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

[groenedraeck]

Dear Nicholas,

thank you for your suggestion. I had some time and tried the following:


First, it was verified that gromacs was not installed system-wide and 
that the package's dependencies (libc6, libfftw3-3, libx11-6, libxml2) 
were all satisfied. In other words, installing gromacs through 
apt(itude) would lead to installation of only gromacs and gromacs-data 
packages. The following command was executed:

$ DEB_BUILD_OPTIONS="noopt debug" apt-get source --build gromacs > 
log.20111116 2>&1

The log was checked multiple times during the build and although I do 
not know the significance of it, a "defined but not used 
[-Wunused-function]"-error showed up and was repeated frequently for 
many .h files, e.g.:
____________________________
$ tail -n 50 ~/gromacs/log.20111116
gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_x86.h:167:21: 
warning: ‘tMPI_Atomic_ptr_swap’ defined but not used [-Wunused-function]
gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_x86.h:194:20: 
warning: ‘tMPI_Spinlock_init’ defined but not used [-Wunused-function]
gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_x86.h:201:20: 
warning: ‘tMPI_Spinlock_lock’ defined but not used [-Wunused-function]
gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_x86.h:230:20: 
warning: ‘tMPI_Spinlock_unlock’ defined but not used [-Wunused-function]
gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_x86.h:240:19: 
warning: ‘tMPI_Spinlock_trylock’ defined but not used [-Wunused-function]
gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_x86.h:256:19: 
warning: ‘tMPI_Spinlock_islocked’ defined but not used [-Wunused-function]
gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_x86.h:262:20: 
warning: ‘tMPI_Spinlock_wait’ defined but not used [-Wunused-function]
[ 24%] Building C object 
src/gmxlib/CMakeFiles/gmx.dir/nonbonded/nb_kernel_c/nb_kernel200.c.o
gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: In 
function ‘nb_kernel200’:
gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:84:42: 
warning: unused variable ‘gbtabscale’ [-Wunused-variable]
gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:84:33: 
warning: variable ‘tabscale’ set but not used [-Wunused-but-set-variable]
gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:83:29: 
warning: variable ‘nthreads’ set but not used [-Wunused-but-set-variable]
gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:83:23: 
warning: variable ‘ntype’ set but not used [-Wunused-but-set-variable]
gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: In 
function ‘nb_kernel200nf’:
gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:286:42: 
warning: unused variable ‘gbtabscale’ [-Wunused-variable]
gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:286:33: 
warning: variable ‘tabscale’ set but not used [-Wunused-but-set-variable]
gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:285:29: 
warning: variable ‘nthreads’ set but not used [-Wunused-but-set-variable]
gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c:285:23: 
warning: variable ‘ntype’ set but not used [-Wunused-but-set-variable]
gromacs-4.5.5/src/gmxlib/nonbonded/nb_kernel_c/nb_kernel200.c: At top level:
gromacs-4.5.5/include/types/../thread_mpi/atomic/gcc_x86.h:105:19: 
warning: ‘tMPI_Atomic_add_return’ defined but not used [-Wunused-function]
____________________________

Please find the complete log file (log.20111116) attached to this message.

I had a feeling that installing the package will probably result in a 
lot of things being broken. It was tried anyway (both .deb files were 
present in the active build folder):

$ sudo dpkg -i gromacs-data_4.5.5-1_all.deb gromacs_4.5.5-1_i386.deb

This command completed without errors and the program pdb2gmx was found 
to be installed in /usr/bin/pdb2gmx, as should be the case.

So, the next step was to try to generate the topology file from the 
lysozyme .pdb input - as described in the aforementioned tutorial.

$ pdb2gmx -f 1AKI_waterless.pdb -o 1AKI_processed.gro -water spce

Which -contrary to what I was expecting because of all the build errors- 
was found to produce the same Illegal instruction error as reported in 
the initial bug report. The log of which is attached as output.pdb2gmx.

I hope the log file can help you zoom in on the current issue. 
Personally, it would not surprise me if this is something AMD Duron 
processor specific and/or kernel-Duron specific. As said, the tutorial 
could be completed without any problems on a amd64 machine running 
Debian GNU/Linux testing (Wheezy).

Let me know when I can try some other things that can help you with 
getting rid of this bug. Good luck!
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: log.20111116
URL: <http://lists.alioth.debian.org/pipermail/debichem-devel/attachments/20111116/897b20ec/attachment-0002.ksh>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: output.pdb2gmx
URL: <http://lists.alioth.debian.org/pipermail/debichem-devel/attachments/20111116/897b20ec/attachment-0003.ksh>