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

Scott Brozell sbrozell at scripps.edu
Thu Sep 27 17:53:57 PDT 2007


Hi,

On Thu, 27 Sep 2007, Francesco Pietra wrote:

> I decided to start from fresh source and compile all programs, again setting
>
> MPICH_HOME=/usr/local
>
> as root of the installation of Open MPI
>
> Surely there was notable progress with respect to previous attempts. This time
> /bin contains a large number of executables though errors were reported about
> anchor_and_grow. I donot understand if this is the single error or it is
> truncated (probably so because the test was short)
>
> make test 2>&1 | tee test.out
>
> Attached is the compressed test.out. Againg, I am sincerely sorry to convey all
> these troubles due to my scarce experience with compilations.
>
> I was surprised to see antechamber.mpi and mopac.mpi. In Amber9 the compilation
> of Antechamber and Divcon is serial.

dock6 is the only parallel executable.
antechamber.mpi, etc is a minor glitch (inappropriate
file extension) that is exercised by unconventional building.
Here is the quick start for an example gnu installation:
    cd install; ./configure gnu; make install; make test;
    make distclean; ./configure gnu parallel;
    setenv MPICH_HOME /bla; make dock; cd test/mpi; make


Since you didnt build a serial dock, the serial dock tests are failing:
Processing test flex1
../../../bin/dock6 -i flex1.dockin -o flex1.dockout
make[3]: ../../../bin/dock6: Command not found


Scott

> --- Francesco Pietra <chiendarret at yahoo.com> wrote:
>
> > Date: Thu, 27 Sep 2007 02:26:48 -0700 (PDT)
> > From: Francesco Pietra <chiendarret at yahoo.com>
> > Subject: Fwd: Re: [Dock-fans] Fwd: Re:  Parallel install
> > To: Scott Brozell <sbrozell at scripps.edu>
> > CC: dock-fans <dock-fans at docking.org>
> >
> > 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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