[Dock-fans] using mpich2 with dock5

Philip Crawford P.Crawford at unsw.edu.au
Mon Oct 3 04:54:30 PDT 2005


Dock 4 doesn't use mpich for parallel execution. On a small testbed cluster 
(2 DP systems, athlon 1.8 DP plus athlon 2 DP, running RHEL 3) I had 
problems with Dock 4 parallelisation.
Terry Lang advised that we download Dock 5.2. The MPI version compiled and 
ran on the same pair of DP systems without any problems. With MPI, one 
process (of 4 in our case) controls the parallel execution, the rest 
actually do the docking calculations. So, using "top" on a Unix system, you 
will only see n-1 processes chewing processor time if you launch n processes.
I compiled against the latest 1.x MPI library, not the 2.x one. As I 
recall, the documentation with the source said Dock 5.2 had been written to 
that interface.

Phil Crawford
UNSW
Sydney

At 01:52 AM 2/10/2005, Kaitlyn Hwang wrote:
>I tested ...
>
>mpiexec -np 2 valgrind ../../../../../dock5_mpi2/bin/dock5 -i dock.in -o
>dockval.out
>
>
>I have a reponse from another dock-fan user that parallel works with
>dock4. Has anyone seen or fix the below error? Or have dock4 working in
>parallel. If so, which mpich did you use?
>________________________________________________________________________
>
>==15884== Invalid read of size 4
>==15884==    at 0x1BA04DD7:
>std::string::_Rep::_M_grab(std::allocator<char> const&,
>std::allocator<char> cons
>t&) (in /usr/lib/gcc-lib/i386-pc-linux-gnu/3.3.5/libstdc++.so.5.0.7)
>==15884==    by 0x1BA061B6: std::string::assign(std::string const&) (in
>/usr/lib/gcc-lib/i386-pc-linux-gnu/3.
>3.5/libstdc++.so.5.0.7)
>==15884==    by 0x1BA05475: std::string::operator=(std::string const&) (in
>/usr/lib/gcc-lib/i386-pc-linux-gnu
>/3.3.5/libstdc++.so.5.0.7)
>==15884==    by 0x80867B5: copy_molecule(DOCKMol&, DOCKMol const&)
>(dockmol.cpp:222)
>==15884==    by 0x8065E08: Base_MPI::get_from_send_queue(DOCKMol&)
>(base_mpi.cpp:464)
>==15884==    by 0x808FFC8: Library_File::get_mol(DOCKMol&)
>(library_file.cpp:779)
>==15884==    by 0x804B36C: main (dock.cpp:94)
>==15884==  Address 0x4F525241 is not stack'd, malloc'd or (recently)
>free'd
>________________________________________________________________________
>
>
>@*-*@
>kaitlyn
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>Dock-fans at docking.org
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Philip Crawford, B.Comp.Sc., MIEEE      Phone:  +61-2-93852564
Computer Systems Officer                Fax:    +61-2-93851059
Educational Media Unit                  Email:
School of Medical Sciences,             P.Crawford at unsw.edu.au
University of New South Wales,
UNSW, NSW, 2052, Australia              Mobile: 0419-294 698 




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