Have you confirmed that the memory in the computer you are using has no
defects? Running MEMTEST would help resolve that question.
Jim
James Kress Ph.D., President
The KressWorksR Institute
An IRS Approved 501 (c)(3) Charitable, Nonprofit Corporation
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-----Original Message-----
From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Sent: Saturday, April 25, 2020 2:33 PM
To: AMBER Mailing List <amber.ambermd.org>; david.case.rutgers.edu
Subject: Re: [AMBER] minimizing a pyridine in water
Error persists even when running on 1 single processor
Date = Sat Apr 25 12:38:00 EDT 2020
Program received signal SIGSEGV: Segmentation fault - invalid memory
reference.
Backtrace for this error:
#0 0x7F4FB8156697
#1 0x7F4FB8156CDE
#2 0x7F4FB765233F
#3 0x597E88 in __ew_recip_MOD_fill_charge_grid
#4 0x5989CC in __ew_recip_MOD_do_pmesh_kspace
#5 0x55DC8A in do_pme_recip_
#6 0x56093A in ewald_force_
#7 0x7406A3 in force_
#8 0x4EFCD9 in runmin_
#9 0x4DA5BF in sander_
#10 0x4D13F5 in MAIN__ at multisander.F90:?
/var/spool/slurmd/job2276907/slurm_script: line 21: 26909 Segmentation fault
(core dumped) $AMBERHOME/bin/sander -O -i 1B_allmin.1.in -o ligand_
only_0_lamda_allmin_1B.out -p ligand_only_0_lamda_solvated.prmtop -c
ligand_only_0_lamda_solvmin.rst -r ligand_only_0_lamda_allmin_1B.rst -ref
ligand
_only_0_lamda_solvated.inpcrd
****************************************************************************
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*********
________________________________
From: Debarati DasGupta <debarati_dasgupta.hotmail.com>
Sent: Saturday, April 25, 2020 1:35:48 PM
To: david.case.rutgers.edu <david.case.rutgers.edu>; AMBER Mailing List
<amber.ambermd.org>
Subject: Re: [AMBER] minimizing a pyridine in water
Hi Prof Case,
First, Make sure that you have examined the output file from the run you
already have to look for problems that may have been reported there.
Till Nstep=750 there are no errors and it looks fine, there is no output
generated after Nstep=750 although my slurm manager says job still running
(WITH NO ERROR in out file) the Slurm.out had the bad memory
allocation...seg fault messages.
If that doesn't help, run on serial sander, and see what happens. If that
works, try sander.MPI with something like 4 threads: it's possible that your
system is so small that something bad is happening with 12 threads. (It
still should not segfault).
The minimization works with normal serial sander -O -i ..... but the moment
I use sander.MPI I get those segfault errors.
I don't know how many waters you have, but my guess is that (especially
using cut=12) that you may simply have a case where your cutoff is too big,
and you are missing the error message telling you that.
My system size is small, I have 675 WAT molecules. I should use a smaller
cut variable, but I am not sure whether I should change it as for my
kinase_PYR complex I use cut =12, and I thought for my TI experiments, I
should follow the same parameters so that it gives us a better comparison of
protein_ligand and ligand_in_water simulations.
I am basically in the initial step ( minimizing and equilibrating the ligand
tethered to a hotspot in the kinase and ligand_in_water, before I actually
plug them into the TI protocol.
Thanks
****************************************************************************
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*******
Sent from Mail<
https://go.microsoft.com/fwlink/?LinkId=550986> for Windows
10
From: David A Case<mailto:david.case.rutgers.edu>
Sent: 25 April 2020 13:29
To: AMBER Mailing List<mailto:amber.ambermd.org>
Subject: Re: [AMBER] minimizing a pyridine in water
On Sat, Apr 25, 2020, Debarati DasGupta wrote:
>I am trying to minimize a 1P3 molecule in TIP3P water and this is my
>input file
>
>Initial Minimization on Whole System
>&cntrl
> imin = 1,
> igb = 0,
> cut = 12,
> ntmin = 2,
>maxcyc = 2000,
> ntb = 1,
>ntr = 1, restraintmask = ':1P3', restraint_WT = 10, /
>
>
>I am using sander.MPI on 12 processors to run this minimization step...
First, Make sure that you have examined the output file from the run you
already have to look for problems that may have been reported there.
If that doesn't help, run on serial sander, and see what happens. If that
works, try sander.MPI with something like 4 threads: it's possible that your
system is so small that something bad is happening with 12 threads. (It
still should not segfault).
I don't know how many waters you have, but my guess is that (especially
using cut=12) that you may simply have a case where your cutoff is too big,
and you are missing the error message telling you that.
...good luck...dac
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Received on Sat Apr 25 2020 - 17:00:02 PDT
