I fixed the compiler error from using cmdstan described here by installing the more updated gcc-4.9.4 locally in my account on a cluster that I don’t have root access. However, bin/stanc keeps looking up the system’s older /lib64/libstdc++.so.6 and complains with the error message below even when I…

This is an issue on our local cluster and we have activate scripts to setup the env vars appropriately. I think you’re just missing LDFLAGS but this is what I use: $ cat /soft/stan/activate ver=2.17.0 echo "activating stan v$ver" export CMDSTAN=/soft/stan/cmdstan-2.17.1 export PATH=/soft/clang/4.0…

Thanks for the suggestion. Appreciated. I tried adding the environment variables in your suggestion but the same error message appears. bin/stanc still stubbornly looks up the libstdc++.so.6 under the system installed /lib64 even though the more updated gcc-4.9.4 installation added by me seems to w…

With the LDFLAGS now added, I removed cmdstan and installed it again. Unfortunately, the same error message continues to appear when trying to compile the example stan model despite that the cmdstan was successfully compiled using the gcc-4.9.4 installed by me!

You may need to check that the LDFLAGS is being used when building CmdStan. At some point, make will show the command used and it should contain the path to your GCC. (You could do just that by removing bin/stanc and doing make build). If it still doesn’t work, run ldd -v on the stanc binary and c…

Thanks for helping troubleshoot this, I know all the info on how do to it is in the various compiler-related docs but it sucks that we have to visit it on users without a detailed non-dev explanation of exactly where all the bits are found. Would be great to have some FAQ items for this so helping …

Well, DIY C++ toolchain is hard on any platform

Thank you very much for the guidance. It’s very useful. I checked accordingly and noticed LDFLAGS was not being used. This led me to suspect it was not set correctly despite echo $LDFLAGS showed the correct value. On the cluster in concern, the setup uses a tcsh shell and does not have the export c…

Thanks for sharing, in particular the difference with tcsh. Under the Slurm job scheduler, an array job is done similarly, though many large Slurm clusters now use the node as the unit of resources to allocate, so one does multiple chains within the job. FWIW, my script looks like this for a hyper…

[image] maedoc: I’m tempted to say that this may be an opportunity for additional tooling wrt. CmdStan, but workflows and such become so opinionated that common abstractions are difficult to identify. In CmdStan make compile_info now (on develop) dumps the call used to the compiler so that’s …

`GLIBCXX_3.4.20' not found (required by bin/stanc) when using cmdstan

Interfaces

maedoc June 3, 2019, 10:01am 3

Also, debug advice: use ldd $model_binary to see what the linker is thinking.

1 Like

Topic		Replies	Views
Cmdstan model compilation fails after conda installation (Big Sur) CmdStan compiler	8	957	July 27, 2022
Model Compilation error on Centos7 Cluster - cmdstanr CmdStan	9	1442	October 14, 2021
Conda cmdstan installation errors on linux CentOS cluster CmdStan installation	1	191	June 10, 2024
Error installing cmdstan in linux: it's trying to use clang Interfaces	7	1165	November 27, 2017
Problems running CmdStan's basic examples CmdStan cmdstan , installation	2	575	January 28, 2021

`GLIBCXX_3.4.20' not found (required by bin/stanc) when using cmdstan

Related topics