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HutchNYC
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Problems with type-b.se batch

Uplinger,

Seems I'm giving this project quite a workout. I had some problems with a couple other WU's.

erlc_c104_se0000_0 and
erlc_c103_se0000_1 so far.

Both ran on an i7-920 w7-64bit.

At just over 3 hours, both units hit the 100% completion mark. They then kept running past until I suspended them at 107%.

Looking at the log for the c104 unit, I get a constant repeat of the error message:

Atom displacement from last update exceeds warning distance.

The log has grown to 31,485k

I have them both suspended. Will advise further as other units in this batch reach 100%

Hutch

edit:

Same error message on both. Also corrected title to type-b.

Edit2: I should also note that this on on a different i7-920 than the machine last night.

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[Edit 3 times, last edit by HutchNYC at Mar 11, 2010 4:43:29 AM]

[Mar 11, 2010 2:22:35 AM]

HutchNYC
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Re: Problems with type-b batch

Some of the other erlc_cXXX_seXXXX_X WU's from one of my other machines have now finished and returned ok.

So far just a problem with the two mentioned.

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[Mar 11, 2010 2:53:47 AM]

uplinger
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Re: Problems with type-b batch

Interesting, These two are known to have been restarted? Or were they running from beginning to end?

-Uplinger

[Mar 11, 2010 2:55:09 AM]

HutchNYC
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Re: Problems with type-b batch

They ran straight thru. Only suspended to investigate once they passed 107% completion.

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[Mar 11, 2010 2:57:11 AM]

HutchNYC
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Re: Problems with type-b batch

Also noted in the log:

NONBOND OPTION FLAGS:
ELEC VDW GROUps CDIElec SWITch VGROup VSWItch
BYGRoup EXTEnd GRADient QUADripo NOEWald
CUTNB = 15.000 CTEXNB =999.000 CTONNB = 15.000 CTOFNB = 15.000
WMIN = 1.200 WRNMXD = 1.200 E14FAC = 0.833 EPS = 1.000
NBXMOD = 5
There are 0 atom pairs and 1377 atom exclusions.
There are 43233 group pairs and 0 group exclusions.
GTNBCT> CUTNB,CTOFNB,CTONNB= 15.0 15.0 15.0

***** LEVEL 1 WARNING FROM <GTNBCT> *****
***** CUTNB,CTOFNB,CTONNB are not in correct order.
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5

DCNTRL> Langevin integration requested.
NSTEP = 200000 NSAVC = 100 NSAVV = 10
ISCALE = 0 ISCVEL = 0 IASORS = 0
IASVEL = 1 ICHECW = 1 NTRFRQ = 0
IHTFRQ = 0 IEQFRQ = 0 NPRINT = 1000
INBFRQ = 100 IHBFRQ = 0 IPRFRQ = 1000
ILBFRQ = 0 IMGFRQ = -1 ISEED = 776562
ISVFRQ = 100 NCYCLE = 100 NSNOS = 10
FIRSTT = 300.000 TEMINC = 5.000 TSTRUC = 300.000
FINALT = 300.000 TWINDH = 10.000 TWINDL = -10.000

TIME STEP = 4.09097E-02 AKMA 2.00000E-03 PS

SHAKE TOLERANCE = 0.10000E-09

***** LEVEL 1 WARNING FROM <DCNTRL> *****
***** Nonbond bond update frequency may be too large.
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5

