Running rstan on grid engine causing compiling error

Interfaces RStan
1

I am trying to run rstan on a grid engine to parallelize multiple scenarios that use the same stan file but with different data inputs.

i keep getting this error that i cant understand what it is the cause for the error.

Loading required package: bindrcpp
Loading required package: rstan
Loading required package: ggplot2
Loading required package: StanHeaders
rstan (Version 2.16.2, packaged: 2017-07-03 09:24:58 UTC, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
rstan_options(auto_write = TRUE)
options(mc.cores = parallel::detectCores())
Loading required package: rlecuyer
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from /data/co/CSL0301/script/lib/rstan/include/rstan/rstaninc.hpp:3:0,
                 from file3f614e46f472.cpp:622:
/data/co/CSL0301/script/lib/rstan/include/rstan/stan_fit.hpp: In function ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector<long unsigned int>&, const std::vector<std::basic_string<char> >&, RNG_t&)’:
/data/co/CSL0301/script/lib/rstan/include/rstan/stan_fit.hpp:438:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<stan::io::var_context> init_context_ptr;
        ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from /data/co/CSL0301/script/lib/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from /data/co/CSL0301/script/lib/BH/include/boost/lexical_cast
Calls: FUN ... stan_model -> cxxfunctionplus -> cxxfunction -> compileCode
In addition: Warning message:
running command '/usr/lib/R/bin/R CMD SHLIB file3f614e46f472.cpp 2> file3f614e46f472.cpp.err.txt' had status 1 
Execution halted

R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] bindrcpp_0.2         rstan_2.16.2         StanHeaders_2.16.0-1 ggplot2_2.2.1       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12       plyr_1.8.4         bindr_0.1          viridis_0.4.0      digest_0.6.12      viridisLite_0.2.0  jsonlite_1.5       tibble_1.3.3       gtable_0.2.0      
[10] lattice_0.20-34    pkgconfig_2.0.1    texPreview_1.0.0   rlang_0.1.1        rstudioapi_0.6     qapply_1.38        magick_0.4         parallel_3.3.3     mvtnorm_1.0-6     
[19] gridExtra_2.2.1    dplyr_0.7.2        httr_1.2.1         xml2_1.1.1         stats4_3.3.3       grid_3.3.3         glue_1.1.1         inline_0.3.14      R6_2.2.2          
[28] svgPanZoom_0.3.3   tidyr_0.6.3        slackr_1.4.3       magrittr_1.5       scales_0.4.1       assertthat_0.2.0   xtable_1.8-2       colorspace_1.3-2   labeling_0.3      
[37] DoseFinding_0.9-15 lazyeval_0.2.0     munsell_0.4.3
2

Do you have -Werror in CXXFLAGS somewhere (either in the sitewide Makevars file or in ~/.R/Makevars)? I am not seeing an error message just a harmless warning about deprecated stuff and then compilation stops.

3

Are you using the same singular Stan file for your different scenarios? I don’t think that will run correctly – you may need to have separate Stan files for each scenario.

I was running something where I used the same Stan model but for 100 different datasets. I had to end up creating 100 identical Stan files (renamed, of course) for each dataset evaluation in order for it to run. I was also using a grid engine for this as well.

Hope that is helpful!

4

yeah. ive tried that too but w no success.

td <- file.path(tempdir(),'stantemp')
  
  dir.create(td,recursive = TRUE)
  
  thisfile <- sprintf('thismodel%s.stan',gsub('[.]','_',as.character(runif(1))))
  
  file.copy(system.file(paste0('stan_models/',endpoint, "SigmoidEmax.stan"),package = 'CSL0301'),
            file.path(td,thisfile)
            )
  
  stan.args <- list(file=file.path(td,thisfile),
                     data=data, init=init , pars = parameters, chains = nChains, iter = nIter, warmup = nBurnin,
                     control = list(adapt_delta = 0.9), thin=nThin,cores=1)
  
  
  fit <- do.call('stan',stan.args)
5

I get same error with simple toy model

f <- function(i,mod) {
  rstan::stan(model_code = mod)
}

model_code='
data {
}
parameters {
  real y;
}
model {
  y ~ normal(0, 1);
}'


x2 <-qapply::qapply(X = 1:30,
                    FUN = f,
                    fargs = list(mod=model_code),
                    nCores = 10,
                    workDir = 'qapply',
                    tag = 'teststan',
                    clearWd=FALSE)
6

That should not be necessary if you have saved the compiled model to the disk by first invoking rstan_options(auto_write = TRUE) and compiling it once.

