[Dock-fans] Fwd: Re: Parallel install

Francesco Pietra chiendarret at yahoo.com
Tue Sep 25 12:38:03 PDT 2007


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
> 
> (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.
> 
> 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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> > 
> > _______________________________________________
> > Dock-fans mailing list
> > Dock-fans at docking.org
> > http://blur.compbio.ucsf.edu/mailman/listinfo/dock-fans
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> >      
> >
>
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> 
> 
> 
>      
>
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