Serialization for sum_to_zero#3308

WardBrian · 2024-08-01T14:42:35Z

Submission Checklist

Run unit tests: ./runTests.py src/test/unit
Run cpplint: make cpplint
Declare copyright holder and open-source license: see below

Summary

Serializer/deserializer for stan-dev/math#3099

The implementation in the math library is still being discussed, so this should not be merged yet. The main purpose is to let me continue building the end-to-end implementation including the compiler

Intended Effect

How to Verify

Side Effects

Documentation

Copyright and Licensing

Please list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company):
Simons Foundation

By submitting this pull request, the copyright holder is agreeing to 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/)

stan-buildbot · 2024-08-01T17:00:58Z

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
arma/arma.stan	0.38	0.35	1.06	5.48% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.01	0.01	0.95	-5.64% slower
gp_regr/gen_gp_data.stan	0.02	0.02	0.96	-4.5% slower
gp_regr/gp_regr.stan	0.12	0.1	1.18	15.27% faster
sir/sir.stan	69.23	74.02	0.94	-6.92% slower
irt_2pl/irt_2pl.stan	4.19	4.58	0.91	-9.42% slower
eight_schools/eight_schools.stan	0.06	0.06	0.97	-3.37% slower
pkpd/sim_one_comp_mm_elim_abs.stan	0.25	0.26	0.96	-4.0% slower
pkpd/one_comp_mm_elim_abs.stan	20.26	20.2	1.0	0.31% faster
garch/garch.stan	0.49	0.41	1.19	15.69% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan	3.16	3.08	1.03	2.58% faster
arK/arK.stan	2.01	1.96	1.03	2.66% faster
gp_pois_regr/gp_pois_regr.stan	3.43	3.0	1.14	12.36% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	10.67	8.64	1.23	19.0% faster
performance.compilation	184.33	206.94	0.89	-12.27% slower
Mean result: 1.0286185720803056

Jenkins Console Log
Blue Ocean
Commit hash: 2cd95be39b0482d0fedb7fe9a1e8c77b7084592a

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 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
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

SteveBronder

Quick Q but looks good

SteveBronder · 2024-08-06T20:34:26Z

src/stan/io/deserializer.hpp

+  inline auto read_constrain_sum_to_zero(LP& lp, size_t size) {
+    stan::math::check_positive("read_sum_to_zero", "size", size);
+    return stan::math::sum_to_zero_constrain<Jacobian>(
+        this->read<Ret>(size - 1), lp);


Should size - 1 be done at the compiler level? Since we would expect size + 1 to be returned

I was just going off of what simplex does in the same case (line 547), which does the -1

stan-buildbot · 2024-08-07T15:42:41Z

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
arma/arma.stan	0.45	0.37	1.19	16.12% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.01	0.01	0.95	-4.72% slower
gp_regr/gen_gp_data.stan	0.03	0.03	1.16	13.92% faster
gp_regr/gp_regr.stan	0.13	0.11	1.24	19.67% faster
sir/sir.stan	80.36	75.44	1.07	6.13% faster
irt_2pl/irt_2pl.stan	4.75	4.45	1.07	6.44% faster
eight_schools/eight_schools.stan	0.06	0.06	1.06	5.52% faster
pkpd/sim_one_comp_mm_elim_abs.stan	0.27	0.27	1.0	-0.2% slower
pkpd/one_comp_mm_elim_abs.stan	22.74	19.83	1.15	12.8% faster
garch/garch.stan	0.51	0.46	1.1	8.99% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan	3.13	2.82	1.11	10.16% faster
arK/arK.stan	2.05	1.91	1.07	6.84% faster
gp_pois_regr/gp_pois_regr.stan	3.23	3.08	1.05	4.57% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	10.11	9.32	1.08	7.74% faster
performance.compilation	203.04	215.59	0.94	-6.18% slower
Mean result: 1.0833294816620653

Jenkins Console Log
Blue Ocean
Commit hash: 4f8838bd96b1d1590209d845f484e5867c6c54a0

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 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
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 · 2024-08-08T16:50:16Z

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
arma/arma.stan	0.35	0.34	1.02	2.3% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.01	0.01	0.9	-11.57% slower
gp_regr/gen_gp_data.stan	0.03	0.03	0.79	-25.88% slower
gp_regr/gp_regr.stan	0.11	0.1	1.02	2.08% faster
sir/sir.stan	74.01	74.5	0.99	-0.66% slower
irt_2pl/irt_2pl.stan	4.49	4.38	1.03	2.47% faster
eight_schools/eight_schools.stan	0.06	0.06	1.04	3.51% faster
pkpd/sim_one_comp_mm_elim_abs.stan	0.27	0.27	1.01	0.87% faster
pkpd/one_comp_mm_elim_abs.stan	21.17	20.45	1.04	3.4% faster
garch/garch.stan	0.46	0.45	1.04	3.49% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan	2.91	2.85	1.02	1.95% faster
arK/arK.stan	1.94	1.87	1.04	3.39% faster
gp_pois_regr/gp_pois_regr.stan	3.04	2.94	1.03	3.19% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	9.47	9.26	1.02	2.26% faster
performance.compilation	207.07	205.32	1.01	0.84% faster
Mean result: 0.9993568971270046

Jenkins Console Log
Blue Ocean
Commit hash: 20b01da689e97de2329d35220bbc1f1b7ba46e43

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 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
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 added 2 commits August 1, 2024 10:36

deserializer impl + tests

753d40f

serializer impl + tests

3baa07d

WardBrian requested a review from SteveBronder August 1, 2024 14:42

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

59d619e

WardBrian mentioned this pull request Aug 5, 2024

Add sum_to_zero transform stan-dev/stanc3#1443

Merged

2 tasks

SteveBronder reviewed Aug 6, 2024

View reviewed changes

WardBrian closed this Aug 7, 2024

WardBrian reopened this Aug 7, 2024

Resolve doxygen warnings in deserializer.hpp

4a60cb9

Merge branch 'develop' into de/serialize-sum-to-zero

6149a9b

SteveBronder approved these changes Aug 8, 2024

View reviewed changes

WardBrian merged commit 658755b into develop Aug 8, 2024

WardBrian deleted the de/serialize-sum-to-zero branch August 8, 2024 17:17

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Serialization for sum_to_zero#3308