7

I think you either are running out of RAM or you have -Werror in your configuration flags somewhere. Just using a deprecated part of Boost should not cause the compilation to stop. When there is a bona fide compilation error it says error: somewhere with a cryptic message following that.

8 
starting worker pid=106375 on localhost:11291 at 18:23:51.061
In file included from /usr/lib/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /usr/lib/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/core.hpp:14,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
                 from file19f05392900cc.cpp:8:
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: error: ‘template<class _Operation> class std::binder2nd’ is deprecated [-Werror=deprecated-declarations]
 struct functor_traits<std::binder2nd<T> >
                            ^~~~~~~~~
In file included from /usr/include/c++/6/bits/stl_function.h:1127:0,
                 from /usr/include/c++/6/string:48,
                 from /usr/include/c++/6/bits/locale_classes.h:40,
                 from /usr/include/c++/6/bits/ios_base.h:41,
                 from /usr/include/c++/6/ios:42,
                 from /usr/include/c++/6/istream:38,
                 from /usr/include/c++/6/sstream:38,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:10,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/core.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
                 from file19f05392900cc.cpp:8:
/usr/include/c++/6/backward/binders.h:143:11: note: declared here
     class binder2nd
           ^~~~~~~~~
In file included from /usr/lib/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /usr/lib/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/core.hpp:14,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
                 from file19f05392900cc.cpp:8:
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: error: ‘template<class _Operation> class std::binder1st’ is deprecated [-Werror=deprecated-declarations]
 struct functor_traits<std::binder1st<T> >
                            ^~~~~~~~~
In file included from /usr/include/c++/6/bits/stl_function.h:1127:0,
                 from /usr/include/c++/6/string:48,
                 from /usr/include/c++/6/bits/locale_classes.h:40,
                 from /usr/include/c++/6/bits/ios_base.h:41,
                 from /usr/include/c++/6/ios:42,
                 from /usr/include/c++/6/istream:38,
                 from /usr/include/c++/6/sstream:38,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/memory/stack_alloc.hpp:10,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/core/autodiffstackstorage.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/core.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
                 from file19f05392900cc.cpp:8:
/usr/include/c++/6/backward/binders.h:108:11: note: declared here
     class binder1st
           ^~~~~~~~~
cc1plus: all warnings being treated as errors
make: *** [file19f05392900cc.o] Error 1

ERROR(s) during compilation: source code errors or compiler configuration errors!

