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Problem with shake when running in parallel
#21152 06/05/09 05:22 PM
Joined: Oct 2007
Posts: 24
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Hello,

I have a very weird problem with a simulation I'm just setting up. I want to use shake for this simulation but any command which follows directly after the shake is not recognized. The strange thing is that I don't have the problem if I do it with single CPU version of CHARMM. Here is one example of an output file but if I put shake in a different place in the input file a different command will not be recognized (it is always the command which directly follows shake):

Code:
1
                 Chemistry at HARvard Macromolecular Mechanics
                   (CHARMM) - Developmental Version 34b2   February 15, 2008   
       Copyright(c) 1984-2001  President and Fellows of Harvard College
                              All Rights Reserved
      Current operating system: Linux-2.6.18-92.1.13.el5(x86_64)@compute-2-8[+ 31]
                 Created on  6/ 5/ 9 at 12:44:26 by user: alexander   

            Maximum number of ATOMS:    240480, and RESidues:       80160
            Current HEAP size:        10240000, and STACK size:  10000000

 RDTITL> * MEMBRANE SYSTEM
 RDTITL> * EQUILIBRATION/PRODUCTION
 RDTITL> *
  
 CHARMM>     
  
 CHARMM>    !FILE NAMES
 CHARMM>    set input equil1       ! INPUT FILE NAMES
 Parameter: INPUT <- "EQUIL1"
  
 CHARMM>    set output equil2      ! OUTOUT FILE NAMES
 Parameter: OUTPUT <- "EQUIL2"
  
 CHARMM>     
  
 CHARMM>    !READ TOPOLOGY
 CHARMM>    open read card unit 10 name /home/alexander/std/top_all32_lipid_prot_cmap.rtf
 VOPEN> Attempting to open::/home/alexander/std/top_all32_lipid_prot_cmap.rtf::
 OPNLGU> Unit 10 opened for READONLY access to /home/alexander/std/top_all32_lipid_prot_cmap.rtf
  
 CHARMM>    read  rtf card unit 10
 MAINIO> Residue topology file being read from unit  10.
 TITLE> *>>>>>>>>CHARMM22 ALL-HYDROGEN TOPOLOGY FILE FOR PROTEINS <<<<<<
 TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<
 TITLE> *>>>>>>>>>>>>>>>>>>>>>> DECEMBER, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
 TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: WWW.CHARMM.ORG
 TITLE> *               PARAMETER SET DISCUSSION FORUM
 TITLE> *
  
 CHARMM>    close unit 10
 VCLOSE: Closing unit   10 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !READ PARAMETERS
 CHARMM>    open read card unit 20 name /home/alexander/std/par_all32_lipid_prot_cmap.prm
 VOPEN> Attempting to open::/home/alexander/std/par_all32_lipid_prot_cmap.prm::
 OPNLGU> Unit 20 opened for READONLY access to /home/alexander/std/par_all32_lipid_prot_cmap.prm
  
 CHARMM>    read para card unit 20

          PARAMETER FILE BEING READ FROM UNIT 20
 TITLE> *>>>>> CHARMM22 ALL-HYDROGEN PARAMETER FILE FOR PROTEINS <<<<<<<<
 TITLE> *>>>>> INCLUDES PHI, PSI CROSS TERM MAP (CMAP) CORRECTION <<<<<<<
 TITLE> *>>>>>>>>>>>>>>>>>>>>>> DECEMBER, 2003 <<<<<<<<<<<<<<<<<<<<<<<<<<
 TITLE> * ALL COMMENTS TO ADM JR. VIA THE CHARMM WEB SITE: WWW.CHARMM.ORG
 TITLE> *               PARAMETER SET DISCUSSION FORUM
 TITLE> *
*****  WARNING  ***** PARRDR no nonbond parameters for atom type: 250  POLO
 NO nonbond interactions will be computed for this atom type.
 PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.
  
 CHARMM>    close unit 20
 VCLOSE: Closing unit   20 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !READ PSF
 CHARMM>    open read card unit 10 name system_big.psf
 VOPEN> Attempting to open::system_big.psf::
 OPNLGU> Unit 10 opened for READONLY access to system_big.psf
  
 CHARMM>    read psf  card unit 10
 MAINIO> Protein structure file being read from unit  10.
 TITLE>  * MEMBRANE SYSTEM
 TITLE>  * EQUILIBRATION/PRODUCTION
 TITLE>  *  DATE:     6/ 5/ 9     11:12:28      CREATED BY USER: alexander
 TITLE>  *
 PSFSUM> PSF modified: NONBOND lists and IMAGE atoms cleared.
 PSFSUM> Summary of the structure file counters :
         Number of segments      =        2   Number of residues   =     8113
         Number of atoms         =    56539   Number of groups     =    15673
         Number of bonds         =    56259   Number of angles     =    71113
         Number of dihedrals     =    87640   Number of impropers  =      560
         Number of cross-terms   =        0
         Number of HB acceptors  =     7833   Number of HB donors  =        0
         Number of NB exclusions =        0   Total charge =    0.00000
  
