Charm++ parallel programming system

[Puneet Singh <singh.punit1990 AT gmail.com>]

Dear Sir/Madam,

I understand that this should be forwarded to namd team (& i have done so) But  this error crops up when i compile charm with smp , hence i am also sending this to you for some hint/resolution.

I am trying to build NAMD for host only (without mic/gpgpu support) hybrid configuration (OpenMP/threaded + MPI) .But i am having trouble running apoa1.namd example with namd2 smp binary. Brief build procedure & errors encountered are as :-

1. I am compiling the charm (with smp) and then compiling NAMD with intel mpi compilers.NAMD smp build script is attached : namd_build_smp.sh .

The script generated namd2 binary successfully, but when i try to run the namd2 + apoa1.namd example i get:

ERROR: Atom 27216 velocity is -10752.9 1207.92 -5988.05 (limit is 12000, atom 268 of 667 on patch 64 pe 18)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 64 pe 18).

(attached: namd_with_smpError.log)

2.
 a) Then i again tried to build the non-smp charm (attached: namd_build.sh), then i was able to run the apoa example using:-

mpirun -np 23 ./namd2 ./apoa1/apoa1.namd

(attached: namd_with_nonsmp.log)

This implies that the input file is okay , the troubles are with my smp build procedure (i guess).

 b) But with non-smp version if i try to run it as multithreaded/smp using:-

mpirun -np 1 ./namd2 +ppn 23 ./apoa1/apoa.namd
(attached: namd_with_nonsmpError.log)
------- Partition 0 Processor 0 Exiting: Called CmiAbort ------
Reason: +ppn cannot be used in non SMP version!

which is obvious.

I want to know that:-
Why the smp configuration fails while non-smp configuration succeeds , weather my build procedure or the input file is at fault? i.e.

•  What improvements are needed in the build procedure (namd_build_smp.sh) so that i cam run the apoa1 example.
• or, What  modifications are needed in input file  apoa1.namd example to make it work  on hybrid configuration(smp) without getting Atom moving fast error ?

Any help/Hint/references in this regard will be very fruitful.

