I am trying to run sampling for 40 iterations and each time i get the following error: Error in unserialize(socklist[[n]]) : error reading from connection Error in serialize(data, node$con, xdr = FALSE) : error writing to connection When i try to do it with chains=1 it crushes… I used all the recommended commands : rstan_options(auto_write=TRUE) options(mc.cores=parallel::detectCores()) Output of sessionInfo: R version 3.5.2 (2018-12-20) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 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] rstan_2.18.2 StanHeaders_2.18.1 ggplot2_3.1.0 loaded via a namespace (and not attached): [1] Rcpp_1.0.0 pillar_1.3.1 compiler_3.5.2 plyr_1.8.4 bindr_0.1.1 [6] prettyunits_1.0.2 tools_3.5.2 pkgbuild_1.0.2 tibble_2.0.1 gtable_0.2.0 [11] pkgconfig_2.0.2 rlang_0.3.1 cli_1.0.1 rstudioapi_0.9.0 parallel_3.5.2 [16] yaml_2.2.0 loo_2.0.0 bindrcpp_0.2.2 gridExtra_2.3 withr_2.1.2 [21] dplyr_0.7.8 stats4_3.5.2 grid_3.5.2 tidyselect_0.2.5 glue_1.3.0 [26] inline_0.3.15 R6_2.3.0 processx_3.2.1 purrr_0.2.5 callr_3.1.1 [31] magrittr_1.5 codetools_0.2-15 scales_1.0.0 ps_1.3.0 matrixStats_0.54.0 [36] assertthat_0.2.0 colorspace_1.4-0 lazyeval_0.2.1 munsell_0.5.0 crayon_1.3.4 I would really appreciate any help. Thanks

There was no error in that example, which is good. Can you run your brms thing with only 1 chain?

R crashed when I only ran it with one chain (see attached image). [crash]

Do you have -march=native and / or -mtune=native in your ~/.R/Makevars{.win} file? Or are you setting those in LOCAL_CPPFLAGS?

Hi, @bgoodri I got the same error as @itpetersen did when trying to use brms. I was trying to reproducible the analysis on this project: https://github.com/kzee/heterogeneityproject/blob/master/Hetero_Analyses_190331.Rmd, which used brm for twice. When I run this rmd file, the first brm function works well, but when it comes to the second, it has this error. I tested the example code, it worked, without error. I tried to change the chain to 1, R just stopped without any error message. Below is the information in my ~/.R/Makevars.win: CXX14=$(BINPREF)g++ -O2 -march=native -mtune=native CXX14FLAGS=-O3 -march=native -mtune=native CXX11FLAGS=-O3 -march=native -mtune=native

This particular model runs fine with one chain when I remove the makevars.win file and don’t set LOCAL_CPPFLAGS to -march=native. I thought I was also getting an error on another model when I didn’t set those, but I can’t confirm. So, the problem might be related to the -march=native and / or -mtune=native, as others above have suggested. Is there any workaround (or anticipated one) for this? Those particular settings result in considerably faster estimation, so I’d prefer to use them, if possible. But, more important is that it isn’t getting an error, so that’s a good start. Thanks for your help!

I would try it without the -march and -mtune stuff. Or change native to corei7.

You might try -mtune=corei7 -march=corei7 instead.

Thanks, I tried both ways, both worked, thanks!

[image] Guoqing_Wang: My solution is to run stanc(), stan_model() sampling() sequentially, rather than simply stan(). My problem solved by Guoqing_Wang’s approach too. Thanks!

I’m getting a very similar problem, though am on linux. I’m fitting a joint model with rstanarm::stan_jm. Generally, it works with 1 core and 1 chain, but otherwise I get the “unserialize” error listed above. Both the stan and parallel example code given above work fine. I can also implement other parallel procedures (like bootstrap) without a problem. Have tried chaging the C++ flags in the .R/Makevars as suggested, but it doesn’t seem to help. Any other thoughts to diagnose the issue differently on ubuntu? R version 3.6.3 (2020-02-29) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.4 LTS Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

Error in unserialize(socklist[[n]]) : error reading from connection Error in serialize(data, node$con, xdr = FALSE) : error writing to connection

Interfaces RStan

danielschad November 29, 2021, 12:18pm 52

Ok, installing the development version of rstan solved the problem; see here:

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Some models run without problems, but more complex give error: Error in unserialize(socklist[[n]]) : error reading/writing from connection RStan	13	1653	November 2, 2021
Error in unserialize(socklist[[n]]) : error reading from connection General rstan	19	3877	June 14, 2023
Error in unserialize(socklist[[n]]) : error reading from connection brms	2	752	May 24, 2023
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Error in unserialize(socklist[[n]]) : error reading from connection Error in serialize(data, node$con, xdr = FALSE) : error writing to connection

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