Program source:
  1: 
  2: // includes from the plugin
  3: 
  4: 
  5: // user includes
  6: #define STAN__SERVICES__COMMAND_HPP// Code generated by Stan version 2.14
  7: 
  8: #include <stan/model/model_header.hpp>
  9: 
 10: namespace model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace {
 11: 
 12: using std::istream;
 13: using std::string;
 14: using std::stringstream;
 15: using std::vector;
 16: using stan::io::dump;
 17: using stan::math::lgamma;
 18: using stan::model::prob_grad;
 19: using namespace stan::math;
 20: 
 21: typedef Eigen::Matrix<double,Eigen::Dynamic,1> vector_d;
 22: typedef Eigen::Matrix<double,1,Eigen::Dynamic> row_vector_d;
 23: typedef Eigen::Matrix<double,Eigen::Dynamic,Eigen::Dynamic> matrix_d;
 24: 
 25: static int current_statement_begin__;
 26: 
 27: class model19f053892e3a2_851b263221b353f53f6e5ee203c5b150 : public prob_grad {
 28: private:
 29: public:
 30:     model19f053892e3a2_851b263221b353f53f6e5ee203c5b150(stan::io::var_context& context__,
 31:         std::ostream* pstream__ = 0)
 32:         : prob_grad(0) {
 33:         typedef boost::ecuyer1988 rng_t;
 34:         rng_t base_rng(0);  // 0 seed default
 35:         ctor_body(context__, base_rng, pstream__);
 36:     }
 37: 
 38:     template <class RNG>
 39:     model19f053892e3a2_851b263221b353f53f6e5ee203c5b150(stan::io::var_context& context__,
 40:         RNG& base_rng__,
 41:         std::ostream* pstream__ = 0)
 42:         : prob_grad(0) {
 43:         ctor_body(context__, base_rng__, pstream__);
 44:     }
 45: 
 46:     template <class RNG>
 47:     void ctor_body(stan::io::var_context& context__,
 48:                    RNG& base_rng__,
 49:                    std::ostream* pstream__) {
 50:         current_statement_begin__ = -1;
 51: 
 52:         static const char* function__ = "model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150";
 53:         (void) function__; // dummy call to supress warning
 54:         size_t pos__;
 55:         (void) pos__; // dummy call to supress warning
 56:         std::vector<int> vals_i__;
 57:         std::vector<double> vals_r__;
 58:         double DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
 59:         (void) DUMMY_VAR__;  // suppress unused var warning
 60: 
 61:         // initialize member variables
 62: 
 63:         // validate, data variables
 64:         // initialize data variables
 65: 
 66:         try {
 67:         } catch (const std::exception& e) {
 68:             stan::lang::rethrow_located(e,current_statement_begin__);
 69:             // Next line prevents compiler griping about no return
 70:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
 71:         }
 72: 
 73:         // validate transformed data
 74: 
 75:         // set parameter ranges
 76:         num_params_r__ = 0U;
 77:         param_ranges_i__.clear();
 78:         ++num_params_r__;
 79:     }
 80: 
 81:     ~model19f053892e3a2_851b263221b353f53f6e5ee203c5b150() { }
 82: 
 83: 
 84:     void transform_inits(const stan::io::var_context& context__,
 85:                          std::vector<int>& params_i__,
 86:                          std::vector<double>& params_r__,
 87:                          std::ostream* pstream__) const {
 88:         stan::io::writer<double> writer__(params_r__,params_i__);
 89:         size_t pos__;
 90:         (void) pos__; // dummy call to supress warning
 91:         std::vector<double> vals_r__;
 92:         std::vector<int> vals_i__;
 93: 
 94:         if (!(context__.contains_r("y")))
 95:             throw std::runtime_error("variable y missing");
 96:         vals_r__ = context__.vals_r("y");
 97:         pos__ = 0U;
 98:         context__.validate_dims("initialization", "y", "double", context__.to_vec());
 99:         // generate_declaration y
100:         double y(0);
101:         y = vals_r__[pos__++];
102:         try {
103:             writer__.scalar_unconstrain(y);
104:         } catch (const std::exception& e) { 
105:             throw std::runtime_error(std::string("Error transforming variable y: ") + e.what());
106:         }
107: 
108:         params_r__ = writer__.data_r();
109:         params_i__ = writer__.data_i();
110:     }
111: 
112:     void transform_inits(const stan::io::var_context& context,
113:                          Eigen::Matrix<double,Eigen::Dynamic,1>& params_r,
114:                          std::ostream* pstream__) const {
115:       std::vector<double> params_r_vec;
116:       std::vector<int> params_i_vec;
117:       transform_inits(context, params_i_vec, params_r_vec, pstream__);
118:       params_r.resize(params_r_vec.size());
119:       for (int i = 0; i < params_r.size(); ++i)
120:         params_r(i) = params_r_vec[i];
121:     }
122: 
123: 
124:     template <bool propto__, bool jacobian__, typename T__>
125:     T__ log_prob(vector<T__>& params_r__,
126:                  vector<int>& params_i__,
127:                  std::ostream* pstream__ = 0) const {
128: 
129:         T__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
130:         (void) DUMMY_VAR__;  // suppress unused var warning
131: 
132:         T__ lp__(0.0);