Eagerly awaiting your reply,

Thanks & Regards,
Puneet Singh

#############| NAMD |###############
Charm++> Running on MPI version: 3.0
Charm++> level of thread support used: MPI_THREAD_FUNNELED (desired: MPI_THREAD_FUNNELED)
Charm++> Running in SMP mode: numNodes 1,  23 worker threads per process
Charm++> The comm. thread both sends and receives messages
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'.  
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (48-way SMP).
Charm++> cpu topology info is gathered in 0.003 seconds.
Info: NAMD 2.10 for Linux-x86_64-MPI-smp
Info: 
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
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 60601 for mpi-linux-x86_64-ifort-smp-mpicxx
Info: Built Mon Jul 27 10:41:25 IST 2015 by puneet on shavak249
Info: 1 NAMD  2.10  Linux-x86_64-MPI-smp  23    shavak249  puneet
Info: Running on 23 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0481691 s
Info: 1600.52 MB of memory in use based on /proc/self/stat
Info: Configuration file is ./apoa1/apoa1.namd
Info: Changed directory to ./apoa1
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               1
Info: NUMBER OF STEPS        500
Info: STEPS PER CYCLE        20
Info: PERIODIC CELL BASIS 1  108.861 0 0
Info: PERIODIC CELL BASIS 2  0 108.861 0
Info: PERIODIC CELL BASIS 3  0 0 77.758
Info: PERIODIC CELL CENTER   0 0 0
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: MIN ATOMS PER PATCH    40
Info: INITIAL TEMPERATURE    300
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: NO DCD TRAJECTORY OUTPUT
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME        apoa1-out
Info: BINARY OUTPUT FILES WILL BE USED
Info: NO RESTART FILE
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                 0
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        16
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    20
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         108 108 80
Info: PME MAXIMUM GRID SPACING    1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.10_Linux-x86_64-MPI-smp.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.10_Linux-x86_64-MPI-smp.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY      4
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RANDOM NUMBER SEED     74269
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         apoa1.pdb
Info: STRUCTURE FILE         apoa1.psf
Info: PARAMETER file: XPLOR format! (default) 
Info: PARAMETERS             par_all22_prot_lipid.xplor
Info: PARAMETERS             par_all22_popc.xplor
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 177 BONDS
Info: 435 ANGLES
Info: 446 DIHEDRAL
Info: 45 IMPROPER
Info: 0 CROSSTERM
Info: 83 VDW
Info: 6 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 2.75224
Info: TIME FOR READING PDB FILE: 1.18482
Info: 
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 92224 ATOMS
Info: 70660 BONDS
Info: 74136 ANGLES
Info: 74130 DIHEDRALS
Info: 1402 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 1568 DIHEDRALS WITH MULTIPLE PERIODICITY (BASED ON PSF FILE)
Info: 276669 DEGREES OF FREEDOM
Info: 32992 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 32992 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 553785 amu
Info: TOTAL CHARGE = -14 e
Info: MASS DENSITY = 0.997951 g/cm^3
Info: ATOM DENSITY = 0.100081 atoms/A^3
Info: *****************************
Info: 
Info: Entering startup at 4.07148 s, 1697.09 MB of memory in use
Info: Startup phase 0 took 0.00229907 s, 1697.09 MB of memory in use
Info: ADDED 218698 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 0.47669 s, 1697.09 MB of memory in use
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Info: Startup phase 2 took 0.00525904 s, 1697.09 MB of memory in use
Info: Startup phase 3 took 0.00245094 s, 1697.09 MB of memory in use
Info: Startup phase 4 took 0.00844121 s, 1697.09 MB of memory in use
Info: Startup phase 5 took 0.00198197 s, 1697.09 MB of memory in use
Info: PATCH GRID IS 6 (PERIODIC) BY 6 (PERIODIC) BY 4 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0.00117959 0.0289175 0.0202933
Info: LARGEST PATCH (56) HAS 718 ATOMS
Info: TORUS A SIZE 23 USING 0
Info: TORUS B SIZE 1 USING 0
Info: TORUS C SIZE 1 USING 0
Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
Info: Placed 100% of base nodes on same physical node as patch
Info: Startup phase 6 took 0.164607 s, 1761.09 MB of memory in use
Info: PME using 22 and 22 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ...
Info: PME TRANS LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ...
Info: PME USING 1 GRID NODES AND 1 TRANS NODES
Info: Startup phase 7 took 0.00711083 s, 1761.09 MB of memory in use
Info: Startup phase 8 took 0.00574899 s, 1761.09 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 9 took 0.00673199 s, 1761.09 MB of memory in use
Info: CREATING 2995 COMPUTE OBJECTS
Info: useSync: 1 useProxySync: 0
Info: Startup phase 10 took 0.0805361 s, 1761.09 MB of memory in use
Info: Startup phase 11 took 0.00224996 s, 1761.09 MB of memory in use
Info: Startup phase 12 took 0.000500917 s, 1761.09 MB of memory in use
Info: Finished startup at 4.83609 s, 1761.09 MB of memory in use

ERROR: Atom 27216 velocity is -10752.9 1207.92 -5988.05 (limit is 12000, atom 268 of 667 on patch 64 pe 18)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 64 pe 18).
ERROR: Atom 348 velocity is 41449.5 -24143.2 -4526.39 (limit is 12000, atom 3 of 604 on patch 65 pe 20)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 65 pe 20).
ERROR: Atom 20231 velocity is 17243 23838.3 -1832.79 (limit is 12000, atom 183 of 637 on patch 14 pe 8)
ERROR: Atoms moving too fast; simulation has become unstable (1 atoms on patch 14 pe 8).
ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP      POTENTIAL         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG

ENERGY:       0     12352.4560     14603.1480      4549.0710        48.1064        -362073.7645   -127660.4690         0.0000         0.0000     82752.2738        -375429.1785       301.0300   -458181.4522  12464127.1863       301.0300        4263437.1823   4107551.8235    921491.4634   4263437.1823   4107551.8235

ERROR: Exiting prematurely; see error messages above.
====================================================
WallClock: 5.376962  CPUTime: 5.191210  Memory: 1761.085938 MB

poa1/
apoa1/apoa1.pdb
apoa1/apoa1.psf
apoa1/par_all22_prot_lipid.xplor
apoa1/par_all22_popc.xplor
apoa1/apoa1.namd
------- Partition 0 Processor 0 Exiting: Called CmiAbort ------
Reason: +ppn cannot be used in non SMP version!

