I’m trying to use rstan and brms in a High-Performance Computing (HPC) system, which runs Linux 3.10.0-327.36.3.el7.x86_64 x86_64. I run the following codes in a Conda environment.
I created the Conda environment with following codes (Conda version: 4.10.1):
conda create -n testenv
conda activate testenv
conda install -c conda-forge r-brms
conda install -c conda-forge r-bh
Then I open R in the env and run the following codes:
library(rstan)
example(stan_model, package = "rstan", run.dontrun = TRUE)
With above code I got the error:
ERROR(s) during compilation: source code errors or compiler configuration errors!
The full output is saved as full_output.txt (35.1 KB). And the part relating to the error is:
make cmd is
make -f '/scratch/hj23/miniconda3/envs/test2/lib/R/etc/Makeconf' -f '/scratch/hj23/miniconda3/envs/test2/lib/R/share/make/shlib.mk' -f '/home/hj23/.R/Makevars' CXX='$(CXX14) $(CXX14STD)' CXXFLAGS='$(CXX14FLAGS)' CXXPICFLAGS='$(CXX14PICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX14LDFLAGS)' SHLIB_LD='$(SHLIB_CXX14LD)' SHLIB='file39106a922ce2.so' OBJECTS='file39106a922ce2.o'
make would use
x86_64-conda-linux-gnu-c++ -std=gnu++14 -I"/scratch/hj23/miniconda3/envs/test2/lib/R/include" -DNDEBUG -I"/scratch/hj23/miniconda3/envs/test2/lib/R/library/Rcpp/include/" -I"/scratch/hj23/miniconda3/envs/test2/lib/R/library/RcppEigen/include/" -I"/scratch/hj23/miniconda3/envs/test2/lib/R/library/RcppEigen/include/unsupported" -I"/scratch/hj23/miniconda3/envs/test2/lib/R/library/BH/include" -I"/scratch/hj23/miniconda3/envs/test2/lib/R/library/StanHeaders/include/src/" -I"/scratch/hj23/miniconda3/envs/test2/lib/R/library/StanHeaders/include/" -I"/scratch/hj23/miniconda3/envs/test2/lib/R/library/RcppParallel/include/" -I"/scratch/hj23/miniconda3/envs/test2/lib/R/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/scratch/hj23/miniconda3/envs/test2/lib/R/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /scratch/hj23/miniconda3/envs/test2/include -I/scratch/hj23/miniconda3/envs/test2/include -Wl,-rpath-link,/scratch/hj23/miniconda3/envs/test2/lib -fpic -O3 -march=native -mtune=native -fPIC -c file39106a922ce2.cpp -o file39106a922ce2.o
if test "zfile39106a922ce2.o" != "z"; then \
echo x86_64-conda-linux-gnu-c++ -std=gnu++14 -shared -L"/scratch/hj23/miniconda3/envs/test2/lib/R/lib" -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/scratch/hj23/miniconda3/envs/test2/lib -Wl,-rpath-link,/scratch/hj23/miniconda3/envs/test2/lib -L/scratch/hj23/miniconda3/envs/test2/lib -o file39106a922ce2.so file39106a922ce2.o '/scratch/hj23/miniconda3/envs/test2/lib/R/library/rstan/lib//libStanServices.a' -L'/scratch/hj23/miniconda3/envs/test2/lib/R/library/StanHeaders/lib/' -lStanHeaders -L'/scratch/hj23/miniconda3/envs/test2/lib/R/library/RcppParallel/lib/' -ltbb -L"/scratch/hj23/miniconda3/envs/test2/lib/R/lib" -lR; \
x86_64-conda-linux-gnu-c++ -std=gnu++14 -shared -L"/scratch/hj23/miniconda3/envs/test2/lib/R/lib" -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/scratch/hj23/miniconda3/envs/test2/lib -Wl,-rpath-link,/scratch/hj23/miniconda3/envs/test2/lib -L/scratch/hj23/miniconda3/envs/test2/lib -o file39106a922ce2.so file39106a922ce2.o '/scratch/hj23/miniconda3/envs/test2/lib/R/library/rstan/lib//libStanServices.a' -L'/scratch/hj23/miniconda3/envs/test2/lib/R/library/StanHeaders/lib/' -lStanHeaders -L'/scratch/hj23/miniconda3/envs/test2/lib/R/library/RcppParallel/lib/' -ltbb -L"/scratch/hj23/miniconda3/envs/test2/lib/R/lib" -lR; \
fi
ERROR(s) during compilation: source code errors or compiler configuration errors!
