[Dock-fans] Fwd: Re: Parallel install

Scott Brozell sbrozell at scripps.edu
Wed Sep 26 09:16:40 PDT 2007


Hi,

On Wed, 26 Sep 2007, Francesco Pietra wrote:

> Please see below the results of the commands suggested.
>
> --- Scott Brozell <sbrozell at scripps.edu> wrote:
>
> > On Tue, 25 Sep 2007, Francesco Pietra wrote:
> >
> > > I forgot to add the config.h. Attached now
> > >
> > > --- Francesco Pietra <chiendarret at yahoo.com> wrote:
> > >
> > > > Date: Tue, 25 Sep 2007 08:25:35 -0700 (PDT)
> > > > From: Francesco Pietra <chiendarret at yahoo.com>
> > > > Subject: Re: [Dock-fans] Parallel install
> > > > To: Sudipto Mukherjee <sudmukh at yahoo.com>, dock-fans
> > <dock-fans at docking.org>
> > > >
> > > > Dear Sudipto:
> > > >
> > > > Thanks. I fear that something was wrong with my installation of dock6.1.
> > > >
> > > > Leaving config.h as it was in my previous mail (attached here again) I
> > did:
> > > >
> > > > (1) set the env var (bash)
> > > > MPICH_HOME=/usr/local
> >
> > This is unlikely to be the correct path.
>
> > Try the command:
> > which mpicxx
> > and the use the part before bin.
>
> which mpicxx
> /usr/local/bin/mpicxx
>
>
> > Or try the command
> > locate mpi.h
>
>
> # updatedb
> $ locate mpi.h
>
> /usr/include/sc/util/group/memmtmpi.h
> /usr/include/sc/util/group/messmpi.h
> /usr/local/dock6/src/dock/base_mpi.h
> /usr/local/include/mpi.h
> /usr/local/openmpi-1.2.3/ompi/include/mpi.h
> /usr/local/openmpi-1.2.3/ompi/include/mpi.h.in
> /usr/local/openmpi-1.2.3/ompi/mpi/f77/prototypes_mpi.h
>
>
> On these basis, having previously set
>
> MPICH_HOME=/usr/local
>
> should I proceed to the next suggestions for env variable, or should I first
> remove the above one?

Based on that info either
MPICH_HOME=/usr/local
or
MPICH_HOME=/usr/local/openmpi-1.2.3/ompi
are probably correct.

