[gmx-users] Re: Install problem
Ibrahim M. Moustafa
I.moustafa at psu.edu
Thu Jul 19 00:52:19 CEST 2007
Hi Jhon,
I have the same issue with GROMACS on Mac PPC 10.4.
The program executes only with the full path
specified. I posted a similar question
before, you can check the archive, but got no solution for the problem.
What I did is that I aliased all modules in
GMXBIN to the full path and it works fine with me.
If you find another solution for the problem, I'd love to know.
thanks,
Ibrahim
At 04:57 PM 7/18/2007, you wrote:
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>Today's Topics:
>
> 1. Re: Implicit solvent simulation (steletch at jouy.inra.fr)
> 2. Re: Implicit solvent simulation (David van der Spoel)
> 3. install problem (John Mercer)
> 4. How to include Mg in the input file? (srinivas aripirala)
>
>
>----------------------------------------------------------------------
>
>Message: 1
>Date: Wed, 18 Jul 2007 21:14:43 +0200
>From: steletch at jouy.inra.fr
>Subject: Re: [gmx-users] Implicit solvent simulation
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <1184786083.469e66a393ffa at www.jouy.inra.fr>
>Content-Type: text/plain; charset=ISO-8859-1
>
>Selon Erik Lindahl <lindahl at cbr.su.se>:
>
> > Hi,
> >
> > On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:
> >
> > > The version used by Alan Mark has never made it into gromacs.
> > > Rather, Erik Lindahl started the implementation of this stuff but
> > > did never finish it completely, due to other priorities I presume.
> > > We should however take out the variables to avoid confusion (unless
> > > someone provides a full implementation).
> >
> > Actually, technically the GB implementation is already in Gromacs
> > (even assembly kernels), and quite correct, it's just that you don't
> > have the born radii yet :-)
> >
> > The last couple of years we've mainly done membrane stuff where it's
> > not useful for my students, and thus not a priority to implement.
> > However, recently Per Larsson has finished C implementations of the
> > Still radius calculations that I've started optimizing.
> >
> > The big remaining task is the SA part of GB/SA, i.e. the surface
> > calculation, which also needs to be optimized and preferrably
> > parallelized (harder) to be useful.
> >
> >
> > Fan Hao actually offered us the code he wrote with Alan, but the
> > challengefor us isn't to write a trivial Still GB implementation, but
> > to make it perform well. There's little point in having a GB
> > implementation that is slower than the fast explicit-solvent
> > simulations in Gromacs!
> >
> >
>
>Happy to hear that, if you need some beta-tester
>for validation and performance
>tests, i'm your man :-)
>
>Cheers,
>
>Stéphane Téletchéa
>
>
>
>------------------------------
>
>Message: 2
>Date: Wed, 18 Jul 2007 22:06:51 +0200
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] Implicit solvent simulation
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <469E72DB.40807 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>steletch at jouy.inra.fr wrote:
> > Selon Erik Lindahl <lindahl at cbr.su.se>:
> >
> >> Hi,
> >>
> >> On Jul 18, 2007, at 5:08 PM, David van der Spoel wrote:
> >>
> >>> The version used by Alan Mark has never made it into gromacs.
> >>> Rather, Erik Lindahl started the implementation of this stuff but
> >>> did never finish it completely, due to other priorities I presume.
> >>> We should however take out the variables to avoid confusion (unless
> >>> someone provides a full implementation).
> >> Actually, technically the GB implementation is already in Gromacs
> >> (even assembly kernels), and quite correct, it's just that you don't
> >> have the born radii yet :-)
> >>
> >> The last couple of years we've mainly done membrane stuff where it's
> >> not useful for my students, and thus not a priority to implement.
> >> However, recently Per Larsson has finished C implementations of the
> >> Still radius calculations that I've started optimizing.
> >>
> >> The big remaining task is the SA part of GB/SA, i.e. the surface
> >> calculation, which also needs to be optimized and preferrably
> >> parallelized (harder) to be useful.
> >>
>
>Erik, didn't you say once that you implemented fast area calculations
>and derivatives?
>
>It's an interesting CS problem, but there certainly are at least a
>couple of papers on these topics.
> >>
> >> Fan Hao actually offered us the code he wrote with Alan, but the
> >> challengefor us isn't to write a trivial Still GB implementation, but
> >> to make it perform well. There's little point in having a GB
> >> implementation that is slower than the fast explicit-solvent
> >> simulations in Gromacs!