Program source:
1:
2: // includes from the plugin
3: // [[Rcpp::plugins(cpp14)]]
4:
5:
6: // user includes
7: #include <Rcpp.h>
8: #include <rstan/io/rlist_ref_var_context.hpp>
9: #include <rstan/io/r_ostream.hpp>
10: #include <rstan/stan_args.hpp>
11: #include <boost/integer/integer_log2.hpp>
12: // Code generated by Stan version 2.21.0
13:
14: #include <stan/model/model_header.hpp>
15:
16: namespace model3910519e785d_16a540c6086086816528e4524def24d9_namespace {
17:
18: using std::istream;
19: using std::string;
20: using std::stringstream;
21: using std::vector;
22: using stan::io::dump;
23: using stan::math::lgamma;
24: using stan::model::prob_grad;
25: using namespace stan::math;
26:
27: static int current_statement_begin__;
28:
29: stan::io::program_reader prog_reader__() {
30: stan::io::program_reader reader;
31: reader.add_event(0, 0, "start", "model3910519e785d_16a540c6086086816528e4524def24d9");
32: reader.add_event(3, 1, "end", "model3910519e785d_16a540c6086086816528e4524def24d9");
33: return reader;
34: }
35:
36: class model3910519e785d_16a540c6086086816528e4524def24d9
37: : public stan::model::model_base_crtp<model3910519e785d_16a540c6086086816528e4524def24d9> {
38: private:
39: double y_mean;
40: public:
41: model3910519e785d_16a540c6086086816528e4524def24d9(rstan::io::rlist_ref_var_context& context__,
42: std::ostream* pstream__ = 0)
43: : model_base_crtp(0) {
44: ctor_body(context__, 0, pstream__);
45: }
46:
47: model3910519e785d_16a540c6086086816528e4524def24d9(stan::io::var_context& context__,
48: unsigned int random_seed__,
49: std::ostream* pstream__ = 0)
50: : model_base_crtp(0) {
51: ctor_body(context__, random_seed__, pstream__);
52: }
53:
54: void ctor_body(stan::io::var_context& context__,
55: unsigned int random_seed__,
56: std::ostream* pstream__) {
57: typedef double local_scalar_t__;
58:
59: boost::ecuyer1988 base_rng__ =
60: stan::services::util::create_rng(random_seed__, 0);
61: (void) base_rng__; // suppress unused var warning
62:
63: current_statement_begin__ = -1;
64:
65: static const char* function__ = "model3910519e785d_16a540c6086086816528e4524def24d9_namespace::model3910519e785d_16a540c6086086816528e4524def24d9";
66: (void) function__; // dummy to suppress unused var warning
67: size_t pos__;
68: (void) pos__; // dummy to suppress unused var warning
69: std::vector<int> vals_i__;
70: std::vector<double> vals_r__;
71: local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
72: (void) DUMMY_VAR__; // suppress unused var warning
73:
74: try {
75: // initialize data block variables from context__
76: current_statement_begin__ = 1;
77: context__.validate_dims("data initialization", "y_mean", "double", context__.to_vec());
78: y_mean = double(0);
79: vals_r__ = context__.vals_r("y_mean");
80: pos__ = 0;
81: y_mean = vals_r__[pos__++];
82:
83:
84: // initialize transformed data variables
85: // execute transformed data statements
86:
87: // validate transformed data
88:
89: // validate, set parameter ranges
90: num_params_r__ = 0U;
91: param_ranges_i__.clear();
92: current_statement_begin__ = 1;
93: num_params_r__ += 1;
94: } catch (const std::exception& e) {
95: stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
96: // Next line prevents compiler griping about no return
97: throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
98: }
99: }
100:
