Charm++ parallel programming system

[Phil Miller <mille121 AT illinois.edu>]

It looks like you're missing the memory allocation library. The
multicore-linux64 build target defaults to the OS/C-library provided
memory allocation routines (per charm/src/arch/multicore-linux64), so
you should link in charm/multicore-linux64/lib/libmemory-os.o as well.
You may need to adapt things to build that as a shared object as well,
but you seem to have a handle on that.

Phil

On Thu, Dec 2, 2010 at 11:05, Michael S. Sellers (Cont, ARL/WMRD)
<michael.s.sellers.ctr AT us.army.mil>
 wrote:
> All,
>
> This message was sent to the NAMD listserv about a week ago, and I haven't
> heard anything back so I thought I would try charm.
> I am trying to build NAMD as a shared library, but having some linking
> trouble.  I realize it can't "work" as is without an interface, but this is
> a first step.
>
> I first compiled Charm++ as a shared libary, as well as FFTW and TCL.  Then
> I edited the NAMD Makefile and added -fPIC in the compiler options, and an
> additional linkage section to create "libnamd.so" with "-charm-shared" and
> "-rdynamic" options.  It seems to compile and link okay via the edited
> Makefile.  "namd2" from the compile runs fine.
>
> I'm testing the libnamd.so library using a simple program that sets
> "dlopen("path-to-library", RTLD_LAZY);" equal to a dummy pointer.  However,
> with this I am getting an error.
>
> ****loadNAMD.C******
>  ....
>
>  cout << "Opening libnamd.so...\n";
>  void* handle = dlopen("software/lib/NAMD/libnamd.so", RTLD_LAZY);
>  if (handle == NULL){
>      printf("%s\n", dlerror());
>      return 0;
>  }
>
> ***********************
>
> []$ g++ loadNAMD.C -o loadNAMD -rdynamic -ldl
> []$ ./loadNAMD
>
> The output of dlerror() is:
>
> Opening libnamd.so...
> software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libconv-core.so:
> undefined symbol: Cpv_CthData_
>
> I'm wondering if this is being caused by a lack of Charm++ (via charmrun or
> charmc), or the fact that dlopen invokes any _init() methods existing in the
> code (I read that somewhere...) ?  I would appreciate any suggestions from
> those who are familiar with this type of thing.  I have included the output
> of "ldd -d libnamd.so" at the bottom of this message.
>
> Thanks,
>
> Michael Sellers
>
> []$ ldd -d ~/software/lib/NAMD/libnamd.so
>      libmoduleNeighborLB.so =>
> software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libmoduleNeighborLB.so
> (0x00002b7fe9318000)
>      libmoduleHybridLB.so =>
> software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libmoduleHybridLB.so
> (0x00002b7fe9524000)
>      libmoduleRefineLB.so =>
> /software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libmoduleRefineLB.so
> (0x00002b7fe9730000)
>      libmoduleGreedyLB.so =>
> software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libmoduleGreedyLB.so
> (0x00002b7fe993b000)
>      libck.so =>
> software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libck.so
> (0x00002b7fe9b48000)
>      libconv-cplus-y.so =>
> software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libconv-cplus-y.so
> (0x00002b7fe9f23000)
>      libconv-core.so =>
> software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libconv-core.so
> (0x00002b7fea138000)
>      libconv-util.so =>
> software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libconv-util.so
> (0x00002b7fea3d4000)
>      libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b7fea61a000)
>      libckqt.so =>
> software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libckqt.so
> (0x00002b7fea835000)
>      libdl.so.2 => /lib64/libdl.so.2 (0x00002b7feaa39000)
>      libtcl8.5.so => software/lib/libtcl8.5.so (0x00002b7feac3d000)
>      libsrfftw.so.2 => software/lib/libsrfftw.so.2 (0x00002b7feaf58000)
>      libsfftw.so.2 => software/lib/libsfftw.so.2 (0x00002b7feb188000)
>      libm.so.6 => /lib64/libm.so.6 (0x00002b7feb3be000)
>      libstdc++.so.6 => /usr/local/lib64/libstdc++.so.6 (0x00002b7feb641000)
>      libgcc_s.so.1 => /usr/local/lib64/libgcc_s.so.1 (0x00002b7feb947000)
>      libc.so.6 => /lib64/libc.so.6 (0x00002b7febb5c000)
>      /lib64/ld-linux-x86-64.so.2 (0x0000003f25000000)
> undefined symbol: Cpv_CthData_
>  
> (software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libconv-core.so)
> undefined symbol: cpd_memory_pup
>  
> (software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libck.so)
> undefined symbol: memory_stack_top
>  
> (software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libck.so)
> undefined symbol: Cpv_CthData_
>  
> (software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libck.so)
> undefined symbol: cpd_memory_length
> (software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libck.so)
> undefined symbol: cpd_memory_getLength
>  
> (software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libck.so)
> undefined symbol: cpdInSystem
> (software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libck.so)
> undefined symbol: cpd_memory_get
>  
> (software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libck.so)
> undefined symbol: memory_status_info
>  
> (software/src/NAMD_CVS_Source/Linux-x86_64-g++/.rootdir/charm-6.2.2/multicore-linux64/lib_so/libck.so)
> []$
>
>
>
>
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