On 10/6/2011 11:18, Steffen Möller wrote:
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
Dear Steffen,
thank you for your quick and detailed reponse. I have little experience
with non-trivial compiling issues. However, I have tried some of the
things you suggested, those are reported below.
On the workstation for which the bug was reported, the installed gromacs
and gromacs-data were purged. Hereafter, the following packages
(including dependencies) were installed: dpkg-dev, debhelper, dpatch,
libmpich2-dev, libopenmpi-dev, lesstif2-dev, libgsl0-dev, libxml2-dev,
cmake. Thereafter, the system was restarted and the following command
was issued:
$ apt-get source --build gromacs > log.20111007 2>&1
When finished, the log was inspected for apparent errors. The log file
frequently contained a MPI implementation error:
> -- Using manually set binary suffix: "_mpi.mpich"
> -- Using manually set library suffix: "_mpi.mpich"
> CMake Warning at CMakeLists.txt:192 (MESSAGE):
>
>
> There are known problems with some MPI implementations:
> OpenMPI version < 1.4.1
> MVAPICH2 version <= 1.4.1
>
>
> -- Checking for MPI_IN_PLACE
> -- Performing Test MPI_IN_PLACE_COMPILE_OK
> -- Performing Test MPI_IN_PLACE_COMPILE_OK - Success
> -- Checking for MPI_IN_PLACE - yes
The built packages were installed using:
$ dpkg -i gromacs_4.5.5-1_i386.deb gromacs-data_4.5.5-1_all.deb
The lysozyme (pdb: 1AKI) tutorial (http://goo.gl/dxzex) was followed and
the bug reported above repeated:
$ pdb2gmx -f 1AKI_waterless.pdb -o 1AKI_processed.gro -water spce
[.. truncated log ..]
> Linking CYS-76 SG-601 and CYS-94 SG-724...
> Start terminus LYS-1: NH3+
> End terminus LEU-129: COO-
> Checking for duplicate atoms....
> Now there are 129 residues with 1960 atoms
> Making bonds...
> Illegal instruction
The self-built and installed gromacs packages were purged, the official
gromacs source package was obtained, extracted and the following two
compilers were used:
== gcc-4.4 ==
$ ./configure CC=gcc-4.4 --prefix=/homedir --with-fft=fftw3
$ make CC=gcc-4.4
$ make install
The pdb2gmx program failed with the same error, at seemingly the same
time. Install files were removed as well as the automake stuff($ make
distclean)
== clang == (all dependencies were installed first)
$ ./configure CC=clang --prefix=/home/not/gromacs/install
--with-fft=fftw3 && make CC=clang && make install
From the start, this produced errors in the make phase, a lot of
'clang: warning: argument unused during compilation' warnings were
reported, i.e.:
> /bin/bash ../../../../libtool --mode=compile clang -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2
-std=gnu99 -pthread -I./include -c -o nb_kernel_ia32_sse_test_asm.lo
nb_kernel_ia32_sse_test_asm.s
> clang -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-msse2 -std=gnu99 -pthread -I./include -c nb_kernel_ia32_sse_test_asm.s
-o nb_kernel_ia32_sse_test_asm.o
> clang: warning: argument unused during compilation:
'-fomit-frame-pointer'
> clang: warning: argument unused during compilation: '-finline-functions'
> clang: warning: argument unused during compilation: '-Wall'
> clang: warning: argument unused during compilation: '-Wno-unused'
> clang: warning: argument unused during compilation: '-msse2'
> clang: warning: argument unused during compilation: '-std=gnu99'
> clang: warning: argument unused during compilation: '-pthread'
> clang: warning: argument unused during compilation: '-I ./include'
This time, the pdb2gmx error was totally broken and returned to prompt
after displaying the GROMACS motd (i.e. names team).
At this point I decided to stop trying to get things to work at the 1
GHz Duron workstation, because I was not sure the CC=clang option was
the right way to do it and after the command completed, results got worse.
So, to verify one of my earlier statements, in virtualbox-ose
(3.2.10_OSE r66523), was started an i386 guest running Debian GNU/Linux
testing (Wheezy), kernel 3.0.0-1-686-pae. Only the base system, standard
system utilities and gromacs packages (including dependencies) were
freshly installed. The error could not be reproduced (following the
lysozyme (pdb: 1AKI) tutorial at http://goo.gl/dxzex).
Indeed, I am starting to think that the problem might be Duron-specific,
as already suggested by Steffen. So, given the nature of the current
problem, the age of the problematic workstation versus the highly
advanced capabilities and applications of GROMACS, I think trying to
squash this bug might not be worth the time and energy of those
involved. At the other hand, however, it is the first occasion that a
Debian package does not work appropriately on the computer I am trying
to run it (and that's what made me report the bug in the first place).
In conclusion, I am willing to contribute and help solving the problem
documented in the bugreport on the given workstation, but only if the
suggested steps are described in sufficient detail for me to quickly
execute, compile, build, install or implement them. I have the given
computer at my disposal, I am subscribed to this bug and -when time
permits- gladly like to try whatever is suggested.
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