[gmx-users] infelicity in installation of 4.0.2

[Martyn Winn]

Hi

I hadn't source'd the GMXRC file, but that doesn't seem to help.
But then I noticed that it ran fine in another terminal window. After a
bit of experimentation, it seems to be to do with the length of PATH. In
the first terminal, PATH is about 2000 characters long (don't ask ;-)
Going to the second terminal where it worked, if I increase the PATH
variable by adding /usr/local/gromacs/bin lots of times, I can make that
crash too. 
A bit of grepping in the source code, I notice that gmxlib/futil.c has a
few hard limits like char system_path[512] (it seems to strcat onto
system_path without checking the length ??).

Might this be the problem?

For the record:
mdw at ccp4v:~/gromacs/test_installation$ ldd /usr/local/gromacs/bin/editconf
	linux-vdso.so.1 =>  (0x00007fff2abfc000)
	libgmxana.so.5 => /usr/local/gromacs/lib/libgmxana.so.5 (0x00007f072254a000)
	libmd.so.5 => /usr/local/gromacs/lib/libmd.so.5 (0x00007f0722258000)
	libgmx.so.5 => /usr/local/gromacs/lib/libgmx.so.5 (0x00007f0721db4000)
	libxml2.so.2 => /usr/lib/libxml2.so.2 (0x00007f0721a6d000)
	libnsl.so.1 => /lib/libnsl.so.1 (0x00007f0721854000)
	libfftw3f.so.3 => /usr/lib/libfftw3f.so.3 (0x00007f072159a000)
	libm.so.6 => /lib/libm.so.6 (0x00007f0721319000)
	libSM.so.6 => /usr/lib/libSM.so.6 (0x00007f0721111000)
	libICE.so.6 => /usr/lib/libICE.so.6 (0x00007f0720ef6000)
	libX11.so.6 => /usr/lib/libX11.so.6 (0x00007f0720bf3000)
	libc.so.6 => /lib/libc.so.6 (0x00007f0720891000)
	libdl.so.2 => /lib/libdl.so.2 (0x00007f072068d000)
	libz.so.1 => /usr/lib/libz.so.1 (0x00007f0720476000)
	libpthread.so.0 => /lib/libpthread.so.0 (0x00007f072025a000)
	libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x00007f0720059000)
	libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007f071fe3e000)
	/lib64/ld-linux-x86-64.so.2 (0x00007f07228d9000)
	libXau.so.6 => /usr/lib/libXau.so.6 (0x00007f071fc3c000)
	libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00007f071fa37000)

Cheers
Martyn

On Tue, 2008-12-02 at 13:52 +0100, Florian Haberl wrote:
> Hi,
> 
> On Tuesday, 2. December 2008, Martyn Winn wrote:
> > Hi all,
> >
> > I've compiled 4.0.2 from source on an EM64T machine running Ubuntu,
> > using ./configure --enable-shared
> > With all executables I've tried, I find:
> >
> > mdw at ccp4v:~/gromacs/test_installation$ editconf
> >
> >                          :-)  G  R  O  M  A  C  S  (-:
> >
> > *** stack smashing detected ***: editconf terminated
> > Segmentation fault
> > mdw at ccp4v:~/gromacs/test_installation$ which editconf
> > /usr/local/gromacs/bin/editconf
> > mdw at ccp4v:~/gromacs/test_installation$ /usr/local/gromacs/bin/editconf
> >
> >                          :-)  G  R  O  M  A  C  S  (-:
> >
> >                  Good ROcking Metal Altar for Chronical Sinners
> >
> >                             :-)  VERSION 4.0.2  (-:
> >
> > i.e. it only runs fine if I specify the full path. Searching the
> > archives, I found that this was reported in April 07, with a reply that
> > it will be fixed in 3.3.2
> >
> > Nothing more recent came up, but apologies if I missed it.
> 
> can you paste the output of ldd $your_executable?
> 
> Have you sourced the GMXRC file?
> 
> 
> Greetings,
> 
> Florian
> 
> 
-- 
***********************************************************************
*                                                                     *
*               Dr. Martyn Winn                                       *
*                                                                     *
*   STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K.   *
*   Tel: +44 1925 603455    E-mail: martyn.winn at stfc.ac.uk            *
*   Fax: +44 1925 603825    Skype name: martyn.winn                   * 
*             URL: http://www.ccp4.ac.uk/martyn/                      *
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