133:         stan::math::accumulator<T__> lp_accum__;
134: 
135:         // model parameters
136:         stan::io::reader<T__> in__(params_r__,params_i__);
137: 
138:         T__ y;
139:         (void) y;  // dummy to suppress unused var warning
140:         if (jacobian__)
141:             y = in__.scalar_constrain(lp__);
142:         else
143:             y = in__.scalar_constrain();
144: 
145: 
146:         // transformed parameters
147: 
148: 
149:         try {
150:         } catch (const std::exception& e) {
151:             stan::lang::rethrow_located(e,current_statement_begin__);
152:             // Next line prevents compiler griping about no return
153:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
154:         }
155: 
156:         // validate transformed parameters
157: 
158:         const char* function__ = "validate transformed params";
159:         (void) function__;  // dummy to suppress unused var warning
160: 
161:         // model body
162:         try {
163: 
164:             current_statement_begin__ = 8;
165:             lp_accum__.add(normal_log<propto__>(y, 0, 1));
166:         } catch (const std::exception& e) {
167:             stan::lang::rethrow_located(e,current_statement_begin__);
168:             // Next line prevents compiler griping about no return
169:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
170:         }
171: 
172:         lp_accum__.add(lp__);
173:         return lp_accum__.sum();
174: 
175:     } // log_prob()
176: 
177:     template <bool propto, bool jacobian, typename T_>
178:     T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
179:                std::ostream* pstream = 0) const {
180:       std::vector<T_> vec_params_r;
181:       vec_params_r.reserve(params_r.size());
182:       for (int i = 0; i < params_r.size(); ++i)
183:         vec_params_r.push_back(params_r(i));
184:       std::vector<int> vec_params_i;
185:       return log_prob<propto,jacobian,T_>(vec_params_r, vec_params_i, pstream);
186:     }
187: 
188: 
189:     void get_param_names(std::vector<std::string>& names__) const {
190:         names__.resize(0);
191:         names__.push_back("y");
192:     }
193: 
194: 
195:     void get_dims(std::vector<std::vector<size_t> >& dimss__) const {
196:         dimss__.resize(0);
197:         std::vector<size_t> dims__;
198:         dims__.resize(0);
199:         dimss__.push_back(dims__);
200:     }
201: 
202:     template <typename RNG>
203:     void write_array(RNG& base_rng__,
204:                      std::vector<double>& params_r__,
205:                      std::vector<int>& params_i__,
206:                      std::vector<double>& vars__,
207:                      bool include_tparams__ = true,
208:                      bool include_gqs__ = true,
209:                      std::ostream* pstream__ = 0) const {
210:         vars__.resize(0);
211:         stan::io::reader<double> in__(params_r__,params_i__);
212:         static const char* function__ = "model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::write_array";
213:         (void) function__; // dummy call to supress warning
214:         // read-transform, write parameters
215:         double y = in__.scalar_constrain();
216:         vars__.push_back(y);
217: 
218:         if (!include_tparams__) return;
219:         // declare and define transformed parameters
220:         double lp__ = 0.0;
221:         (void) lp__; // dummy call to supress warning
222:         stan::math::accumulator<double> lp_accum__;
223: 
224:         double DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
225:         (void) DUMMY_VAR__;  // suppress unused var warning
226: 
227: 
228: 
229:         try {
230:         } catch (const std::exception& e) {
231:             stan::lang::rethrow_located(e,current_statement_begin__);
232:             // Next line prevents compiler griping about no return
233:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
234:         }
235: 
236:         // validate transformed parameters
237: 
238:         // write transformed parameters
239: 
240:         if (!include_gqs__) return;
241:         // declare and define generated quantities
242: 
243: 
244:         try {
245:         } catch (const std::exception& e) {
246:             stan::lang::rethrow_located(e,current_statement_begin__);
247:             // Next line prevents compiler griping about no return
248:             throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
249:         }
250: 
251:         // validate generated quantities
252: 
253:         // write generated quantities
254:     }
255: 
256:     template <typename RNG>
257:     void write_array(RNG& base_rng,
258:                      Eigen::Matrix<double,Eigen::Dynamic,1>& params_r,
259:                      Eigen::Matrix<double,Eigen::Dynamic,1>& vars,
260:                      bool include_tparams = true,
261:                      bool include_gqs = true,
262:                      std::ostream* pstream = 0) const {
263:       std::vector<double> params_r_vec(params_r.size());
264:       for (int i = 0; i < params_r.size(); ++i)
