[gmx-users] install problem
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jul 18 23:59:56 CEST 2007
John Mercer wrote:
> 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"
> 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.
> 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.
> 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
> 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.
have you tried using csh?
just guessing at this point, but on my mac it works fins under a
c-shell, an always has.
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
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