Hi This is my first post to this group and I am a novice. I am working with Imperial’s covid model 3 on an Imac and have just updated to R 4.0.0
I had to move to an old machine not running Catalina to run and experiment with their earlier models because of the reasons that have been discussed between Stan and Catalina. However this machine is MUCH more powerful so need to move my research now onto this machine. So Rstan now works but I have the same problem by bgoodri above- I cannot get 4 cores to sample just 1 works. Is there anything I can do to overcome this please??? this is the error message from R
[1] “First non-zero cases is on day 64, and 30 days before 10 deaths is day 53”
[1] “Portugal has 64 days of data”
[1] “First non-zero cases is on day 60, and 30 days before 10 deaths is day 46”
[1] “Netherlands has 71 days of data”
starting worker pid=45437 on localhost:11120 at 20:50:04.418
starting worker pid=45434 on localhost:11120 at 20:50:04.418
starting worker pid=45436 on localhost:11120 at 20:50:04.419
starting worker pid=45435 on localhost:11120 at 20:50:04.419
Error in unserialize(node$con) : error reading from connection
Calls: → slaveLoop → makeSOCKmaster
Error in unserialize(node$con) : error reading from connection
Calls: → slaveLoop → makeSOCKmaster
Execution halted
Execution halted
Error in unserialize(node$con) : error reading from connection
Calls: → slaveLoop → makeSOCKmaster
Error in unserialize(node$con) : error reading from connection
Calls: → slaveLoop → makeSOCKmaster
Execution halted
Execution halted
Error in makePSOCKcluster(names = spec, …) :
Cluster setup failed. 4 of 4 workers failed to connect.
and this is my set up
sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.4
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] rstanarm_2.19.3 xts_0.12-0 zoo_1.8-7 rstantools_2.0.0 Rcpp_1.0.4.6 abind_1.4-5 ggpubr_0.2.5 magrittr_1.5
[9] bayesplot_1.7.1 scales_1.1.0 stringr_1.4.0 optparse_1.6.6 EnvStats_2.3.1 tidyr_1.0.2 dplyr_0.8.5 gdata_2.18.0
[17] data.table_1.12.8 rstan_2.19.3 ggplot2_3.3.0 StanHeaders_2.19.2 lubridate_1.7.8 httr_1.4.1 readr_1.3.1
loaded via a namespace (and not attached):
[1] nlme_3.1-147 matrixStats_0.56.0 threejs_0.3.3 tools_4.0.0 R6_2.4.1 DT_0.13 colorspace_1.4-1 withr_2.2.0
[9] tidyselect_1.0.0 gridExtra_2.3 prettyunits_1.1.1 processx_3.4.2 curl_4.3 compiler_4.0.0 cli_2.0.2 shinyjs_1.1
[17] colourpicker_1.0 dygraphs_1.1.1.6 ggridges_0.5.2 callr_3.4.3 digest_0.6.25 minqa_1.2.4 base64enc_0.1-3 pkgconfig_2.0.3
[25] htmltools_0.4.0 lme4_1.1-23 fastmap_1.0.1 htmlwidgets_1.5.1 rlang_0.4.5 shiny_1.4.0.2 generics_0.0.2 crosstalk_1.1.0.1
[33] gtools_3.8.2 inline_0.3.15 loo_2.2.0 Matrix_1.2-18 munsell_0.5.0 fansi_0.4.1 lifecycle_0.2.0 stringi_1.4.6
[41] MASS_7.3-51.5 pkgbuild_1.0.6 plyr_1.8.6 grid_4.0.0 promises_1.1.0 crayon_1.3.4 miniUI_0.1.1.1 lattice_0.20-41
[49] splines_4.0.0 hms_0.5.3 ps_1.3.2 pillar_1.4.3 igraph_1.2.5 boot_1.3-24 markdown_1.1 ggsignif_0.6.0
[57] shinystan_2.5.0 reshape2_1.4.4 codetools_0.2-16 stats4_4.0.0 glue_1.4.0 packrat_0.5.0 nloptr_1.2.2.1 vctrs_0.2.4
[65] httpuv_1.5.2 gtable_0.3.0 getopt_1.20.3 purrr_0.3.3 assertthat_0.2.1 mime_0.9 xtable_1.8-4 later_1.0.0
[73] survival_3.1-12 rsconnect_0.8.16 tibble_3.0.1 shinythemes_1.1.2 statmod_1.4.34 ellipsis_0.3.0
many thanks for your help
Mark