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Fold grad_inc_beta into grad_reg_inc_beta #3159

Merged
merged 2 commits into from
Mar 13, 2025
Merged

Fold grad_inc_beta into grad_reg_inc_beta #3159

merged 2 commits into from
Mar 13, 2025

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andrjohns
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@andrjohns andrjohns commented Mar 5, 2025 •
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Summary

The grad_inc_beta function is currently only used in the grad_reg_inc_beta function. The two functions share similar variables, leading to redundant computation.

This PR folds the computations for grad_inc_beta into the existing grad_reg_inc_beta function.

Tests

N/A - Existing tests should still pass (no existing tests for grad_inc_beta)

Side Effects

N/A

Release notes

Removed redundant computation in grad_reg_inc_beta

Checklist

  • Copyright holder: Andrew Johnson

    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

@stan-buildbot
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Name Old Result New Result Ratio Performance change( 1 - new / old )
arma/arma.stan 0.37 0.4 0.93 -7.12% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.01 0.01 1.0 0.13% faster
gp_regr/gen_gp_data.stan 0.03 0.02 1.03 3.08% faster
gp_regr/gp_regr.stan 0.11 0.11 1.01 1.36% faster
sir/sir.stan 77.58 75.42 1.03 2.78% faster
irt_2pl/irt_2pl.stan 4.57 4.7 0.97 -2.99% slower
eight_schools/eight_schools.stan 0.07 0.07 0.97 -2.95% slower
pkpd/sim_one_comp_mm_elim_abs.stan 0.28 0.28 0.99 -0.66% slower
pkpd/one_comp_mm_elim_abs.stan 22.08 21.79 1.01 1.31% faster
garch/garch.stan 0.47 0.45 1.06 5.7% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan 3.0 2.83 1.06 5.84% faster
arK/arK.stan 2.04 1.87 1.09 8.61% faster
gp_pois_regr/gp_pois_regr.stan 3.22 2.99 1.08 7.2% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 10.28 9.78 1.05 4.87% faster
performance.compilation 244.47 225.77 1.08 7.65% faster
Mean result: 1.0257703848581108

Jenkins Console Log
Blue Ocean
Commit hash: 0f8dd4fc4b9973d67f612f68473daae100089e5c

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

@stan-buildbot
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Name Old Result New Result Ratio Performance change( 1 - new / old )
arma/arma.stan 0.44 0.47 0.94 -6.67% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.01 0.01 0.86 -16.23% slower
gp_regr/gen_gp_data.stan 0.03 0.03 0.99 -1.29% slower
gp_regr/gp_regr.stan 0.14 0.12 1.24 19.49% faster
sir/sir.stan 78.11 86.31 0.9 -10.5% slower
irt_2pl/irt_2pl.stan 6.01 6.28 0.96 -4.57% slower
eight_schools/eight_schools.stan 0.11 0.07 1.54 35.02% faster
pkpd/sim_one_comp_mm_elim_abs.stan 0.85 0.33 2.6 61.5% faster
pkpd/one_comp_mm_elim_abs.stan 23.59 24.81 0.95 -5.18% slower
garch/garch.stan 0.58 0.64 0.91 -10.39% slower
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.98 3.69 0.81 -23.84% slower
arK/arK.stan 1.91 2.4 0.79 -26.02% slower
gp_pois_regr/gp_pois_regr.stan 3.06 3.77 0.81 -23.17% slower
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 10.13 12.2 0.83 -20.44% slower
performance.compilation 202.71 212.77 0.95 -4.96% slower
Mean result: 1.0718003480625022

Jenkins Console Log
Blue Ocean
Commit hash: 0f8dd4fc4b9973d67f612f68473daae100089e5c

