write lowest energy coordinates fail with CG - Redmine #2554
Archive from user: Carlo Camilloni
Step 405, Epot=–8.872469e+04, Fnorm=7.410e+00, Fmax=7.881e+01 (atom 3770)
writing lowest energy coordinates.
Program: gmx mdrun, version 2018.2
Source file: src/gromacs/mdlib/minimize.cpp (line 582)
Function: void write_em_traj(FILE , t_commrec, gmx_mdoutf_t, gmx_bool, gmx_bool, const char , gmx_mtop_t, t_inputrec , gmx_int64_t, em_state_t, t_state , ObservablesHistory)
The code below assumes that (with domain decomposition), x is collected to
state_global in the call above.
For more information and tips for troubleshooting, please check the
website at http://www.gromacs.org/Documentation/Errors
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
(from redmine: issue id 2554, created on 2018-06-14 by gmxdefault, closed on 2018-08-21)
- relates #2578 (closed)
- Revision 9232fa9a by Mark Abraham on 2018-07-30T15:49:53Z:
Fix CG with multiple domains The global state can only be accessed on master rank, so we should set the flags there and then permit the DD code to propagate the setup of the cg_p vector. Fixes #2554 Change-Id: If294bf000eb0266125ecc6c6bf937aac0390e2b8
- Revision 0fe41117 by Berk Hess on 2018-08-20T08:29:21Z:
Really fix CG with multiple domains Commit 9232fa9a incorrectly claimed to fix CG with multiple domains. The change fixes all issues due to the change of the global state only being available on the master rank. Note that there is still an issue with writing the final trajectory frame. Refs #2554 Change-Id: I1ed3363f722daad9e6aef00d9ded6647acc820f2
- Revision 1fadc372 by Berk Hess on 2018-08-20T08:29:40Z:
Fix assertion failure in CG When the final step coincided with a coordinate output step, conjugate gradient minimization would exit with an assertion failure instead of writing confout.gro. Fixes #2554 Change-Id: I53fffccb5310259132724b83ee452ef01f8ac9c8