101: ~model3910519e785d_16a540c6086086816528e4524def24d9() { }
102:
103:
104: void transform_inits(const stan::io::var_context& context__,
105: std::vector<int>& params_i__,
106: std::vector<double>& params_r__,
107: std::ostream* pstream__) const {
108: typedef double local_scalar_t__;
109: stan::io::writer<double> writer__(params_r__, params_i__);
110: size_t pos__;
111: (void) pos__; // dummy call to supress warning
112: std::vector<double> vals_r__;
113: std::vector<int> vals_i__;
114:
115: current_statement_begin__ = 1;
116: if (!(context__.contains_r("y")))
117: stan::lang::rethrow_located(std::runtime_error(std::string("Variable y missing")), current_statement_begin__, prog_reader__());
118: vals_r__ = context__.vals_r("y");
119: pos__ = 0U;
120: context__.validate_dims("parameter initialization", "y", "double", context__.to_vec());
121: double y(0);
122: y = vals_r__[pos__++];
123: try {
124: writer__.scalar_unconstrain(y);
125: } catch (const std::exception& e) {
126: stan::lang::rethrow_located(std::runtime_error(std::string("Error transforming variable y: ") + e.what()), current_statement_begin__, prog_reader__());
127: }
128:
129: params_r__ = writer__.data_r();
130: params_i__ = writer__.data_i();
131: }
132:
133: void transform_inits(const stan::io::var_context& context,
134: Eigen::Matrix<double, Eigen::Dynamic, 1>& params_r,
135: std::ostream* pstream__) const {
136: std::vector<double> params_r_vec;
137: std::vector<int> params_i_vec;
138: transform_inits(context, params_i_vec, params_r_vec, pstream__);
139: params_r.resize(params_r_vec.size());
140: for (int i = 0; i < params_r.size(); ++i)
141: params_r(i) = params_r_vec[i];
142: }
143:
144:
145: template <bool propto__, bool jacobian__, typename T__>
146: T__ log_prob(std::vector<T__>& params_r__,
147: std::vector<int>& params_i__,
148: std::ostream* pstream__ = 0) const {
149:
150: typedef T__ local_scalar_t__;
151:
152: local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
153: (void) DUMMY_VAR__; // dummy to suppress unused var warning
154:
155: T__ lp__(0.0);
156: stan::math::accumulator<T__> lp_accum__;
157: try {
158: stan::io::reader<local_scalar_t__> in__(params_r__, params_i__);
159:
160: // model parameters
161: current_statement_begin__ = 1;
162: local_scalar_t__ y;
163: (void) y; // dummy to suppress unused var warning
164: if (jacobian__)
165: y = in__.scalar_constrain(lp__);
166: else
167: y = in__.scalar_constrain();
168:
169: // model body
170:
171: current_statement_begin__ = 1;
172: lp_accum__.add(normal_log<propto__>(y, y_mean, 1));
173:
174: } catch (const std::exception& e) {
175: stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
176: // Next line prevents compiler griping about no return
177: throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
178: }
179:
180: lp_accum__.add(lp__);
181: return lp_accum__.sum();
182:
183: } // log_prob()
184:
185: template <bool propto, bool jacobian, typename T_>
186: T_ log_prob(Eigen::Matrix<T_,Eigen::Dynamic,1>& params_r,
187: std::ostream* pstream = 0) const {
188: std::vector<T_> vec_params_r;
189: vec_params_r.reserve(params_r.size());
190: for (int i = 0; i < params_r.size(); ++i)
191: vec_params_r.push_back(params_r(i));
192: std::vector<int> vec_params_i;
193: return log_prob<propto,jacobian,T_>(vec_params_r, vec_params_i, pstream);
194: }
