VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Mar 09 2004 - 13:29:03 CST

hmmm
That patch fixed the source, but oooo it sure messed up ls and such.
The errors were not severe like a seg fault, but ls wouldn't work because
it couldn't find uncompress.o. I had to turn it off just to see where
uncompress got put after make install.

I will look at it later....

Brian

On Tue, 9 Mar 2004, Zampighi, Lorenzo wrote:

> Hello Brian,
>
> You need to install the patch, zlibc-0.9j-20040228.diff.gz, to make it work.
>
> Of note, after I got it working whenever I do a "ls" I get a segmentation
> fault. I am not sure this is related but it seems to have a lot of issues
> with glibc 2.3.
>
> Lorenzo
>
> -----Original Message-----
> From: Brian Bennion
> To: Axel Kohlmeyer
> Cc: vmd-l_at_ks.uiuc.edu; Diss Romain; John Stone
> Sent: 3/9/04 9:08 AM
> Subject: Re: vmd-l: gziped files
>
> Hello Axel,
>
> (sorry john if this is off topic)
>
> That is a clever idea.... As I tried to get the library compiled I ran
> across some nasty errors in the kernel_stat.h header.
>
> I am running 2.4.21-9.ELsmp #1 SMP on a dual athlon. gcc version 3.2.3
> 20030502 (Red Hat Linux 3.2.3-24
>
> The errors are below
> gcc -DHAVE_CONFIG_H -DSYSCONFDIR=\"/usr/local/etc\" -Di686 -Dpc -Dlinux
> -fpic -I. -I. -c open.c
> In file included from zlibc.h:205,
> from sysincludes.h:142,
> from open.c:10:
> kernel_stat.h:21: warning: no semicolon at end of struct or union
> kernel_stat.h:21: syntax error before '.' token
> kernel_stat.h:24: syntax error before '.' token
> kernel_stat.h:27: syntax error before '.' token
> kernel_stat.h:34: syntax error before '}' token
> In file included from sysincludes.h:142,
> from open.c:10:
> zlibc.h:219:13: warning: extra tokens at end of #undef directive
> zlibc.h:241:13: warning: extra tokens at end of #undef directive
>
>
> On Tue, 9 Mar 2004, Axel Kohlmeyer wrote:
>
> >
> > hi folks,
> >
> > if you run on linux (don't know which other OSs are supported)
> > you could use zlibc (<http://zlibc.linux.lu/).
> >
> > after you installed it, you do
> >
> > export LD_PRELOAD=/usr/local/lib/uncompress.o
> > vmd some.pdb
> >
> > and it will pick up some.pdb.gz if it cannot find some.pdb.
> > works very nicely.
> >
> > axel.
> >
> >
> > >>> "JS" == John Stone <johns_at_ks.uiuc.edu> writes:
> >
> > JS> Diss,
> > JS> At present VMD can't automatically decompress files, but that's
> > JS> something I'd like to implement as a new class of plugin sometime
> soon.
> > JS> Ideally it'd work for all filetypes then, and would work with
> Unix,
> > JS> Windows, etc.
> >
> > JS> John
> >
> > JS> On Mon, Mar 08, 2004 at 05:00:49PM +0100, Diss Romain wrote:
> > >> Hi,
> > >> Is it possible for VMD to directly read a gziped file (.pdb.gz,
> .crd.gz, ...)
> > >> or do i have to gunzip it by hand (or with a script) ?
> > >>
> > >> Thanks you
> >
> > JS> --
> > JS> NIH Resource for Macromolecular Modeling and Bioinformatics
> > JS> Beckman Institute for Advanced Science and Technology
> > JS> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > JS> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > JS> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
> >
> > --
> >
> >
> =======================================================================
> > Axel Kohlmeyer e-mail:
> axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> > Lehrstuhl fuer Theoretische Chemie Phone: ++49
> (0)234/32-26673
> > Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49
> (0)234/32-14045
> > D-44780 Bochum
> http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> >
> =======================================================================
> > If you make something idiot-proof, the universe creates a better
> idiot.
> >
>
> *****************************************************************
> **Brian Bennion, Ph.D. **
> **Computational and Systems Biology Division **
> **Biology and Biotechnology Research Program **
> **Lawrence Livermore National Laboratory **
> **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> **7000 East Avenue phone: (925) 422-5722 **
> **Livermore, CA 94550 fax: (925) 424-6605 **
> *****************************************************************
>

*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************