[Dock-fans] using mpich2 with dock5

Philip Crawford p.crawford at unsw.edu.au
Wed Oct 19 16:44:34 PDT 2005


Ricardo,
Hi. I was running on RHEL 3. compiled MPICH 1.something (whatever was the
latest release at the time). I chose that because the Dock-umentation said
that was what it should be compiled against.

MPICH 1.2 wanted to use rsh for inter-system communication. I renamed the
rsh executable and copied the ssh executable as rsh, as I had ssh working
and RHEL3 didn't want to use rsh without Kerberos authentication. That
worked fine.

Didn't pursue this option far as we were using a borrowed cluster and didn't
have funds to put in our own.
I hope that this clarifies where I was at.
 
Cheers,
 
Phil
__________________________________________________
Philip Crawford, B. Comp. Sc., MIEEE
Structural BioInformatics and Drug Design Group
http://www.sbio.med.unsw.edu.au/sbio
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 Ricardo Nicoluci
Sent: Wednesday, 19 October 2005 11:53 PM
To: dock-fans at docking.org
Subject: Re: [Dock-fans] using mpich2 with dock5

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
> >
> >
> _______________________________________________
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>


--
Ricardo de Paula Nicoluci
PhD Student
Medicinal Chemistry Laboratory
IFSC - University of Sao Paulo
Sao Carlos - SP - Brazil
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