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

@stan-buildbot
Copy link
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Name Old Result New Result Ratio Performance change( 1 - new / old )
arma/arma.stan 0.51 0.4 1.27 21.05% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.01 0.01 0.97 -3.55% slower
gp_regr/gen_gp_data.stan 0.03 0.03 1.02 1.71% faster
gp_regr/gp_regr.stan 0.1 0.1 1.03 3.09% faster
sir/sir.stan 78.19 74.24 1.05 5.06% faster
irt_2pl/irt_2pl.stan 5.12 4.66 1.1 9.0% faster
eight_schools/eight_schools.stan 0.09 0.06 1.45 30.81% faster
pkpd/sim_one_comp_mm_elim_abs.stan 0.28 0.27 1.05 4.46% faster
pkpd/one_comp_mm_elim_abs.stan 21.09 20.87 1.01 1.01% faster
garch/garch.stan 0.51 0.46 1.1 8.72% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.99 3.25 0.92 -8.76% slower
arK/arK.stan 1.94 1.9 1.02 2.01% faster
gp_pois_regr/gp_pois_regr.stan 3.27 3.04 1.08 6.99% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 9.73 9.25 1.05 4.93% faster
performance.compilation 203.02 200.68 1.01 1.15% faster
Mean result: 1.0740210592120576

Jenkins Console Log
Blue Ocean
Commit hash: 41fb879c2b057722f0b8d4e3462ddede193cb95e

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
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Test failure looks like it's just something being flakey up in cmdstan?

@stan-buildbot
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Name Old Result New Result Ratio Performance change( 1 - new / old )
arma/arma.stan 0.34 0.31 1.1 8.78% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.01 0.01 1.05 4.66% faster
gp_regr/gen_gp_data.stan 0.03 0.02 1.07 6.76% faster
gp_regr/gp_regr.stan 0.1 0.09 1.08 7.03% faster
sir/sir.stan 70.06 67.29 1.04 3.95% faster
irt_2pl/irt_2pl.stan 4.19 4.03 1.04 3.81% faster
eight_schools/eight_schools.stan 0.06 0.06 1.03 2.8% faster
pkpd/sim_one_comp_mm_elim_abs.stan 0.26 0.28 0.9 -10.63% slower
pkpd/one_comp_mm_elim_abs.stan 19.64 18.95 1.04 3.5% faster
garch/garch.stan 0.43 0.42 1.03 3.18% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.76 2.64 1.04 4.18% faster
arK/arK.stan 1.8 1.76 1.02 2.04% faster
gp_pois_regr/gp_pois_regr.stan 2.87 2.75 1.04 4.13% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 8.9 8.52 1.05 4.33% faster
performance.compilation 181.97 185.56 0.98 -1.97% slower
Mean result: 1.033960006282594

Jenkins Console Log
Blue Ocean
Commit hash: 41fb879c2b057722f0b8d4e3462ddede193cb95e

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
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Huh, it seems to be repeatable here. @andrjohns are you on a Mac to try plugging this branch into cmdstan?

@andrjohns
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Huh, it seems to be repeatable here. @andrjohns are you on a Mac to try plugging this branch into cmdstan?

Absolutely bizarre! Yeah I'll do some testing locally and see what gremlin I've unleashed in the code

@andrjohns
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I can't reproduce locally unfortunately, and the error on Jenkins seems strange.

It's failing because it can't find some of the object files during linking:

--- Linking model ---

clang++  -Wp,-D_GLIBCXX_ASSERTIONS -std=c++17 -Wno-unknown-warning-option -Wno-tautological-compare -Wno-sign-compare -D_REENTRANT -Wno-ignored-attributes      -I stan/lib/stan_math/lib/tbb_2020.3/include    -O3 -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_1.84.0 -I stan/lib/stan_math/lib/sundials_6.1.1/include -I stan/lib/stan_math/lib/sundials_6.1.1/src/sundials -I stan/lib/stan_math/lib/benchmark_1.5.1/googletest/googletest/include -I stan/lib/stan_math/lib/benchmark_1.5.1/googletest/googletest -I stan/lib/rapidjson_1.1.0/     -DBOOST_DISABLE_ASSERTS                -Wl,-L,"/Users/jenkins/workspace/Stan_CmdStan_downstream_tests/stan/lib/stan_math/lib/tbb"   -Wl,-rpath,"/Users/jenkins/workspace/Stan_CmdStan_downstream_tests/stan/lib/stan_math/lib/tbb"      src/test/test-models/proper.o src/cmdstan/main.o       -ltbb   stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_nvecserial.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_cvodes.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_idas.a stan/lib/stan_math/lib/sundials_6.1.1/lib/libsundials_kinsol.a  stan/lib/stan_math/lib/tbb/libtbb.dylib stan/lib/stan_math/lib/tbb/libtbbmalloc.dylib stan/lib/stan_math/lib/tbb/libtbbmalloc_proxy.dylib -o src/test/test-models/proper

clang: error: no such file or directory: 'src/test/test-models/proper.o'

And I can see earlier in the log that the object files are getting cleaned up in a different step before the linking call.