 CHARMM>    close unit 10
 VCLOSE: Closing unit   10 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !READ COORDINATES
 CHARMM>    open read card unit 10 name equil1.crd
 VOPEN> Attempting to open::equil1.crd::
 OPNLGU> Unit 10 opened for READONLY access to equil1.crd
  
 CHARMM>    read coor card unit 10
          SPATIAL COORDINATES BEING READ FROM UNIT 10
 TITLE> * MEMBRANE SYSTEM
 TITLE> * EQUILIBRATION/PRODUCTION
 TITLE> *  DATE:     6/ 5/ 9     12:21: 2      CREATED BY USER: ALEXANDER
 TITLE> *
  
 CHARMM>    close unit 10
 VCLOSE: Closing unit   10 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !HEXAGONAL PERIODIC BOUNDARY CONDITIONS
 CHARMM>    crystal define hexagonal 98.075 98.075 60 90.00 90.00 120.00
 Crystal Parameters : Crystal Type = HEXA
           A     =   98.07500 B    =   98.07500 C     =   60.00000
           Alpha =   90.00000 Beta =   90.00000 Gamma =  120.00000
  
 CHARMM>     
  
 CHARMM>    !READ CRYSTAL FILE
 CHARMM>    open read unit 10 card name /home/alexander/std/hexagonal.cry
 VOPEN> Attempting to open::/home/alexander/std/hexagonal.cry::
 OPNLGU> Unit 10 opened for READONLY access to /home/alexander/std/hexagonal.cry
  
 CHARMM>    crystal read unit 10 card
 CRYSTAL FILE BEING READ FROM UNIT    10
 TITLE> * CHARMM 25 TESTCASE ALLXTL.INP
 TITLE> * BERNARD R. BROOKS, 15-JUL-97, C25B1
 TITLE> * CRYSTAL SYMMETRY TEST CASE.  TEST ALL OF THE CRYSTAL TYPES.
 TITLE> *  DATE:    10/24/ 7     13:23:12      CREATED BY USER: ALEXANDER
 TITLE> *
 TITLE>  * CHARMM 25 TESTCASE ALLXTL.INP
 TITLE>  * BERNARD R. BROOKS, 15-JUL-97, C25B1
 TITLE>  * CRYSTAL SYMMETRY TEST CASE.  TEST ALL OF THE CRYSTAL TYPES.
 TITLE>  *  DATE:    10/24/ 7     13:23:12      CREATED BY USER: ALEXANDER
 TITLE>  *
                     THERE ARE NO ROTATIONS FOR THIS TRANSFORMATION SET
    56 Transformations have been processed.

  
 CHARMM>    close unit 10
 VCLOSE: Closing unit   10 with status "KEEP"
  
 CHARMM>     
  
 CHARMM>    !IMAGE SETUP
 CHARMM>    image byresid xcen 0.0 ycen 0.0 zcen 0.0 -
 CHARMM>    sele resname TIP3 .or. resname DMPC end
 SELRPN>  56539 atoms have been selected out of  56539
 IMAGE CENTERING ON FOR SOME ATOMS
  
 CHARMM>     
  
 CHARMM>    !FIX HYDROGENS
 CHARMM>    shake bonh param fast
 SHKCOM> SHAKE parameters: TOL =   0.1000D-09 MXITer =    500

            1077 constraints will held by SHAKE.
 FSSHKINI: Fast shake initialized with    1077 bond contraints and        0 water constraints (3-center).
 FSSHKINI:     1077 constraints are in groups of:        0
 FSSHKINI:     15 2-body (CH),    420 3-body(CH2),     74 4-body(CH3),      0 >4-body. 
 FSSHKINI: Fast shake initialized with    1077 bond contraints and        0 water constraints (3-center).
 FSSHKINI:     1077 constraints are in groups of:        0
 FSSHKINI:     15 2-body (CH),    420 3-body(CH2),     74 4-body(CH3),      0 >4-body. 
   ==== COLLCT_FSTSHK ====
 FSSHKINI: =========== Totals for all nodes:   43659 total constraints
 FSSHKINI: Fast shake initialized with   20160 bond contraints and     7833 water constraints (3-center).
 FSSHKINI:    280 2-body (CH),   7840 3-body(CH2),   1400 4-body(CH3),      0 >4-body. 
  