[0] Stack Traceback:
  [0:0] CmiAbortHelper+0x71  [0x6ebaf1]
  [0:1] ConverseInit+0x30a  [0x6ed0da]
  [0:2] _ZN7BackEnd4initEiPPc+0x89  [0xf00cb9]
  [0:3] main+0x41  [0x864201]
  [0:4] __libc_start_main+0xfd  [0x339c61ed5d]
  [0:5]   [0x580039]

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 25338 RUNNING AT shavak249
=   EXIT CODE: 139
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)

apoa1/
apoa1/apoa1.pdb
apoa1/apoa1.psf
apoa1/par_all22_prot_lipid.xplor
apoa1/par_all22_popc.xplor
apoa1/apoa1.namd
Charm++> Running on MPI version: 3.0
Charm++> level of thread support used: MPI_THREAD_SINGLE (desired: MPI_THREAD_SINGLE)
Charm++> Running in non-SMP mode: numPes 23
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'.  
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (48-way SMP).
Charm++> cpu topology info is gathered in 0.010 seconds.
Info: NAMD 2.10 for Linux-x86_64-MPI
Info: 
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
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 60601 for mpi-linux-x86_64-ifort-mpicxx
Info: Built Mon Jul 27 15:39:43 IST 2015 by puneet on shavak249
Info: 1 NAMD  2.10  Linux-x86_64-MPI  23    shavak249  puneet
Info: Running on 23 processors, 23 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.030926 s
Info: 290.902 MB of memory in use based on /proc/self/stat
Info: Configuration file is ./apoa1/apoa1.namd
Info: Changed directory to ./apoa1
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               1
Info: NUMBER OF STEPS        500
Info: STEPS PER CYCLE        20
Info: PERIODIC CELL BASIS 1  108.861 0 0
Info: PERIODIC CELL BASIS 2  0 108.861 0
Info: PERIODIC CELL BASIS 3  0 0 77.758
Info: PERIODIC CELL CENTER   0 0 0
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: MIN ATOMS PER PATCH    40
Info: INITIAL TEMPERATURE    300
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: NO DCD TRAJECTORY OUTPUT
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME        /usr/tmp/apoa1-out
Info: BINARY OUTPUT FILES WILL BE USED
Info: NO RESTART FILE
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                 0
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        16
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    20
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         108 108 80
Info: PME MAXIMUM GRID SPACING    1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.10_Linux-x86_64-MPI.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.10_Linux-x86_64-MPI.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY      4
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RANDOM NUMBER SEED     74269
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         apoa1.pdb
Info: STRUCTURE FILE         apoa1.psf
Info: PARAMETER file: XPLOR format! (default) 
Info: PARAMETERS             par_all22_prot_lipid.xplor
Info: PARAMETERS             par_all22_popc.xplor
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 177 BONDS
Info: 435 ANGLES
Info: 446 DIHEDRAL
Info: 45 IMPROPER
Info: 0 CROSSTERM
Info: 83 VDW
Info: 6 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PSF FILE: 1.02327
Info: TIME FOR READING PDB FILE: 0.130059
Info: 
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 92224 ATOMS
Info: 70660 BONDS
Info: 74136 ANGLES
Info: 74130 DIHEDRALS
Info: 1402 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 1568 DIHEDRALS WITH MULTIPLE PERIODICITY (BASED ON PSF FILE)
Info: 276669 DEGREES OF FREEDOM
Info: 32992 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 32992 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 553785 amu
Info: TOTAL CHARGE = -14 e
Info: MASS DENSITY = 0.997951 g/cm^3
Info: ATOM DENSITY = 0.100081 atoms/A^3
Info: *****************************
Info: 
Info: Entering startup at 32.2657 s, 413.086 MB of memory in use
Info: Startup phase 0 took 0.000956059 s, 413.086 MB of memory in use
Info: ADDED 218698 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 0.177169 s, 435.109 MB of memory in use
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 769 POINTS
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000325096 AT 11.9556
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000324844 AT 11.9556
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Info: Startup phase 2 took 0.00177193 s, 435.109 MB of memory in use
Info: Startup phase 3 took 0.00086689 s, 435.109 MB of memory in use
Info: Startup phase 4 took 0.00143814 s, 435.109 MB of memory in use
Info: Startup phase 5 took 0.000895023 s, 435.109 MB of memory in use
Info: PATCH GRID IS 6 (PERIODIC) BY 6 (PERIODIC) BY 4 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0.00117959 0.0289175 0.0202933
Info: LARGEST PATCH (56) HAS 718 ATOMS
Info: TORUS A SIZE 23 USING 0
Info: TORUS B SIZE 1 USING 0
Info: TORUS C SIZE 1 USING 0
Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
Info: Placed 100% of base nodes on same physical node as patch
Info: Startup phase 6 took 0.0327508 s, 453.512 MB of memory in use
Info: PME using 22 and 22 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ...
Info: PME TRANS LOCATIONS: 1 2 3 4 5 6 7 8 9 10 ...
Info: PME USING 22 GRID NODES AND 22 TRANS NODES
Info: Startup phase 7 took 0.00365806 s, 454.02 MB of memory in use
Info: Startup phase 8 took 0.00569391 s, 459.098 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 9 took 0.00113821 s, 459.098 MB of memory in use
Info: CREATING 2995 COMPUTE OBJECTS
Info: Startup phase 10 took 0.00198698 s, 459.098 MB of memory in use
Info: useSync: 1 useProxySync: 0
Info: Startup phase 11 took 0.000846863 s, 459.098 MB of memory in use
Info: Startup phase 12 took 0.000128031 s, 459.098 MB of memory in use
Info: Finished startup at 32.495 s, 459.098 MB of memory in use