Not entirely sure how/why it's happening there tbh

@andrjohns andrjohns force-pushed the remove-grad_inc_beta branch from 314398e to 96b8a66 Compare March 7, 2025 12:02
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Just rebased onto develop to see if that does anything

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Name Old Result New Result Ratio Performance change( 1 - new / old )
arma/arma.stan 0.32 0.33 0.98 -1.83% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.01 0.01 0.97 -2.97% slower
gp_regr/gen_gp_data.stan 0.02 0.02 1.02 1.5% faster
gp_regr/gp_regr.stan 0.09 0.09 1.0 0.23% faster
sir/sir.stan 69.49 69.38 1.0 0.16% faster
irt_2pl/irt_2pl.stan 4.18 4.0 1.04 4.12% faster
eight_schools/eight_schools.stan 0.06 0.05 1.07 6.61% faster
pkpd/sim_one_comp_mm_elim_abs.stan 0.25 0.24 1.02 2.36% faster
pkpd/one_comp_mm_elim_abs.stan 19.38 18.84 1.03 2.8% faster
garch/garch.stan 0.44 0.41 1.06 5.9% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.68 2.66 1.01 0.74% faster
arK/arK.stan 1.79 1.75 1.02 2.17% faster
gp_pois_regr/gp_pois_regr.stan 2.81 2.75 1.02 1.85% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 8.67 8.58 1.01 1.11% faster
performance.compilation 179.69 187.43 0.96 -4.31% slower
Mean result: 1.0146806701974573

Jenkins Console Log
Blue Ocean
Commit hash: fa89f3f2eeace783e24dc5d33e94f737d6e7f2f7

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
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It's weird, because other PRs haven't seen the same failures, so it does seem like this change would be responsible, but I can't imagine why

@WardBrian
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@andrjohns independent of the failures, it looks like there are a few comments in the grad_2F1 file that should be updated (they specifically mention grad_inc_beta)

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Name Old Result New Result Ratio Performance change( 1 - new / old )
arma/arma.stan 0.38 0.34 1.12 10.33% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.01 0.01 0.94 -6.11% slower
gp_regr/gen_gp_data.stan 0.03 0.03 0.99 -1.02% slower
gp_regr/gp_regr.stan 0.11 0.1 1.11 9.8% faster
sir/sir.stan 78.23 74.49 1.05 4.78% faster
irt_2pl/irt_2pl.stan 4.86 4.6 1.06 5.27% faster
eight_schools/eight_schools.stan 0.06 0.06 1.03 2.51% faster
pkpd/sim_one_comp_mm_elim_abs.stan 0.28 0.26 1.05 4.59% faster
pkpd/one_comp_mm_elim_abs.stan 22.58 20.62 1.09 8.66% faster
garch/garch.stan 0.68 0.45 1.5 33.31% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.88 2.87 1.0 0.47% faster
arK/arK.stan 1.92 1.9 1.01 0.96% faster
gp_pois_regr/gp_pois_regr.stan 3.08 3.01 1.02 2.32% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 9.12 9.26 0.98 -1.56% slower
performance.compilation 213.6 199.6 1.07 6.56% faster
Mean result: 1.068201926838794

Jenkins Console Log
Blue Ocean
Commit hash: fa89f3f2eeace783e24dc5d33e94f737d6e7f2f7

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
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I manually ran https://jenkins.flatironinstitute.org/blue/organizations/jenkins/Stan%2FCmdStan/detail/downstream_tests/829/pipeline/6 with this branch but using -j1 for the make command and it passed, so I think it's just a dependency issue in the tests makefile up at the cmdstan level.

We might be able to use --shuffle to run it down?

