R Session Aborted

dhunfini · November 20, 2018, 1:36am

Hi,
I am repeatedly getting the following error when I run my stan() function. Please help to overcome the error.
‘R session Aborted. R encountered a fatal error. The session was terminated’

If your question relates to installation please provide the following information:

Operating System = Windows 10
RStan Version = 2.18.2
Output of writeLines(readLines(file.path(Sys.getenv("HOME"), ".R/Makevars")))

CXX14FLAGS=-O3 -Wno-unused-variable -Wno-unused-function
CXX14 = $(BINPREF)g++ -m$(WIN) -std=c++1y
CXX11FLAGS=-O3 -Wno-unused-variable -Wno-unused-function

CXX14FLAGS=-O3 -Wno-unused-variable -Wno-unused-function
CXX14 = $(BINPREF)g++ -m$(WIN) -std=c++1y
CXX11FLAGS=-O3 -Wno-unused-variable -Wno-unused-function

CXX14FLAGS=-O3 -Wno-unused-variable -Wno-unused-function
CXX14 = $(BINPREF)g++ -m$(WIN) -std=c++1y
CXX11FLAGS=-O3 -Wno-unused-variable -Wno-unused-function

CXX14FLAGS=-O3 -Wno-unused-variable -Wno-unused-function
CXX14 = $(BINPREF)g++ -m$(WIN) -std=c++1y
CXX11FLAGS=-O3 -Wno-unused-variable -Wno-unused-function

CXX14FLAGS=-O3 -Wno-unused-variable -Wno-unused-function
CXX14 = g++ -std=c++1y

CXX14FLAGS=-O3 -Wno-unused-variable -Wno-unused-function
CXX14 = g++ -std=c++1y

Output of devtools::session_info("rstan")

- Session info --------------------------------------------------------------------------------------------------------------
 setting  value                       
 version  R version 3.5.1 (2018-07-02)
 os       Windows 10 x64              
 system   x86_64, mingw32             
 ui       RStudio                     
 language (EN)                        
 collate  English_Australia.1252      
 ctype    English_Australia.1252      
 tz       Australia/Brisbane          
 date     2018-11-20                  

- Packages ------------------------------------------------------------------------------------------------------------------
 package      * version   date       lib source        
 assertthat     0.2.0     2017-04-11 [1] CRAN (R 3.5.1)
 backports      1.1.2     2017-12-13 [1] CRAN (R 3.5.0)
 base64enc      0.1-3     2015-07-28 [1] CRAN (R 3.5.0)
 BH             1.66.0-1  2018-02-13 [2] CRAN (R 3.5.0)
 callr          3.0.0     2018-08-24 [1] CRAN (R 3.5.1)
 cli            1.0.1     2018-09-25 [1] CRAN (R 3.5.1)
 colorspace     1.3-2     2016-12-14 [2] CRAN (R 3.5.1)
 crayon         1.3.4     2017-09-16 [1] CRAN (R 3.5.1)
 desc           1.2.0     2018-05-01 [1] CRAN (R 3.5.1)
 digest         0.6.18    2018-10-10 [2] CRAN (R 3.5.1)
 fansi          0.4.0     2018-10-05 [2] CRAN (R 3.5.1)
 ggplot2        3.1.0     2018-10-25 [1] CRAN (R 3.5.1)
 glue           1.3.0     2018-07-17 [2] CRAN (R 3.5.1)
 gridExtra      2.3       2017-09-09 [2] CRAN (R 3.5.1)
 gtable         0.2.0     2016-02-26 [2] CRAN (R 3.5.1)
 inline         0.3.15    2018-05-18 [2] CRAN (R 3.5.1)
 labeling       0.3       2014-08-23 [2] CRAN (R 3.5.0)
 lattice        0.20-35   2017-03-25 [2] CRAN (R 3.5.1)
 lazyeval       0.2.1     2017-10-29 [2] CRAN (R 3.5.1)
 loo            2.0.0     2018-04-11 [2] CRAN (R 3.5.1)
 magrittr       1.5       2014-11-22 [1] CRAN (R 3.5.1)
 MASS           7.3-50    2018-04-30 [2] CRAN (R 3.5.1)
 Matrix         1.2-14    2018-04-13 [2] CRAN (R 3.5.1)
 matrixStats    0.54.0    2018-07-23 [2] CRAN (R 3.5.1)
 mgcv           1.8-24    2018-06-23 [2] CRAN (R 3.5.1)
 munsell        0.5.0     2018-06-12 [2] CRAN (R 3.5.1)
 nlme           3.1-137   2018-04-07 [2] CRAN (R 3.5.1)
 pillar         1.3.0     2018-07-14 [2] CRAN (R 3.5.1)
 pkgbuild       1.0.2     2018-10-16 [2] CRAN (R 3.5.1)
 plyr           1.8.4     2016-06-08 [2] CRAN (R 3.5.1)
 prettyunits    1.0.2     2015-07-13 [1] CRAN (R 3.5.1)
 processx       3.2.0     2018-08-16 [1] CRAN (R 3.5.1)
 ps             1.2.0     2018-10-16 [1] CRAN (R 3.5.1)
 R6             2.3.0     2018-10-04 [1] CRAN (R 3.5.1)
 RColorBrewer   1.1-2     2014-12-07 [2] CRAN (R 3.5.0)
 Rcpp           0.12.19   2018-10-01 [2] CRAN (R 3.5.1)
 RcppEigen      0.3.3.4.0 2018-02-07 [2] CRAN (R 3.5.1)
 reshape2       1.4.3     2017-12-11 [2] CRAN (R 3.5.1)
 rlang          0.3.0.1   2018-10-25 [1] CRAN (R 3.5.1)
 rprojroot      1.3-2     2018-01-03 [1] CRAN (R 3.5.1)
 rstan          2.18.1    2018-10-16 [2] CRAN (R 3.5.1)
 scales         1.0.0     2018-08-09 [2] CRAN (R 3.5.1)
 StanHeaders    2.18.0    2018-10-07 [2] CRAN (R 3.5.1)
 stringi        1.2.4     2018-07-20 [2] CRAN (R 3.5.1)
 stringr        1.3.1     2018-05-10 [2] CRAN (R 3.5.1)
 tibble         1.4.2     2018-01-22 [2] CRAN (R 3.5.1)
 utf8           1.1.4     2018-05-24 [2] CRAN (R 3.5.1)
 viridisLite    0.3.0     2018-02-01 [2] CRAN (R 3.5.1)
 withr          2.1.2     2018-03-15 [1] CRAN (R 3.5.1)