265:         params_r_vec[i] = params_r(i);
266:       std::vector<double> vars_vec;
267:       std::vector<int> params_i_vec;
268:       write_array(base_rng,params_r_vec,params_i_vec,vars_vec,include_tparams,include_gqs,pstream);
269:       vars.resize(vars_vec.size());
270:       for (int i = 0; i < vars.size(); ++i)
271:         vars(i) = vars_vec[i];
272:     }
273: 
274:     static std::string model_name() {
275:         return "model19f053892e3a2_851b263221b353f53f6e5ee203c5b150";
276:     }
277: 
278: 
279:     void constrained_param_names(std::vector<std::string>& param_names__,
280:                                  bool include_tparams__ = true,
281:                                  bool include_gqs__ = true) const {
282:         std::stringstream param_name_stream__;
283:         param_name_stream__.str(std::string());
284:         param_name_stream__ << "y";
285:         param_names__.push_back(param_name_stream__.str());
286: 
287:         if (!include_gqs__ && !include_tparams__) return;
288: 
289:         if (!include_gqs__) return;
290:     }
291: 
292: 
293:     void unconstrained_param_names(std::vector<std::string>& param_names__,
294:                                    bool include_tparams__ = true,
295:                                    bool include_gqs__ = true) const {
296:         std::stringstream param_name_stream__;
297:         param_name_stream__.str(std::string());
298:         param_name_stream__ << "y";
299:         param_names__.push_back(param_name_stream__.str());
300: 
301:         if (!include_gqs__ && !include_tparams__) return;
302: 
303:         if (!include_gqs__) return;
304:     }
305: 
306: }; // model
307: 
308: } // namespace
309: 
310: typedef model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150 stan_model;
311: 
312: #include <rstan/rstaninc.hpp>
313: /**
314:  * Define Rcpp Module to expose stan_fit's functions to R.
315:  */
316: RCPP_MODULE(stan_fit4model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_mod){
317:   Rcpp::class_<rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150,
318:                boost::random::ecuyer1988> >("stan_fit4model19f053892e3a2_851b263221b353f53f6e5ee203c5b150")
319:     // .constructor<Rcpp::List>()
320:     .constructor<SEXP, SEXP>()
321:     // .constructor<SEXP, SEXP>()
322:     .method("call_sampler",
323:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::call_sampler)
324:     .method("param_names",
325:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::param_names)
326:     .method("param_names_oi",
327:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::param_names_oi)
328:     .method("param_fnames_oi",
329:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::param_fnames_oi)
330:     .method("param_dims",
331:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::param_dims)
332:     .method("param_dims_oi",
333:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::param_dims_oi)
334:     .method("update_param_oi",
335:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::update_param_oi)
336:     .method("param_oi_tidx",
337:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::param_oi_tidx)
338:     .method("grad_log_prob",
339:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::grad_log_prob)
340:     .method("log_prob",
341:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::log_prob)
342:     .method("unconstrain_pars",
343:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::unconstrain_pars)
344:     .method("constrain_pars",
345:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::constrain_pars)
346:     .method("num_pars_unconstrained",
347:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::num_pars_unconstrained)
348:     .method("unconstrained_param_names",
349:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::unconstrained_param_names)
350:     .method("constrained_param_names",
351:             &rstan::stan_fit<model19f053892e3a2_851b263221b353f53f6e5ee203c5b150_namespace::model19f053892e3a2_851b263221b353f53f6e5ee203c5b150, boost::random::ecuyer1988>::constrained_param_names)
352:     ;
353: }
354: 
355: // declarations
356: extern "C" {
357: SEXP file19f05392900cc( ) ;
358: }
359: 
360: // definition
361: 
362: SEXP file19f05392900cc(  ){
363:  return Rcpp::wrap("851b263221b353f53f6e5ee203c5b150");
364: }
365: 
366: 
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from /usr/lib/R/library/RcppEigen/include/Eigen/Core:276:0,
                 from /usr/lib/R/library/RcppEigen/include/Eigen/Dense:1,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/core/matrix_vari.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/core.hpp:14,
                 from /usr/lib/R/library/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/stan/math.hpp:4,
                 from /usr/lib/R/library/StanHeaders/include/src/stan/model/model_header.hpp:4,
                 from file19f05392900cc.cpp:8:
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:973:28: error: ‘templat
In addition: Warning message:
running command '/usr/lib/R/bin/R CMD SHLIB file19f05392900cc.cpp 2> file19f05392900cc.cpp.err.txt' had status 1
9

