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

Francesco Pietra chiendarret at yahoo.com
Fri Sep 28 14:38:28 PDT 2007


Commenting out the two last lines on my .bashrc

#For amber9
MPI_HOME=/usr/local
export MPI_HOME
AMBERHOME=/usr/local/amber9
PATH=$PATH:$AMBERHOME/exe; export AMBERHOME PATH

the issue was fixed:

install/test/amber_score_181l
shows
Running: $DOCK_HOME/bin/mopac.sh
and the pdb was generated as can be seen from the attached file.

Of course, I am now going to define again AMBERHOME as it was in my .bashrc. Do
you believe that this may have other consequences than when using Amber score?
If not, I'll try to compile dock parallel.

I could install DOCK as another user, though it makes everything less easy.

Thanks
francesco

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

> Hi,
> 
> On Fri, 28 Sep 2007, Francesco Pietra wrote:
> 
> > Yes, amberize_ligand failed and that was reflected on the other *.out
> files.
> > All three are attached.
> >
> > I can't foresee if Amber score  will become useful. Though, being somewhat
> > familiar with Amber9, and having it, if there is any chance to fix this
> problem
> > ...
> >
> > To this regard, why was Antechamber calling divcon at
> $AMBERHOME/bin/divcon?
> > Which can't be found in DOCK. Divcon is available on my machine, though at
> > $AMBERHOME/exe/divcon (where also antechamber is present).
> 
> Ahh, this is a known problem that has been fixed in Amber/antechamber
> land, but not yet released.
> The patch is to undefine AMBERHOME and rerun the tests.
> 
> Scott
> 
> > --- Scott Brozell <sbrozell at scripps.edu> wrote:
> >
> > > Hi,
> > >
> > > On Fri, 28 Sep 2007, Francesco Pietra wrote:
> > >
> > > > 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.
> > >
> > >
> > > These difs look innocuous.  Unfortunately, changes in the number of
> > > Conformations cause a cascade of difs.  This is on the long term todo
> list.
> > >
> > > ./anchor_and_grow/flex2.dockout.dif
> > > 58c58
> > > <  Conformations:    13
> > > ---
> > > >  Conformations:    14
> > >
> > >
> > > > 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).
> > >
> > >
> > > ../../../bin/prepare_amber.pl completed.
> > > Processing test move_ligand
> > > ../../../bin/dock6 -i move_ligand.dockin -o move_ligand.dockout
> > > getpdb: can't open file lig.1.amber.pdb
> > > make[3]: *** [move_ligand.dockout] Error 1
> > >
> > > If you plan to use Amber score then the missing lig.1.amber.pdb should
> > > be investigated:  in install/test/amber_score_181l look at the
> > > files *.out
> > > It is likely that amberize_ligand failed.
> > >
> > > Scott
> > >
> > > > 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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> > > > > > >
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> > > >
> > >
> >
>
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