From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Mar 29 2011 - 02:51:19 CDT
Hello Jim:
It starts to become clear this morning (hopefully). It seems to me
that the problem is the simultaneous presence of colvars and ramd (a
situation that I have emphasized on previous posts, without having any
reason for that). Both involve individual atom requests, which is not
allowed in parallel simulations.
Thus, sourcing ramd script from only the ramd portion of namd conf
file, and having "numsteps" (probably the same having "run") at the
end of namd conf file (after ramd), the error is:
FATAL ERROR: Due to a design error, GlobalMasterServer does not
support individual atom requests from multiple global force clients on
parallel runs.
Here the relevant portions of the log file, where I have shortened the
portion related to colvars:
arm++> cpu topology info is gathered in 0.001 seconds.
Info: NAMD CVS-2011-02-14 for Linux-x86_64
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60202 for net-linux-x86_64-iccstatic
Info: Built Mon Feb 14 02:16:25 CST 2011 by jim on lisboa.ks.uiuc.edu
Info: 1 NAMD CVS-2011-02-14 Linux-x86_64 4 tya64 francesco
Info: Running on 4 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.078851 s
Info: 1.63774 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is ramd_acc-03.conf
Info: Working in the current directory
/home/francesco/work_hasic1a_GLUP_ASPP_allHSP_S-S/9.ramd_04-1.1
TCL: Suspending until startup complete.
Info: EXTENDED SYSTEM FILE ./press-02.restart.xsc
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 100
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 122.1 0 0
Info: PERIODIC CELL BASIS 2 0 119.2 0
Info: PERIODIC CELL BASIS 3 0 0 148.634
Info: PERIODIC CELL CENTER -0.0430445 -1.34946 -7.98849
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER.
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 20
Info: MAX PAIR PARTITIONS 8
Info: SELF PARTITION ATOMS 154
Info: SELF2 PARTITION ATOMS 154
Info: PAIR PARTITION ATOMS 318
Info: PAIR2 PARTITION ATOMS 637
Info: MIN ATOMS PER PATCH 100
Info: VELOCITY FILE ./press-02.restart.vel
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 ELECTROSTATICS SCALED BY 1
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME ./ramd_acc-03.dcd
Info: DCD FREQUENCY 100
Info: DCD FIRST STEP 100
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME ./ramd_acc-03
Info: RESTART FILENAME ./ramd_acc-03.restart
Info: RESTART FREQUENCY 10
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 13.5
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 3
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 19
Info: ENERGY OUTPUT STEPS 10
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 100
Info: TCL GLOBAL FORCES ACTIVE
Info: TCL GLOBAL FORCES SCRIPT
/usr/local/namd_2.8nb/lib/ramd/scripts/ramd-4.1_script.tcl
Info: COLLECTIVE VARIABLES CALCULATION REQUESTED
Info: COLLECTIVE VARIABLES CONFIGURATION ./CLA-ligands_colvars_press01.in
Info: COLLECTIVE VARIABLES RESTART INFORMATION
./press-02.restart.colvars.state
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: OSCILLATION PERIOD IS 200 FS
Info: DECAY TIME IS 100 FS
Info: PISTON TEMPERATURE IS 310 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 1.30719e-05 3.88275e-05 2.39687e-06
Info: CELL FLUCTUATION IS ANISOTROPIC
Info: CONSTANT AREA PRESSURE CONTROL ACTIVE
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.257952
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 128 120 160
Info: PME MAXIMUM GRID SPACING 1
Info: Attempting to read FFTW data from
FFTW_NAMD_CVS-2011-02-14_Linux-x86_64.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_CVS-2011-02-14_Linux-x86_64.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 5
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : WATER
Info: ERROR TOLERANCE : 1e-06
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 15343
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB ./complex.r.pdb
Info: STRUCTURE FILE ./complex.r.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS ./par_all27_prot_lipid.prm
Info: PARAMETERS ./AP1.r.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: BINARY COORDINATES ./press-02.restart.coor