[1] \\CompanyName/documents/StaffHome/StaffGroups$/Name/Documents/R/win-library/3.5
[2] C:/R-3.5.1/library

I have been using RCloud to run Rstan before changing to Windows desktop. But often using Cloud gives me an error regarding out of memory and had to change to Windows desktop.

I would really appreciate your help

bgoodri · November 20, 2018, 1:42am

Can you tell us what the Stan program is? Are you sure it did not run out of RAM? Was this with or without first doing Sys.setenv(LOCAL_CPP = "-mtune = native")? Etc.

Also, it would be better if you upgraded the rstan 2.18.2 on CRAN, although that may not fix this issue.

dhunfini · November 20, 2018, 1:56am

Thanks for the quick reply.
My stan program is as follows


//This is stan code for simulating fake data 

  functions {
     real[] ode(real t,
     real[] y,
     real[] params,
     real[] x_r, // x_r:real data, x_i: integer data
     int[] x_i) {

     real dydt[6];
    
     real A;
     real beta;
     real delta;
     real gamma;
     real omega;
     real sigma;
     real kappa;
     real eta;
     delta =params[1]; 
     A = x_r[1];
     beta = x_r[2];
     gamma = x_r[3];
     omega = x_r[4];
     sigma = x_r[5];
     kappa = x_r[6];
     eta = x_r[7];
     
     dydt[1] =  A - beta * y[5] * y[1] - beta * y[6] * y[1];                 
     dydt[2] = beta * y[1] * y[5] - beta * y[6] * y[2]- delta * y[2];      
     dydt[3] = beta * y[6] * y[1] - beta * y[5] * y[3] ;                   
     dydt[4]=  beta * y[6] * y[2] +  beta * y[5] * y[3] - gamma * y[4];        
     dydt[5] = omega * y[2] + omega * (1-sigma) * y[4] - kappa * y[5];          
     dydt[6] = eta * sigma* y[4] - kappa * y[6];                         
    
  return dydt;
 }

}

data {
    int<lower=1> T; //max time
     real y0[6];   //initial condition of ode
     real t0;      //initial time
     real ts[T];    //time span
     real A;
     real beta;
     real delta;
     real gamma;
     real omega;
     real sigma;
     real kappa;
     real eta;
}

transformed data {
      real params[1];
      real x_r[7];
      int x_i[0];
     
      params[1] = delta;
      x_r[1] = A;
      x_r[2] = beta;
      x_r[3] = gamma;
      x_r[4]= omega;
      x_r[5]= sigma;
      x_r[6] = kappa;
      x_r[7] = eta;
}
model {
  
