[gmx-developers] Release 4.6 fails to compile

Christoph Junghans junghans at votca.org
Thu Jun 7 02:03:23 CEST 2012

> Hi All,
> I just wanted to point out that based on the latest change to the 4.6
> release branch (free energy, etc) there is a small bug that breaks
> compilation for mdrun-gpu.  The problem comes from the changes to idef.h -
> the introduction of A and B states for bonded parameters causes the
> following:
> Building C object src/gmxlib/CMakeFiles/gmx.dir/invblock.c.o
> In file included from
> /home/jalemkul/ATHENA/software/openmm-2.0/include/OpenMM.h:43,
>                 from
> /home/jalemkul/ATHENA/software/git/release-4-6/src/kernel/openmm_wrapper.cpp:59:
> /home/jalemkul/ATHENA/software/openmm-2.0/include/openmm/CustomHbondForce.h:
> In constructor ‘OpenMM::CustomHbondForce::GroupInfo::GroupInfo(int, int,
> int, const std::vector<double, std::allocator<double> >&)’:
> /home/jalemkul/ATHENA/software/openmm-2.0/include/openmm/CustomHbondForce.h:439:
> warning: ‘OpenMM::CustomHbondForce::GroupInfo::p3’ will be initialized after
> /home/jalemkul/ATHENA/software/openmm-2.0/include/openmm/CustomHbondForce.h:438:
> warning:   ‘std::vector<double, std::allocator<double> >
> OpenMM::CustomHbondForce::GroupInfo::parameters’
> /home/jalemkul/ATHENA/software/openmm-2.0/include/openmm/CustomHbondForce.h:442:
> warning:   when initialized here
> [  7%] [  7%] Building C object src/gmxlib/CMakeFiles/gmx.dir/macros.c.o
> /home/jalemkul/ATHENA/software/git/release-4-6/src/kernel/openmm_wrapper.cpp:
> In function ‘void* openmm_init(FILE*, const char*, t_inputrec*, gmx_mtop_t*,
> gmx_localtop_t*, t_mdatoms*, t_forcerec*, t_state*)’:
> /home/jalemkul/ATHENA/software/git/release-4-6/src/kernel/openmm_wrapper.cpp:929:
> error: ‘struct t_iparams::<anonymous>’ has no member named ‘r13’
> /home/jalemkul/ATHENA/software/git/release-4-6/src/kernel/openmm_wrapper.cpp:929:
> error: ‘struct t_iparams::<anonymous>’ has no member named ‘kUB’
> /home/jalemkul/ATHENA/software/git/release-4-6/src/kernel/openmm_wrapper.cpp:932:
> error: ‘struct t_iparams::<anonymous>’ has no member named ‘theta’
> /home/jalemkul/ATHENA/software/git/release-4-6/src/kernel/openmm_wrapper.cpp:932:
> error: ‘struct t_iparams::<anonymous>’ has no member named ‘ktheta’
> Adding 'A' to the end of each of these terms solves the problem, though that
> is a bit of a hack, but would work assuming free energy features are not
> intended to be run on GPU.  A more elegant solution should probably be
> found, but I didn't care about elegance when I was trying to compile ;)
> I just thought I should point this out so that perhaps a fix will be put in
> place.  I can file this on redmine if necessary so no one forgets.
Can you push a patch to gerrit?

Related question, do we want to keep OpenMM support in 4.6? OpenMM-2.0
is more than obsolete, they have released 4.1 last month and porting
Gromacs to it will need some time. I have unsuccessfully tried porting
Gromacs to OpenMM-3.0 at some point. And the new hybrid kernels will
use cuda, so GPUs will be supported anyway.


2012/6/6 Justin A. Lemkul <jalemkul at vt.edu>:
> --
> ========================================
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
> --
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-developers-request at gromacs.org.

Christoph Junghans
Web: http://www.compphys.de

More information about the gromacs.org_gmx-developers mailing list