[Dock-fans] using mpich2 with dock5

Kaitlyn Hwang hwang at mcs.anl.gov
Wed Oct 19 07:44:20 PDT 2005


btw, dock5 works with mpich2. If you see your program segfault,
it is probably because of patch 6 and 8. So don't put those two patches
in.

Your time in the output will be off.

kaitlyn

On Wed, 19 Oct 2005, Ricardo Nicoluci wrote:

> Hi,
>
> I applied all the patches to Dock 5.2 and I tried to run it with
> mpich2.1. I didnt get any error message, it simply stops with 0
> molecules processed !
> Is this the same "message" that you guys got !?
>
> Thanks.
>
> On 10/6/05, Philip Crawford <p.crawford at unsw.edu.au> wrote:
> > Kaitlyn,
> > Hi. My apologies. The success I reported with Dock 5.2 and MPI was before I
> > found the Bugfixes. I no longer have the cluster to test this on.
> >
> > Cheers,
> >
> > Phil
> > __________________________________________________
> > Philip Crawford, B. Comp. Sc., MIEEE
> > School of Medical Sciences
> > The University of NSW
> > Phone: +61-2-9385 2564
> > Mobile: +61-419-294 698
> > Fax: +61-2-9385 1059
> > Email: p.crawford at unsw.edu.au
> > __________________________________________________
> >
> > -----Original Message-----
> > From: dock-fans-bounces at docking.org [mailto:dock-fans-bounces at docking.org]
> > On Behalf Of Kaitlyn Hwang
> > Sent: Thursday, 6 October 2005 3:36 PM
> > To: Philip Crawford
> > Cc: dock-fans at docking.org
> > Subject: Re: [Dock-fans] using mpich2 with dock5
> >
> > Got dock5 working in parallel with mpich2-1.0.2p1  if I take out the
> > bugfixes 6 & 8 from
> > http://dock.compbio.ucsf.edu/DOCK_5/5.2.0/5.2.0_bugfixes.htm
> >
> > Here's some dock5 errors with bugfixes 6&8 patched in and debug with gdb
> >
> > 94        while(c_library.get_mol(mol)) {
> > (gdb) n
> >
> > Program received signal SIGSEGV, Segmentation fault.
> > 0x40119dd7 in std::string::_Rep::_M_grab(std::allocator<char> const&,
> > std::allocator<char> const&) ()
> >    from /usr/lib/gcc-lib/i386-pc-linux-gnu/3.3.5/libstdc++.so.5
> > (gdb) up
> > #1  0x4011b1b7 in std::string::assign(std::string const&) ()
> >    from /usr/lib/gcc-lib/i386-pc-linux-gnu/3.3.5/libstdc++.so.5
> > (gdb) up
> > #2  0x4011a476 in std::string::operator=(std::string const&) ()
> >    from /usr/lib/gcc-lib/i386-pc-linux-gnu/3.3.5/libstdc++.so.5
> > (gdb) up
> > #3  0x080867b6 in copy_molecule(DOCKMol&, DOCKMol const&)
> > (target=@0xbfffcb30,
> >     original=@0x8168c10) at dockmol.cpp:222
> > 222             target.current_data = original.current_data;
> >
> >
> >
> > kaitlyn
> >
> > On Mon, 3 Oct 2005, Philip Crawford wrote:
> >
> > > 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
> > > >_______________________________________________
> > > >Dock-fans mailing list
> > > >Dock-fans at docking.org
> > > >http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> > >
> > > 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
> > >
> > >
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> >
>
>
> --
> Ricardo de Paula Nicoluci
> PhD Student
> Medicinal Chemistry Laboratory
> IFSC - University of Sao Paulo
> Sao Carlos - SP - Brazil
> _______________________________________________
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>
>



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