В Tue, 24 Oct 2023 10:37:48 +0000
"Helske, Jouni" <jouni.hel...@jyu.fi> пишет:
> Examples with CPU time > 2.5 times elapsed time
> user system elapsed ratio
> exchange 1.196 0.04 0.159 7.774
I've downloaded the archived copy of the package from the CRAN FTP
server, installed it and tried:
library(bssm)
Sys.setenv("OMP_THREAD_LIMIT" = 2)
data("exchange")
model <- svm(
exchange, rho = uniform(0.97,-0.999,0.999),
sd_ar = halfnormal(0.175, 2), mu = normal(-0.87, 0, 2)
)
system.time(particle_smoother(model, particles = 500))
# user system elapsed
# 0.515 0.000 0.073
I set a breakpoint on clone() [*] and got quite a few calls creating
OpenMP threads with the following call stack:
#0 clone () at ../sysdeps/unix/sysv/linux/x86_64/clone.S:52
<...>
#4 0x00007ffff7314e0a in GOMP_parallel () from
/usr/lib/x86_64-linux-gnu/libgomp.so.1
<-- RcppArmadillo code below
#5 0x00007ffff38f5f00 in
arma::eglue_core<arma::eglue_div>::apply<arma::Mat<double>,
arma::eOp<arma::eOp<arma::Col<double>, arma::eop_exp>,
arma::eop_scalar_times>, arma::eOp<arma::eOp<arma::Col<double>,
arma::eop_scalar_div_post>, arma::eop_square> > (outP=..., x=...) at
.../library/RcppArmadillo/include/armadillo_bits/mp_misc.hpp:69
#6 0x00007ffff3a31246 in
arma::Mat<double>::operator=<arma::eOp<arma::eOp<arma::Col<double>,
arma::eop_exp>, arma::eop_scalar_times>,
arma::eOp<arma::eOp<arma::Col<double>, arma::eop_scalar_div_post>,
arma::eop_square>, arma::eglue_div> (X=..., this=0x7fffffff36f0) at
.../library/RcppArmadillo/include/armadillo_bits/Proxy.hpp:226
#7
arma::Col<double>::operator=<arma::eGlue<arma::eOp<arma::eOp<arma::Col<double>,
arma::eop_exp>, arma::eop_scalar_times>,
arma::eOp<arma::eOp<arma::Col<double>, arma::eop_scalar_div_post>,
arma::eop_square>, arma::eglue_div> > ( X=..., this=0x7fffffff36f0) at
.../library/RcppArmadillo/include/armadillo_bits/Col_meat.hpp:535
<-- bssm code below
#8 ssm_ung::laplace_iter (this=0x7fffffff15e0, signal=...) at
model_ssm_ung.cpp:310
#9 0x00007ffff3a36e9e in ssm_ung::approximate (this=0x7fffffff15e0) at
.../library/RcppArmadillo/include/armadillo_bits/arrayops_meat.hpp:27
#10 0x00007ffff3a3b3d3 in ssm_ung::psi_filter
(this=this@entry=0x7fffffff15e0, nsim=nsim@entry=500, alpha=...,
weights=..., indices=...) at model_ssm_ung.cpp:517
#11 0x00007ffff3948cd7 in psi_smoother (model_=..., nsim=nsim@entry=500,
seed=seed@entry=1092825895, model_type=model_type@entry=3) at
R_psi.cpp:131
What does arma::eglue_core do?
(gdb) list
/* reformatted a bit */
library/RcppArmadillo/include/armadillo_bits/mp_misc.hpp:64
int n_threads = (std::min)(
int(arma_config::mp_threads),
int((std::max)(int(1), int(omp_get_max_threads())))
);
(gdb) p arma_config::mp_threads
$3 = 8
(gdb) p (int)omp_get_max_threads()
$4 = 16
(gdb) p (char*)getenv("OMP_THREAD_LIMIT")
$7 = 0x555556576b91 "2"
(gdb) p /x (int)omp_get_thread_limit()
$9 = 0x7fffffff
Sorry for misinforming you about the OMP_THREAD_LIMIT environment
variable: the OpenMP specification requires the program to ignore
modifications to the environment variables after the program has
started [**], so it only works if R is started with OMP_THREAD_LIMIT
set. Additionally, the OpenMP thread limit is not supposed to be
adjusted at runtime at all [***].
Unfortunately for our situation, Armadillo is very insistent in setting
its own number of threads from arma_config::mp_threads (which is
constexpr 8 unless you set preprocessor directives while compiling it)
and omp_get_max_threads (which is the upper bound on the number of
threads that cannot be adjusted at runtime).
What I'm about to suggest is a terrible hack, but since Armadillo seems
to lack the option to set the number of threads at runtime, there might
be no other option.
Before you #include an Armadillo header, every time:
1. #include <omp.h> so that the OpenMP functions are declared and the
#include guard is set
2. Define a static inline function get_number_of_threads returning the
desired number of threads as an int (e.g. referencing an extern int
number_of_threads stored elsewhere)
3. #define omp_get_max_threads get_number_of_threads
Now if you provide an API for the R code to get and set this number, it
should be possible to control the number of threads used by OpenMP code
in Armadillo. Basically, a data.table::setDTthreads() for the copy of
Armadillo inlined inside your package.
If you then compile your package with a large #define
ARMA_OPENMP_THREADS, it will both be able to use more than 8 threads
*and* limit itself when needed.
An alternative course of action is compiling your package with #define
ARMA_OPENMP_THREADS 2 and giving up on more OpenMP threads inside calls
to Armadillo.
--
Best regards,
Ivan
[*]
https://github.com/tidymodels/textrecipes/pull/251#issuecomment-1775549814
[**]
https://www.openmp.org/spec-html/5.2/openmpch21.html#x432-59000021
[***]
https://www.openmp.org/wp-content/uploads/OpenMPRefCard-5-2-web.pdf#page=15
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