: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz
Stepping: 4
CPU MHz: 2400.000
CPU max MHz: 3700.0000
CPU min MHz: 1000.0000
BogoMIPS: 4800.00
Virtualization: VT-x
L1d cache: 1.3 MiB
L1i cache: 1.3 MiB
L2 cache: 40 MiB
L3 cache: 55 MiB
NUMA node0 CPU(s): 0,2,4,6,8,10,12,14,16,18,20,22,24,26,28,30,32,34,36,38,40,42,44,46,48,50,52,54,56,58,60,62,64,66,68,70,72,74,76,78
NUMA node1 CPU(s): 1,3,5,7,9,11,13,15,17,19,21,23,25,27,29,31,33,35,37,39,41,43,45,47,49,51,53,55,57,59,61,63,65,67,69,71,73,75,77,79
Vulnerability Gather data sampling: Mitigation; Microcode
Vulnerability Itlb multihit: KVM: Mitigation: VMX disabled
Vulnerability L1tf: Mitigation; PTE Inversion; VMX conditional cache flushes, SMT vulnerable
Vulnerability Mds: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Meltdown: Mitigation; PTI
Vulnerability Mmio stale data: Mitigation; Clear CPU buffers; SMT vulnerable
Vulnerability Reg file data sampling: Not affected
Vulnerability Retbleed: Mitigation; IBRS
Vulnerability Spec rstack overflow: Not affected
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; IBRS; IBPB conditional; STIBP conditional; RSB filling; PBRSB-eIBRS Not affected; BHI Not affected
Vulnerability Srbds: Not affected
Vulnerability Tsx async abort: Mitigation; Clear CPU buffers; SMT vulnerable
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc art arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt tsc_deadline_timer aes xsave avx f16c rdrand lahf_lm abm 3dnowprefetch cpuid_fault epb cat_l3 cdp_l3 invpcid_single pti intel_ppin ssbd mba ibrs ibpb stibp tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 hle avx2 smep bmi2 erms invpcid rtm cqm mpx rdt_a avx512f avx512dq rdseed adx smap clflushopt clwb intel_pt avx512cd avx512bw avx512vl xsaveopt xsavec xgetbv1 xsaves cqm_llc cqm_occup_llc cqm_mbm_total cqm_mbm_local dtherm ida arat pln pts hwp hwp_act_window hwp_epp hwp_pkg_req pku ospke md_clear flush_l1d arch_capabilities

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

No response

WardBrian · 2025-08-15T14:30:27Z

@SteveBronder it looks like a few of the SoA signatures aren't compiling any more:
https://jenkins.flatironinstitute.org/blue/organizations/jenkins/Stan%2FStanc3/detail/PR-1527/7/pipeline

'../test/integration/good/function-signatures/math/matrix/trigamma.stan' had fails '[]' and errors '['Did not compile!']'
'../test/integration/good/function-signatures/math/matrix/trunc.stan' had fails '[]' and errors '['Did not compile!']'
'../test/integration/good/function-signatures/math/matrix/bessel_second_kind.stan' had fails '[]' and errors '['Did not compile!']'
'../test/integration/good/function-signatures/math/matrix/round.stan' had fails '[]' and errors '['Did not compile!']'

All of the errors are error: no matching function for call to 'NAME', except for the bessel second kind, which is

