Charm++ parallel programming system

[Phil Miller <mille121 AT illinois.edu>]

I may have been a bit too hasty. You'll also need one of the thread
libraries as well. It looks like multicore-linux64 uses context
threads, so libthreads-context.o.

On Thu, Dec 2, 2010 at 11:35, Michael S. Sellers (Cont, ARL/WMRD)
<michael.s.sellers.ctr AT us.army.mil>
 wrote:
> Phil,
>
> Thanks a lot for the quick response.
>
> -Mike
>
> Phil Miller wrote:
>>
>> 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)
>>> []$
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> charm mailing list
>>> charm AT cs.uiuc.edu
>>> http://lists.cs.uiuc.edu/mailman/listinfo/charm
>>>
>>> _______________________________________________
>>> ppl mailing list
>>> ppl AT cs.uiuc.edu
>>> http://lists.cs.uiuc.edu/mailman/listinfo/ppl
>>>
>>>
>>>
>