Info: SUMMARY OF PARAMETERS:
Info: 195 BONDS
Info: 485 ANGLES
Info: 608 DIHEDRAL
Info: 54 IMPROPER
Info: 6 CROSSTERM
Info: 130 VDW
Info: 0 VDW_PAIRS
Info: TIME FOR READING PSF FILE: 2.7509
Info: TIME FOR READING PDB FILE: 0.902384
Info:
Info: Reading from binary file ./press-02.restart.coor
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 219393 ATOMS
Info: 156441 BONDS
Info: 119832 ANGLES
Info: 82263 DIHEDRALS
Info: 3446 IMPROPERS
Info: 1264 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 188277 RIGID BONDS
Info: 469902 DEGREES OF FREEDOM
Info: 77450 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 77450 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 1.34691e+06 amu
Info: TOTAL CHARGE = -0.000173653 e
Info: MASS DENSITY = 1.03392 g/cm^3
Info: ATOM DENSITY = 0.101417 atoms/A^3
Info: *****************************
Info:
Info: Entering startup at 3.82823 s, 57.3364 MB of memory in use
Info: Startup phase 0 took 0.192449 s, 57.336 MB of memory in use
Info: Startup phase 1 took 1.98068 s, 95.3553 MB of memory in use
Info: Startup phase 2 took 0.056417 s, 97.0344 MB of memory in use
Info: Startup phase 3 took 0.0479629 s, 97.0343 MB of memory in use
Info: PATCH GRID IS 6 (PERIODIC) BY 6 (PERIODIC) BY 7 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: Reading from binary file ./press-02.restart.vel
Info: REMOVING COM VELOCITY 0.00292499 0.0305455 0.0250787
Info: LARGEST PATCH (51) HAS 943 ATOMS
Info: Startup phase 4 took 0.242286 s, 124.273 MB of memory in use
Info: PME using 4 and 4 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 0 1 2 3
Info: PME TRANS LOCATIONS: 0 1 2 3
Info: Optimizing 4 FFT steps. 1... 2... 3... 4... Done.
Info: Startup phase 5 took 0.0777831 s, 129.158 MB of memory in use
Info: Startup phase 6 took 0.124777 s, 109.334 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 7 took 1.33913 s, 109.481 MB of memory in use
Info: CREATING 16022 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
TCL: RAMD:
TCL: RAMD: -------------------------------------------------------------------
TCL: RAMD: Random Acceleration Molecular Dynamics Simulation version 4.1
TCL: RAMD: -------------------------------------------------------------------
TCL: RAMD:
TCL: RAMD: mdSteps = 0
TCL: RAMD: accel = 0.3
TCL: RAMD: ramdSeed = 14257
TCL: RAMD: forceOutFreq = 50
TCL: RAMD: maxDist = 50
TCL: RAMD: firstProtAtom = 1
TCL: RAMD: rMinRamd = 0.02
TCL: RAMD: debugLevel = 0
TCL: RAMD: mdStart = no
TCL: RAMD: ramdSteps = 50
TCL: RAMD: firstRamdAtom = 219371
TCL: RAMD: lastRamdAtom = 219393
TCL: RAMD: lastProtAtom = 20137
TCL: RAMD: Pure RAMD simulation is performed
TCL: RAMD:
TCL: RAMD: Atoms subject to the random acceleration are: 219371 219372
219373 219374 219375 219376 219377 219378 219379 219380 219381 219382
219383 219384 219385 219386 219387 219388 219389 219390 219391 219392
219393
colvars: ----------------------------------------------------------------------
colvars: Initializing the collective variables module, version 2011-01-03.
colvars: # analysis = off [default]
colvars: # colvarsTrajFrequency = 100
colvars: # colvarsRestartFrequency = 200
colvars: # colvarsTrajAppend = off [default]
colvars: The restart output state file will be
"./ramd_acc-03.restart.colvars.state".
colvars: The final output state file will be "./ramd_acc-03.colvars.state".
colvars: The trajectory file will be "./ramd_acc-03.colvars.traj".
colvars: ----------------------------------------------------------------------
colvars: Initializing a new collective variable.
colvars: # name = colvar1
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 1 initialized: total mass = 35.45.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 2 initialized: total mass = 28.014.
colvars: All components initialized.
colvars: # width = 1
colvars: # lowerBoundary = -10
colvars: # lowerWallConstant = 100
colvars: # lowerWall = -5
colvars: # upperBoundary = 10
colvars: # upperWallConstant = 100
colvars: # upperWall = 5
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = on
colvars: # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
.................................................
