Bug #1156
mdrun -nt > 1 crashes with old tpr
Description
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.
Associated revisions
fix imcompatibility with tpr vers<64 with free energy option
should fix to redmine #1156
Change-Id: I6e60f1efbb03bf460009b8bc59f80f2e0e15bf44
History
#1 Updated by David van der Spoel over 6 years ago
- Target version set to 4.6.1
#2 Updated by Peter Kasson over 6 years ago
I have also encountered this problem on multiple TPR files FWIW.
#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.
#4 Updated by Michael Shirts over 6 years ago
Looks like it's probably my fault, then. I'll see what I can come up with to fix.
#5 Updated by Michael Shirts over 6 years ago
Posted a fix. I believe this only affects tprs with version < 64.
#6 Updated by Berk Hess over 6 years ago
- Assignee set to Michael Shirts
Is this a duplicate of #1131?
#7 Updated by Daniel Wang over 6 years ago
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: iwnking@gmail.com
Thanks a lot:)
#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: iwnking@gmail.com
Thanks a lot:)
You can download a patch to the development code at https://gerrit.gromacs.org/#/c/2196/.
#9 Updated by Mark Abraham over 6 years ago
- Status changed from New to Accepted
- Affected version set to 4.6
#10 Updated by Mark Abraham over 6 years ago
- Status changed from Accepted to In Progress
#11 Updated by Mark Abraham over 6 years ago
- Status changed from In Progress to Resolved
#12 Updated by Rossen Apostolov over 5 years ago
- Status changed from Resolved to Closed
fix imcompatibility with tpr vers<64 with free energy option
should fix to redmine #1156
Change-Id: I6e60f1efbb03bf460009b8bc59f80f2e0e15bf44