}
generated quantities {
     real y_hat[T,6];
     y_hat = integrate_ode_bdf(ode, y0, t0, ts, params, x_r, x_i);
// generate fake data and add measurement error
   for (t in 1:T) {
   y_hat[t,1] = y_hat[t,1] + normal_rng(0, 0.1);
   y_hat[t,2] = y_hat[t,2] + normal_rng(0, 0.1);
   y_hat[t,3] = y_hat[t,3] + normal_rng(0, 0.1);
   y_hat[t,4] = y_hat[t,4] + normal_rng(0, 0.1);
   y_hat[t,5] = y_hat[t,5] + normal_rng(0, 0.1);
   y_hat[t,6] = y_hat[t,6] + normal_rng(0, 0.1);
  }
}

And R code used to run the stan program is

#use typical values to simulate fake data from ode
sim_data <- list(T = 10, y0 = c(1e8, 0, 0, 0, 1, 1), t0 = 0,
                 ts = 1:10,
                 A= 1.4e6, beta = 3.8e-11, delta =3.3, gamma = 0.14, omega = 1e4, sigma = 0.5, kappa = 3.5, eta = 20000)

#simulate fake data using the system of ODEs
fit1 <- stan("myModel-sim.stan", data = sim_data,
             chains = 1, iter = 1,
             algorithm = "Fixed_param")

When I ran this on RCloud it gave me the following error, which I think says ran out of RAM as you said.

Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! clang: error: unable to execute command: Killed
clang: error: clang frontend command failed due to signal (use -v to see invocation)
clang version 3.8.0-2ubuntu4 (tags/RELEASE_380/final)
Target: x86_64-pc-linux-gnu
Thread model: posix
InstalledDir: /usr/bin
clang: note: diagnostic msg: PLEASE submit a bug report to http://llvm.org/bugs/ and include the crash backtrace, preprocessed source, and associated run script.
clang: note: diagnostic msg: 
********************

PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT:
Preprocessed source(s) and associated run script(s) are located at:
clang: note: diagnostic msg: /tmp/file52fa66d38f76-ce4303.cpp
clang: note: diagnostic msg: /tmp/file52fa66d38f76-ce4303.sh
clang: note: diagnostic msg: 

********************
make: *** [file52fa66d38f76.o] Error 254
In addition: Warning message:
In system(cmd, intern = !verbose) :
  running command '/opt/R/3.5.0/lib/R/bin/R CMD SHLIB file52fa66d38f76.cpp 2> file52fa66d38f76.cpp.err.txt' had status 1

The stan program worked fine in RCloud early today. The error from Cloud is given after using Cloud for sometime most of the days.

The error from desktop is given without using
Sys.setenv(LOCAL_CPP = “-mtune = native”)

Thanks

bgoodri · November 20, 2018, 2:14am

This looks similar to a crash we saw on Windows last week when using algebra_solver. Unfortunately, we have not figured out why it is happening yet. RStudio Cloud will probably work at this time of night.

dhunfini · November 20, 2018, 11:48pm

@bgoodri ,
I am trying to run the above stan code from RCloud today and still getting the above error regarding CompileCode. Is there anyway I could overcome this error. Please help. I really need to speedup my simulation, and most of the time getting the CompileCode error is slowing down things.

Thanks

bgoodri · November 21, 2018, 5:16am

I’ll try to figure it out tomorrow

bgoodri · November 28, 2018, 1:54pm

Haven’t figured it out yet but am still working on it

bgoodri · November 29, 2018, 5:18pm

I still haven’t figured out the Windows bug, but I can get the example to compile on RStudio Cloud now (which has recently upgraded its compiler).

I had to add

LDFLAGS += -fuse-ld=gold

to the Makevars_Stan file in addition to changing the CXX* lines from clang++ to clang++-5.0 and adding -flto=thin to the CXX*FLAGS lines.

dhunfini · December 3, 2018, 12:36am

Thanks @bgoodri .

