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<font size="+1"><font face="Arial">hello:<br>
I am running NPT on a blue gene cluster, but the jobs always
failed with following messages. However, everything goes well if
I run it on my local cluster:<br>
<br>
<br>
---------------log-----------------------------------<br>
ol 0.66! imb F 6% pme/F 0.45 step 900, will finish Mon Apr 30
04:46:31 2012<br>
vol 0.66! imb F 6% pme/F 0.46 step 1000, will finish Mon Apr 30
04:41:19 2012<br>
<br>
Step 1053, time 2.106 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 0.000303, max 0.005164 (between atoms 18949 and 18948)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
18949 18948 42.3 0.1112 0.1117 0.1111<br>
<br>
Step 1054, time 2.108 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 3.732914, max 37.515310 (between atoms 18947 and 18945)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
18948 18949 90.0 0.1117 4.2691 0.1111<br>
18947 18945 90.0 0.1110 4.2791 0.1111<br>
<br>
Step 1054, time 2.108 (ps) LINCS WARNING<br>
relative constraint deviation after LINCS:<br>
rms 1.580342, max 37.414397 (between atoms 18949 and 18948)<br>
bonds that rotated more than 30 degrees:<br>
atom 1 atom 2 angle previous, current, constraint length<br>
18949 18948 90.0 0.1117 4.2678 0.1111<br>
18945 18947 89.9 0.1110 4.2789 0.1111<br>
Wrote pdb files with previous and current coordinates<br>
Wrote pdb files with previous and current coordinates<br>
<br>
Step 1055:<br>
<br>
Step 1055:<br>
The charge group starting at atom 18949 moved than the distance
allowed by the domain decomposition (0.920188) in direction Z<br>
The charge group starting at atom 18947 moved than the distance
allowed by the domain decomposition (0.920188) in direction Z<br>
distance out of cell -2.676795<br>
distance out of cell 1.235327<br>
Old coordinates: 5.667 0.005 7.374<br>
Old coordinates: 5.792 6.019 7.474<br>
New coordinates: 3.633 6.161 3.620<br>
New coordinates: 8.203 -0.016 10.910<br>
Old cell boundaries in direction Z: 6.295 7.449<br>
Old cell boundaries in direction Z: 7.351 9.673<br>
New cell boundaries in direction Z: 6.297 7.450<br>
New cell boundaries in direction Z: 7.357 9.674<br>
<br>
<br>
Program mdrun_mpi_bg, VERSION 4.5.5<br>
Source code file: ../../../src/mdlib/domdec.c, line: 4124<br>
<br>
Fatal error:<br>
A charge group moved too far between two domain decomposition
steps<br>
This usually means that your system is not well equilibrated<br>
For more information and tips for troubleshooting, please check
the GROMACS<br>
website at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
<br>
"They Were So Quiet About It" (Pixies)<br>
<br>
Error on node 53, will try to stop all the nodes<br>
Halting parallel program mdrun_mpi_bg on CPU 53 out of 64<br>
<br>
-------------------------------------------------------<br>
Program mdrun_mpi_bg, VERSION 4.5.5<br>
Source code file: ../../../src/mdlib/domdec.c, line: 4124<br>
<br>
Fatal error:<br>
A charge group moved too far between two domain decomposition
steps<br>
This usually means that your system is not well equilibrated<br>
For more information and tips for troubleshooting, please check
the GROMACS<br>
website at <a class="moz-txt-link-freetext" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a><br>
-------------------------------------------------------<br>
<br>
"They Were So Quiet About It" (Pixies)<br>
<br>
Error on node 62, will try to stop all the nodes<br>
Halting parallel program mdrun_mpi_bg on CPU 62 out of 64<br>
<br>
gcq#37: "They Were So Quiet About It" (Pixies)<br>
<br>
Abort(-1) on node 53 (rank 53 in comm 1140850688): application
called MPI_Abort(MPI_COMM_WORLD, -1) - process 53<br>
<br>
gcq#37: "They Were So Quiet About It" (Pixies)<br>
<br>
Abort(-1) on node 62 (rank 62 in comm 1140850688): application
called MPI_Abort(MPI_COMM_WORLD, -1) - process 62<br>
<br>
<br>
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