# Bin/stanc segfault on cluster

**URL:** <https://discourse.mc-stan.org/t/bin-stanc-segfault-on-cluster/336>\
**Category:** CmdStan\
**Tags:** stanc\
**Created:** [April 12, 2017, 3:11pm UTC](https://discourse.mc-stan.org/t/bin-stanc-segfault-on-cluster/336 "2017-04-12T15:11:31Z")\
**Posts on this page:** 4\
**Page:** 1

<div class="post-metadata">

**Author:** ![sakrejda](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/sakrejda/32/845_2.png) [@sakrejda](https://discourse.mc-stan.org/u/sakrejda)\
**Post date:** [April 12, 2017, 3:11pm UTC](https://discourse.mc-stan.org/t/bin-stanc-segfault-on-cluster/336/1 "2017-04-12T15:11:31Z")

</div>

So I’m trying to get CmdStan going on a cluster and I get:

```
--- Translating Stan model to C++ code ---
bin/stanc examples/bernoulli/bernoulli.stan --o=examples/bernoulli/bernoulli.hpp
make: *** [examples/bernoulli/bernoulli.hpp] Segmentation fault

```

I requested plenty of memory, I cloned develop and pulled in the submodules, it has  
sane modules loaded:

```
[ks79a@ghpcc06 cmdstan]$ module list
Currently Loaded Modulefiles:
  1) gcc/5.1.0 2) glibc/2.23 3) cmake/3.2.2 4) git/2.1.3 5) R/3.3.1

```

uname -a gives:

```
Linux c35b15 2.6.32-642.4.2.el6.x86_64 #1 SMP Mon Aug 15 02:06:41 EDT 2016 x86_64 x86_64 x86_64 GNU/Linux

```

I’m confused. Ring any bells for you guys?

