Hi,<div><br></div><div>what is the error message? Look at stdout/stderr and log file.</div><div><br></div><div>Roland<br><br><div class="gmail_quote">On Tue, Aug 3, 2010 at 11:21 AM, Da-Wei Li <span dir="ltr"><<a href="mailto:lidawei@gmail.com">lidawei@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hello<br>
<br>
I tried the Gromacs 4.5 beta. However, my MPI mdrun died. Here it is<br>
the output. The Gromacs-4.0.7 work fine for the same system. It is<br>
"protein in water" system. There are about 22000 atoms.<br>
***************************************************************************************<br>
Will use 9 particle-particle and 7 PME only nodes<br>
This is a guess, check the performance at the end of the log file<br>
Making 1D domain decomposition 9 x 1 x 1<br>
<br>
Steepest Descents:<br>
Tolerance (Fmax) = 1.00000e+03<br>
Number of steps = 50000<br>
rank 9 in job 1 hpc-8-16.local_53455 caused collective abort of all ranks<br>
exit status of rank 9: killed by signal 9<br>
************************************************************<br>
<br>
<br>
<br>
dawei<br>
<div><div></div><div class="h5"><br>
On Fri, Jul 30, 2010 at 3:20 PM, Rossen Apostolov<br>
<<a href="mailto:rossen.apostolov@cbr.su.se">rossen.apostolov@cbr.su.se</a>> wrote:<br>
><br>
> After months of hard work and 2449 patches, the new gromacs-4.5-beta1 is<br>
> out!<br>
><br>
> It is full of many new and exciting features, please try them out!<br>
><br>
> If something is not working as expected, please send a mail or file a<br>
> bugzilla report.<br>
><br>
> For developers: there is a new branch for stable releases called<br>
> "release-4-5-patches". Bugfixes should be applied there *first*, and if<br>
> needed, merged from that branch into the master after the fix. See<br>
> <a href="http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes" target="_blank">http://www.gromacs.org/Developer_Zone/Git/Git_Tutorial#Bugfixes</a> for more<br>
> information.<br>
><br>
><br>
> New features:<br>
><br>
> 2D decomposition support for PME: improved load balancing with up to 40%<br>
> overall performance improvement for large systems.<br>
> Memory usage is improved for very large systems, allowing simulations of<br>
>>100 million atoms.<br>
> Running on multi-core nodes now automatically uses threads for domain<br>
> decomposition through the built-in threaded MPI library<br>
> GPU computing support<br>
> Check-pointing is made more secure:MD5sum are used to verify that all files<br>
> are correctly in-place before a simulation is appended. Output file<br>
> appending at continuation is turned on by default<br>
> Full Cmake support. Autoconf/automake will be deprecated after the final 4.5<br>
> release!<br>
> Full support for 7 AMBER force fields<br>
> Support for CHARMM27, including cmap for dihedrals<br>
> Efficient Generalized-Born implicit solvent support including the<br>
> Still/HCT/OBC-models to compute the Born radii, a novel way of tabulating<br>
> the generalized Born-interaction formula for greater speed, and optimized<br>
> SSE-routines for both cut-off and all-vs-all simulations.<br>
> Support for nucleic acid simulations<br>
> Support for Velocity-Verlet integrators for reversible T- and P-coupling;<br>
> MTTK pressure control integrators; Nose-Hoover chains<br>
> Support for Bennett acceptance ratio (BAR) free energy calculations<br>
> Decoupling group setup for free energy<br>
> File formats: All GROMACS tools can now read any VMD supported trajectory<br>
> format, without converting trajectory first. (VMD is required)<br>
> g_rdf was a little bit enhanced that structure factors can be calculated for<br>
> any system, by supplying the necessary data via sfactor.dat. Most of the<br>
> common atomtypes are already contained, but everybody who needs more freedom<br>
> can enhance the table<br>
> Library support for "dynamic index groups" based on textual selections<br>
> (experimental feature). See the tool g_select, the included template.c, or<br>
> Doxygen documentation for information on how to write analysis tools using<br>
> the library. Existing tools have not (yet) been converted.<br>
> g_tune_pme: For a given number of processes or threads this tool<br>
> systematically times mdrun with various numbers of PME-only nodes and<br>
> determines which setting is fastest. It also checks whether performance can<br>
> be enhanced by shifting load between the real and the reciprocal space part<br>
> of the Ewald sum.<br>
> g_membed: a very convenient utility for embedding membrane proteins into<br>
> equilibrated lipid bilayers<br>
><br>
> Big thanks to all developers, contributors and users!<br>
><br>
</div></div><div class="im">> --<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>865-241-1537, ORNL PO BOX 2008 MS6309<br>
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