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

Francesco Pietra chiendarret at yahoo.com
Fri Sep 28 00:53:35 PDT 2007


Yes, I badly forgot to carry out first serial compilation. Now done, which
resulted in a seemingly major error. Please see below at your directions how to
carry that out.

--- Scott Brozell <sbrozell at scripps.edu> wrote:

> 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;

I removed all binaries generated from previous faulty parallel compilation.
Then (after "make clean") I followed the above directions for serial
compilation. The following binaries were generated in /bin:

am1bcc, amberize_complex, amberize_ligand, amberize_receptor, antechamber,
atomtype, bondtype, chemgrid, distmap, dock6, espgen, grid, grid_convert,
grid_convrds, make_phimap, mopac, mopac.sh, nchemgrid_GB, nchemgrid_SA,
parmcal, parmchk, prepare_amber.pl, prepgen, resp, respgen, showbox,
showsphere, solvgrid, solvmap, sphere_selector, sphgen, teLeap, tleap.

make test 2>&1 | tee test_serial.out (attached)

revealed 29 instances of Possible Failure. I examined with make check the dif
files finding irrelevant differences in tails of floating points, and more
difficult to understand problems with the number of conformations. Probably one
should be familiar with dock to fully grasp the message of these dif files. It
is much more complicated than with Amber9 dif.

The end of the test_serial.out reveals a possible major error (can't open file
lig.1.amber.pdb). I don't understand if this issue should be resolved before
parallel compilation (which, in fact, I have not carried out).

cd test
make check 2>&1 | tee check_serial.out

is also attached.

>From the mailing list I fear I am the single guy experiencing so much troubles
in compiling dock. I deeply apologize.

Thanks

francesco




>     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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