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:
[EMAIL PROTECTED]:~/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:
> >
> > [EMAIL PROTECTED]:~/gromacs/test_installation$ editconf
> >
> > :-) G R O M A C S (-:
> >
> > *** stack smashing detected ***: editconf terminated
> > Segmentation fault
> > [EMAIL PROTECTED]:~/gromacs/test_installation$ which editconf
> > /usr/local/gromacs/bin/editconf
> > [EMAIL PROTECTED]:~/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: [EMAIL PROTECTED] *
* Fax: +44 1925 603825 Skype name: martyn.winn *
* URL: http://www.ccp4.ac.uk/martyn/ *
***********************************************************************
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