AMBER Archive (2009)

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

From: Hashem Taha (hashemt_at_gmail.com)
Date: Thu Dec 03 2009 - 23:29:38 CST

to followup on this:

I recompiled sander using with intel compilers and debugging symbols (-g)
and ran the tip4p job inside of idbc (intel debugger). Here is what it
barfed out:

Reading symbols from /home/john/amber-intel/
amber10/bin/sander...done.
(idb) 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
[New Thread 47575108185088 (LWP 3426)]
[New Thread 47575108185088 (LWP 3426)]
Starting program: /home/john/amber-intel/amber10/bin/sander
Program received signal SIGSEGV
ewald_force (crd=<no value>, numatoms=-220440305, iac=<no value>, ico=(...),
nntypes=1676387787, charge=(...), cn1=(...), cn2=(...), asol=(...),
bsol=(...), eelt=0, epol=0, frc=(...), x=(...), ix=(...), ipairs=(...),
xr=(...), virvsene=0, pol=(...), qm_pot_only=.FALSE., cn114=(...),
cn214=(...)) at /home/john/amber-intel/amber10/src/sander/_ew_force.f:947
Warning: Source file '/home/john/amber-intel/amber10/src/sander/_ew_force.f'
more recent than executable file
'/home/john/amber-intel/amber10/bin/sander'.
947 if ( mpoltype == 0 )then

So the weird things I see right away in that dump is that numatoms is
-220440305

Help???

On Thu, Dec 3, 2009 at 7:26 PM, Hashem Taha <hashemt_at_gmail.com> wrote:

> 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
>>>
>>>
>>>
>>
>>
>> _______________________________________________
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>> AMBER_at_ambermd.org
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>>
>
>
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