[Debichem-devel] Bug#725013: gromacs-openmpi: grompp crashes with invalid opcode

[Vassilis Virvilis]

Package: gromacs-openmpi
Version: 4.6.3-4
Severity: important

Dear Maintainer,

   * What led up to the situation?

Trying to run grompp grompp_d

   * What exactly did you do (or not do) that was effective (or
     ineffective)?

It crashes

dmesg output:
[ 1699.966132] traps: grompp_d[9667] trap invalid opcode ip:7fb9311ac95d sp:7ffff7700ee8 error:0 in libgmx_d.so.8[7fb9310d0000+4e9000]
[ 1728.255893] traps: grompp[9684] trap invalid opcode ip:7f6807c2c65d sp:7fff560ed648 error:0 in libgmx.so.8[7f6807b51000+51b000]

   * What was the outcome of this action?

crash.

   * What outcome did you expect instead?

The problem looks like a miscompilation. I am working on i7 system. If I
compile gromacs from source it works. If I use dpkg-buildpackage it doesn't
work.

The problem is on libgmx/rando.c

-- System Information:
Debian Release: jessie/sid
  APT prefers unstable
  APT policy: (500, 'unstable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.10-3-amd64 (SMP w/24 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages gromacs-openmpi depends on:
ii  libblas3 [libblas.so.3]      1.2.20110419-7
ii  libc6                        2.17-93
ii  libfftw3-double3             3.3.3-5+b1
ii  libfftw3-single3             3.3.3-5+b1
ii  libgomp1                     4.8.1-10
ii  libhwloc5                    1.7.2-1
ii  liblapack3 [liblapack.so.3]  3.4.2+dfsg-4
ii  libopenmpi1.6                1.6.5-5
ii  openmpi-bin                  1.6.5-5

Versions of packages gromacs-openmpi recommends:
ii  gromacs  4.6.3-4

Versions of packages gromacs-openmpi suggests:
ii  gromacs-data  4.6.3-4

-- no debconf information