 CHARMM>     
  
 CHARMM>    !SETUP NONBOND OPTION
 CHARMM>    nbonded  atom vatom vswitch bycb -
 CHARMM>             ctonnb 11.0 ctofnb 12.0 cutnb 16.0 cutim 20.0 -
 CHARMM>             inbfrq -1 imgfrq -1 wmin 1.0 cdie eps 1.0 -
 CHARMM>             ewald pmew fftx 96 ffty 96 fftz 64 kappa 0.316 spline order 6

 SELECTED IMAGES ATOMS BEING CENTERED ABOUT  0.000000  0.000000  0.000000
 RESIDUE  431 OPERATED ON BY TRANSFORMATION C010
 RESIDUE  470 OPERATED ON BY TRANSFORMATION C010
 RESIDUE  656 OPERATED ON BY TRANSFORMATION C033
 RESIDUE  714 OPERATED ON BY TRANSFORMATION C033
 RESIDUE  822 OPERATED ON BY TRANSFORMATION C010
 RESIDUE  932 OPERATED ON BY TRANSFORMATION C010
 RESIDUE 2115 OPERATED ON BY TRANSFORMATION C033
 RESIDUE 2364 OPERATED ON BY TRANSFORMATION C033
 RESIDUE 2622 OPERATED ON BY TRANSFORMATION C033
 RESIDUE 2646 OPERATED ON BY TRANSFORMATION C017
 RESIDUE 2913 OPERATED ON BY TRANSFORMATION C047
 RESIDUE 3054 OPERATED ON BY TRANSFORMATION C010
 RESIDUE 3258 OPERATED ON BY TRANSFORMATION C010
 RESIDUE 3403 OPERATED ON BY TRANSFORMATION C047
 RESIDUE 3892 OPERATED ON BY TRANSFORMATION C018
 RESIDUE 4013 OPERATED ON BY TRANSFORMATION C018
 RESIDUE 4037 OPERATED ON BY TRANSFORMATION C048
 RESIDUE 4096 OPERATED ON BY TRANSFORMATION C018
 RESIDUE 4171 OPERATED ON BY TRANSFORMATION C048
 RESIDUE 4198 OPERATED ON BY TRANSFORMATION C033
 RESIDUE 4267 OPERATED ON BY TRANSFORMATION C048
 RESIDUE 4318 OPERATED ON BY TRANSFORMATION C033
 RESIDUE 4383 OPERATED ON BY TRANSFORMATION C010
 RESIDUE 4668 OPERATED ON BY TRANSFORMATION C048
 RESIDUE 4743 OPERATED ON BY TRANSFORMATION C033
 RESIDUE 5107 OPERATED ON BY TRANSFORMATION C033
 RESIDUE 5112 OPERATED ON BY TRANSFORMATION C022
 RESIDUE 5383 OPERATED ON BY TRANSFORMATION C010
 RESIDUE 5489 OPERATED ON BY TRANSFORMATION C022
 RESIDUE 5662 OPERATED ON BY TRANSFORMATION C033
 RESIDUE 5889 OPERATED ON BY TRANSFORMATION C017
 RESIDUE 5923 OPERATED ON BY TRANSFORMATION C010
 RESIDUE 6102 OPERATED ON BY TRANSFORMATION C010
 RESIDUE 6147 OPERATED ON BY TRANSFORMAT
      ***** LEVEL  0 WARNING FROM <CHARMM> *****
      ***** Unrecognized command: nbon
      ******************************************
      BOMLEV (  0) IS REACHED - TERMINATING. WRNLEV IS -5

                    ABNORMAL TERMINATION
                    MAXIMUM STACK SPACE USED IS  601260
                    STACK CURRENTLY IN USE IS         0
                    MOST SEVERE WARNING WAS AT LEVEL  0

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     3.59  SECONDS 
                         CPU TIME:     3.59  SECONDS 

      ***** LEVEL  0 WARNING FROM <CHARMM> *****
      ***** Unrecognized command: nbon
      ******************************************
      BOMLEV (  0) IS REACHED - TERMINATING. WRNLEV IS -5

                    ABNORMAL TERMINATION
                    MAXIMUM STACK SPACE USED IS  601260
                    STACK CURRENTLY IN USE IS         0
                    MOST SEVERE WARNING WAS AT LEVEL  0

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     3.69  SECONDS 
                         CPU TIME:     3.68  SECONDS 

      ***** LEVEL  0 WARNING FROM <CHARMM> *****
      ***** Unrecognized command: nbon
      ******************************************
      BOMLEV (  0) IS REACHED - TERMINATING. WRNLEV IS -5