@WardBrian WardBrian mentioned this pull request Mar 10, 2025
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Name Old Result New Result Ratio Performance change( 1 - new / old )
arma/arma.stan 0.33 0.31 1.07 6.47% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.01 0.01 1.03 2.61% faster
gp_regr/gen_gp_data.stan 0.02 0.02 1.07 6.74% faster
gp_regr/gp_regr.stan 0.09 0.09 1.04 3.74% faster
sir/sir.stan 69.21 66.93 1.03 3.29% faster
irt_2pl/irt_2pl.stan 4.13 3.97 1.04 3.87% faster
eight_schools/eight_schools.stan 0.06 0.05 1.08 7.32% faster
pkpd/sim_one_comp_mm_elim_abs.stan 0.26 0.24 1.08 7.25% faster
pkpd/one_comp_mm_elim_abs.stan 19.37 18.57 1.04 4.16% faster
garch/garch.stan 0.44 0.4 1.08 7.61% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.7 2.61 1.04 3.6% faster
arK/arK.stan 1.83 1.72 1.06 5.67% faster
gp_pois_regr/gp_pois_regr.stan 2.82 2.74 1.03 2.99% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 8.82 8.37 1.05 5.06% faster
performance.compilation 183.75 182.19 1.01 0.85% faster
Mean result: 1.0502981811572827

Jenkins Console Log
Blue Ocean
Commit hash: dfc21285f1149f6ea7bcc073ecbf5129975375f2

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
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clang: error: no such file or directory: 'src/test/test-models/empty.o'
clang: error: no such file or directory: 'src/test/test-models/proper.o'
clang: error: no such file or directory: 'src/test/test-models/test_model.o'
clang: error: no such file or directory: 'src/test/test-models/bern_gq_model.o'
make: *** [src/test/test-models/empty] Error 1
make: *** Waiting for unfinished jobs....
make: *** [src/test/test-models/proper] Error 1
make: *** [src/test/test-models/test_model] Error 1
make: *** [src/test/test-models/bern_gq_model] Error 1
rm test/interface/generated_quantities_test.o test/interface/fixed_param_sampler_test.o src/test/test-models/bern_extra_model.hpp src/test/test-models/gq_non_scalar.hpp src/test/test-models/bern_extra_model.o src/test/test-models/gq_non_scalar.o
make -j8 test/interface/generated_quantities_test test/interface/fixed_param_sampler_test failed
exit now (03/11/25 21:37:35 EDT)
------------------------------------------------------------
make -j8 build
------------------------------------------------------------
make -j8 test/interface/opencl_test test/interface/optimization_output_test test/interface/output_sig_figs_test test/interface/pathfinder_test test/interface/model_output_test test/interface/tbb_threadpool_test test/interface/save_metric_json_test test/interface/diagnose_test test/interface/variational_output_test test/interface/file_test test/interface/stansummary_test test/interface/datetime_test test/interface/print_test test/interface/print_uninitialized_test test/interface/laplace_test test/interface/mpi_test test/interface/metric_test test/interface/command_test test/interface/log_prob_test test/interface/multi_chain_init_test test/interface/elapsed_time_test test/interface/multi_chain_test test/interface/csv_header_consistency_test test/interface/var_context_loading_test test/interface/config_json_test
------------------------------------------------------------
make -j8 test/interface/generated_quantities_test test/interface/fixed_param_sampler_test

I cannot fathom why this is still happening... and it's only for this PR,

@andrjohns
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Hmmm, could a workaround for now be to run the tests with KEEP_OBJECT so that test objects don't get cleaned up between targets?

@WardBrian
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That would probably fix it, but I'm still suspicious there might be an actual issue here we just don't understand. If you look at the history for the downstream branch, the recent failures are exclusively for this PR, and there are plenty of other successes

@stan-dev stan-dev deleted a comment from stan-buildbot Mar 12, 2025
@stan-dev stan-dev deleted a comment from stan-buildbot Mar 12, 2025
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Name Old Result New Result Ratio Performance change( 1 - new / old )
arma/arma.stan 0.33 0.32 1.0 0.16% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.01 0.01 1.01 0.77% faster
gp_regr/gen_gp_data.stan 0.02 0.02 1.05 4.51% faster
gp_regr/gp_regr.stan 0.1 0.09 1.07 6.43% faster
sir/sir.stan 68.73 67.02 1.03 2.49% faster
irt_2pl/irt_2pl.stan 4.34 3.99 1.09 8.16% faster
eight_schools/eight_schools.stan 0.06 0.05 1.03 3.3% faster
pkpd/sim_one_comp_mm_elim_abs.stan 0.26 0.24 1.08 7.4% faster
pkpd/one_comp_mm_elim_abs.stan 19.62 18.63 1.05 5.03% faster
garch/garch.stan 0.43 0.4 1.08 7.14% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.75 2.63 1.05 4.55% faster
arK/arK.stan 1.8 1.71 1.05 4.88% faster
gp_pois_regr/gp_pois_regr.stan 2.86 2.78 1.03 2.95% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 8.57 8.41 1.02 1.88% faster
performance.compilation 181.29 180.58 1.0 0.4% faster
Mean result: 1.0424122200993475