In file included from ../../test/integration/good/function-signatures/math/matrix/bessel_second_kind.hpp:1:
In file included from stan/src/stan/model/model_header.hpp:6:
In file included from /home/jenkins/workspace/Stan_Stanc3_PR-1527@2/compile-good-O1/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math.hpp:19:
In file included from /home/jenkins/workspace/Stan_Stanc3_PR-1527@2/compile-good-O1/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/rev.hpp:11:
In file included from /home/jenkins/workspace/Stan_Stanc3_PR-1527@2/compile-good-O1/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/rev/constraint.hpp:24:
In file included from /home/jenkins/workspace/Stan_Stanc3_PR-1527@2/compile-good-O1/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/prim/constraint.hpp:4:
In file included from /home/jenkins/workspace/Stan_Stanc3_PR-1527@2/compile-good-O1/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/prim/fun.hpp:32:
/home/jenkins/workspace/Stan_Stanc3_PR-1527@2/compile-good-O1/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/prim/fun/bessel_second_kind.hpp:59:16: error: function 'bessel_second_kind<const std::vector<int, std::allocator<int> > &, stan::math::var_value<Eigen::Matrix<double, -1, 1, 0, -1, 1>, void>, nullptr>' with deduced return type cannot be used before it is defined
        return bessel_second_kind(std::forward<decltype(c)>(c),
               ^
/home/jenkins/workspace/Stan_Stanc3_PR-1527@2/compile-good-O1/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/rev/functor/apply_scalar_binary.hpp:53:10: note: in instantiation of function template specialization 'stan::math::bessel_second_kind(const std::vector<int, std::allocator<int> > &&, stan::math::var_value<Eigen::Matrix<double, -1, 1, 0, -1, 1>, void> &&)::(anonymous class)::operator()<const std::vector<int, std::allocator<int> > &, stan::math::var_value<Eigen::Matrix<double, -1, 1, 0, -1, 1>, void> >' requested here
  return std::forward<F>(f)(std::forward<T1>(x), std::forward<T2>(y));
         ^
/home/jenkins/workspace/Stan_Stanc3_PR-1527@2/compile-good-O1/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/prim/fun/bessel_second_kind.hpp:57:10: note: in instantiation of function template specialization 'stan::math::apply_scalar_binary<(lambda at /home/jenkins/workspace/Stan_Stanc3_PR-1527@2/compile-good-O1/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/prim/fun/bessel_second_kind.hpp:58:7), const std::vector<int, std::allocator<int> > &, stan::math::var_value<Eigen::Matrix<double, -1, 1, 0, -1, 1>, void>, nullptr, nullptr>' requested here
  return apply_scalar_binary(
         ^
../../test/integration/good/function-signatures/math/matrix/bessel_second_kind.hpp:1798:21: note: in instantiation of function template specialization 'stan::math::bessel_second_kind<const std::vector<int, std::allocator<int> > &, stan::math::var_value<Eigen::Matrix<double, -1, 1, 0, -1, 1>, void>, nullptr>' requested here
        stan::math::bessel_second_kind(d_int_array,
                    ^
/home/jenkins/workspace/Stan_Stanc3_PR-1527@2/compile-good-O1/performance-tests-cmdstan/cmdstan/stan/lib/stan_math/stan/math/prim/fun/bessel_second_kind.hpp:56:13: note: 'bessel_second_kind<const std::vector<int, std::allocator<int> > &, stan::math::var_value<Eigen::Matrix<double, -1, 1, 0, -1, 1>, void>, nullptr>' declared here
inline auto bessel_second_kind(T1&& a, T2&& b) {

WardBrian · 2025-08-15T14:36:45Z

I'm guessing it is because the rev specializations of those functions hardcode var or var_value rather than using template traits

WardBrian · 2025-08-15T14:57:03Z

Jenkins also failed during the merge in this repo:
https://jenkins.flatironinstitute.org/blue/organizations/jenkins/Stan%2FMath/detail/develop/357/pipeline

WardBrian · 2025-08-15T15:25:17Z

@SteveBronder do you have a sense of how easy this would be to fix?

If it ends up being complicated I would advocate for reverting this and leaving math as-is in the release, for the sake of getting all the other bugfixes in the last 8 months in the hands of users

SteveBronder · 2025-08-15T15:27:14Z

'../test/integration/good/function-signatures/math/matrix/trigamma.stan' had fails '[]' and errors '['Did not compile!']'
'../test/integration/good/function-signatures/math/matrix/trunc.stan' had fails '[]' and errors '['Did not compile!']'
'../test/integration/good/function-signatures/math/matrix/bessel_second_kind.stan' had fails '[]' and errors '['Did not compile!']'
'../test/integration/good/function-signatures/math/matrix/round.stan' had fails '[]' and errors '['Did not compile!']'

