Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. set sim = 1PO5_tmi/angle set mpirun = mpirun -np 32 -machinefile /uufs/updraft.arches/host/var/torque/aux//37164.uprm.privatearch.arches set pmemd = ~/pmemd-a10-updraft set cur = 13 set pre = 12 cd ~/biodata2/P450/1PO5_tmi/angle mpirun -np 32 -machinefile /uufs/updraft.arches/host/var/torque/aux//37164.uprm.privatearch.arches /uufs/chpc.utah.edu/common/home/u0181375/pmemd-a10-updraft -O -i mdin -o mdout.13 -p prmtop -c restrt.12 -r restrt.13 -x traj.13 -e ener.13 MPIRUN.up012: MPI progress Quiescence Detected after 900 seconds. MPIRUN.up012: 32 out of 32 ranks showed no MPI send or receive progress. MPIRUN.up012: Per-rank details are the following: MPIRUN.up012: Rank 0 (up012 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 1 (up012 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 2 (up012 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 3 (up012 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 4 (up012 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 5 (up012 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 6 (up012 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 7 (up012 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 8 (up049 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 9 (up049 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 10 (up049 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 11 (up049 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 12 (up049 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 13 (up049 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 14 (up049 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 15 (up049 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 16 (up050 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 17 (up050 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 18 (up050 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 19 (up050 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 20 (up050 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 21 (up050 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 22 (up050 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 23 (up050 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 24 (up051 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 25 (up051 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 26 (up051 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 27 (up051 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 28 (up051 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 29 (up051 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 30 (up051 ) caused MPI progress Quiescence. MPIRUN.up012: Rank 31 (up051 ) caused MPI progress Quiescence. MPIRUN.up012: both MPI progress and Ping Quiescence Detected after 900 seconds. MPIRUN.up012: 32 out of 32 ranks showed no MPI send or receive progress. MPIRUN.up012: 32 out of 32 ranks could not return a ping request. MPIRUN.up012: Per-rank details are the following: MPIRUN.up012: Rank 0 (up012 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 1 (up012 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 2 (up012 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 3 (up012 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 4 (up012 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 5 (up012 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 6 (up012 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 7 (up012 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 8 (up049 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 9 (up049 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 10 (up049 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 11 (up049 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 12 (up049 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 13 (up049 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 14 (up049 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 15 (up049 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 16 (up050 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 17 (up050 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 18 (up050 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 19 (up050 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 20 (up050 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 21 (up050 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 22 (up050 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 23 (up050 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 24 (up051 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 25 (up051 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 26 (up051 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 27 (up051 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 28 (up051 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 29 (up051 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 30 (up051 ) caused both MPI progress and Ping Quiescence. MPIRUN.up012: Rank 31 (up051 ) caused both MPI progress and Ping Quiescence.  **** Segmentation fault! Fault address: (nil) This is likely to have been caused by either a null pointer dereference or a general protection fault. pmemd-a10-updraft:7021 terminated with signal 6 at PC=2a9604626d SP=403ff5c8. Backtrace: /lib64/tls/libc.so.6(gsignal+0x3d)[0x2a9604626d] /lib64/tls/libc.so.6(abort+0xfe)[0x2a96047a6e] /uufs/arches/sys/pkg/pscale/3.2/lib/3.2/libpathfortran.so.1(__f90_segv+0x289)[0x2a95999f3b] /lib64/tls/libc.so.6[0x2a96046300] /lib64/tls/libc.so.6(_IO_vfprintf+0xcb)[0x2a960578cb] /lib64/tls/libc.so.6(vsprintf+0x79)[0x2a96075319] /uufs/arches/sys/pkg/pscale/3.2/lib/3.2/libpathfortran.so.1(_lmessage+0x109)[0x2a95af2c72] echo Done with 1PO5_tmi/angle... Done with 1PO5_tmi/angle...