AMBER Archive (2009)

Subject: Re: [AMBER] help with TIP4P and mpi pmemd

From: Hashem Taha (hashemt_at_gmail.com)
Date: Fri Dec 04 2009 - 15:01:50 CST

yes pmemd 10. And yes, all the bugfixes have been applied. Moreover, this
problem also affects sander.

On Thu, Dec 3, 2009 at 10:58 PM, Robert Duke <rduke_at_email.unc.edu> wrote:

> Are we talking pmemd 10? If so, has bugfix 8 been applied?
> Regards - Bob
>
> ----- Original Message ----- From: "Hashem Taha" <hashemt_at_gmail.com>
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Sent: Thursday, December 03, 2009 9:26 PM
> Subject: Re: [AMBER] help with TIP4P and mpi pmemd
>
>
>
> Hi Bob,
>>
>> I have tried this tip4p system before with the same molecule, and it
>> worked
>> fine (using serial sander, parallel sander and parallel pmemd). The same
>> exact input files were used in this case. There are no comment lines in
>> the
>> input file before &cntrl.
>>
>> I tried running the same job using a serial version of sander but I
>> encountered the same problem. I've recompiled sander using gcc with
>> debugging flags and this is what I get when I run sander in GDB:
>>
>> (gdb) run -O -i minwat.in -o minwat.out -p alpha_ara_ome_tip4p.top -c
>> alpha_ara_ome_tip4p.crd -r minwat.rst -ref alpha_ara_ome_tip4p.crd
>> Starting program: /home/john/amber10/bin/sander -O -i minwat.in -o
>> minwat.out -p alpha_ara_ome_tip4p.top -c alpha_ara_ome_tip4p.crd -r
>> minwat.rst -ref alpha_ara_ome_tip4p.crd
>>
>> Program received signal SIGSEGV, Segmentation fault.
>> 0x00000000004bb74e in nb_adjust_ ()
>> (gdb) backtrace
>> #0 0x00000000004bb74e in nb_adjust_ ()
>> #1 0x00000000004bdd42 in ewald_force_ ()
>> #2 0x00000000005f8259 in force_ ()
>> #3 0x0000000000483797 in runmin_ ()
>> #4 0x00000000004734e3 in sander () at _sander.f:1296
>> #5 0x0000000000470124 in MAIN__ () at _multisander.f:291
>> #6 0x0000000000a2c6ae in main ()
>>
>> I don't have much experience with gdb but from the looks of it the error
>> is
>> originating from nb_adjust().
>>
>> I've tried recompiling sander and pmemd with different MPI libraries
>> (openmpi and mpich2) and no MPI, with and without MKL and using gfortran
>> and
>> ifort, all the these combinations resulted in a SIGSEGV fault error.
>> Although, I only added the debug flags to the gfortran/no parallel
>> version.
>>
>>
>>
>> On Thu, Dec 3, 2009 at 3:37 PM, Robert Duke <rduke_at_email.unc.edu> wrote:
>>
>> Have you done this (tip4p) before? Try your prmtop/inpcrd/mdin with
>>> single
>>> processor sander, then single processor pmemd, and then pmemd mpi. I bet
>>> you have setup problems, or pmemd build problems, but this will sort that
>>> out. I will let others expond on setting up an extra points simulation
>>> if
>>> that is the problem. As an aside, why did you modify the elec and vdw
>>> screening parms for 1-4 interactions, scnb and scee. This is I believe
>>> generally not recommended, but maybe you are doing something I don't know
>>> about... Also, do you really have two comment lines in front of &cntrl?
>>> I
>>> have never tried that, maybe it is inconsequential but I don't know...
>>> (because there are multiple reading passes, namelist i/o combined with
>>> group
>>> i/o, I would not do anything nonstandard. May work fine, but namelist
>>> read
>>> errors can be really obscure, especially in parallel - one reason to
>>> switch
>>> to a single processor test case if something wierd happens.
>>> Regards - Bob Duke
>>> ----- Original Message ----- From: "Hashem Taha" <hashemt_at_gmail.com>
>>> To: <amber_at_ambermd.org>
>>> Sent: Thursday, December 03, 2009 5:16 PM
>>> Subject: [AMBER] help with TIP4P and mpi pmemd
>>>
>>>
>>> I have a problem with trying to run some jobs using TIP4P water as the
>>>
>>>> solvent. I have tried running the same exact files with TIP3P water and
>>>> the
>>>> calculations started and completed perfectly. However, upon changing
>>>> from
>>>> TIP3P to TIP4P, my calculations would stop without reason. the file that
>>>> I
>>>> am trying to run is just a water minimization and it results in the
>>>> following errors. The input file is also included below. The
>>>> calculations
>>>> start but after a few steps they come to a halt. Any help would be
>>>> appreciated, and if you require further information please let me
>>>> know...
>>>>
>>>> HT
>>>>
>>>> the errors are:
>>>>
>>>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>>>>
>>>>>
>>>>> Image PC Routine Line
>>>> Source
>>>> pmemd 000000000048265A Unknown Unknown
>>>> Unknown
>>>> pmemd 00000000004777C3 Unknown Unknown
>>>> Unknown
>>>> pmemd 00000000004AA1D5 Unknown Unknown
>>>> Unknown
>>>> pmemd 00000000004CA1CE Unknown Unknown
>>>> Unknown
>>>> pmemd 000000000040744C Unknown Unknown
>>>> Unknown
>>>> libc.so.6 0000003F4D81D8B4 Unknown Unknown
>>>> Unknown
>>>> pmemd 0000000000407359 Unknown Unknown
>>>> Unknown
>>>> rank 7 in job 55 compute-0-8.local_45343 caused collective abort of
>>>> all
>>>> ranks
>>>> exit status of rank 7: killed by signal 9
>>>>
>>>> the input file...
>>>>
>>>> Constant Volume Minimization
>>>> # Control section
>>>> &cntrl
>>>> ntwx = 50, ntpr = 1, ntwr = 1,
>>>> scnb = 1.0, scee = 1.0, nsnb = 25, dielc = 1, cut = 8.0,
>>>> ntb = 1,
>>>> maxcyc = 1000, ntmin = 0, dx0 = 0.01, drms = 0.0001,
>>>> ntp = 0,
>>>> ibelly = 0, ntr = 1,
>>>> imin = 1,
>>>> &end
>>>> Group Input for restrained atoms
>>>> 5.0
>>>> RES 1 2
>>>> END
>>>> END
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER_at_ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER_at_ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> _______________________________________________
>> AMBER mailing list
>> AMBER_at_ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber