MPICH from macports missing symbols

StackOverflow https://stackoverflow.com/questions/12748491

  •  05-07-2021
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Question

I'm trying to write a program with Rmpi, unfortunately a symbol required is undefined, and tracking it down with otool and nm seems to just lead me to libmpich.3.3.dylib. Unfortunately the symbol MPI_Comm_dup, is undefined in this dynamic library.

However, I'm not an expert on OSX dynamic libraries, and am wondering if I am correct in my approach and conclusion. Furthermore I am open to any suggestions to resolve this issue.

Thanks,

Error : .onLoad failed in loadNamespace() for 'Rmpi', details:
  call: dyn.load(file, DLLpath = DLLpath, ...)
  error: unable to load shared object '/home/jonathan.lisic/R/x86_64-apple-darwin12.2.0-library/2.15/Rmpi/libs/x86_64/Rmpi.so':
  dlopen(/home/jonathan.lisic/R/x86_64-apple-darwin12.2.0-library/2.15/Rmpi/libs/x86_64/Rmpi.so, 6): Symbol not found: _MPI_Comm_dup
  Referenced from: /opt/local/lib/libmpich.3.3.dylib
  Expected in: flat namespace
 in /opt/local/lib/libmpich.3.3.dylib
Error: package/namespace load failed for Rmpi

jonathan.lisic@server:/opt/local$ otool -L /home/jonathan.lisic/R/x86_64-apple-darwin12.2.0-library/2.15/Rmpi/libs/x86_64/Rmpi.so
/home/jonathan.lisic/R/x86_64-apple-darwin12.2.0-library/2.15/Rmpi/libs/x86_64/Rmpi.so:
        Rmpi.so (compatibility version 0.0.0, current version 0.0.0)
        /opt/local/lib/libmpich.3.3.dylib (compatibility version 0.0.0, current version 3.0.0)
        /opt/local/lib/libmpl.1.dylib (compatibility version 3.0.0, current version 3.0.0)
        /opt/local/lib/libopa.1.dylib (compatibility version 2.0.0, current version 2.0.0)
        /opt/local/lib/R/lib/x86_64/libR.dylib (compatibility version 2.15.0, current version 2.15.1)
        /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1669.0.0)
        /opt/local/lib/gcc45/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 169.3.0)

jonathan.lisic@server:/opt/local/lib$ otool -L libmpich.dylib
libmpich.dylib:
        /opt/local/lib/libmpich.3.3.dylib (compatibility version 0.0.0, current version 3.0.0)
        /opt/local/lib/gcc43/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 169.3.0)

jonathan.lisic@server:/opt/local/lib$ otool -L libmpich.3.3.dylib
libmpich.3.3.dylib:
        /opt/local/lib/libmpich.3.3.dylib (compatibility version 0.0.0, current version 3.0.0)
        /opt/local/lib/gcc43/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1.0.0)
        /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 169.3.0)

jonathan.lisic@server:/opt/local/lib$ nm  -u libmpich.3.3.dylib | egrep dup
_MPI_Comm_dup
_MPL_trstrdup
_dup2
_strdup
Was it helpful?

Solution

The symbol you are looking for (or at least, Rmpi is looking for) lives in libpmpich.*.dylib. Note the p in that name. The details of why this extra library exists are mostly historical and uninteresting, but it does exist. It contains almost all of the MPI_ symbols in the library, while libmpich.*.dylib contains all of the PMPI_ symbols in the library as well as all of the actual implementation code for the MPI library.

I've never used Rmpi myself, but perhaps there's a way to configure it to look in a different library or to add more libraries to the searched set? IIRC, Open MPI does not separate these two libraries, which could be the source of a single-library assumption by the Rmpi developers.

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