[Debichem-devel] Bug#644397: Bug#644397: gromacs: pdb2gmx, version 4.5.5, fails with 'Illegal instruction' on i686, 3.0.0.1-686-pae (testing)

[Steffen Möller]

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