mm_pbsa.pl has no MPI. If you are running Amber11, then it has an option to
fork processes (thereby running in parallel), but it is NOT MPI, and it
can't be run on distributed systems (i.e., only one node). This is
described in the manual.
If you want to use an MPI version of MM/PBSA, you'll have to use the Python
version.
All the best,
Jason
On Tue, Apr 5, 2011 at 11:06 AM, vani panguluri <vanipanguluri.gmail.com>wrote:
> Hello Dwight,
>
> The following is the command
> mpirun -np $NPROCS /usr/local/packages/amber/11/intel-11.1-mvapich-1.1/exe/
> mm_pbsa.pl binding_energy.mmpbsa > binding_energy.log
>
> and the binding_energy.mmpbsa is
> .GENERAL
> PREFIX snapshot
> PATH ./
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> COMPT ./pdb1k4u_apo2.prmtop
> RECPT ./1k4u.prmtop
> LIGPT ./apocynin.prmtop
> GC 0
> AS 0
> DC 0
> MM 1
> GB 1
> PB 1
> MS 1
> NM 0
> .PB
> PROC 2
> REFE 0
> INDI 1.0
> EXDI 80.0
> SCALE 2
> LINIT 1000
> PRBRAD 1.4
> ISTRNG 0.0
> RADIOPT 0
> NPOPT 1
> CAVITY_SURFTEN 0.0072
> CAVITY_OFFSET 0.00
> SURFTEN 0.0072
> SURFOFF 0.00
> .MM
> DIELC 1.0
> .GB
> IGB 2
> GBSA 1
> SALTCON 0.00
> EXTDIEL 80.0
> INTDIEL 1.0
> SURFTEN 0.0072
> SURFOFF 0.00
> .MS
> PROBE 0.0
>
> could please check why i got that error.
> Regards ,
> Vani
>
> On Tue, Apr 5, 2011 at 10:37 AM, Dwight McGee <dwight.mcgee.gmail.com
> >wrote:
>
> > Hi,
> >
> > Can you provide the following information so that it can help us
> diagnose
> > your problem. What did you specifically type on the command line to run
> > this
> > calculation (inputs/outputs if any)? Have you applied all bug fixes? Do
> you
> > pass all the amber tests when you run *test_amber_parallel.sh?*
> >
> > On Mon, Apr 4, 2011 at 7:11 PM, vani panguluri <vanipanguluri.gmail.com
> > >wrote:
> >
> > > Hello amber users,
> > >
> > > I am get the following error while executing mm_pbsa.pl.
> > >
> > > Exit code -5 signaled from qb504
> > > Killing remote processes... At-entry must be first
> > > For details see:
> > > http://ambermd.org/Questions/mm_pbsa.html#read_input_at_entry_first
> > > At-entry must be first For details see:
> > > http://ambermd.org/Questions/mm_pbsa.html#read_input_at_entry_first
> > > At-entry must be first For details see:
> > > http://ambermd.org/Questions/mm_pbsa.html#read_input_at_entry_first
> > > At-entry must be first For details see:
> > > http://ambermd.org/Questions/mm_pbsa.html#read_input_at_entry_first
> > > MPI process terminated unexpectedly
> > > DONE
> > > ------------------------------------------------------
> > > Running PBS epilogue script - 04-Apr-2011 18:06:06
> > > ------------------------------------------------------
> > > Checking node qb504 (MS)
> > > -> Killing process of vani: bash
> > > -> Killing process of vani:
> > > /home/packages/mvapich/1.1/intel-11.1/bin/mpispawn
> > > -> Killing process of vani: [mm_pbsa.pl]
> > > /usr/local/sbin/node_cleaner: line 86: kill: (3307) - No such process
> > > -> Killing process of vani: [mm_pbsa.pl]
> > > /usr/local/sbin/node_cleaner: line 86: kill: (3308) - No such process->
> > > Killing process of vani: [mm_pbsa.pl]
> > > /usr/local/sbin/node_cleaner: line 86: kill: (3309) - No such process
> > > -> Killing process of vani: [mm_pbsa.pl]/usr/local/sbin/node_cleaner:
> > line
> > > 86: kill: (3310) - No such process
> > > -> Killing process of vani: [mm_pbsa.pl]
> > > /usr/local/sbin/node_cleaner: line 86: kill: (3311) - No such process->
> > > Killing process of vani: [mm_pbsa.pl]
> > > /usr/local/sbin/node_cleaner: line 86: kill: (3313) - No such process
> > > -> Killing process of vani: [mm_pbsa.pl]/usr/local/sbin/node_cleaner:
> > line
> > > 86: kill: (3314) - No such process
> > > Checking node qb504 ok
> > >
> > >
> > > can anyone help me to solve this error.
> > >
> > > Regards,
> > > Vani
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > T. Dwight McGee Jr.
> > Quantum Theory Project
> > University of Florida
> > Graduate Student
> > dwight.mcgee.gmail.com
> >
> > "Problems cannot be solved at the same level of awareness that created
> > them."
> > Albert Einstein
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Apr 05 2011 - 11:30:07 PDT