I'm looking at these functions and idt trigamma, trunc, and round should have worked for SoA matrices in the first place. Like looking at trigamma they all use trigama_impl which is only made for scalar types. And round and trunc do not have SoA specializations either. So I think in the compiler we should turn those ones off.

The Bessel function one I think is a real error from ADL since the perfect forwarding function is being chosen over the others. I can open up a PR for that one rn

WardBrian · 2025-08-15T15:39:36Z

I'm looking at these functions and idt trigamma, trunc, and round should have worked for SoA matrices in the first place.

Are you sure? They've been marked as SoA supported since the first compiler pr stan-dev/stanc3#955.
Why have they been compiling until now?

SteveBronder and others added 18 commits July 9, 2025 17:58

First pass and passes mix fun test

df9a9b2

apply_scalar_binary. loglogistic now passes

b6e0a45

fix apply vector

13c4fd0

update ternary

dd3458c

[Jenkins] auto-formatting by clang-format version 10.0.0-4ubuntu1

45128f6

fix docs

aa5eb5e

fix docs

6ff0b0e

update test_ad_test to not use apply::return_t

4edea9f

[Jenkins] auto-formatting by clang-format version 10.0.0-4ubuntu1

696d2b2

fix template for sub_col and sub_row

2c8c9c5

update log1m_exp template constraints

2c1a328

[Jenkins] auto-formatting by clang-format version 10.0.0-4ubuntu1

912855d

fix templates for var and var matrix funs

dce5a63

[Jenkins] auto-formatting by clang-format version 10.0.0-4ubuntu1

fd7ad01

fix exp2

021e150

fix exp2

c677470

[Jenkins] auto-formatting by clang-format version 10.0.0-4ubuntu1

a77c2b6

remover binary operators for +/- etc from holder

f385fd2

WardBrian mentioned this pull request Jul 14, 2025

Release CmdStan 2.37 stan-dev/cmdstan#1324

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SteveBronder and others added 3 commits July 14, 2025 12:42

make operators for holder into free functions

1d5a64c

[Jenkins] auto-formatting by clang-format version 10.0.0-4ubuntu1

f5f0ead

have expr test on jenkins use gcc with sanitizer

e884013

WardBrian reviewed Jul 14, 2025

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revert before merge: have expr test on jenkins use gcc with sanitizer…

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SteveBronder added 2 commits July 15, 2025 11:09

fix templates for trigamma

b7336d2

revert changes to jenkinsfile

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stan-buildbot and others added 3 commits July 31, 2025 15:31

[Jenkins] auto-formatting by clang-format version 10.0.0-4ubuntu1

cef520c

allow as_array_or_scalar to return a holder of a map for std vector t…

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…ypes

[Jenkins] auto-formatting by clang-format version 10.0.0-4ubuntu1

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WardBrian requested a review from andrjohns August 4, 2025 13:57

WardBrian reviewed Aug 11, 2025

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SteveBronder and others added 4 commits August 11, 2025 14:12

update with brians review

4f97d77

[Jenkins] auto-formatting by clang-format version 10.0.0-4ubuntu1

bb37bf9

fix all places with Eigen maps and size functions for perfect forwarding

04fe232

[Jenkins] auto-formatting by clang-format version 10.0.0-4ubuntu1

3f3a52f

WardBrian previously approved these changes Aug 12, 2025

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remove use of Eigen::Map in divide_columns

acd3426

SteveBronder dismissed WardBrian’s stale review via acd3426 August 12, 2025 16:56

WardBrian approved these changes Aug 14, 2025

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SteveBronder merged commit a2d0372 into develop Aug 14, 2025
34 checks passed

WardBrian deleted the fix/exprs-apply branch August 14, 2025 19:54

SteveBronder restored the fix/exprs-apply branch August 15, 2025 14:56

WardBrian mentioned this pull request Aug 15, 2025

Fix some scalar functions being mislabeled as SoA stan-dev/stanc3#1540

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