Jenkins Console Log
Blue Ocean
Commit hash: dfc21285f1149f6ea7bcc073ecbf5129975375f2

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

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Okay, I think it is probably just a race condition on the disk. For some reason, the cmdstan runTests python script does batching, and I think that these batches end up running with some small overlap in time to each other, so the next batch sees that the previous batch built the .os, but didn't see that it deleted them?

Increasing the batch size large enough so that there is only one batch both seem to fix it. The entire runCmdStanTests.py script is pretty ugly, so I'm not too miffed at just bumping the BATCH to like 50 (from 25) and moving on...

@WardBrian WardBrian mentioned this pull request Mar 12, 2025
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Name Old Result New Result Ratio Performance change( 1 - new / old )
arma/arma.stan 0.35 0.33 1.07 6.24% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.01 0.01 1.0 0.43% faster
gp_regr/gen_gp_data.stan 0.03 0.03 1.16 13.65% faster
gp_regr/gp_regr.stan 0.1 0.1 1.01 0.66% faster
sir/sir.stan 72.27 70.56 1.02 2.37% faster
irt_2pl/irt_2pl.stan 4.43 4.13 1.07 6.82% faster
eight_schools/eight_schools.stan 0.06 0.06 0.99 -1.22% slower
pkpd/sim_one_comp_mm_elim_abs.stan 0.27 0.25 1.06 5.87% faster
pkpd/one_comp_mm_elim_abs.stan 20.2 19.27 1.05 4.6% faster
garch/garch.stan 0.47 0.44 1.05 4.89% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.83 2.77 1.02 2.13% faster
arK/arK.stan 1.9 1.83 1.04 3.54% faster
gp_pois_regr/gp_pois_regr.stan 2.92 2.94 0.99 -0.66% slower
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 8.93 8.3 1.08 7.09% faster
performance.compilation 189.0 182.85 1.03 3.26% faster
Mean result: 1.042981747857559

Jenkins Console Log
Blue Ocean
Commit hash: dfc21285f1149f6ea7bcc073ecbf5129975375f2

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

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Name Old Result New Result Ratio Performance change( 1 - new / old )
arma/arma.stan 0.31 0.31 1.0 0.21% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan 0.01 0.01 1.02 2.42% faster
gp_regr/gen_gp_data.stan 0.02 0.02 1.04 4.3% faster
gp_regr/gp_regr.stan 0.09 0.09 1.05 5.02% faster
sir/sir.stan 67.13 66.83 1.0 0.44% faster
irt_2pl/irt_2pl.stan 4.07 3.97 1.02 2.27% faster
eight_schools/eight_schools.stan 0.06 0.05 1.05 4.57% faster
pkpd/sim_one_comp_mm_elim_abs.stan 0.25 0.25 1.01 1.28% faster
pkpd/one_comp_mm_elim_abs.stan 18.7 18.65 1.0 0.23% faster
garch/garch.stan 0.45 0.41 1.11 9.58% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan 2.78 2.6 1.07 6.57% faster
arK/arK.stan 1.83 1.73 1.06 5.43% faster
gp_pois_regr/gp_pois_regr.stan 2.82 2.72 1.04 3.55% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan 8.62 8.45 1.02 1.92% faster
performance.compilation 180.02 181.81 0.99 -1.0% slower
Mean result: 1.03303778839186

Jenkins Console Log
Blue Ocean
Commit hash: 0d6bd650ebd331395197dd352b2d23d459fb7626

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 WardBrian merged commit 8b8057a into develop Mar 13, 2025
24 checks passed
@WardBrian WardBrian deleted the remove-grad_inc_beta branch March 13, 2025 13:27
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@andrjohns @stan-buildbot @WardBrian @SteveBronder