Parallel Charmm (MMFF Problems)

David Chalmers david.chalmers at vcp.monash.edu.au
Fri Jun 22 01:38:56 EDT 2001


Hi again All,

Thanks to Tru Huynh who pointed out that I was not running version of
Charmm that was compiled with the parallel flags.

>
> 3) the latest lam-mpi is 6.5.2, you might consider upgrading ;)
>

He also pointed out that I am using an old version of lam-mpi.  I tried
the the current version - but I could not get Charmm to link with this
version.  Does anyone know how to do this?

Once I was using the properly compiled parallel version of Charmm I found
that I could get the charmm ace2.inp test to run in parallel.  However, I
would like to do a parallel calculation using the MMFF forcefield.  In my
hands these are dying with fortran end of file errors (see below).  Is it
possible to do MMFF calculations in parallel?

Again, any insights would be appreciated.

David


<grendel04 /test/cmmfftest> lamboot -v ~/charmm/hostfile

LAM 6.3.1/MPI 2 C++ - University of Notre Dame

Executing hboot on n0 (grendel04)...
Executing hboot on n1 (grendel03)...
topology done

<grendel04 /test/cmmfftest> mpirun -np 2 charmm_f2c_p < mmff_amino.inp
1
                 Chemistry at HARvard Macromolecular Mechanics
                   (CHARMM) - Developmental Version 27b4   February 15, 2001
       Copyright(c) 1984,1992  President and Fellows of Harvard College
                              All Rights Reserved
                     Current operating system: GNU LINUX
                 Created on  6/22/ 1 at 15:30:43 by user: david

            Maximum number of ATOMS:     60120, and RESidues:       32000
            Current HEAP size:        10240000, and STACK size:    900000

 RDTITL> * MMFF.INP
 RDTITL> * AUTHOR:  RYSZARD CZERMINSKI (MAY 11, 1993)
 RDTITL> * PURPOSE: TO TEST NEW MMFF RING PERCEPTION CODE
 RDTITL> * EXTERNAL FILES: MMFFANG.PAR MMFFBOND.PAR MMFFCHG.PAR MMFFDEF.PAR
 RDTITL> *                 MMFFOOP.PAR MMFFSTBN.PAR MMFFSUP.PAR MMFFSYMB.PAR
 RDTITL> *                 MMFFTOR.PAR MMFFVDW.PAR
 RDTITL> *

<----- Lots of stuff deleted ------>

 CHARMM>    read parameter card mmff HDEF name @0mmffhdef.par
 Parameter: 0 -> "/GRENDEL/APPS/CHARMM27/C27B4/TEST/DATA/"
 VOPEN> Attempting to open::/grendel/apps/charmm27/c27b4/test/data/mmffhdef.par::

          PARAMETER FILE BEING READ FROM UNIT 90
RDHDEF>   102 MMFF HYDROGEN SYMBOLIC TYPE DEFINITIONS READ FROM UNIT    90
 PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
 VCLOSE: Closing unit   90 with status "KEEP"

 CHARMM>    read parameter card mmff AROM name @0mmffarom.par
 Parameter: 0 -> "/GRENDEL/APPS/CHARMM27/C27B4/TEST/DATA/"
 VOPEN> Attempting to open::/grendel/apps/charmm27/c27b4/test/data/mmffarom.par::

          PARAMETER FILE BEING READ FROM UNIT 90
rdarom>   45 MMFF AROMATIC SYMBOLIC TYPE DEFINITIONS READ FROM UNIT    90
 PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
 VCLOSE: Closing unit   90 with status "KEEP"

 CHARMM>    read parameter card mmff VDW  name @0mmffvdw.par
 Parameter: 0 -> "/GRENDEL/APPS/CHARMM27/C27B4/TEST/DATA/"
 VOPEN> Attempting to open::/grendel/apps/charmm27/c27b4/test/data/mmffvdw.par::

          PARAMETER FILE BEING READ FROM UNIT 90
rdvdwm2>    99 VDW PARAMETERS READ FROM UNIT    90
fmt: end of file
apparent state: unit 1 named fort.1
last format: (8I5)
lately reading sequential formatted external IO
28629 (n1) exited with status 1

<grendel04 /test/cmmfftest>


_____________________________________________________________________________

David Chalmers						       Lab: 9903 9110
Victorian College of Pharmacy				       Fax: 9903 9582
381 Royal Pde, Parkville, Vic 3053           http://synapse.vcp.monash.edu.au
Australia			  	     David.Chalmers at vcp.monash.edu.au
_____________________________________________________________________________


_______________________________________________
Beowulf mailing list, Beowulf at beowulf.org
To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf



More information about the Beowulf mailing list