I can run the code on desktop (Windows 10) but using integrate_ode_rk45() instead of integrate_ode_bdf(). I also had to use Sys.setenv(LOCAL_CPPFLAGS = ‘-march=native’) in the R file for the stan code to run.

bgoodri · December 3, 2018, 12:49am

Interesting. That helps narrow it down a bit.

Ziyi_Chen · May 11, 2019, 7:56pm

@bgoodri
Have you solved it now?

I installed rstan from https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started (I think it is the latest), and run on Windows 10. I also got R session abort as shown below, even if I use only 1 chain, warmup=5, iter=10, and takes small memory.

Sometimes when running 4 chains in parallel, It said “Error reading from connection”.

However, the same code runs well on my mac system.

Thank you.

bgoodri · May 11, 2019, 9:09pm

No, but anything that works serially but does not work in parallel is likely (if not due to running out of RAM) some sort of antivirus like thing that shuts a program down if it launches multiple threads.

Ziyi_Chen · May 11, 2019, 9:14pm

@bgoodri
R also aborts with 1 chain (no parallel).

bgoodri · May 11, 2019, 9:30pm

Some of the ODE functions cause problems on Windows. Other than that, it is hard to say. Do the functions in rstanarm work? That would indicate whether there is a problem running compiled code on your machine.

Ziyi_Chen · May 11, 2019, 11:01pm

It may take time to try.
Before that, I found another interesting issue:

On another Windows computer, the first time runs well, while at the second time, R said

STARTING SAMPLER FOR MODEL ‘GMMBLCA_constrained_Givens_fixC_noZ20190428’ NOW.
Error in unserialize(socklist[[n]]) : error reading from connection
In addition: Warning messages:
1: In sink() : no sink to remove
2: In sink() : no sink to remove
3: In rnorm(n = max.num.nonGauss * max.GMM.num, mean = log(sigma.free.init[, :
NAs produced
4: In rnorm(n = max.num.nonGauss * max.GMM.num, mean = log(sigma.free.init[, :
NAs produced
5: In rnorm(n = max.num.nonGauss * max.GMM.num, mean = log(sigma.free.init[, :
NAs produced

Enter a frame number, or 0 to exit

1: GMMBLCA_fixC_noZ_Stan_function(X = simData$sim.X, whiten.option = “sqrtprec”, GMMBLCA.stan.model = GMMBLCA.stan.model
2: #198: sampling(object = GMMBLCA.stan.model, data = list(TT = TT, Q = num.nonGauss, C = GMM.init$Ck[1:num.nonGauss], V
3: sampling(object = GMMBLCA.stan.model, data = list(TT = TT, Q = num.nonGauss, C = GMM.init$Ck[1:num.nonGauss], V = num
4: .local(object, …)
5: parallel::parLapplyLB(cl, X = 1:chains, fun = callFun)
6: do.call(c, clusterApplyLB(cl, x = splitList(X, length(cl)), fun = lapply, fun, …), quote = TRUE)
7: clusterApplyLB(cl, x = splitList(X, length(cl)), fun = lapply, fun, …)
8: dynamicClusterApply(cl, fun, length(x), argfun)
9: recvOneResult(cl)
10: recvOneData(cl)
11: recvOneData.SOCKcluster(cl)
12: unserialize(socklist[[n]])

bgoodri · May 11, 2019, 11:05pm

It looks as if your R code is failing you.

Ziyi_Chen · May 11, 2019, 11:07pm

@bgoodri No, I know this NA happens somewhere outside stan sampling. That does not matter.

bgoodri · May 11, 2019, 11:56pm

If you call tempdir() before calling stan or sampling, there might be something in one of the .txt files in that directory that has more information about the error.

Ziyi_Chen · May 13, 2019, 2:18am

Thanks.
Later I just changed to linux server offered by my university, installing rstan per https://github.com/stan-dev/rstan/wiki/Installing-RStan-on-Linux. Then it works well.

Lucius · May 15, 2019, 3:54pm

My problem is the same as yours. I tried to reinstall it, but I still couldn’t solve it. Have you solved it?

Topic		Replies	Views
R Session Aborted General	4	585	December 4, 2019
A parade of errors trying to run rstan on Windows 10 RStan	10	1347	March 28, 2020
R Session Aborted when Replicating a Stan Factor Analysis model RStan	2	1251	December 24, 2018
Compilation error with 8 schools example RStan	4	1652	April 17, 2019
Rstan sampling "R session aborted" error Modeling	7	3318	February 19, 2021

R Session Aborted

Related topics