NUMBER OF DEGREES OF FREEDOM = 2488

SEED FOR RANDOM NUMBER GENERATOR IS 776562
GAUSSIAN OPTION IS 1
VELOCITIES ASSIGNED AT TEMPERATURE = 300.0000

DETAILS ABOUT CENTRE OF MASS
POSITION : -2.85634563E-02 -0.10284680 0.14059009
VELOCITY : -2.07384261E-03 7.15068421E-03 -2.27412201E-03
ANGULAR MOMENTUM : -587.32357 -573.04777 -877.73359
KINETIC ENERGY : 0.22691966
LNGFIL: TBATH = 300.000000 DELTA = 0.040910
LNGFIL: Langevin dynamics setup for 420 atoms
LNGFIL: RBUF = 0.000000
LNGFIL: SXREF = 0.000000 SYREF = 0.000000 SZREF = 0.000000
DYNA DYN: Step Time TOTEner TOTKe ENERgy TEMPerature
DYNA PROP: GRMS HFCTote HFCKe EHFCor VIRKe
DYNA INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
DYNA EXTERN: VDWaals ELEC HBONds ASP USER
DYNA IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
DYNA RESTR: CDROplet EHARmonic SHAPe DMC RGY
DYNA MMFP: GEO MDIP SSBP SHEL DROFfa
DYNA PRESS: VIRE VIRI PRESSE PRESSI VOLUme
---------- --------- --------- --------- --------- ---------
DYNA> 0 0.00000 -3505.14337 756.62286 -4261.76623 306.06909
DYNA PROP> 20.18231 -3503.19210 757.06595 1.95127 -435.05501
DYNA INTERN> 1.06780 9.13986 0.00000 17.17347 0.01614
DYNA EXTERN> 867.17991 -5379.60308 0.00000 0.00000 0.00000
DYNA IMAGES> 0.00000 0.00000 0.00000 0.00000 -3.20218
DYNA RESTR> 0.28621 0.00000 0.00000 0.00000 0.00000
DYNA MMFP> 0.00000 0.00000 226.17565 0.00000 0.00000
DYNA PRESS> -21.02292 311.05959 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.20 Atom = 1235
Average distance = 0.22
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.24 Atom = 1235
Average distance = 0.23
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.27 Atom = 1235
Average distance = 0.23
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.29 Atom = 1235
Average distance = 0.24
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.31 Atom = 1235
Average distance = 0.24
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.32 Atom = 1235
Average distance = 0.25
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.33 Atom = 1235
Average distance = 0.26
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.33 Atom = 1235
Average distance = 0.26
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.32 Atom = 1235
Average distance = 0.27
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.32 Atom = 1235
Average distance = 0.28
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.31 Atom = 1235
Average distance = 0.28
EXELEC> Atom displacement from last update exceeds warning distance.

This repeats for the bulk of the log.

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[Mar 11, 2010 3:11:15 AM]

uplinger
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Re: Problems with type-b batch

The Atom displacement is ok. Do not worry about that.

Search for the last word "DYNAMICS" all caps. Then paste the next 30-50 lines after that.

Also, search for wcg_restart, and then paste the 5 lines above and below that.

As well as search for the last occurance of "HARVard" and paste the 20 lines above and below that.

These will give me an insight into the work unit.

-Uplinger

[Mar 11, 2010 3:21:15 AM]

HutchNYC
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Re: Problems with type-b batch

DYNAMICS (last)

CHARMM>

CHARMM> DYNAMICS restart nstep @Nstep timestp 0.002 iprfrq 1000 -
CHARMM> nprint 1000 echeck 1000.0 -
CHARMM> -
CHARMM> iasvel 1 firstt 300.0 finalt 300.0 tstruc 300.0 -
CHARMM> langevin tbath 300.0 rbuf 0.0 -
CHARMM> -
CHARMM> inbfrq 100 imgfrq -1 ihbfrq 0 ilbfrq 0 -
CHARMM> -
CHARMM> iunread 53 isvfrq 100 -
CHARMM> iunwrite 51 iuncrd 52 nsavcrd 100
Parameter: NSTEP -> "200000"
IUNREA = 53 IUNWRI = 51 IUNOS = -1
IUNCRD = 52 IUNVEL = -1 KUNIT = -1
READYN> dynamics restart file was read. Current step= 142600
NSTEP =200000 JHSTRT =142600

NONBOND OPTION FLAGS:
ELEC VDW GROUps CDIElec SWITch VGROup VSWItch
BYGRoup EXTEnd GRADient QUADripo NOEWald
CUTNB = 15.000 CTEXNB =999.000 CTONNB = 15.000 CTOFNB = 15.000
WMIN = 1.200 WRNMXD = 1.200 E14FAC = 0.833 EPS = 1.000
NBXMOD = 5
There are 0 atom pairs and 1377 atom exclusions.
There are 41689 group pairs and 0 group exclusions.
GTNBCT> CUTNB,CTOFNB,CTONNB= 15.0 15.0 15.0

***** LEVEL 1 WARNING FROM <GTNBCT> *****
***** CUTNB,CTOFNB,CTONNB are not in correct order.
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5

NBONDG>> Maximum group spatial extent (12A) exceeded.
Size is 12.35 Angstroms and starts with atom: 1
Please check group boundary definitions.
*** LEVEL -1 WARNING *** BOMLEV IS -2
PRNHBD: CUToff Hydrogen Bond distance = 0.5000 Angle = 90.0000
CuT switching ON HB dist. = 3.5000 OFf HB dist. = 4.0000
CuT switching ON Hb Angle = 50.0000 OFf Hb Angle = 70.0000
ACCEptor antecedents included
All hydrogen bonds for each hydrogen will be found
Hydrogen bonds between excluded atoms will be kept

