[AMBER] segmentation fault using GPUs

From: Ouaray Z. <zo1g10.soton.ac.uk>
Date: Fri, 16 Dec 2011 11:38:36 +0000


I am trying to run a simulation from the last structure of a previous MD simulation (100ns), where the mutated struture is mutated back to the wild-type (that concern only one residu). i prepared the back mutant via tleap (keeping all the parameters from the last simulation: water box, ion, zinc parametrization) and i did a minimization only on the residue mutated. but once i try to run the simulation (using GPUs) with this command:

time mpirun -np 2 pmemd.cuda.MPI -O -o MutChang_MD.out -i mdrun.in -p MutChang.parm7 -c MutChangVMin.rst -ref MutChangVMin.rst -r MutChang_MD.rst -x MutChang_MD.mdcrd

i have this error message:

forrtl: severe (174): SIGSEGV, segmentation fault occurred
mpirun has exited due to process rank 1 with PID 7062 on
node purple007 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).

I attached the output file, tleap, minimization file and the MD file.
can someone help me with this please?
Kind regards,

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Received on Fri Dec 16 2011 - 04:00:02 PST
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