Hi, what is the error message? Look at stdout/stderr and log file.
Roland On Tue, Aug 3, 2010 at 11:21 AM, Da-Wei Li <[email protected]> wrote: > Hello > > I tried the Gromacs 4.5 beta. However, my MPI mdrun died. Here it is > the output. The Gromacs-4.0.7 work fine for the same system. It is > "protein in water" system. There are about 22000 atoms. > > *************************************************************************************** > Will use 9 particle-particle and 7 PME only nodes > This is a guess, check the performance at the end of the log file > Making 1D domain decomposition 9 x 1 x 1 > > Steepest Descents: > Tolerance (Fmax) = 1.00000e+03 > Number of steps = 50000 > rank 9 in job 1 hpc-8-16.local_53455 caused collective abort of all > ranks > exit status of rank 9: killed by signal 9 > ************************************************************ > > > > dawei > > On Fri, Jul 30, 2010 at 3:20 PM, Rossen Apostolov > <[email protected]> wrote: > > > > After months of hard work and 2449 patches, the new gromacs-4.5-beta1 is > > out! > > > > It is full of many new and exciting features, please try them out! > > > > If something is not working as expected, please send a mail or file a > > bugzilla report. > > > > For developers: there is a new branch for stable releases called > > "release-4-5-patches". Bugfixes should be applied there *first*, and if > > needed, merged from that branch into the master after the fix. See > > http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes for more > > information. > > > > > > New features: > > > > 2D decomposition support for PME: improved load balancing with up to 40% > > overall performance improvement for large systems. > > Memory usage is improved for very large systems, allowing simulations of > >>100 million atoms. > > Running on multi-core nodes now automatically uses threads for domain > > decomposition through the built-in threaded MPI library > > GPU computing support > > Check-pointing is made more secure:MD5sum are used to verify that all > files > > are correctly in-place before a simulation is appended. Output file > > appending at continuation is turned on by default > > Full Cmake support. Autoconf/automake will be deprecated after the final > 4.5 > > release! > > Full support for 7 AMBER force fields > > Support for CHARMM27, including cmap for dihedrals > > Efficient Generalized-Born implicit solvent support including the > > Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating > > the generalized Born-interaction formula for greater speed, and optimized > > SSE-routines for both cut-off and all-vs-all simulations. > > Support for nucleic acid simulations > > Support for Velocity-Verlet integrators for reversible T- and P-coupling; > > MTTK pressure control integrators; Nose-Hoover chains > > Support for Bennett acceptance ratio (BAR) free energy calculations > > Decoupling group setup for free energy > > File formats: All GROMACS tools can now read any VMD supported trajectory > > format, without converting trajectory first. (VMD is required) > > g_rdf was a little bit enhanced that structure factors can be calculated > for > > any system, by supplying the necessary data via sfactor.dat. Most of the > > common atomtypes are already contained, but everybody who needs more > freedom > > can enhance the table > > Library support for "dynamic index groups" based on textual selections > > (experimental feature). See the tool g_select, the included template.c, > or > > Doxygen documentation for information on how to write analysis tools > using > > the library. Existing tools have not (yet) been converted. > > g_tune_pme: For a given number of processes or threads this tool > > systematically times mdrun with various numbers of PME-only nodes and > > determines which setting is fastest. It also checks whether performance > can > > be enhanced by shifting load between the real and the reciprocal space > part > > of the Ewald sum. > > g_membed: a very convenient utility for embedding membrane proteins into > > equilibrated lipid bilayers > > > > Big thanks to all developers, contributors and users! > > > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [email protected]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
