Hello,
On 10/05/2011 03:37 PM, groenedraeck wrote:
> Package: gromacs
> Version: 4.5.5-1
> Severity: important
>
> It was found that the pdb2gmx (v4.5.5) from the GROMACS (gromacs v4.5.5-1)
> fails with an 'Illegal instruction' after the 'Making bonds...' operation
> (see below).
>
> The bug was first noted in gromacs 4.5.4-2 (bug report not filed, prior
> versions of gromacs not tested at this workstation), and persists in the
> recent gromacs 4.5.5-1. In both cases the gromacs packages and all
> dependencies were installed through aptitude. Although reproducible on a
> virtual machine (see below), the bug first appeared on a physical computer,
> equipped with a single 1 GHz AMD Duron processor, 514340k RAM, md0 raid1
> controlled by mdadm.
This could be a problem with some optimisation that goes beyond what the
Duron can do. The folks from debichem may have a different opinion, but
I suggest to compile it yourself to see what happens. You may want to
substitute the compiler with gcc-4.4, but I think, given how simple it
seems to reproduce your problem on your platform, I would just start
with the default:
apt-get source --build gromacs
should be doing that. You may need to install some extra build
dependencies. Then use dpkg -i to install the packages. If this solved
the issue, then please report with your compiler version. If the error
still persists, I see two things to do:
* use another compiler (clang, gcc-snapshot or gcc-4.4)
* add a debug package for gromacs and start pdb2gmx from within gdb
I have pasted a respective patch for the debug package below and have
just built gromacs with it. Worked here. @Debichem: It would be nice to
see a future version of gromacs with something like it. For the problem
at hand I do not think the -dbg package to be helping too much since
illegal instuctions just should not happen and may IMHO more be pointing
to a compiler issue.
--- debian/control (revision 3036)
+++ debian/control (working copy)
@@ -112,3 +112,12 @@
This package contains only the core simulation engine with parallel
support using the OpenMPI interface. It is suitable for nodes of a
processing cluster, or for multiprocessor machines.
+
+Package: gromacs-dbg
+Architecture: any
+Depends: gromacs (= ${binary:Version})
+Description: debug sysmbols for gromacs
+ This package contains information to identify problems with the executed
+ code. Those may be platform-specific issues or programming errors. You
+ may be asked to install the package prior to reproducing the issue you
+ were reporting.
Index: debian/rules
===================================================================
--- debian/rules (revision 3036)
+++ debian/rules (working copy)
@@ -239,7 +239,7 @@
dh_testroot -s
dh_installchangelogs -s
dh_installdocs -s
- dh_strip -A
+ dh_strip -A --dbg-package=gromacs-dbg
dh_link -s
dh_compress -s
dh_fixperms -s
Hope to have somewhat helped
Steffen
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