[gmx-users] help with mpirun and system exploding during heating

[Justin A. Lemkul]

These aren't mpi problems, they are problems with your system.  This type of
question is all over the mailing list, so do have a thorough look through the
archives to search for solutions.  Also, read here for a bit of background:

http://wiki.gromacs.org/index.php/blowing_up

If you need further help fixing the problem, please provide a description of
your system, what you have done so far, and your .mdp file.

-Justin

Quoting fabracht sdf <fabracht at gmail.com>:

> I finallly managed to compile gromacs with mpi support, thanks to this
> mailing list, but i encountered some problems during my heating process.
> I typed the command grompp -np 4 ....
> and then mpirun -np 4 mdrun -...
> that work out just fine for my minimization, but my heating well i think it
> all collapsed. the warning comes out like this.
> This first line is the end of many others that look almost the same.
> Well, I am new at doing parallel runs, but I didn't use to have this type of
> problem when i used mdrun without parallel support.
> I would like, if possible, some advice on the problem.
> Thank you in advance.
> Fabrício Bracht
>
>    2780   2782   86.4    0.1251
>
10293535107740740517837563833443348857967447872767677507395291864535498202923000697921266631802318051677748694356690233134327724315919817320285963619926665436209667405260044702144728804850275940332715881909506291349877903079274820737742355599362145056132495305476834829176742035319916407745130558128128.0000
> 0.1250
> step 0
> Warning: 1-4 interaction between 1 and 8 at distance
>
43885648070156953668679170455683956179476920623456280845667077863696278941602310820546250146687554479097819048903759400566246209207791071928566884060437161360627600451028963901489648585765463696505095004653577791267904813562400454512943804592192332319886212529061114941178128342988027402519363840901120.000
> which is larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
>
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.2
> Source code file: nsgrid.c, line: 220
>
> Fatal error:
> Number of grid cells is zero. Probably the system and box collapsed.
>
> -------------------------------------------------------
>
> "I'd Be Water If I Could" (Red Hot Chili Peppers)
>
> Error on node 0, will try to stop all the nodes
> Halting parallel program mdrun on CPU 0 out of 4
>
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.2
> Source code file: nsgrid.c, line: 220
>
> Fatal error:
> Number of grid cells is zero. Probably the system and box collapsed.
>
> -------------------------------------------------------
>
> "I'd Be Water If I Could" (Red Hot Chili Peppers)
>
> Error on node 2, will try to stop all the nodes
> Halting parallel program mdrun on CPU 2 out of 4
>
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.2
> Source code file: nsgrid.c, line: 220
>
> Fatal error:
> Number of grid cells is zero. Probably the system and box collapsed.
>
> -------------------------------------------------------
>
> "I'd Be Water If I Could" (Red Hot Chili Peppers)
>
> Error on node 1, will try to stop all the nodes
> Halting parallel program mdrun on CPU 1 out of 4
>
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.2
> Source code file: nsgrid.c, line: 220
>
> Fatal error:
> Number of grid cells is zero. Probably the system and box collapsed.
>
> -------------------------------------------------------
>
> "I'd Be Water If I Could" (Red Hot Chili Peppers)
>
>
> gcq#257: "I'd Be Water If I Could" (Red Hot Chili Peppers)
>
> Error on node 3, will try to stop all the nodes
> Halting parallel program mdrun on CPU 3 out of 4
>
> gcq#257: "I'd Be Water If I Could" (Red Hot Chili Peppers)
>
>
> gcq#257: "I'd Be Water If I Could" (Red Hot Chili Peppers)
>
>
> gcq#257: "I'd Be Water If I Could" (Red Hot Chili Peppers)
>
> -----------------------------------------------------------------------------
> One of the processes started by mpirun has exited with a nonzero exit
> code.  This typically indicates that the process finished in error.
> If your process did not finish in error, be sure to include a "return
> 0" or "exit(0)" in your C code before exiting the application.
>
> PID 6888 failed on node n0 (127.0.0.1) with exit status 1.
> -----------------------------------------------------------------------------
>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================