Dear Amber developers,
I have applied all the patches to AMBER 11 on my GPU machine, which has 4 C2050 cards. But sometimes the jobs still fail. AMBER 11 is compiled with Intel Compiler 11.0.081. Intel MPI 3.2.1.009 is used for parallel run. CUDA 3.2 RC2 does not work well with intel 11.0 compiler, so I installed CUDA 3.1 stable version.
In the first job, the system has 12157 atoms only, and the simulation is under NPT ensemble. If cut is set to 8A, this job runs fine. But if cut is set to 10, it dies with a lot of NaN in energy terms and coordinates.
In the second job, the system has 34116 atoms. The serial cuda run is OK. But in parallel CUDA run, it dies with error message "max pairlist cutoff must be less than unit cell max sphere radius". However, cut is set to 8A, and the distance between the protein and cell boundary is set to 10A.
Can anyone help me out?
Ye MEI
2010-11-15
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Received on Sun Nov 14 2010 - 20:00:04 PST
