Charm++ parallel programming system

[Phil Miller <mille121 AT illinois.edu>]

On Thu, Dec 2, 2010 at 12:59, Michael S. Sellers (Cont, ARL/WMRD)
<michael.s.sellers.ctr AT us.army.mil>
 wrote:
> Does this mean that the cause of the problem is different, or should I still
> look at the memory and thread library linking?

It means your problem is very likely what I thought was going on. Yes,
you'll need to make shared objects of those and link against them as
well.

> -Mike
>
> Abhinav S Bhatele wrote:
>>
>> NAMD uses charmc to link the executable.
>>
>>
>> On Thu, Dec 2, 2010 at 12:02 PM, Phil Miller 
>> <mille121 AT illinois.edu
>> <blockedmailto:mille121 AT illinois.edu>>
>>  wrote:
>>
>>    On Thu, Dec 2, 2010 at 11:53, Michael S. Sellers (Cont, ARL/WMRD)
>>    
>> <michael.s.sellers.ctr AT us.army.mil
>>    
>> <blockedmailto:michael.s.sellers.ctr AT us.army.mil>>
>>  wrote:
>>    > Okay, so I need to have charm build these as shared libraries
>>    (memory-os and
>>    > threads-context), and then link them when I build the NAMD
>>    shared library?
>>    >
>>    > Is there a short answer to why I need to do this, but it's not
>>    necessary for
>>    > the NAMD executable?
>>
>>    I'm not too familiar with NAMD's build system, but if it uses charmc
>>    (the Charm compiler wrapper) to link the executable, that
>>    automatically links in memory allocation and threading libraries,
>>    either the platform default or whatever was specified on the command
>>    line.
>>
>>    Please let us know if you encounter other issues like this, or have in
>>    the past, even if you figured out the solution on your own. We'll
>>    definitely look at fixing things to make life easier.
>>
>>    > Thanks,
>>    >
>>    > Mike
>>    >
>>    > Phil Miller wrote:
>>    >>
>>    >> 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
>>    
>> <blockedmailto: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
>>    
>> <blockedmailto: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 <blockedhttp://libtcl8.5.so> =>
>>    software/lib/libtcl8.5.so <blockedhttp://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
>>  
>> <blockedmailto:charm AT cs.uiuc.edu>
>>    >>>>> http://lists.cs.uiuc.edu/mailman/listinfo/charm
>>    <blockedhttp://lists.cs.uiuc.edu/mailman/listinfo/charm>
>>    >>>>>
>>    >>>>> _______________________________________________
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>>    >>>>> 
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>> <blockedmailto:ppl AT cs.uiuc.edu>
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>>    >>>>>
>>    >>>>>
>>    >>>>>
>>    >>>>>
>>    >
>>
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>>    
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>>
>>
>>
>> --
>> Abhinav S Bhatele, Ph. D.
>> Webpage: www.bhatele.org <blockedhttp://www.bhatele.org>
>