[Dock-fans] Fwd: Re: Parallel install

Francesco Pietra chiendarret at yahoo.com
Thu Sep 27 00:55:57 PDT 2007


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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