Hello:
I try to run amber GPU MPI job with command line:
mpirun -np 2 pmemd.cuda.MPI -O -i step6.0_minimization.mdin -p
step5_charmm2amber.parm7 -c step5_charmm2amber.rst7 -o test.mdout -r
test.rst7 -inf test.mdinfo
however, it failed with messages:
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Here is my csh for Amber. I compiled Amber with Intel Compiler:
setenv AMBERHOME /soft/amber/16
source /soft/amber/16/amber.csh
alias acpype '/soft/amber/acpype/acpype.py'
setenv MPI_HOME /soft/intel/impi/5.1.3.223/intel64/
set path=(/soft/amber/16/bin $path)
source /soft/intel/bin/compilervars.csh intel64
source /soft/intel/impi/5.1.3.223/bin64/mpivars.csh
set path=(/soft/intel/impi/5.1.3.223/intel64/bin $path)
setenv CUDA_HOME /usr/local/cuda
setenv MKL_HOME /soft/intel/mkl/
setenv LD_LIBRARY_PATH
/soft/amber/16/lib:/soft/intel/impi/5.1.3.223/intel64/lib:/usr/local/cuda/lib64:/soft/intel/lib/intel64:/soft/intel/lib/ia32:/soft/intel/mkl/lib/intel64:/soft/intel/mkl/lib/ia32:{$LD_LIBRARY_PATH}
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Received on Thu Aug 11 2016 - 02:00:02 PDT
