CODEWITHSUNDEEP
pythonmpiundefined-symbol
Adam
Adam

Reputation: 17329

creating a C++ MPI module for Python, import error

I have a Python module which wraps a C++ library. The library uses MPI and is compiled with mpicxx. Everything works great on some machines, but on others I get this:

ImportError: ./_pyCombBLAS.so: undefined symbol: _ZN3MPI3Win4FreeEv

So there's an undefined symbol from the MPI library. As far as I can tell mpicxx should link everything in, yet it doesn't. Any ideas why?

Upvotes: 0

Views: 1489

Answers (3)

user744629
user744629

Reputation: 2041

symbol ZN3MPI3Win4FreeEv is defined is libmpi_cxx.so, so one have to link with -lmpi_cxx instead of -lmpi

Upvotes: 0

Adam
Adam

Reputation: 17329

It turns out that the fault was that the wrong libraries were being loaded. As you know, a cluster is likely to have several versions of MPI installed, sometimes the same version is compiled with several compilers. These are all likely to have the same filenames. In my case even though I compiled with, say MPICH GNU, the default path was to the OpenMPI PGI libraries. I didn't realize this, I thought compiling with MPICH GNU would mean the MPICH GNU libraries would be found at runtime.

Of course I couldn't actually use PGI-compiled OpenMPI because Python was compiled with GCC and PGI doesn't emit binaries fully compatible with GCC.

The solution is to set the LD_LIBRARY environment variable to match the MPI distribution you used to compile your code.

Upvotes: 1

stderr
stderr

Reputation: 8722

It's a shared library problem. Try running ldd on the extension module on both the system where it works and the system where it fails.

ldd _extension.so

This should show you all the libraries your extension depends on so you can make sure they're available.

A simple way to work around it may be to statically link the dependencies into your extension.

Upvotes: 0

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