I finallly managed to compile gromacs with mpi support, thanks to this mailing list, but i encountered some problems during my heating process.<br>I typed the command grompp -np 4 ....<br>and then mpirun -np 4 mdrun -...<br>
that work out just fine for my minimization, but my heating well i think it all collapsed. the warning comes out like this.<br>This first line is the end of many others that look almost the same.<br>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.<br>
I would like, if possible, some advice on the problem.<br>Thank you in advance.<br>Fabrício Bracht<br><br> 2780 2782 86.4 0.1251 10293535107740740517837563833443348857967447872767677507395291864535498202923000697921266631802318051677748694356690233134327724315919817320285963619926665436209667405260044702144728804850275940332715881909506291349877903079274820737742355599362145056132495305476834829176742035319916407745130558128128.0000 0.1250<br>
step 0<br>Warning: 1-4 interaction between 1 and 8 at distance 43885648070156953668679170455683956179476920623456280845667077863696278941602310820546250146687554479097819048903759400566246209207791071928566884060437161360627600451028963901489648585765463696505095004653577791267904813562400454512943804592192332319886212529061114941178128342988027402519363840901120.000 which is larger than the 1-4 table size 1.000 nm<br>
These are ignored for the rest of the simulation<br>This usually means your system is exploding,<br>if not, you should increase table-extension in your mdp file<br><br>-------------------------------------------------------<br>
Program mdrun, VERSION 3.3.2<br>Source code file: nsgrid.c, line: 220<br><br>Fatal error:<br>Number of grid cells is zero. Probably the system and box collapsed.<br><br>-------------------------------------------------------<br>
<br>"I'd Be Water If I Could" (Red Hot Chili Peppers)<br><br>Error on node 0, will try to stop all the nodes<br>Halting parallel program mdrun on CPU 0 out of 4<br><br>-------------------------------------------------------<br>
Program mdrun, VERSION 3.3.2<br>Source code file: nsgrid.c, line: 220<br><br>Fatal error:<br>Number of grid cells is zero. Probably the system and box collapsed.<br><br>-------------------------------------------------------<br>
<br>"I'd Be Water If I Could" (Red Hot Chili Peppers)<br><br>Error on node 2, will try to stop all the nodes<br>Halting parallel program mdrun on CPU 2 out of 4<br><br>-------------------------------------------------------<br>
Program mdrun, VERSION 3.3.2<br>Source code file: nsgrid.c, line: 220<br><br>Fatal error:<br>Number of grid cells is zero. Probably the system and box collapsed.<br><br>-------------------------------------------------------<br>
<br>"I'd Be Water If I Could" (Red Hot Chili Peppers)<br><br>Error on node 1, will try to stop all the nodes<br>Halting parallel program mdrun on CPU 1 out of 4<br><br>-------------------------------------------------------<br>
Program mdrun, VERSION 3.3.2<br>Source code file: nsgrid.c, line: 220<br><br>Fatal error:<br>Number of grid cells is zero. Probably the system and box collapsed.<br><br>-------------------------------------------------------<br>
<br>"I'd Be Water If I Could" (Red Hot Chili Peppers)<br><br><br>gcq#257: "I'd Be Water If I Could" (Red Hot Chili Peppers)<br><br>Error on node 3, will try to stop all the nodes<br>Halting parallel program mdrun on CPU 3 out of 4<br>
<br>gcq#257: "I'd Be Water If I Could" (Red Hot Chili Peppers)<br><br><br>gcq#257: "I'd Be Water If I Could" (Red Hot Chili Peppers)<br><br><br>gcq#257: "I'd Be Water If I Could" (Red Hot Chili Peppers)<br>
<br>-----------------------------------------------------------------------------<br>One of the processes started by mpirun has exited with a nonzero exit<br>code. This typically indicates that the process finished in error.<br>
If your process did not finish in error, be sure to include a "return<br>0" or "exit(0)" in your C code before exiting the application.<br><br>PID 6888 failed on node n0 (<a href="http://127.0.0.1">127.0.0.1</a>) with exit status 1.<br>
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