like this?
/usr/lib/R/library/RcppEigen/include/Eigen/src/Core/Functors.h:977:28: error: ‘template<class _Operation> class std::binder1st’ is deprecated [-Werror=deprecated-declarations]?

10

Yes, you need to get -Werror out of your configuration.

11

and putting in the Makevars CXXFLAGS= -Werror will do that?

12

No, removing -Werror from CXXFLAGS in Makevars will do that.

13 
> rstan::stan(model_code = model_code)
In file included from /data/co/CSL0301/script/lib/rstan/include/rstan/rstaninc.hpp:3:0,
                 from file76f20b5be95.cpp:319:
/data/co/CSL0301/script/lib/rstan/include/rstan/stan_fit.hpp: In function ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector<long unsigned int>&, const std::vector<std::basic_string<char> >&, RNG_t&)’:
/data/co/CSL0301/script/lib/rstan/include/rstan/stan_fit.hpp:438:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<stan::io::var_context> init_context_ptr;
        ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from /data/co/CSL0301/script/lib/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from /data/co/CSL0301/script/lib/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from /data/co/CSL0301/script/lib/BH/include/boost/lexical_cast/try_lexical_convert.hpp:42,
                 from /data/co/CSL0301/script/lib/BH/include/boost/lexical_cast.hpp:32,
                 from /data/co/CSL0301/script/lib/BH/include/boost/math/tools/convert_from_string.hpp:15,
                 from /data/co/CSL0301/script/lib/BH/include/boost/math/constants/constants.hpp:13,
                 from /data/co/CSL0301/script/lib/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
                 from /data/co/CSL0301/script/lib/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
                 from /data/co/CSL0301/script/lib/StanHeaders/include/stan/math/rev/core.hpp:34,
                 from /data/co/CSL0301/script/lib/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /data/co/CSL0301/script/lib/StanHeaders/include/stan/math.hpp:4,
                 from /data/co/CSL0301/script/lib/StanHeaders/include/src/stan/model/model_header.hpp:4,
                 from file76f20b5be95.cpp:8:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from /data/co/CSL0301/script/lib/rstan/include/rstan/rstaninc.hpp:3:0,
                 from file76f20b5be95.cpp:319:
/data/co/CSL0301/script/lib/rstan/include/rstan/stan_fit.hpp:547:10: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     std::auto_ptr<rstan_sample_writer> sample_writer_ptr;
          ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from /data/co/CSL0301/script/lib/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from /data/co/CSL0301/script/lib/BH/include/boost/lexical_cast/detail/converter_lexical.hpp:54,
                 from /data/co/CSL0301/script/lib/BH/include/boost/lexical_cast/try_lexical_convert.hpp:42,
                 from /data/co/CSL0301/script/lib/BH/include/boost/lexical_cast.hpp:32,
                 from /data/co/CSL0301/script/lib/BH/include/boost/math/tools/convert_from_string.hpp:15,
                 from /data/co/CSL0301/script/lib/BH/include/boost/math/constants/constants.hpp:13,
                 from /data/co/CSL0301/script/lib/StanHeaders/include/stan/math/prim/scal/fun/constants.hpp:4,
                 from /data/co/CSL0301/script/lib/StanHeaders/include/stan/math/rev/core/operator_unary_plus.hpp:7,
                 from /data/co/CSL0301/script/lib/StanHeaders/include/stan/math/rev/core.hpp:34,
                 from /data/co/CSL0301/script/lib/StanHeaders/include/stan/math/rev/mat.hpp:4,
                 from /data/co/CSL0301/script/lib/StanHeaders/include/stan/math.hpp:4,
                 from /data/co/CSL0301/script/lib/StanHeaders/include/src/stan/model/model_header.hpp:4,
                 from file76f20b5be95.cpp:8:
/usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
Error in .Object$initialize(...) : 
  could not find function "cpp_object_initializer"
trying deprecated constructor; please alert package maintainer
Error in .Object$initialize(...) : 
  could not find function "cpp_object_initializer"
failed to create the sampler; sampling not done
14

