The Bad magic number error has been mentioned by other users in previous
threads, such as
http://archive.ambermd.org/201103/0259.html. This means
that the version of python being used to execute the python scripts is
incompatible with the version of python that was used to originally compile
the scripts. You will need to make sure you are using the same version of
python to both compile and execute MMPBSA.py.
Good luck!
-Bill
On Tue, Apr 5, 2011 at 4:44 PM, vani panguluri <vanipanguluri.gmail.com>wrote:
> 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
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue Apr 05 2011 - 14:00:06 PDT