                    ABNORMAL TERMINATION
                    MAXIMUM STACK SPACE USED IS  601260
                    STACK CURRENTLY IN USE IS         0
                    MOST SEVERE WARNING WAS AT LEVEL  0

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     3.55  SECONDS 
                         CPU TIME:     3.55  SECONDS 


      ***** LEVEL  0 WARNING FROM <CHARMM> *****
      ***** Unrecognized command: nbon
      ******************************************
      BOMLEV (  0) IS REACHED - TERMINATING. WRNLEV IS -5

                    ABNORMAL TERMINATION
                    MAXIMUM STACK SPACE USED IS  601260
                    STACK CURRENTLY IN USE IS         0
                    MOST SEVERE WARNING WAS AT LEVEL  0

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     3.64  SECONDS 
                         CPU TIME:     3.63  SECONDS 
      ***** LEVEL  0 WARNING FROM <CHARMM> *****
      ***** Unrecognized command: nbon
      ******************************************
      BOMLEV (  0) IS REACHED - TERMINATING. WRNLEV IS -5

                    ABNORMAL TERMINATION
                    MAXIMUM STACK SPACE USED IS  601260
                    STACK CURRENTLY IN USE IS         0
                    MOST SEVERE WARNING WAS AT LEVEL  0

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     3.74  SECONDS 
                         CPU TIME:     3.70  SECONDS 
ION C033
 RESIDUE 6271 OPERATED ON BY TRANSFORMATION C033
 RESIDUE 6492 OPERATED ON BY TRANSFORMATION C010
 RESIDUE 7738 OPERATED ON BY TRANSFORMATION C010
 RESIDUE 7790 OPERATED ON BY TRANSFORMATION C033

 <MKIMAT>: updating the image atom lists and remapping
 Transformation   Atoms  Groups  Residues  Upper-Bound 

      ***** LEVEL  0 WARNING FROM <CHARMM> *****
      ***** Unrecognized command: nbon
      ******************************************
      BOMLEV (  0) IS REACHED - TERMINATING. WRNLEV IS -5

                    ABNORMAL TERMINATION
                    MAXIMUM STACK SPACE USED IS  601260
                    STACK CURRENTLY IN USE IS         0
                    MOST SEVERE WARNING WAS AT LEVEL  0

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     3.59  SECONDS 
                         CPU TIME:     3.56  SECONDS 

      ***** LEVEL  0 WARNING FROM <CHARMM> *****
      ***** Unrecognized command: nbon
      ******************************************
      BOMLEV (  0) IS REACHED - TERMINATING. WRNLEV IS -5

                    ABNORMAL TERMINATION
                    MAXIMUM STACK SPACE USED IS  601260
                    STACK CURRENTLY IN USE IS         0
                    MOST SEVERE WARNING WAS AT LEVEL  0

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     3.69  SECONDS 
                         CPU TIME:     3.66  SECONDS 

      ***** LEVEL  0 WARNING FROM <CHARMM> *****
      ***** Unrecognized command: nbon
      ******************************************
      BOMLEV (  0) IS REACHED - TERMINATING. WRNLEV IS -5

                    ABNORMAL TERMINATION
                    MAXIMUM STACK SPACE USED IS  601260
                    STACK CURRENTLY IN USE IS         0
                    MOST SEVERE WARNING WAS AT LEVEL  0

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     3.55  SECONDS 
                         CPU TIME:     3.51  SECONDS 

      ***** LEVEL  0 WARNING FROM <CHARMM> *****
      ***** Unrecognized command: nbon
      ******************************************
      BOMLEV (  0) IS REACHED - TERMINATING. WRNLEV IS -5

                    ABNORMAL TERMINATION
                    MAXIMUM STACK SPACE USED IS  601260
                    STACK CURRENTLY IN USE IS         0
                    MOST SEVERE WARNING WAS AT LEVEL  0

                    $$$$$ JOB ACCOUNTING INFORMATION $$$$$
                     ELAPSED TIME:     3.64  SECONDS 
                         CPU TIME:     3.61  SECONDS 
6 additional processes aborted (not shown)


Any ideas? The CHARMM version is c34b2. Thanks a lot,

Alexander

Re: Problem with shake when running in parallel
Melbourne #21153 06/05/09 05:24 PM
Joined: Oct 2007
Posts: 24
M
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Joined: Oct 2007
Posts: 24
Another strange thing is that other simulations using virtually the same commands in the same order work in parallel...

Alexander

Re: Problem with shake when running in parallel
Melbourne #21154 06/05/09 05:48 PM
Joined: Sep 2003
Posts: 8,470
rmv Online Content
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Joined: Sep 2003
Posts: 8,470
At times, the FAST option can be troublesome with SHAKE; try removing that keyword.


Rick Venable
computational chemist


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