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#14357 05/13/07 06:46 AM
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preeti Offline OP
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Hello,

I checked GBMV with c31b2 version since c33b2 vesion had bug writing the dcd file.

With c31b2, the serial run (ibmaix) recognizes the GBMV version but the paralle gave this fillowing output which says it dosen't know what "GBMV" is! How can this be possible? I wasted computer and my time testing in serial and just checked the parallel output to see that it was wrong? Could anyone tell mw what's wrong? (for parallel i use ibmaixmp)

preeti

CHARMM>

CHARMM> GBMV BETA -20 EPSILON 80 DN 1.0 watr 1.4 GEOM -
CHARMM> TOL 1e-8 BUFR 0.5 Mem 10 CUTA 20 HSX1 -0.125 HSX2 0.25 -
CHARMM> ALFRQ 1 EMP 1.5 P4 0.0 P6 8.0 P3 0.70 ONX 1.9 OFFX 2.1 -
CHARMM> WTYP 2 NPHI 38 SHIFT -0.102 SLOPE 0.9085 CORR 1

***** LEVEL 0 WARNING FROM <CHARMM> *****
***** Unrecognized command: GBMV
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5

**** Warning **** The following extraneous characters
were found while command processing in CHARMM
BETA -20 EPSILON 80 DN 1.0 WATR 1.4 GEOM TOL 1E-8 BUFR 0.5 MEM 10 CUTA 20 HSX1
-0.125 HSX2 0.25 ALFRQ 1 EMP 1.5 P4 0.0 P6 8.0 P3 0.70 ONX 1.9 OFFX 2.1 WTYP 2
NPHI 38 SHIFT -0.102 SLOPE 0.9085 CORR 1

CHARMM>

CHARMM> shake fast bonh tol 1.0e-8 para
SHKCOM> SHAKE parameters: TOL = 0.1000D-07 MXITer = 500

7841 constraints will held by SHAKE.

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rmv Online Content
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If the 'lite' keyword for install.com was used for the parallel ibmaixmp build, then the GBMV feature would not be present.

Put the SHOW command (miscom.doc) at the beginning of an input script, and CHARMM will list a bunch of interesting things, including the installed features.

Last edited by rmv; 05/13/07 06:35 PM.
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preeti Offline OP
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Rick,

Here' the output of show command: I tried:

./install.com ibmaixmp xxlarge 64

we have following supercomputer:

http://scv.bu.edu/SCV/pSeries.html

1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 31b2 February 15, 2005
Copyright(c) 1984-2001 President and Fellows of Harvard College
All Rights Reserved
Current operating system: IBM AIX
Created on 5/13/ 7 at 14:51:31 by user: mankoo

Maximum number of ATOMS: 360720, and RESidues: 90180
Current HEAP size: 10240000, and STACK size: 10000000

