mdrun -nt > 1 crashes with old tpr
As reported here http://lists.gromacs.org/pipermail/gmx-users/2013-February/078961.html mdrun 4.6 crashes with more than one thread when run with a particular old tpr file. Initial debugging points to initiation of new data structures that are not present in the old tpr file (line 569 below).
567 block_bc(cr, fep->n_lambda);
568 snew_bc(cr, fep->all_lambda, efptNR);
569 nblock_bc(cr, efptNR, fep->all_lambda);
It runs with one thread.
fix imcompatibility with tpr vers<64 with free energy option
should fix to redmine #1156
#3 Updated by David van der Spoel over 6 years ago
Additional information: the routine
static void do_expandedvals(t_fileio *fio, t_expanded *expand, t_lambda *fepvals, gmx_bool bRead, int file_version)
is only called for new files (tpx_version > 79) therefore the rest will be initialized with NULL or 0.
#8 Updated by Justin Lemkul over 6 years ago
Daniel Wang wrote:
Michael Shirts wrote:
Posted a fix. I believe this only affects tprs with version < 64.
Could you send me the patch? I prefer to use gromacs4.6 because it runs slightly faster than 4.5.
Here is my email address: email@example.com
Thanks a lot:)
You can download a patch to the development code at https://gerrit.gromacs.org/#/c/2196/.