Just a public service announcement :) This error has been bothering me on and off lately, I hadn’t connected it to the change to using mtune=native and march=native in makevars on windows, but at least in my case this is apparently still a problem. Using Win7 64 and a Xeon e-5 1650.
What happens if you just do -march=native rather than also -mtune=native? Also, what is the error messages you are seeing?
Also, what is
system("wmic cpu get caption, deviceid, name, numberofcores, maxclockspeed, status")
?
Other way around actually – it’s ok (seemingly, so far) with just mtune=native, which I’m fairly sure was also the case at some point in the past on this machine.
Caption DeviceID MaxClockSpeed Name NumberOfCores Status
Intel64 Family 6 Model 45 Stepping 7 CPU0 3201 Intel(R) Xeon(R) CPU E5-1650 0 @ 3.20GHz 6 OKWhat about with -march=sandybridge? Also, what is the error message produced when there is one?
Error in unserialize(socklist[[n]]) : error reading from connection
Error in serialize(data, node$con, xdr = FALSE) :
error writing to connection
sandybridge still breaks things.
So, it compiles and runs and then has trouble with the serialization as it comes back to R?
No, it compiles but breaks down in the beginning of sampling, sometime after the initial gradient calculation.
Can I get a
native <- system("g++ -dM -E - -march=native", intern = TRUE)
basic <- system("g++ -dM -E - ", intern = TRUE)
setdiff(native, basic)
?
No. g++ not in path, then when I run it in CMD from ming_64\bin it’s just hung.
In CMD, it would be something like
C:\Rtools\mingw_64\bin> echo "" | g++ -dM -E -march=native -
but I guess you would have to write it to a file and read it into R to figure out what are the differences with the -march=native option.
I probably should have just temp broken my path in the first place.
[1] "#define __SSE4_1__ 1" "#define __POPCNT__ 1" "#define __corei7_avx 1" "#define __sandybridge 1"
[5] "#define __XSAVEOPT__ 1" "#define __BIGGEST_ALIGNMENT__ 32" "#define __SSE4_2__ 1" "#define __tune_corei7_avx__ 1"
[9] "#define __AVX__ 1" "#define __PCLMUL__ 1" "#define __XSAVE__ 1" "#define __sandybridge__ 1"
[13] "#define __corei7_avx__ 1" "#define __tune_sandybridge__ 1" "#define __SSSE3__ 1" "#define __AES__ 1"If you do -march=core2 does it crash?
No crashes, that works fine.
Is there any difference betweeen
echo "" | g++ -dM -E -march=core2 -
echo "" | g++ -dM -E -
?
core2 <- system("g++ -dM -E - -march=core2 ", intern = TRUE)
basic <- system("g++ -dM -E - ", intern = TRUE)
setdiff(core2, basic)
[1] "#define __core2__ 1" "#define __SSSE3__ 1" "#define __core2 1"
native <- system("g++ -dM -E - -march=native ", intern = TRUE)
core2 <- system("g++ -dM -E - -march=core2", intern = TRUE)
setdiff(native, core2)
[1] "#define __SSE4_1__ 1" "#define __POPCNT__ 1" "#define __corei7_avx 1" "#define __sandybridge 1"
[5] "#define __XSAVEOPT__ 1" "#define __BIGGEST_ALIGNMENT__ 32" "#define __SSE4_2__ 1" "#define __tune_corei7_avx__ 1"
[9] "#define __AVX__ 1" "#define __PCLMUL__ 1" "#define __XSAVE__ 1" "#define __sandybridge__ 1"
[13] "#define __corei7_avx__ 1" "#define __tune_sandybridge__ 1" "#define __AES__ 1"OK. I guess we might get a bit of speed from enabling SSSE3 instructions by default with -march=core2 and users can add -march=native themselves if it does not crash on their computer.