should i remove -Wdeprecated-declarations?

15

I suspect you are calling your .R file from Rscript. In that case, you need library(Rcpp) in your .R file or you need to put --default-packages=Rcpp into the invocation of Rscript.

16 
library(rstan)
library(Rcpp)

f <- function(i,mod) {
  rstan::stan(model_code = mod)
}

model_code='
data {
}
parameters {
  real y;
}
model {
  y ~ normal(0, 1);
}'


x2 <-qapply::qapply(X = 1:30,
                    FUN = f,
                    fargs = list(mod=model_code),
                    nCores = 10,
                    workDir = 'qapply',
                    tag = 'teststan',
                    clearWd=FALSE)

Loading required package: Rcpp
Loading required package: rstan
Loading required package: ggplot2
Loading required package: StanHeaders
rstan (Version 2.16.2, packaged: 2017-07-03 09:24:58 UTC, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
rstan_options(auto_write = TRUE)
options(mc.cores = parallel::detectCores())
Loading required package: rlecuyer
Error in compileCode(f, code, language = language, verbose = verbose) : 
  Compilation ERROR, function(s)/method(s) not created! In file included from /data/co/CSL0301/script/lib/rstan/include/rstan/rstaninc.hpp:3:0,
                 from file275a7dd10e58.cpp:319:
/data/co/CSL0301/script/lib/rstan/include/rstan/stan_fit.hpp: In function ‘int rstan::{anonymous}::command(rstan::stan_args&, Model&, Rcpp::List&, const std::vector<long unsigned int>&, const std::vector<std::basic_string<char> >&, RNG_t&)’:
/data/co/CSL0301/script/lib/rstan/include/rstan/stan_fit.hpp:438:8: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
   std::auto_ptr<stan::io::var_context> init_context_ptr;
        ^~~~~~~~
In file included from /usr/include/c++/6/bits/locale_conv.h:41:0,
                 from /usr/include/c++/6/locale:43,
                 from /data/co/CSL0301/script/lib/BH/include/boost/lexical_cast/detail/converter_lexical_streams.hpp:43,
                 from /data/co/CSL0301/script/lib/BH/include/boost/lexical_cast
Calls: do.call ... stan_model -> cxxfunctionplus -> cxxfunction -> compileCode
In addition: Warning message:
running command '/usr/lib/R/bin/R CMD SHLIB file275a7dd10e58.cpp 2> file275a7dd10e58.cpp.err.txt' had status 1 
Execution halted
17

This output does not state what the error is. You may need to load Rcpp on the compute nodes.

But again, you should be able to write a .stan program on the disk, compile it once with auto_write = TRUE, and pass the (perhaps full) path to the .stan program to each compute node and they should read the compiled model off the disk.

18

that output was from a compute node (shows Rcpp being loaded). I’ll try loading the compiled program

19

i would need to copy the .h, .so created in the tempdir of the master node after compilation to the tempdir of a compute node, for rstan to pick it up?

20

That would only work if the different grid nodes use the same tempdir, which they ordinarily would not if they are different R processes. You can force them to with an environmental variable, which is documented in ?tempdir.