> >>
> >>
> >
> > Happy to hear that, if you need some
> beta-tester for validation and performance
> > tests, i'm your man :-)
> >
>You can help already now, by heading over to
>http://wiki.gromacs.org/index.php/Implicit_Solvent
>and adding more documentation.
>
>Although I realize it is the holiday season, at least in Europe, I would
>like to once more recommend the development wiki for documenting this
>kind of discussion, and for publishing specifications for algorithms,
>like (totally unrelated, but came up earlier today):
>http://wiki.gromacs.org/index.php/Cpp_replacement
>
>Cheers,
>--
>David van der Spoel, Ph.D.
>Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
>spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>
>
>------------------------------
>
>Message: 3
>Date: Wed, 18 Jul 2007 16:20:41 -0400
>From: John Mercer <jmercer at duke.edu>
>Subject: [gmx-users] install problem
>To: gmx-users at gromacs.org
>Message-ID: <77F8B904-7457-4BF6-8720-0F7A2F7356CB at duke.edu>
>Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
>Hi,
>
>I am a beginning user of GROMACS, and am just now trying to get a
>functional installation. There is something not quite right about
>the installations I have tried. I have spent considerable time
>testing ideas about what might be the problem, but have not nailed
>it. I am hoping someone will have a suggestion (perhaps obvious)
>that will reduce the time I am spending getting GROMACS operational.
>I can duplicate the problem with multiple GROMACS subprograms but
>will only refer to "luck" (luck.c).
>
>Platform: Mac OS X 10.4.10
>
>Installations tried:
> 1. Binary package install of
> gromacs-3.3.dmg.gz (from www.gromacs.org)
> 2. Fink with compile; first standalone, then remove standalone and
>install openmpi
>In both cases, GMXRC.bash is sourced in "profile".
> 3. All installations exhibit the same problem so I'll stick to fink.
>
>Indications:
> 1. luck -c executes with a segmentation fault from any directory.
> 2. /sw/bin/luck -c executes normally
> from any directory. (/usr/local/
>bin installation exhibits same problem.)
> 3. Not a UNIX PATH problem as non GROMACS functions in /sw/bin
>execute normally from the same shell.
> 4. A shorter PATH value does function normally without regard to
>where fink subdirectories are placed in the PATH, causing me to
>wonder whether PATH is parsed in code with a fixed memory variable.
>
>
>Diagnostics:
> 1. luck -c prints the GROMACS banner before it's segmentation fault
> 2. /sw/bin/luck -c prints the banner, a wording for the GROMACS
>acronym, a version number, the authors, software information, and a
>user friendly quote.
> 3. Comparing 1. & 2. with luck.c,
> copyrite.c, etc suggestions that a
>call to bromacs() in CopyRight() migh be where the problem manifests
>itself.
> 4. The call sequence could be CopyRight() -> bromacs() -> pukeit() -
> > low_lib_libopen() -> low_libfn().
> 5. Note: I haven't tested all these functions to verify they are
>each involved, but suggest them as a hypothesis based on the output
>and looking at traces of system calls.
> 6. One thing that puzzles me is that it looks as if low_libfn()
>expects "GMXLIB" as an environment variable, but the script
>GMXRC.bash sets up "GMXLDLIB as the library environment variable.
>
>Whatever the problem, the program executes from any directory, but
>only with the full path specified does it execute without a
>segmentation fault.
>
>
>Any advice on how to fix this problem would be greatly appreciated.
>
>John Mercer
>
>
>------------------------------
>
>Message: 4
>Date: Wed, 18 Jul 2007 16:50:22 -0400
>From: "srinivas aripirala" <srinivas.aripirala at gmail.com>
>Subject: [gmx-users] How to include Mg in the input file?
>To: gmx-users at gromacs.org
>Message-ID:
> <811592db0707181350j5d255bafpb0df787fbad4d29f at mail.gmail.com>
>Content-Type: text/plain; charset="iso-8859-1"
>
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>------------------------------
>
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>End of gmx-users Digest, Vol 39, Issue 69
>*****************************************
----------------------------------------------------------------------------------------------------------
Ibrahim M. Moustafa, Ph.D.
Biochemistry and Molecular Biology Dept.
201 Althouse Lab., University Park
Pennsylvania State University, PA16802
Tel. (814)863-8703
Fax. (814)865-7927
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