Archive from user: Maud Jusot I don’t manage to restart correctly REMD simulation (I posted it on the gmx-users mailing list here : https://www.mail-archive.com/gromacs.org\_gmx-users@maillist.sys.kth.se/msg18550.html ) but to summarize it : the first simulation has no problem and finish correctly after maxh time, but when it restarts no checkpoint files are written anymore and gromacs does not stop at maxh time (even if it says it does in the output). I tried it with 3 different versions of gromacs (4.6.5, 5.1.0 and 5.1.2) on two different clusters, so I am quite sure the problem does not come from the installation nor from the version. *(from redmine: issue id 1942, created on 2016-04-06 by gmxdefault, closed on 2016-06-27)* * Relations: * relates #692 * Changesets: * Revision bc98987b97d294362c19e34be45d527587f035c7 by Mark Abraham on 2016-06-23T12:53:55Z: ``` Prevent use of mdrun -maxh -multi A proper fix can probably be made in release-2016, and if so, the content of this commit should not be merged forward. Refs #1942 Change-Id: Ie7e6c0ca25fba09ad1794cacbe116b03e95ff0f9 ``` * Revision d5bd278b11bccc0e3d1a5bd4ee417c570fea133c by Mark Abraham on 2016-06-27T17:31:02Z: ``` Removed unnecessary inter-simulation signalling Generally, multi-simulation runs do not need to couple the simulations (discussion at #692). Individual algorithms implemented with multi-simulations might need to do so, but should take care of their own details, and now do. Scaling should improve in the cases where simulations are now decoupled. It is unclear what the expected behaviour of a multi-simulation should be if the user supplies any of the possible non-uniform distributions of init_step and nsteps, sourced from any of .mdp, .cpt or command line. Instead, we report on the non-uniformity and proceed. It's always possible that the user knows what they are doing. In particular, now that multi-simulations are no longer explicitly coupled, any heterogeneity in the execution environment will lead to checkpoints and -maxh acting at different time steps, unless a user-selected algorithm requires that the simulations stay coordinated (e.g. REMD or ensemble restraints). In the implementation of signalling, we have stopped checking gs for NULL as a proxy for whether we should be doing signalling at that communication phase. Replaced with a helper object in which explicit flags are set. Added unit tests of that functionality. Improved documentation of check_nstglobalcomm. mdrun now reports the number of steps between intra-simulation communication to the log file. Noted minor TODOs for future cleanup. Added some trivial test cases for termination by maxh in normal-MD, multi-sim and REMD cases. Refactored multi-sim tests to make this possible without duplication. This is complicated by the way filenames get changed by mdrun -multi by the former par_fn, so cleaned up the way that is handled so it can work and be re-used better. Introduced mdrun integration-test object library to make that build system work a little better. Made some minor improvements to Doxygen setup for integration tests. Fixes #860, #692, #1857, #1942. Change-Id: I5f7b98f331db801b058ae2b196d79716b5912b09 ``` * Uploads: * [tpr_files.tar.gz](/uploads/e45f9c056f1646fa464043ad238a4732/tpr_files.tar.gz) all the tpr files * [output_files.tar.gz](/uploads/5ddd21c9f35a839f379e88988d36e038/output_files.tar.gz) output files and script