195:
196:
197: void get_param_names(std::vector<std::string>& names__) const {
198: names__.resize(0);
199: names__.push_back("y");
200: }
201:
202:
203: void get_dims(std::vector<std::vector<size_t> >& dimss__) const {
204: dimss__.resize(0);
205: std::vector<size_t> dims__;
206: dims__.resize(0);
207: dimss__.push_back(dims__);
208: }
209:
210: template <typename RNG>
211: void write_array(RNG& base_rng__,
212: std::vector<double>& params_r__,
213: std::vector<int>& params_i__,
214: std::vector<double>& vars__,
215: bool include_tparams__ = true,
216: bool include_gqs__ = true,
217: std::ostream* pstream__ = 0) const {
218: typedef double local_scalar_t__;
219:
220: vars__.resize(0);
221: stan::io::reader<local_scalar_t__> in__(params_r__, params_i__);
222: static const char* function__ = "model3910519e785d_16a540c6086086816528e4524def24d9_namespace::write_array";
223: (void) function__; // dummy to suppress unused var warning
224:
225: // read-transform, write parameters
226: double y = in__.scalar_constrain();
227: vars__.push_back(y);
228:
229: double lp__ = 0.0;
230: (void) lp__; // dummy to suppress unused var warning
231: stan::math::accumulator<double> lp_accum__;
232:
233: local_scalar_t__ DUMMY_VAR__(std::numeric_limits<double>::quiet_NaN());
234: (void) DUMMY_VAR__; // suppress unused var warning
235:
236: if (!include_tparams__ && !include_gqs__) return;
237:
238: try {
239: if (!include_gqs__ && !include_tparams__) return;
240: if (!include_gqs__) return;
241: } catch (const std::exception& e) {
242: stan::lang::rethrow_located(e, current_statement_begin__, prog_reader__());
243: // Next line prevents compiler griping about no return
244: throw std::runtime_error("*** IF YOU SEE THIS, PLEASE REPORT A BUG ***");
245: }
246: }
247:
248: template <typename RNG>
249: void write_array(RNG& base_rng,
250: Eigen::Matrix<double,Eigen::Dynamic,1>& params_r,
251: Eigen::Matrix<double,Eigen::Dynamic,1>& vars,
252: bool include_tparams = true,
253: bool include_gqs = true,
254: std::ostream* pstream = 0) const {
255: std::vector<double> params_r_vec(params_r.size());
256: for (int i = 0; i < params_r.size(); ++i)
257: params_r_vec[i] = params_r(i);
258: std::vector<double> vars_vec;
259: std::vector<int> params_i_vec;
260: write_array(base_rng, params_r_vec, params_i_vec, vars_vec, include_tparams, include_gqs, pstream);
261: vars.resize(vars_vec.size());
262: for (int i = 0; i < vars.size(); ++i)
263: vars(i) = vars_vec[i];
264: }
265:
266: std::string model_name() const {
267: return "model3910519e785d_16a540c6086086816528e4524def24d9";
268: }
269:
270:
271: void constrained_param_names(std::vector<std::string>& param_names__,
272: bool include_tparams__ = true,
273: bool include_gqs__ = true) const {
274: std::stringstream param_name_stream__;
275: param_name_stream__.str(std::string());
276: param_name_stream__ << "y";
277: param_names__.push_back(param_name_stream__.str());
278:
279: if (!include_gqs__ && !include_tparams__) return;
280:
281: if (include_tparams__) {
282: }
283:
284: if (!include_gqs__) return;
285: }
286:
287:
288: void unconstrained_param_names(std::vector<std::string>& param_names__,
289: bool include_tparams__ = true,
290: bool include_gqs__ = true) const {
291: std::stringstream param_name_stream__;
292: param_name_stream__.str(std::string());
