Hello all. I am trying to implement reduce_sum_static to parallelize over N (participants; this is why grainsize=1), but when I compile my model in PyStan3, I get an error Process finished with exit code 139 (interrupted by signal 11: SIGSEGV) functions { real partial_sum(real[,] RTu_rdm, int …

I have an error while downloading CmdStan to the cluster using install_cmdstan(): INFO:cmdstanpy:stan/lib/stan_math/stan/math/prim/prob/neg_binomial_2_log_glm_lpmf.hpp:139:17: error: expected ?;? before ?theta_tmp? WARNING:cmdstanpy:CmdStan installation failed This is the last lines. Is there a w…

But when I compile it on my local machine using CmdStanPy, it compiles without errors.

I don’t know if that helps, but PyStan3 fails to compile models that were complied fine with PyStan2.19.

Check the version of the c++ compiler on the cluster in that case.

Checked that on the cluster: >g++ --version >g++ (GCC) 4.8.5 20150623 (Red Hat 4.8.5-36) On my local machine it’s g++ --version Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 9.0.0 (clang-900.0.39.2) Ta…

Your local compiler is clang 9.0, which is why ot works locally. I can confirm it will definitely not work with 4.8.5.

ok, that’s good to know about clang! Thanks! I asked my system admins if C++ compiler can be updated, so let’s hope for the best. Is this also why PyStan3 models don’t compile?

On the cluster you will not be able to compile with g++ 4.8.5 with any Stan interface, so I would imagine so. All interfaces have the same backend that requires g++ 4.9.3 or clang 5.0+ (we officially say 6 because that is what we test).

Hmm are you sure about that? I run models just fine with pystan2.19 on this cluster… Also, is there a way to easily change g++ to clang? Maybe cluster’s clang version is ok.

On the cluster run: clang++ --version to see if it exists. pystan2.19 uses the older version of the Math backend that could be used with older compiler pre-4.9.3.

Reduce_sum_static fails to compile with SIGSEGV error - PyStan3

Modeling

ahartikainen August 2, 2020, 3:46pm 18

conda has its own compilers too (conda install possible), but I recommend following the official route on clusters.

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Reduce_sum_static fails to compile with SIGSEGV error - PyStan3

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