Full output below but…

```
Job <make examples/bernoulli/bernoulli> was submitted from host <ghpcc06> by user <ks79a> in cluster <umghpcc>.
Job was executed on host(s) <c35b15>, in queue <condo_uma_nicholas_reich>, as user <ks79a> in cluster <umghpcc>.
</home/ks79a> was used as the home directory.
</home/ks79a/cmdstan/.> was used as the working directory.
Started at Wed Apr 12 10:52:46 2017
Results reported on Wed Apr 12 10:57:43 2017

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
make examples/bernoulli/bernoulli
------------------------------------------------------------

Exited with exit code 2.

Resource usage summary:

    CPU time : 251.83 sec.
    Max Memory : 1823 MB
    Average Memory : 689.25 MB
    Total Requested Memory : 4096.00 MB
    Delta Memory : 2273.00 MB
    Max Processes : 6
    Max Threads : 7
    Run time : 297 sec.
    Turnaround time : 302 sec.

The output (if any) follows:

g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -c -O3 -o bin/cmdstan/stanc.o src/cmdstan/stanc.cpp
g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -c -O0 -o bin/stan/lang/grammars/expression07_grammar_inst.o stan/src/stan/lang/grammars/expression07_grammar_inst.cpp
g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -c -O0 -o bin/stan/lang/grammars/statement_grammar_inst.o stan/src/stan/lang/grammars/statement_grammar_inst.cpp
g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -c -O0 -o bin/stan/lang/grammars/indexes_grammar_inst.o stan/src/stan/lang/grammars/indexes_grammar_inst.cpp
g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -c -O0 -o bin/stan/lang/grammars/functions_grammar_inst.o stan/src/stan/lang/grammars/functions_grammar_inst.cpp
g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -c -O0 -o bin/stan/lang/grammars/whitespace_grammar_inst.o stan/src/stan/lang/grammars/whitespace_grammar_inst.cpp
g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -c -O0 -o bin/stan/lang/grammars/expression_grammar_inst.o stan/src/stan/lang/grammars/expression_grammar_inst.cpp
g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -c -O0 -o bin/stan/lang/grammars/bare_type_grammar_inst.o stan/src/stan/lang/grammars/bare_type_grammar_inst.cpp
g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -c -O0 -o bin/stan/lang/grammars/term_grammar_inst.o stan/src/stan/lang/grammars/term_grammar_inst.cpp
g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -c -O0 -o bin/stan/lang/grammars/var_decls_grammar_inst.o stan/src/stan/lang/grammars/var_decls_grammar_inst.cpp
g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -c -O0 -o bin/stan/lang/grammars/statement_2_grammar_inst.o stan/src/stan/lang/grammars/statement_2_grammar_inst.cpp
g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -c -O0 -o bin/stan/lang/grammars/program_grammar_inst.o stan/src/stan/lang/grammars/program_grammar_inst.cpp
g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -c -O0 -o bin/stan/lang/grammars/semantic_actions_def.o stan/src/stan/lang/grammars/semantic_actions_def.cpp
g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -c -O0 -o bin/stan/lang/ast_def.o stan/src/stan/lang/ast_def.cpp
ar -rs bin/libstanc.a bin/stan/lang/grammars/expression07_grammar_inst.o bin/stan/lang/grammars/statement_grammar_inst.o bin/stan/lang/grammars/indexes_grammar_inst.o bin/stan/lang/grammars/functions_grammar_inst.o bin/stan/lang/grammars/whitespace_grammar_inst.o bin/stan/lang/grammars/expression_grammar_inst.o bin/stan/lang/grammars/bare_type_grammar_inst.o bin/stan/lang/grammars/term_grammar_inst.o bin/stan/lang/grammars/var_decls_grammar_inst.o bin/stan/lang/grammars/statement_2_grammar_inst.o bin/stan/lang/grammars/program_grammar_inst.o bin/stan/lang/grammars/semantic_actions_def.o bin/stan/lang/ast_def.o
ar: creating bin/libstanc.a
g++ -I src -I stan/src -isystem stan/lib/stan_math/ -isystem stan/lib/stan_math/lib/eigen_3.2.9 -isystem stan/lib/stan_math/lib/boost_1.62.0 -isystem stan/lib/stan_math/lib/cvodes_2.9.0/include -Wall -DEIGEN_NO_DEBUG -DBOOST_RESULT_OF_USE_TR1 -DBOOST_NO_DECLTYPE -DBOOST_DISABLE_ASSERTS -DFUSION_MAX_VECTOR_SIZE=12 -DNO_FPRINTF_OUTPUT -pipe -lpthread -O0 -o bin/stanc bin/cmdstan/stanc.o -Lbin -lstanc

--- Translating Stan model to C++ code ---
bin/stanc examples/bernoulli/bernoulli.stan --o=examples/bernoulli/bernoulli.hpp
make: *** [examples/bernoulli/bernoulli.hpp] Segmentation fault

```

---

<div class="post-metadata">

**Author:** ![sakrejda](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/sakrejda/32/845_2.png) [@sakrejda](https://discourse.mc-stan.org/u/sakrejda)\
**Post date:** [April 12, 2017, 5:23pm UTC](https://discourse.mc-stan.org/t/bin-stanc-segfault-on-cluster/336/2 "2017-04-12T17:23:50Z")

</div>

Huh, this segfaults when I just run `stanc --version` and it segfaults _before_ the first line in `main`… ok.

---

<div class="post-metadata">

**Author:** ![Bob\_Carpenter](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/bob_carpenter/32/9230_2.png) [@Bob\_Carpenter](https://discourse.mc-stan.org/u/Bob_Carpenter)\
**Post date:** [April 12, 2017, 6:37pm UTC](https://discourse.mc-stan.org/t/bin-stanc-segfault-on-cluster/336/3 "2017-04-12T18:37:19Z")

</div>

This can happen if you compiled on one platform and are trying to run on another. The binaries have to match.

---

<div class="post-metadata">

**Author:** ![sakrejda](https://yyz2.discourse-cdn.com/flex030/user_avatar/discourse.mc-stan.org/sakrejda/32/845_2.png) [@sakrejda](https://discourse.mc-stan.org/u/sakrejda)\
**Post date:** [April 12, 2017, 6:37pm UTC](https://discourse.mc-stan.org/t/bin-stanc-segfault-on-cluster/336/4 "2017-04-12T18:37:54Z")

</div>

Actually I just learned that _everything_ I compile on this cluster segfaults, so… yeah… fixing that first.