Charmrun> IBVERBS version of charmrun Charmrun> client 4 connected Charmrun> client 6 connected Charmrun> client 2 connected Charmrun> client 7 connected Charmrun> client 1 connected Charmrun> client 5 connected Charmrun> client 0 connected Charmrun> client 3 connected Charm++: scheduler running in netpoll mode. Charm++> cpu topology info is being gathered. Charm++> Running on 1 unique compute nodes (8-way SMP). Info: NAMD 2.7b2 for Linux-x86_64-ibverbs Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/ Info: and send feedback or bug reports to namd@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 60103 for net-linux-x86_64-ibverbs-iccstatic Info: Built Thu Nov 12 22:12:37 CST 2009 by jim on dakar.ks.uiuc.edu Info: 1 NAMD 2.7b2 Linux-x86_64-ibverbs 8 cn13 root Info: Running on 8 processors. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.014868 s Info: 84.4922 MB of memory in use based on /proc/self/stat Info: Changed directory to output Info: Configuration file is fold_alanin.job0.0.log.nrc TCL: SERVER CONNECTED TCL: SERVER: eval {cd /data/liuyz/replica-parallel/example; pwd } TCL: CLIENT: /data/liuyz/replica-parallel/example TCL: SERVER: eval {set NEWTEMP 300 } TCL: CLIENT: 300 TCL: SERVER: eval {set base_seed 92698 } TCL: CLIENT: 92698 TCL: SERVER: eval {set job_output_root output/fold_alanin.job0 } TCL: CLIENT: output/fold_alanin.job0 TCL: SERVER: eval { proc save_callback {labels values} { global saved_labels saved_values set saved_labels $labels set saved_values $values } callback save_callback proc save_array {} { global saved_labels saved_values saved_array foreach label $saved_labels value $saved_values { set saved_array($label) $value } } seed [expr int(0*srand($base_seed + 100*$replica_id) + 100000*rand())] langevin on langevinDamping 10.0 langevinTemp $NEWTEMP outputname $job_output_root.$replica_id } TCL: Reduction callback proc set to save_callback TCL: CLIENT: TCL: SERVER: eval { temperature $NEWTEMP } TCL: CLIENT: TCL: SERVER: eval {outputEnergies 100 } TCL: CLIENT: TCL: SERVER: eval {dcdFreq 10000 } TCL: CLIENT: TCL: SERVER: eval {source alanin_base.namd; run 0; save_array } TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 100 Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB Info: LDB PERIOD 20000 steps Info: FIRST LDB TIMESTEP 500 Info: LAST LDB TIMESTEP -1 Info: LDB BACKGROUND SCALING 1 Info: HOM 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: INITIAL TEMPERATURE 300 Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 0.4 Info: DCD FILENAME output/fold_alanin.job0.0.dcd Info: DCD FREQUENCY 10000 Info: DCD FIRST STEP 10000 Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME output/fold_alanin.job0.0 Info: BINARY OUTPUT FILES WILL BE USED Info: NO RESTART FILE Info: SWITCHING ACTIVE Info: SWITCHING ON 7 Info: SWITCHING OFF 8 Info: PAIRLIST DISTANCE 10 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 10 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 22.5 Info: ENERGY OUTPUT STEPS 100 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 1000 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 300 Info: LANGEVIN DAMPING COEFFICIENT IS 10 INVERSE PS Info: LANGEVIN DYNAMICS APPLIED TO HYDROGENS 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 28988 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB unfolded.pdb Info: STRUCTURE FILE alanin.psf Info: PARAMETER file: XPLOR format! (default) Info: PARAMETERS alanin.params Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: SUMMARY OF PARAMETERS: Info: 61 BONDS Info: 179 ANGLES Info: 38 DIHEDRAL Info: 42 IMPROPER Info: 0 CROSSTERM Info: 21 VDW Info: 0 VDW_PAIRS Info: TIME FOR READING PSF FILE: 0.000846863 