[Dock-fans] Fwd: Re: Fwd: Re: Parallel install

Francesco Pietra chiendarret at yahoo.com
Thu Sep 27 02:26:48 PDT 2007


I forgot to mention that I plan to use Antechamber from Amber9. Summarizing
this and questions below:
(1) What to do with legacy_accessories.tar.gz?
(2) Delete antechamber and mopac from /src before compiling dock? Or what
better in order to avoid installing antechamber to save spece
Thanks
francesco 


--- Francesco Pietra <chiendarret at yahoo.com> wrote:

> Date: Thu, 27 Sep 2007 00:55:57 -0700 (PDT)
> From: Francesco Pietra <chiendarret at yahoo.com>
> Subject: Re: [Dock-fans] Fwd: Re:  Parallel install
> To: Scott Brozell <sbrozell at scripps.edu>
> CC: dock-fans <dock-fans at docking.org>
> 
> Please, read below. My main question before cleaning and re-install, is what
> to
> do with
> 
> 
> legacy_accessories.tar.gz
> 
> 
> --- Scott Brozell <sbrozell at scripps.edu> wrote:
> 
> > Hi,
> > 
> > Did you read the test output ?
> 
> Yes, I noticed that, though I was unable to decide what to do. Please see
> below.
> > 
> > ...
> > make[3]: Entering directory `/usr/local/dock6/install/test/bump_filter'
> > cd ../grid_generation && make test
> > make[4]: Entering directory `/usr/local/dock6/install/test/grid_generation'
> > # Construct box to enclose spheres
> > ../../../bin/showbox < box.in > /dev/null
> > /bin/sh: ../../../bin/showbox: No such file or directory
> > 
> > Obviously, you should confirm that bin/showbox does not exist
> > and investigate its installation.
> > 
> > Scott
> 
> 
> /usr/local/dock6//bin only contains two binary files, dock6 (generated by
> serial install) and dock6.mpi (generated by parallel install). Details below.
> 
> The download contained
> dock.6.1_source.tar.gz
> and
> legacy_accessories.tar.gz
> 
> 
> I did nothing with the latter tar.gz file.
> 
> Decompressing dock.6.1.... into
> 
> /usr/local
> 
> as described in the manual, gave 
> /usr/local/dock6
> containing:
> bin;
> install;
> parameters;
> src (accessories, antechamber, dock, docktools, gbsa_grids, grid, mopac6,
> resp,
> tleap, Makefile);
> tutorials.
> 
> As I am the only user of the computing machine, I did:
> 
> chown -R francesco dock6
> chgrp -R francesco dock6
> 
> Install g++ 4.1.2 from Debian package (g77-doc g77-3.4 gcc-3.4 lib2c0-dev)
> (as
> Open MPI was compiled with Intel, like Amber9)
> 
> ./configure gnu
> 
> make dock # builds only dock programs
> make dock # builds the accessory programs
> 
> I made the test and probably overlooked the problems (see later)
> 
> Then configure parallel:
>  
> 
> ./configure gnu parallel
> 
> Then set
> 
> MPICH_HOME=/usr/local
> 
> Then
> make clean
> make dock # builds only the dock program
> make utils # builds only the accessory programs
> 
> 
> 
> Then 
> make  clean
> make test 2>&1 | tee test.out
> make check 2>&1 | tee check.out
> 
> Surely there was a mistake in the serial install, where
> 
> make dock # builds the accessory programs
> should have been
> make utils # builds the accessory programs
> 
> I guess the best is deleting everything and start from fresh
> dock.6.1_source.tar.gz, first serial, then reliable make test, then parallel.
> Though, I wait until I know what to do with the legacy file where I see many
> fortran sources.
> 
> Thanks
> francesco
> 
> 
> > 
> > On Wed, 26 Sep 2007, Francesco Pietra wrote:
> > 
> > > Attached the tests according to the correct synthax for generating .out
> > >
> > > Thanks
> > > francesco
> > >
> > >
> > > --- Scott Brozell <sbrozell at scripps.edu> wrote:
> > >
> > > > Hi,
> > > >
> > > > On Wed, 26 Sep 2007, Francesco Pietra wrote:
> > > >
> > > > > The whole thread is below for record, though, new events are all
> > summarized
> > > > > here.
> > > > >
> > > > > There are two compilations, dock6 and dock6.mpi, in:
> > > > >
> > > > > /usr/local/dock6/bin
> > > > >
> > > > > I stick at
> > > > >
> > > > > MPICH_HOME=/usr/local
> > > > >
> > > > > Then I delete the outputs of previous "make test" and carry out new
> > ones as
> > > > > follows
> > > > >
> > > > > (1) From the directory
> > > > > /usr/local/dock6/install
> > > > >
> > > > > make clean
> > > > > make test | tee test.out
> > > > >
> > > > > (2) From the directory
> > > > >
> > > > > /usr/local/dock6/install/test
> > > > >
> > > > > make check | tee check.out
> > > > >
> > > > > The two output files are attached. Again, test.out is very short and
> > looks
> > > > very
> > > > > similar to previous trials. I am quite sorry to give these troubles.
> > > >
> > > >
> > > > The tests are failing as before.  The error message is not being
> > > > redirected.  Watch the actual full output as it is emitted or
> > > > use the correct syntax to pipe stderr (for bash):
> > > >
> > > > make test 2>&1 | tee test.out
> > > >
> > > > Scott
> > >
> > >
> > 
> 
> 
> 
>      
>
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