Scott

> Thanks
> francesco
>
>
>
>
> > Also use the command export:
> > MPICH_HOME=/bla
> > export MPICH_HOME
> >
> > > > (the daemons of openmpi are in /usr/local/bin, which is on my PATH)
> > > >
> > > > (2) make dock # builds only the dock program
> > > >
> > > > (the attached test_parallel_onlydock.out reports the "make test")
> > > >
> > > >
> > > > (3) make utils # builds only the accessory programs
> > > >
> > > > (the attached test_parallel_dockandaccessory.out reports the "make test")
> > > >
> > > > Attached is also test_serial.out from the "make test" for the serial
> > > > installation.
> >
> > Yes, something is wrong; test_serial.out appears to be truncated
> > as do the others; this is the tail:
> > make[2]: Leaving directory `/usr/local/dock6/install/test/anchor_and_grow'
> > cd bump_filter && make test
> > make[2]: Entering directory `/usr/local/dock6/install/test/bump_filter'
> > cd ../grid_generation && make test
> > make[3]: Entering directory `/usr/local/dock6/install/test/grid_generation'
> > # Construct box to enclose spheres
> > ../../../bin/showbox < box.in > /dev/null
> > make[3]: Leaving directory `/usr/local/dock6/install/test/grid_generation'
> > make[2]: Leaving directory `/usr/local/dock6/install/test/bump_filter'
> > make[1]: Leaving directory `/usr/local/dock6/install/test'
> >
> >
> > Retry the tests, reporting the verbatim output via:
> > cd install;make test
> >
> > Scott
> >
> > > > In all case the "make test" was extremely short.
> > > >
> > > > The system is amd64opteron Debian Linux amd64 etch.
> > > >
> > > > Thanks for any advice
> > > >
> > > > francesco
> > > >
> > > >
> > > >
> > > > --- Sudipto Mukherjee <sudmukh at yahoo.com> wrote:
> > > >
> > > > > Dear Francesco,
> > > > >
> > > > > MPICH_HOME needs to be set as an environment variable.
> > > > > You should not have to make any modifications to config.h
> > > > > For example, if your login shell is csh, add the following to your
> > .cshrc
> > > > > setenv MPICH_HOME      /path/to/openmpi
> > > > >
> > > > > Please also note that MPICH_HOME needs to be the root of the MPI
> > > > installation
> > > > > folder.
> > > > > In your case, this is most likely /usr/local/openmpi or similar.
> > > > >
> > > > > Regards
> > > > > Sudipto Mukherjee
> > > > > Graduate Student, Robert C. Rizzo Lab
> > > > > Dept. of Applied Math & Statistics, Stony Brook University
> > > > > Lab: 631-632-8519, Mobile: 631-220-5744
> > > > >
> > > > >
> > > > > ----- Original Message ----
> > > > > From: Francesco Pietra <chiendarret at yahoo.com>
> > > > > To: dock-fans <dock-fans at docking.org>
> > > > > Sent: Friday, September 21, 2007 5:14:56 PM
> > > > > Subject: [Dock-fans] Parallel install
> > > > >
> > > > > On a shared memory computer with two dual-opterons, OS Linux Debian
> > amd64
> > > > > etch,
> > > > > I have successfully installed
> > > > >
> > > > > /usr/local/dock6
> > > > >
> > > > > serial dock and accessory (DOCK 6.1) with g++ 4.1.2, gcc 3.4, g77 3.4.
> > > > >
> > > > > On this computer, Amber9 is installed in /usr/local/amber9 with openmpi
> > > > > support
> > > > >
> > > > > MPI_HOME=/usr/local
> > > > >
> > > > > where openmpi is compiled with Intel.
> > > > >
> > > > > I would be very grateful for suggesting me how to rearrange the
> > config.h
> > > > file
> > > > > (please, see below) so that  MPICH_HOME points to openmpi:
> > > > >
> > > > > # DOCK configuration file for GNU compilers with MPICH2 based
> > parallelism.
> > > > > # This configuration file can be used on many platforms:
> > > > > #  Linux, Macintosh OS X, Windows with Cygwin, etc.
> > > > > # If g77 is not available then change FC below to gfortran or g95.
> > > > >
> > > > > # REQUIREMENTS - define these environment variables:
> > > > > # MPICH_HOME is the root directory of the MPICH2 MPI implementation
> > > > > # END REQUIREMENTS
> > > > >
> > > > > # TROUBLESHOOTING
> > > > > # 1. Linking problems, such as undefined references, cannot find
> > -lbla_bla,
> > > > > # and command not found errors:
> > > > > # ensure that mpicxx exists;  ensure that the compiler invoked by
> > mpicxx
> > > > > exists
> > > > > # (for best results it should be g++); in the worst case try manual
> > > > linking:
> > > > > # change the LOAD definition below to g++, execute the command
> > > > > # $MPICH_HOME/bin/mpicc -show
> > > > > # and add to the LIBS definition below the output related to link
> > flags,
> > > > e.g
> > > > > # LIBS= -lm -Lyada -Lyada_yada -lbla -lbla_bla ...
> > > > > # 2. General advice: build a serial dock first then build a parallel
> > > > > # dock using a validated MPI implementation.
> > > > > # 3. Best practice advice:  the most straightforward route to
> > successful
> > > > > # parallel executable building is to use the same compilers for
> > building
> > > > > # the MPI implementation and dock.
> > > > > # END TROUBLESHOOTING
> > > > >
> > > > > # CC is the C compiler
> > > > > # CXX is the C++ compiler
> > > > > # CFLAGS is the flags for the C and C++ compilers
> > > > > # FC is the Fortran compiler
> > > > > # FFLAGS is the flags for the Fortran compiler
> > > > > # LIBS is the flags for the linker
> > > > > # LOAD is the command to invoke the linker
> > > > > # MPICH_IGNORE_CXX_SEEK  see
> > > > > #   http://www-unix.mcs.anl.gov/mpi/mpich2/faq.htm#cxxseek
> > > > > # MPICH_SKIP_MPICXX  Dock does not use MPI C++ bindings; see
> > > > > #
> > http://www-unix.mcs.anl.gov/mpi/mpi-standard/mpi-report-2.0/node226.htm
> > > > > # SFX is the suffix for the executable
> > > > >
> > > > > CC=          gcc
> > > > > CXX=         g++
> > > > > CFLAGS=      -DBUILD_DOCK_WITH_MPI -DMPICH_IGNORE_CXX_SEEK
> > > > > -DMPICH_SKIP_MPICXX
> > > > > -I$(MPICH_HOME)/include -O2
> > > > > FC=          g77
> > > > > FFLAGS=      -O2 -fno-automatic -fno-second-underscore
> > > > > LOAD=        $(MPICH_HOME)/bin/mpicxx
> > > > > LIBS=        -lm
> > > > > SFX=         .mpi
> > > > >
> > > > > # Macro definitions for NAB
> > > > > # AR is the library archiver
> > > > > # LEX is the lexical analyzer generator
> > > > > # OCFLAGS is the flags for the C compilers with high optimization
> > > > > # RANLIB is the library index generator
> > > > > AR=          ar rv
> > > > > LEX=         flex
> > > > > OCFLAGS=     -O3 -D_ANSI_SOURCE
> > > > > RANLIB=      ranlib
> > > > > DOCKHOME=/usr/local/dock6
> > > > > # Created at Fri Sep 21 18:36:29 CEST 2007 via ./configure gnu parallel
> > > > >
> > > > >
> > > > > I plan to use Antechamber in Amber9.
> > > > >
> > > > > Thanks
> > > > >
> > > > > francesco pietra
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> > > >
> > >
> >
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