DCNTRL> Langevin integration requested.
NSTEP = 200000 NSAVC = 100 NSAVV = 10
ISCALE = 0 ISCVEL = 0 IASORS = 0
IASVEL = 1 ICHECW = 1 NTRFRQ = 0
IHTFRQ = 0 IEQFRQ = 0 NPRINT = 1000
INBFRQ = 100 IHBFRQ = 0 IPRFRQ = 1000
ILBFRQ = 0 IMGFRQ = -1 ISEED = 1301799587
ISVFRQ = 100 NCYCLE = 100 NSNOS = 10
FIRSTT = 300.000 TEMINC = 5.000 TSTRUC = 300.000
FINALT = 300.000 TWINDH = 10.000 TWINDL = -10.000

TIME STEP = 4.09097E-02 AKMA 2.00000E-03 PS

SHAKE TOLERANCE = 0.10000E-09

***** LEVEL 1 WARNING FROM <DCNTRL> *****
***** Nonbond bond update frequency may be too large.
******************************************
BOMLEV ( -2) IS NOT REACHED. WRNLEV IS 5

NUMBER OF DEGREES OF FREEDOM = 2488
LNGFIL: TBATH = 300.000000 DELTA = 0.040910
LNGFIL: Langevin dynamics setup for 420 atoms
LNGFIL: RBUF = 0.000000
LNGFIL: SXREF = 0.000000 SYREF = 0.000000 SZREF = 0.000000
DYNA DYN: Step Time TOTEner TOTKe ENERgy TEMPerature
DYNA PROP: GRMS HFCTote HFCKe EHFCor VIRKe
DYNA INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
DYNA EXTERN: VDWaals ELEC HBONds ASP USER
DYNA IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
DYNA RESTR: CDROplet EHARmonic SHAPe DMC RGY
DYNA MMFP: GEO MDIP SSBP SHEL DROFfa
DYNA PRESS: VIRE VIRI PRESSE PRESSI VOLUme
---------- --------- --------- --------- --------- ---------
DYNA> 0 285.20000 -2635.58325 760.01925 -3395.60250 307.44299
DYNA PROP> 16.92039 -2634.08098 766.66733 1.50227 1917.11533
DYNA INTERN> 10.62657 24.28721 0.00000 8.16936 0.17114
DYNA EXTERN> 474.71346 -4148.84718 0.00000 0.00000 0.00000
DYNA IMAGES> 0.00000 0.00000 0.00000 0.00000 -6.83687
DYNA RESTR> 1.94102 0.00000 0.00000 0.00000 0.00000
DYNA MMFP> 0.00000 0.00000 240.17280 0.00000 0.00000
DYNA PRESS> -28.13111 -1249.94578 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.20 Atom = 1235
Average distance = 0.32
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.28 Atom = 1235
Average distance = 0.34
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.35 Atom = 1235
Average distance = 0.36
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.41 Atom = 1235
Average distance = 0.37
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.47 Atom = 1235
Average distance = 0.39
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 1.53 Atom = 1235
Average distance = 0.40
EXELEC> Atom displacement from last update exceeds warning distance.

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[Mar 11, 2010 3:36:29 AM]

HutchNYC
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Re: Problems with type-b batch

wcg_restart (last)

CHARMM>

CHARMM> ! set friction constant for required relaxation time
CHARMM> shake bonh para
SHKCOM> SHAKE parameters: TOL = 0.1000D-09 MXITer = 500

1214 constraints will held by SHAKE.

CHARMM> scalar fbeta set 5.0 select .not. type H* end
SELRPN> 420 atoms have been selected out of 1234

CHARMM>

CHARMM> if @loop .eq. 1 goto wcg_restart
Parameter: LOOP -> "1"
Comparing "1" and "1".
IF test evaluated as true. Performing command

CHARMM>

CHARMM> open write unformatted unit 51 name @system_gsbp_@Rwater_1.rst
Parameter: SYSTEM -> "SOLV_C104"
Parameter: RWATER -> "18"
VOPEN> Attempting to open::SOLV_C104_GSBP_18_1.RST::
OPNLGU> Unit 51 opened for WRITE access to C:\ProgramData\BOINC\slots\5\SOLV_C104_GSBP_18_1.RST

CHARMM> open read unformatted unit 53 name wcgrestart.rst
VOPEN> Attempting to open::WCGRESTART.RST::
OPNLGU> Unit 53 opened for READONLY access to C:\ProgramData\BOINC\slots\5\WCGRESTART.RST

