Hello,
By using MMPBSA.py also i am getting the below error
killing remote processes...Traceback (most recent call last):
File
"/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/bin/MMPBSA.py.MPI",
line 43, in ?
import inputparse, utils, alamdcrd # (2)
ImportError: Bad magic number in
/home/packages/amber/11/intel-11.1-mvapich-1.1/bin/inputparse.pyc
MPI process terminated unexpectedly
'import site' failed; use -v for traceback
Traceback (most recent call last):
import sys, os, time, math # (1)
KeyboardInterrupt
'import site' failed; use -v for traceback
'import site' failed; use -v for traceback
'import site' failed; use -v for traceback
'import site' failed; use -v for traceback
'import site' failed; use -v for traceback
File
"/usr/local/packages/amber/11/intel-11.1-mvapich-1.1/bin/MMPBSA.py.MPI",
line 43, in ?
import inputparse, utils, alamdcrd # (2)
ImportError: Bad magic number in
/home/packages/amber/11/intel-11.1-mvapich-1.1/bin/inputparse.pyc
Could you please check that one.
Regards,
Vani
On Tue, Apr 5, 2011 at 1:29 PM, Jason Swails <jason.swails.gmail.com> wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Apr 05 2011 - 14:00:04 PDT