.................................................
colvars: # name = colvar9
colvars: Initializing a new "distance" component.
colvars: # componentCoeff = 1 [default]
colvars: # componentExp = 1 [default]
colvars: # period = 0 [default]
colvars: # wrapAround = 0 [default]
colvars: # forceNoPBC = off [default]
colvars: # oneSiteSystemForce = off [default]
colvars: Initializing atom group "group1".
colvars: Atom group "group1" defined, 1 initialized: total mass = 35.45.
colvars: Initializing atom group "group2".
colvars: Atom group "group2" defined, 1 initialized: total mass = 15.999.
colvars: All components initialized.
colvars: # width = 1
colvars: # lowerBoundary = -10
colvars: # lowerWallConstant = 100
colvars: # lowerWall = -5
colvars: # upperBoundary = 10
colvars: # upperWallConstant = 100
colvars: # upperWall = 5
colvars: # expandBoundaries = off [default]
colvars: # extendedLagrangian = off [default]
colvars: # outputValue = on [default]
colvars: # outputVelocity = off [default]
colvars: # outputSystemForce = on
colvars: # outputAppliedForce = off [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables initialized, 9 in total.
colvars: ----------------------------------------------------------------------
colvars: Initializing a new "harmonic" instance.
colvars: # name = CLA_harmonic
colvars: # colvars = { colvar1, colvar2, colvar3, colvar4, colvar5,
colvar6, colvar7, colvar8, colvar9 }
colvars: # forceConstant = 5
colvars: # centers = { 3.6, 4.9, 3, 3.2, 3, 4, 3.5, 3.1, 5 }
colvars: # targetCenters = { 3.6, 4.9, 3, 3.2, 3, 4, 3.5, 3.1, 5 } [default]
colvars: # targetForceConstant = 0 [default]
colvars: ----------------------------------------------------------------------
colvars: Collective variables biases initialized, 1 in total.
colvars: ----------------------------------------------------------------------
colvars: Restarting from file "./press-02.restart.colvars.state".
colvars: Restarting collective variable "colvar1" from value: 3.48985
colvars: Restarting collective variable "colvar2" from value: 4.50437
colvars: Restarting collective variable "colvar3" from value: 3.32463
colvars: Restarting collective variable "colvar4" from value: 3.04155
colvars: Restarting collective variable "colvar5" from value: 2.99285
colvars: Restarting collective variable "colvar6" from value: 3.1526
colvars: Restarting collective variable "colvar7" from value: 3.20845
colvars: Restarting collective variable "colvar8" from value: 3.11906
colvars: Restarting collective variable "colvar9" from value: 5.10255
colvars: Restarting harmonic bias "CLA_harmonic".
colvars: ----------------------------------------------------------------------
colvars: Collective variables module initialized.
colvars: ----------------------------------------------------------------------
Info: Startup phase 8 took 0.171692 s, 125.178 MB of memory in use
Info: Startup phase 9 took 0.000221014 s, 133.126 MB of memory in use
Info: Finished startup at 8.06162 s, 133.126 MB of memory in use
FATAL ERROR: Due to a design error, GlobalMasterServer does not
support individual atom requests from multiple global force clients on
parallel runs.
If the colvar module in the conf file is commented out, ramd runs fine
and the final pdb (coor) file is also obtained. Conversely, without
ramd, colvars run fine. It seems to be a matter for developers unless
(hopefully) it is simply mishandling from my side. Attached hehe
please find the whole conf file (with colvars commented out), which is
where errors from my side could be detected.
