Hi David,
I did try to run the minimization using the CPU.
- sander returned after running first half with CG minimization (crashed
after switching to steepest descent minimization)
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x2B4328F584B7
#1 0x2B4328F576B0
#2 0x2B43296E81FF
#3 0x660170 in nb_adjust_
#4 0x661E92 in ewald_force_
#5 0x5A1F93 in force_
#6 0x5FB5BC in runmin_
#7 0x5E763C in sander_
#8 0x5E0214 in MAIN__ at multisander.F90:?
Segmentation fault (core dumped)
- pmemd returned after running first half with CG minimization (crashed
after switching to steepest descent minimization)
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x2B5842FBF4B7
#1 0x2B5842FBE6B0
#2 0x2B584374F1FF
#3 0x4C6CA8 in __nb_exclusions_mod_MOD_nb_adjust
#4 0x4BC093 in __pme_force_mod_MOD_pme_force
#5 0x4EE4A8 in __runmin_mod_MOD_runmin_master
#6 0x520140 in MAIN__ at pmemd.F90:?
Segmentation fault (core dumped)
With mpirun -np 10 sander.MPI or mpirun -np 10 pmemd.MPI, the simulation
didn't go anywhere.
It stopped at...
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
default_name
begin time read from input coords = 0.000 ps
Number of triangulated 3-point waters found: 43483
Any hint?
On Tue, Oct 13, 2020 at 12:05 PM David A Case <david.case.rutgers.edu>
wrote:
> On Tue, Oct 13, 2020, Állan Ferrari wrote:
> >
> >I am interested in running an MD simulation with a protein-ligand system.
> >Nonetheless, I keep running into a memory access error in the first MD
> >computation (after minimization) which I can't figure out how to solve. To
> >simplify everything, I ran an MD simulation of the protein alone and
> >everything worked smoothly. With the ligand alone, it keeps returning this
> >error though.
>
> Have you run a (short) ligand MD simulation using CPU version. That can
> often give better error messages than the GPU version provides. (The
> GPU version is optimized for speed, and does not always provide a lot of
> information when things go wrong.)
>
> It is not uncommon that initial equilibration of a system may need to be
> done on the CPU.
>
> ....regards...dac
>
>
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>
--
*Állan*
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Received on Wed Oct 14 2020 - 13:00:02 PDT