1 Like
I am getting this error as well. I have two models, one that does an analytical solution for an ode system, and another that does a numerical solution. The analytical one compiles and samples just fine; the numerical one compiles but sometimes gives many warnings about closing unused connections after compiling. Trying sampling() gives the following errors:
Error in unserialize(socklist[[n]]) : error reading from connection
12.
unserialize(socklist[[n]])
11.
recvOneData.SOCKcluster(cl)
10.
recvOneData(cl)
9.
recvOneResult(cl)
8.
dynamicClusterApply(cl, fun, length(x), argfun)
7.
clusterApplyLB(cl = cl, x = splitList(X, nchunks), fun = lapply, FUN = fun, ...)
6.
do.call(c, clusterApplyLB(cl = cl, x = splitList(X, nchunks), fun = lapply, FUN = fun, ...), quote = TRUE)
5.
parallel::parLapplyLB(cl, X = 1:chains, fun = callFun)
4.
.local(object, ...)
3.
sampling(comp_model, pars = c("P_hat", "P_rep"), chains = 9, iter = 1, algorithm = "Fixed_param", init = params, refresh = 0)
2.
sampling(comp_model, pars = c("P_hat", "P_rep"), chains = 9, iter = 1, algorithm = "Fixed_param", init = params, refresh = 0) at functions.r#80
1.
prior_predict(model_s2, 2)
Error in serialize(data, node$con, xdr = FALSE) : error writing to connection
11.
serialize(data, node$con, xdr = FALSE)
10.
sendData.SOCK0node(con, list(type = type, data = value, tag = tag))
9.
sendData(con, list(type = type, data = value, tag = tag))
8.
postNode(n, "DONE")
7.
stopNode(n)
6.
stopCluster.default(cl)
5.
parallel::stopCluster(cl)
4.
.local(object, ...)
3.
sampling(comp_model, pars = c("P_hat", "P_rep"), chains = 9, iter = 1, algorithm = "Fixed_param", init = params, refresh = 0)
2.
sampling(comp_model, pars = c("P_hat", "P_rep"), chains = 9, iter = 1, algorithm = "Fixed_param", init = params, refresh = 0) at functions.r#80
1.
prior_predict(model_s2, 2)
I’ll attach both models, but I doubt the problem is in the Stan program. I’ve looked through a few threads on this error and I’ve tried multiple configuration of the Makevars file as well as reinstalling rstan but I haven’t found a working solution.
stage1.stan (4.2 KB)
stage2.stan (4.6 KB)
System Info:
sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] bayesplot_1.6.0 rstan_2.18.2 StanHeaders_2.18.0
[4] ggplot2_3.1.0
system("wmic cpu get caption, deviceid, name, numberofcores, maxclockspeed, status")
Caption DeviceID MaxClockSpeed Name NumberOfCores Status
Intel64 Family 6 Model 142 Stepping 10 CPU0 1800 Intel(R) Core(TM) i5-8250U CPU @ 1.60GHz 4 OK
M <- file.path(Sys.getenv("HOME"), ".R", ifelse(.Platform$OS.type == "windows", "Makevars.win", "Makevars"))
writeLines(readLines(M))
CXXFLAGS=-O3 -Wno-unused-variable -Wno-unused-function -Wno-unused-local-typedefs
CXXFLAGS=-O3 -Wno-unused-variable -Wno-unused-function
CXXFLAGS=-O3 -Wno-unused-variable -Wno-unused-function
CXX14FLAGS=-O3 -march=native -mtune=native
CXX11FLAGS=-O3 -march=native -mtune=native
Do the errors persist when you comment out any lines in ~/.R/Makevars that mention -march and / or -mtune?
1 Like
I’m not sure what syntax to use for comments in the Makevars file, so I just removed those lines and kept this:
CXXFLAGS=-O3 -Wno-unused-variable -Wno-unused-function -Wno-unused-local-typedefs
CXXFLAGS=-O3 -Wno-unused-variable -Wno-unused-function
CXXFLAGS=-O3 -Wno-unused-variable -Wno-unused-function
and still got the errors
Error in unserialize(socklist[[n]]) : error reading from connection
Error in serialize(data, node$con, xdr = FALSE) : error writing to connection