293: param_name_stream__ << "y";
294: param_names__.push_back(param_name_stream__.str());
295:
296: if (!include_gqs__ && !include_tparams__) return;
297:
298: if (include_tparams__) {
299: }
300:
301: if (!include_gqs__) return;
302: }
303:
304: }; // model
305:
306: } // namespace
307:
308: typedef model3910519e785d_16a540c6086086816528e4524def24d9_namespace::model3910519e785d_16a540c6086086816528e4524def24d9 stan_model;
309:
310: #ifndef USING_R
311:
312: stan::model::model_base& new_model(
313: stan::io::var_context& data_context,
314: unsigned int seed,
315: std::ostream* msg_stream) {
316: stan_model* m = new stan_model(data_context, seed, msg_stream);
317: return *m;
318: }
319:
320: #endif
321:
322:
323:
324: #include <rstan_next/stan_fit.hpp>
325:
326: struct stan_model_holder {
327: stan_model_holder(rstan::io::rlist_ref_var_context rcontext,
328: unsigned int random_seed)
329: : rcontext_(rcontext), random_seed_(random_seed)
330: {
331: }
332:
333: //stan::math::ChainableStack ad_stack;
334: rstan::io::rlist_ref_var_context rcontext_;
335: unsigned int random_seed_;
336: };
337:
338: Rcpp::XPtr<stan::model::model_base> model_ptr(stan_model_holder* smh) {
339: Rcpp::XPtr<stan::model::model_base> model_instance(new stan_model(smh->rcontext_, smh->random_seed_), true);
340: return model_instance;
341: }
342:
343: Rcpp::XPtr<rstan::stan_fit_base> fit_ptr(stan_model_holder* smh) {
344: return Rcpp::XPtr<rstan::stan_fit_base>(new rstan::stan_fit(model_ptr(smh), smh->random_seed_), true);
345: }
346:
347: std::string model_name(stan_model_holder* smh) {
348: return model_ptr(smh).get()->model_name();
349: }
350:
351: RCPP_MODULE(stan_fit4model3910519e785d_16a540c6086086816528e4524def24d9_mod){
352: Rcpp::class_<stan_model_holder>("stan_fit4model3910519e785d_16a540c6086086816528e4524def24d9")
353: .constructor<rstan::io::rlist_ref_var_context, unsigned int>()
354: .method("model_ptr", &model_ptr)
355: .method("fit_ptr", &fit_ptr)
356: .method("model_name", &model_name)
357: ;
358: }
359:
360:
361: // declarations
362: extern "C" {
363: SEXP file39106a922ce2( ) ;
364: }
365:
366: // definition
367: SEXP file39106a922ce2() {
368: return Rcpp::wrap("16a540c6086086816528e4524def24d9");
369: }
Compilation ERROR, function(s)/method(s) not created!
Error in compileCode(f, code, language = language, verbose = verbose) :
650 | return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~/scratch/hj23/miniconda3/envs/test2/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: /scratch/hj23/miniconda3/envs/test2/lib/R/library/rstan/lib//libStanServices.a(stan_fit.o): relocation R_X86_64_PC32 against undefined hidden symbol `_ZTCN5boost10wrapexceptISt14overflow_errorEE0_NS_16exception_detail10clone_implINS3_19error_info_injectorIS1_EEEE' can not be used when making a shared object/scratch/hj23/miniconda3/envs/test2/bin/../lib/gcc/x86_64-conda-linux-gnu/9.3.0/../../../../x86_64-conda-linux-gnu/bin/ld: final link failed: bad valuecollect2: error: ld returned 1 exit statusmake: *** [/scratch/hj23/miniconda3/envs/test2/lib/R/share/make/shlib.mk:10: file39106a922ce2.so] Error 1
I also tried the above codes in Conda env in a local iMac and it works well (it can sample). Thus, I guess the error is relating to HPC.
Please let me know what I can try and the potential limitations that the HPC may have.
Thanks in advance!