# Job
# System mod21-popc-AP1 TIP3-water-solvated, NaCl isotonic
# ramd with CLA-ligands colvars, PME following press-02.conf
# forcefield
paratypecharmm on
parameters ./par_all27_prot_lipid.prm
parameters ./AP1.r.prm
# molecules
structure ./complex.r.psf
coordinates ./complex.r.pdb
bincoordinates ./press-02.restart.coor
binvelocities ./press-02.restart.vel
extendedSystem ./press-02.restart.xsc
# constraints
# colvars on # provide a colvarsConfig (and colvarsINput if restart)
# colvarsConfig ./CLA-ligands_colvars_press01.in
# colvarsInput ./press-02.restart.colvars.state
# constant temp control
langevin on
langevinTemp 310
langevinDamping 5
langevinHydrogen off
# constant pressure control
useGroupPressure yes
useFlexibleCell yes
useConstantRatio no
LangevinPiston on
LangevinPistonTarget 1.01325
LangevinPistonPeriod 200.
LangevinPistonDecay 100.
LangevinPistonTemp 310
UseConstantArea yes
# integrator
timestep 1.0 ;# 1fs/step
nonbondedFreq 1 ;# nonbonded forces every step
fullElectFrequency 5 ;# PME only every five step
stepspercycle 20 ;# redo pairlist every 20 steps
# Approximations_1
# rigidBonds all ;# needed for 2fs/step
rigidBonds water
rigidTolerance 0.000001
exclude scaled1-4
cutoff 12.0
switching on
switchdist 10.0
pairlistdist 13.5 ;# cutoff +3.5
margin 3
1-4scaling 1.0
PME yes
# cellBasisVector1 122.1 0. 0.
# cellBasisVector2 0. 119.2 0.
# cellBasisVector3 0. 0. 153.99
# Don't set the periodic cell basis if you have also specified an .xsc
# restart file
cellOrigin -0.043044526129961014 -1.3494617938995361 -7.98848533630371
PMEGridSpacing 1.0
# output
outputName ./ramd_acc-03
outputEnergies 10 # multiple of fullElectFrequency or viceversa
restartfreq 10
DCDfreq 100
binaryrestart yes
binaryoutput no
wrapNearest on
wrapAll on
#############################################################
#*** Random Acceleration Molecular Dynamics
*************************************
source /usr/local/namd_2.8nb/lib/ramd/scripts/ramd-4.1.tcl
#*** sources the wrapper script ramd-4.1.tcl;
#*** please change the directory '../scripts/' to '' ( the correct path );
#*** directory '' should contain the scripts: ramd-4.1.tcl,
ramd-4.1_script.tcl, and vectors.tcl
ramd debugLevel 0
#*** activates verbose output if set to something else than 0
ramd ramdSteps 50
#*** specifies the number of steps in 1 ramd stint;
#*** defaults to 50
ramd accel 0.3
#*** specifies the acceleration to be applied;
#*** defaults to 0.25 kcal/mol*A*amu
ramd rMinRamd 0.02
#*** specifies the minimum distance to be travelled by the ligand in 1
ramd stint;
#*** defaults to 0.01 Angstr
ramd forceOutFreq 50
#*** every 'forceOutFreq' steps detailed output of forces will be written;
#*** defaults to 0 (no detailed output)
ramd maxDist 50
#*** specifies the distance between the COMs of the ligand and the
protein when the simulation is stopped
#*** defaults to 50 Angstr (myoglobin max with 43 A)
ramd firstProtAtom 1
#*** specifies the index of the first protein atom
#*** defaults to 1 (assumes first atom in the system corresponds to
first protein atom
ramd lastProtAtom 20137
#*** specifies the index of the last protein atom
#*** required; simulation exits if this parameter is not set
ramd firstRamdAtom 219371
#*** specifies the index of the first ligand atom
#*** required; simulation exits if this parameter is not set
ramd lastRamdAtom 219393
#*** specifies the index of the last ligand atom
#*** required; simulation exits if this parameter is not set
ramd ramdSeed 14257
#*** specifies the seed for the random number generator (for the
generation of acceleration directions)
#*** defaults to 14253
#*** please change if you wish to run different trajectories
######################
# Run protocol (steps multiple of stepspercycle)
seed 15343
numsteps 100
thanks
francesco
On Mon, Mar 28, 2011 at 11:52 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>
> You only want the tclForce on that's in the ramd.tcl file. You need to look
> at the RAMD example since I'm not familiar with how it works.
