---------- Forwarded message ----------
Dear Amber users,
after equilibrating a cyclohexane box, I have put inside a cromophore (78
atoms) and did constrained minimization and NVT equilibration. Now I want to
do NPT equilibration, starting from restart file representing the last point
of NVT simulation. Here is my input file npt.in:
md npt equilibration
&cntrl
imin = 0, irest = 1, ntx = 7,
ntb = 2, pres0 = 1.0, ntp = 1,
taup = 2.0,
cut = 10.0, ntr = 1,
ntc = 2, ntf = 2,
tempi = 300.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 100000, dt = 0.001,
ntpr = 1000, ntwx = 1000, ntwr = 1000, ntwv = 1000
/
Keep cromophore restrainted
50.0
RES 1 3
END
END
Error message that is printed is:
***** Processor 7
***** System must be very inhomogeneous.
***** Readjusting recip sizes.
In this slab, Atoms found: 14064 Allocated: 3472
[eniac:17614] *** Process received signal ***
[eniac:17614] Signal: Segmentation fault (11)
[eniac:17614] Signal code: Address not mapped (1)
[eniac:17614] Failing at address: 0x7f06e4f29aa8
[eniac:17614] [ 0] /lib/libpthread.so.0 [0x7f16fc153a80]
[eniac:17614] [ 1] sander.MPI(nb_adjust_+0x4ea) [0x520e3a]
[eniac:17614] [ 2] sander.MPI(ewald_force_+0x12e6) [0x523976]
[eniac:17614] [ 3] sander.MPI(force_+0x3004) [0x6df404]
[eniac:17614] [ 4] sander.MPI(runmd_+0x1671) [0x4f8c61]
[eniac:17614] [ 5] sander.MPI(sander_+0x61c5) [0x4c1f39]
[eniac:17614] [ 6] sander.MPI(MAIN__+0xee7) [0x4bbce3]
[eniac:17614] [ 7] sander.MPI(main+0x2c) [0x965a2c]
[eniac:17614] [ 8] /lib/libc.so.6(__libc_start_main+0xe6) [0x7f16fbe101a6]
[eniac:17614] [ 9] sander.MPI [0x4448a9]
[eniac:17614] *** End of error message ***
.
.
.
[eniac:17606] [0,0,0] ORTE_ERROR_LOG: Timeout in file
base/pls_base_orted_cmds.c at line 275
[eniac:17606] [0,0,0] ORTE_ERROR_LOG: Timeout in file pls_rsh_module.c at
line 1166
[eniac:17606] [0,0,0] ORTE_ERROR_LOG: Timeout in file errmgr_hnp.c at line
90
mpirun noticed that job rank 1 with PID 17610 on node eniac exited on signal
11 (Segmentation fault).
5 additional processes aborted (not shown)
[eniac:17606] [0,0,0] ORTE_ERROR_LOG: Timeout in file
base/pls_base_orted_cmds.c at line 188
[eniac:17606] [0,0,0] ORTE_ERROR_LOG: Timeout in file pls_rsh_module.c at
line 1198
--------------------------------------------------------------------------
mpirun was unable to cleanly terminate the daemons for this job. Returned
value Timeout instead of ORTE_SUCCESS.
--------------------------------------------------------------------------
If a simulation is started on one processor only, 'Segmentation fault'
message is thrown. I get the same error messages If I try to start NPT
equilibration prior minimization (from input.inpcrd file generated by
xleap), or after minimization (5000 steps, without NVT equilibration). What
I have done wrong?
Thanks in advance,
Jura
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Received on Wed Aug 17 2011 - 09:30:04 PDT