RDTITL> * STARTING WITH PDB FILE 1MBC...
RDTITL> * THIS IS THE KURIYAN,PETSKO,KARPLUS,WILZ STRUCTURE
RDTITL> *

CHARMM>

CHARMM> show
MISCOM: List of command substitution parameter values
MISCOM: label: NBFACT value: 1.500000
MISCOM: label: PI value: 3.141593
MISCOM: label: KBLZ value: 0.001987
MISCOM: label: TIMFAC value: 0.048888
MISCOM: label: CCELEC value: 332.071600
MISCOM: label: CNVFRQ value: 108.591993
MISCOM: label: SPEEDL value: 0.029979
MISCOM: label: MINGRMS value: 0.000000
MISCOM: label: XTLA value: 0.000000
MISCOM: label: XTLB value: 0.000000
MISCOM: label: XTLC value: 0.000000
MISCOM: label: XTLALPHA value: 0.000000
MISCOM: label: XTLBETA value: 0.000000
MISCOM: label: XTLGAMMA value: 0.000000
MISCOM: label: BOMLEV value: 0
MISCOM: label: PRNLEV value: 5
MISCOM: label: IOLEV value: 1
MISCOM: label: MYNODE value: 0
MISCOM: label: NUMNODE value: 1
MISCOM: label: IBMAIX value: 1
MISCOM: label: UNIX value: 1
MISCOM: label: SCALAR value: 1
MISCOM: label: PARALLEL value: 1
MISCOM: label: PARAFULL value: 1
MISCOM: label: MPI value: 1
MISCOM: label: INTEGER8 value: 1
MISCOM: label: I4BINARY value: 1
MISCOM: label: IBMAIX_M value: 1
MISCOM: label: XXLARGE value: 1
MISCOM: label: EXPAND value: 1
MISCOM: label: PUTFCM value: 1
MISCOM: label: NOGRAPHI value: 1
MISCOM: label: FASTER value: 0
MISCOM: label: NCPU value: 1
MISCOM: label: FNBL value: 0
MISCOM: label: FLUSH value: 1
MISCOM: label: MINECALL value: 0
MISCOM: label: MINSTEPS value: 0
MISCOM: label: MINCONVR value: 0
MISCOM: label: XTLXDIM value: 0
MISCOM: label: MAXSEG value: 10000
MISCOM: label: MAXA value: 360720
MISCOM: label: MAXB value: 360720
MISCOM: label: MAXT value: 721440
MISCOM: label: MAXP value: 1082160
MISCOM: label: MAXIMP value: 180360
MISCOM: label: MAXNB value: 17200
MISCOM: label: MAXPAD value: 72000
MISCOM: label: MAXRES value: 90180
MISCOM: label: MAXATC value: 500
MISCOM: label: MAXCB value: 1500
MISCOM: label: MAXCT value: 5500
MISCOM: label: MAXCP value: 1500
MISCOM: label: MAXCI value: 600
MISCOM: label: MAXCH value: 3200
MISCOM: label: MAXCN value: 20100
MISCOM: label: MAXCSP value: 500

CHARMM>

CHARMM>

CHARMM> stop
Parallel load balance (sec.):
Node Eext Eint Wait Comm List Integ Total
0 0.0 0.0 0.0 0.0 0.0 0.0 0.0

NORMAL TERMINATION BY NORMAL STOP
MAXIMUM STACK SPACE USED IS 0
STACK CURRENTLY IN USE IS 0
NO WARNINGS WERE ISSUED
HEAP PRINTOUT- HEAP SIZE 10240000
SPACE CURRENTLY IN USE IS 0
MAXIMUM SPACE USED IS 500
FREE LIST
PRINHP> ADDRESS: 1 LENGTH: 10240000 NEXT: 0

$$$$$ JOB ACCOUNTING INFORMATION $$$$$
ELAPSED TIME: 0.00 SECONDS
CPU TIME: 0.02 SECONDS

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rmv Online Content
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The feature list is so short that the LITE keyword of install.com must have been used; the (default) FULL feature list would include the list below. A new parallel CHARMM executable will probably be needed, built w/o the LITE keyword.

ACE
ADUMB
ASPENER
ASPMEMB
BANBA
BLOCK
CFF
CHEQ
CMAP
DIMB
DMCONS
DOCK
DYNVV2
EMAP
ESTATS
FASTEW
FLEXPARM
FLUCQ
FMA
FOURD
FSSHK
GBBLCK
GBFIXAT
GBIM
GBINLINE
GBMV
GBSW
GBSWIT
GENETIC
GENBORN
GOMODEL
GRID
GSBP
HMCM
IMCUBES
LATTICE
LDM
LDLAN
LDMGEN
LONEPAIR
LMC
LRST
LRVDW
MC
MEHMC
MMFF
MOLVIB
MULTCAN
NEWTIMER
OLDDYN
OPLS
OVERLAP
PATHINT
PBEQ
PBOUND
PERT
POLAR
PSSP
PM1
PMEPLSMA
PNOE
PRIMSH
RCFFT
RDFSOL
REPLICA
RGYCONS
RXNCOR
SASAE
SCPISM
SGLD
SHAPES
SHELL
SOFTVDW
TNPACK
TPS
TRAVEL
TSM
TSALLIS
QUANTUM

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preeti Offline OP
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Rick,

Soonn after i posted earlier message, I tried reinstallation with FULL and now "gbmv" is being recognized by parallel version. may be the default if not trustworthy.

thanks so much for your help.
best, preeti


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