>
> -Jim
>
>
> On Mon, 28 Mar 2011, Francesco Pietra wrote:
>
>> On Mon, Mar 28, 2011 at 9:33 PM, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
>>>
>>> It looks like you have "tclForces on" after run or minimize in your
>>> config
>>> file, so possibly your tclForces script was not active during the RAMD
>>> run
>>> at all.
>>
>> Hi Jim:
>> Yes, "tclforces on" is in the sourced ramd script, which comes after
>> the "run" command in namd conf file. I had checked that against namd
>> 2.7 with external namd: there was the same order of statements.
>>
>> Now, if "tclforces on" is located in namd conf file, at the top:
>>
>>
>> # forcefield
>> paratypecharmm on
>> parameters ./par_all27_prot_lipid.prm
>> parameters ./AP1.r.prm
>> tclForces on
>>
>> the error is:
>>
>> Info: Configuration file is ramd_acc-03.conf
>> Info: Working in the current directory
>> /home/francesco/work_hasic1a_GLUP_ASPP_allHSP_S-S/9.ramd_04-1.1
>> TCL: Suspending until startup complete.
>> ERROR: 'tclForcesScript' is a required configuration option
>> ERROR: when 'tclForces' is set
>> ERROR: tclForcesScript defines: Tcl script for global forces
>> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>>
>>
>>
>> Where should "tclforces on" be now located?
>>
>> thanks
>> francesco
>>
>>
>>
>>>
>>> -Jim
>>>
>>> On Mon, 28 Mar 2011, Francesco Pietra wrote:
>>>
>>>> Hi:
>>>> I carried out a trial RAMD simulation with namd.2.8 (from binary
>>>> Linux64) charmmff for a protein-organic-ligand in a lipidic membrane.
>>>>
>>>> The simulation ended correctly at the bare 100 chosen steps, the
>>>> ligand did not move - as expected from 1000 steps acc 0.3 ts 1fs.
>>>> Everything seems OK except the error below. I vaguely remember that
>>>> Vlad warned me in the past to compile namd in order that ramd exists
>>>> correctly. Was that the same errior message or anything new about
>>>> which I should now care?
>>>>
>>>> thanks
>>>> francesco pietra
>>>>
>>>> **************************
>>>>
>>>> ENERGY: 1000 10573.6218 17958.2104 9301.2411
>>>> 779.3272 -763083.0117 55270.6864 0.0000
>>>> 1.9652 144208.1552 -524989.8044 308.8680
>>>> -669197.9596 -524727.0908 309.0692 -173.1971
>>>> -32.1881 2166358.3052 -35.4825 -31.7813
>>>>
>>>> WRITING EXTENDED SYSTEM TO RESTART FILE AT STEP 1000
>>>> WRITING COORDINATES TO DCD FILE AT STEP 1000
>>>> WRITING COORDINATES TO RESTART FILE AT STEP 1000
>>>> FINISHED WRITING RESTART COORDINATES
>>>> The last position output (seq=1000) takes 0.134 seconds, 744.610 MB of
>>>> memory in use
>>>> WRITING VELOCITIES TO RESTART FILE AT STEP 1000
>>>> FINISHED WRITING RESTART VELOCITIES
>>>> The last velocity output (seq=1000) takes 0.021 seconds, 744.609 MB of
>>>> memory in use
>>>> TCL: Setting parameter TclForces to on
>>>> FATAL ERROR: Setting parameter TclForces from script failed!
>>>>
>>>> FATAL ERROR: Setting parameter TclForces from script failed!
>>>>
>>>> ------------- Processor 1 Exiting: Called CmiAbort ------------
>>>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>>>>
>>>>
>>>> FATAL ERROR: Setting parameter TclForces from script failed!
>>>>
>>>> ------------- Processor 3 Exiting: Called CmiAbort ------------
>>>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>>>>
>>>>
>>>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>>>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>>>>
>>>>
>>>> FATAL ERROR: Setting parameter TclForces from script failed!
>>>>
>>>> ------------- Processor 2 Exiting: Called CmiAbort ------------
>>>> Reason: FATAL ERROR: Setting parameter TclForces from script failed!
>>>> **************************
>>>>
>>>
>
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