[gmx-users] Test suite failures
r.nobes at fle.fujitsu.com
Tue Mar 2 15:08:00 CET 2004
Thanks for explaining why some of the tests appear to fail.
One more observation: three of the test jobs terminate with a SIGSEGV (both
on our Linux box and on the Fujitsu PRIMEPOWER). These are angles1,
angles125 and rb1. For example:
cluster.fle.fujitsu.com ~/gmxtest > cd d.angles1
cluster.fle.fujitsu.com d.angles1 > grompp -norenum -normdumbds >&
cluster.fle.fujitsu.com d.angles1 > mdrun
starting mdrun 'This_incredible_box_of_butane'
50 steps, 0.0 ps.
Segmentation fault (core dumped)
or, under gdb,
Program received signal SIGSEGV, Segmentation fault.
0x40093d80 in angles () from /usr/local/lib/libgmx.so.3
#0 0x40093d80 in angles () from /usr/local/lib/libgmx.so.3
#1 0xbfffd988 in ?? ()
> -----Original Message-----
> From: David van der Spoel [mailto:spoel at xray.bmc.uu.se]
> Sent: 02 March 2004 08:39
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Test suite failures
> On Tue, 2 Mar 2004, Ross Nobes wrote:
> >I am trying to confirm that (non-MPI) version 3.2.1 runs correctly on our
> >Linux Xeon machine. If I install GROMACS via the RPM package, and then
> >the test suite (obtained from the CVS server), I get failures for a
> >of jobs:
> >Testing dec+water . . . FAILED. Check files in d.dec+water
> >Testing acetonitrilRF . . . FAILED. Check files in d.acetonitrilRF
> >Testing tip4p . . . FAILED. Check files in d.tip4p
> >Testing sw . . . FAILED. Check files in d.sw
> A number of these fail because the reference states are very old. Rather
> than updating the reference states with each release, which some defies
> the purpose of "honest" tests, I left them in. If you check the
> differences (checkedr.out) you will see that they are small, in most cases
> negligable because of the large inherent fluctuations in pressure. Sine
> the gmxcheck program checks the relative energy/pressure you get
> deviations when the values are close to zero. Most of the failures are
> harmless therefore.
> Nevertheless it is very important to check this stuff. I don't know
> offhand whether the examples you mention should be OK, dec+water has
> failed consistently for a while. I'll have a look.
> David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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