CHARMM> open append unfo unit 52 name @{system}_gsbp_@Rwater_1.trj
Parameter: SYSTEM -> "SOLV_C104"
Parameter: RWATER -> "18"
VOPEN> Attempting to open::SOLV_C104_GSBP_18_1.TRJ::
OPNLGU> Unit 52 opened for APPEND access to C:\ProgramData\BOINC\slots\5\SOLV_C104_GSBP_18_1.TRJ

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[Mar 11, 2010 3:38:37 AM]

HutchNYC
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Re: Problems with type-b batch

HARVard (last)

EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 2.71 Atom = 1235
Average distance = 0.85
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 2.70 Atom = 1235
Average distance = 0.85
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 2.72 Atom = 1235
Average distance = 0.85
EXELEC> Atom displacement from last update exceeds warning distance.
Maximum distance = 2.75 Atom = 1235
Average distance = 0.86
WRIDYN: RESTart file was written at step 142600
Processing passed argument "WCGTYPE:1"
Parameter: WCGTYPE <- "1"
Processing passed argument "i:1"
Parameter: i <- "1"
Processing passed argument "loop:1"
Parameter: loop <- "1"
Processing passed argument "restartnstep:57400"
Parameter: restartnstep <- "57400"
1
Chemistry at HARvard Macromolecular Mechanics
(CHARMM) - Developmental Version 34a2 February 15, 2007
Copyright(c) 1984-2001 President and Fellows of Harvard College
All Rights Reserved
Created on 0/ 0/ 0 at 0: 0: 0

Maximum number of ATOMS: 60120, and RESidues: 20040
Current HEAP size: 2048000, and STACK size: 10000000

Processing passed argument "system:solv_c104"
Parameter: SYSTEM <- "SOLV_C104"
Processing passed argument "title:solv"
Parameter: TITLE <- "SOLV"
Processing passed argument "stitle:c104"
Parameter: STITLE <- "C104"
Processing passed argument "rtffile:top_all22_prot_cmap.inp"
Parameter: RTFFILE <- "TOP_ALL22_PROT_CMAP.INP"
Processing passed argument "paramfile:par_all22_prot_cmap.inp"
Parameter: PARAMFILE <- "PAR_ALL22_PROT_CMAP.INP"
Processing passed argument "gaff:c104"
Parameter: GAFF <- "C104"
Processing passed argument "nwater:400"
Parameter: NWATER <- "400"
Processing passed argument "ligcrd:erlc"
Parameter: LIGCRD <- "ERLC"
Processing passed argument "rforce:0"
Parameter: RFORCE <- "0"
Processing passed argument "gsbpf:erlc"
Parameter: GSBPF <- "ERLC"
Processing passed argument "iseed:776562"
Parameter: ISEED <- "776562"
Processing passed argument "rwater:18"
Parameter: RWATER <- "18"
Processing passed argument "nstep:200000"
Parameter: NSTEP <- "200000"
Processing passed argument "minstep:1000"
Parameter: MINSTEP <- "1000"
Processing passed argument "skipstep:100"
Parameter: SKIPSTEP <- "100"
Processing passed argument "startstep:10000"
Parameter: STARTSTEP <- "10000"
Processing passed argument "WCGIN:solv_stup_eqlb.inp"
Processing passed argument "WCGOUT:result.out"
Processing passed argument "WCGTYPE:1"
Parameter: WCGTYPE <- "1"
Processing passed argument "i:1"
Parameter: I <- "1"
Processing passed argument "loop:1"
Parameter: LOOP <- "1"
Processing passed argument "restartnstep:57400"
Parameter: RESTARTNSTEP <- "57400"
RDTITL> * EQUILIBRIUM MOLECULAR DYNAMICS USING THE
RDTITL> * SPHERICAL SOLVENT BOUNDARY POTENTIAL (SSBP) METHOD
RDTITL> *

CHARMM>

CHARMM> bomlev -2

CHARMM>

CHARMM> open read card unit 1 name @rtffile
Parameter: RTFFILE -> "TOP_ALL22_PROT_CMAP.INP"

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[Mar 11, 2010 3:41:51 AM]

HutchNYC
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Re: Problems with type-b batch

It looks like it's progressing in a loop. Just hoping that it's not an infinite loop or that it'll hit some max and error out.

If you think it'll finish ok eventually, I'll let it run. Was only hoping to avoid having replacements sent if there is some problem with the WU itself.

Meantime, it's still suspended and I have plenty of other work to crunch, so no rush for you to get back to me with a quick answer.

Hutch

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[Mar 11, 2010 4:02:35 AM]

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