Parallel Charmm and RedHat 7.1

David Chalmers david.chalmers at vcp.monash.edu.au
Thu Jun 21 04:12:59 EDT 2001


Hi All,

I am trying to run the parallel version of Charmm (27b4) on our
Linux/Intel cluster.  I have managed to get Charmm compiled using both f2c
g77 (the lite version) with lam-6.3.1.  I can get Charmm to run using
mpirun on a single processor but it dies (or is killed) with two.
Can anybody help me with a pointer to where I am going wrong?

David


Here is some input and output:

<grendel04 /test/c27test> lamboot -v 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/c27test> cat schema
/grendel/apps/charmm27/c27b4_f2c_p/exec/gnu/charmm n0 --
/grendel/apps/charmm27/c27b4_f2c_p/exec/gnu/charmm n1 --

<grendel04 /test/c27test> mpirun -c2c -w -O schema < ace2.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  6/21/ 1 at 18: 7:51 by user: david

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

 RDTITL> * CHARMM TESTCASE ENUM.INP
 RDTITL> * AUTHOR: CHRISTIAN BARTELS
 RDTITL> * FILES:  TOPH19.RTF, PARAM19-1.2.INP
 RDTITL> * TESTS:  ACE + ADAPTIVE UMBRELLA SAMPLING OF THE POTENTIAL ENERGY
 RDTITL> *         (PEPTIDE FOLDING SIMULATIONS)
 RDTITL> *

 CHARMM>

 CHARMM>    ! setup system
 CHARMM>    stream /grendel/apps/charmm27/c27b4/test/datadir.def
 VOPEN> Attempting to open::/grendel/apps/charmm27/c27b4/test/datadir.def::
 OPNLGU> Unit 99 opened for READONLY access to /grendel/apps/charmm27/c27b4/test/datadir.def

                    INPUT STREAM SWITCHING TO UNIT    99
 RDTITL> * CHARMM TESTCASE DATA DIRECTORY ASSIGNMENT
 RDTITL> *
 Parameter: IN1 <- "" <empty>

 CHARMM>    faster on
 MISCOM> FAST option ON.
         Scalar FAST Mode

 CHARMM>    set 0 /grendel/apps/charmm27/c27b4/test/data/     ! input data directory
 Parameter: 0 <- "/GRENDEL/APPS/CHARMM27/C27B4/TEST/DATA/"

 CHARMM>    set 9 /grendel/apps/charmm27/c27b4/test/scratch/  ! scratch directory
 Parameter: 9 <- "/GRENDEL/APPS/CHARMM27/C27B4/TEST/SCRATCH/"

 CHARMM>    return
 VCLOSE: Closing unit   99 with status "KEEP"

                    RETURNING TO INPUT STREAM     5

 CHARMM>

 CHARMM>    open unit 11 read form name @0toph19.rtf
 Parameter: 0 -> "/GRENDEL/APPS/CHARMM27/C27B4/TEST/DATA/"
 VOPEN> Attempting to open::/grendel/apps/charmm27/c27b4/test/data/toph19.rtf::
 OPNLGU> Unit 11 opened for READONLY access to /grendel/apps/charmm27/c27b4/test/data/toph19.rtf

 CHARMM>    read rtf card unit 11
 MAINIO> Residue topology file being read from unit  11.
 TITLE> * TOPOLOGY FILE FOR PROTEINS USING EXPLICIT HYDROGEN ATOMS: VERSION 19
 TITLE> *
mpirun: process terminated before completing MPI_Init()
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  6/21/ 1 at 18: 4:57 by user: david

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

 RDTITL> No title read.

      ***** LEVEL  1 WARNING FROM <RDTITL> *****
      ***** Title expected.
      ******************************************
      BOMLEV (  0) IS NOT REACHED. WRNLEV IS  5



                    NORMAL TERMINATION BY END OF FILE
                    MAXIMUM STACK SPACE USED IS       0
                    STACK CURRENTLY IN USE IS         0
                    MOST SEVERE WARNING WAS AT LEVEL  1
                    HEAP PRINTOUT-  HEAP SIZE  10240000
                    SPACE CURRENTLY IN USE IS         0
                    MAXIMUM SPACE USED IS           480
                    FREE LIST
            PRINHP> ADDRESS:         1 LENGTH:  10240000 NEXT:         0

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:      .00  SECONDS
                         CPU TIME:      .02  SECONDS
Killed
<grendel04 /test/c27test>


_____________________________________________________________________________

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
_____________________________________________________________________________




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