ETITLE:      TS           BOND          ANGLE          DIHED          IMPRP               ELECT            VDW       BOUNDARY           MISC        KINETIC               TOTAL           TEMP      POTENTIAL         TOTAL3        TEMPAVG            PRESSURE      GPRESSURE         VOLUME       PRESSAVG      GPRESSAVG

ENERGY:       0     12352.4560     14603.1480      4549.0710        48.1064        -362073.7644     24229.5343         0.0000         0.0000     82752.2738        -223539.1750       301.0300   -306291.4488   -223524.8476       301.0300          -2568.6725     -3582.2555    921491.4634     -2568.6725     -3582.2555

ENERGY:       1     18844.4109     15785.9133      4571.2456        53.5350        -361670.8138     24319.4022         0.0000         0.0000     75223.8495        -222872.4573       273.6437   -298096.3068   -223478.1937       273.6437          -3192.4049     -3497.3102    921491.4634     -3192.4049     -3497.3102

ENERGY:       2     29488.6214     18758.6024      4637.0922        69.5538        -360338.7682     24512.0178         0.0000         0.0000     61082.0538        -221790.8268       222.1997   -282872.8806   -223476.2577       222.1997          -4269.6708     -3354.1998    921491.4634     -4269.6708     -3354.1998

ENERGY:       3     29918.6891     22271.8869      4734.9573        94.3383        -358090.2897     24689.8970         0.0000         0.0000     54714.9832        -221665.5378       199.0381   -276380.5211   -223477.2859       199.0381          -4381.8243     -3200.6936    921491.4634     -4381.8243     -3200.6936
-----------
ENERGY:     500     20974.8940     19756.6576      5724.4523       179.8271        -337741.4197     23251.1008         0.0000         0.0000     45359.0786        -222495.4093       165.0039   -267854.4878   -222061.0911       165.0039          -3197.5170     -2425.4142    921491.4634     -3197.5170     -2425.4142

WRITING EXTENDED SYSTEM TO OUTPUT FILE AT STEP 500
WRITING COORDINATES TO OUTPUT FILE AT STEP 500
The last position output (seq=-2) takes 0.002 seconds, 463.621 MB of memory in use
WRITING VELOCITIES TO OUTPUT FILE AT STEP 500
The last velocity output (seq=-2) takes 0.002 seconds, 463.621 MB of memory in use
====================================================

WallClock: 66.561104  CPUTime: 66.561104  Memory: 463.621094 MB
(namd_build.sh)

Attachment: namd_build_smp.sh
Description: Bourne shell script

Attachment: namd_build.sh
Description: Bourne shell script