Info: TIME FOR READING PDB FILE: 0.000463963 Info: Info: **************************** Info: STRUCTURE SUMMARY: Info: 66 ATOMS Info: 65 BONDS Info: 96 ANGLES Info: 31 DIHEDRALS Info: 32 IMPROPERS Info: 0 CROSSTERMS Info: 0 EXCLUSIONS Info: 198 DEGREES OF FREEDOM Info: 55 HYDROGEN GROUPS Info: TOTAL MASS = 783.886 amu Info: TOTAL CHARGE = 8.19564e-08 e Info: ***************************** Info: Info: Entering startup at 0.344687 s, 84.75 MB of memory in use Info: Startup phase 0 took 0.000593185 s, 84.75 MB of memory in use Info: Startup phase 1 took 0.00304699 s, 84.8789 MB of memory in use Info: Startup phase 2 took 0.000595808 s, 84.8789 MB of memory in use Info: PATCH GRID IS 1 BY 1 BY 1 Info: PATCH GRID IS 2-AWAY BY 2-AWAY BY 2-AWAY Info: REMOVING COM VELOCITY -0.402696 -0.578146 -0.264158 Info: LARGEST PATCH (0) HAS 66 ATOMS Info: CREATING 11 COMPUTE OBJECTS Info: Startup phase 3 took 0.00122213 s, 85.0078 MB of memory in use Info: Startup phase 4 took 0.000352859 s, 85.0078 MB of memory in use Info: Startup phase 5 took 0.000343084 s, 85.0078 MB of memory in use LDB: Measuring processor speeds ... Done. Info: Startup phase 6 took 1.19697 s, 85.0078 MB of memory in use Info: CREATING 11 COMPUTE OBJECTS [0] useProxySync is turned on. Info: useSync: 0 useProxySync: 0 Info: Building spanning tree ... send: 1 recv: 0 Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625 Info: NONBONDED TABLE SIZE: 705 POINTS Info: ABSOLUTE IMPRECISION IN FAST TABLE ENERGY: 3.38813e-21 AT 7.99609 Info: RELATIVE IMPRECISION IN FAST TABLE ENERGY: 1.27241e-16 AT 7.99609 Info: ABSOLUTE IMPRECISION IN FAST TABLE FORCE: 6.77626e-21 AT 7.99609 Info: RELATIVE IMPRECISION IN FAST TABLE FORCE: 1.1972e-16 AT 7.99609 Info: Startup phase 7 took 0.00167513 s, 85.375 MB of memory in use Info: Startup phase 8 took 8.79765e-05 s, 85.5039 MB of memory in use Info: Finished startup at 1.54958 s, 85.5039 MB of memory in use TCL: Running for 0 steps ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG ENERGY: 0 44.6127 52.1232 8.6023 20.3617 -191.4874 6.6678 0.0000 0.0000 60.7929 1.6732 309.0140 -59.1198 2.1286 309.0140 TCL: CLIENT: TCL: SERVER: eval {expr $saved_array(TEMP) } TCL: CLIENT: 309.013957789 TCL: SERVER: eval {expr $saved_array(TOTAL) - $saved_array(KINETIC) } TCL: CLIENT: -59.1197535725 TCL: SERVER: eval {run 1000; save_array } TCL: Running for 1000 steps ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG ENERGY: 0 44.6127 52.1232 8.6023 20.3617 -191.4874 6.6678 0.0000 0.0000 60.7929 1.6732 309.0140 -59.1198 2.1286 309.0140 ENERGY: 100 22.7357 28.7076 13.5654 12.8757 -184.8476 -8.0448 0.0000 0.0000 66.3733 -48.6346 337.3796 -115.0080 -48.7249 401.8837 ENERGY: 200 19.8691 24.7865 9.3536 9.3029 -188.5687 -9.3794 0.0000 0.0000 73.8351 -60.8009 375.3082 -134.6361 -59.3305 334.1866 ENERGY: 300 15.8584 24.7070 6.6806 7.1951 -185.1026 -6.5057 0.0000 0.0000 62.9630 -74.2042 320.0449 -137.1672 -73.4533 328.2516 ENERGY: 400 15.6045 27.4716 6.2442 9.6366 -190.4854 -6.7635 0.0000 0.0000 61.0690 -77.2230 310.4173 -138.2919 -77.0794 304.0066 LDB: ============= START OF LOAD BALANCING ============== 1.69077 LDB: ============== END OF LOAD BALANCING =============== 1.69087 Info: Initial time: 8 CPUs 0.000111834 s/step 0.00129437 days/ns 85.5039 MB memory ENERGY: 500 17.3288 20.6684 6.8482 5.7683 -188.0331 -8.5673 0.0000 0.0000 61.8130 -84.1737 314.1993 -145.9867 -83.9230 291.6319 ENERGY: 600 14.9149 26.6230 5.7124 7.3298 -186.4362 -5.8722 0.0000 0.0000 56.4026 -81.3257 286.6976 -137.7282 -81.7841 264.8654 ENERGY: 700 18.9219 23.4449 6.0039 14.0176 -191.9033 -7.9267 0.0000 0.0000 59.9247 -77.5171 304.6007 -137.4417 -76.2631 294.0258 ENERGY: 800 18.5689 19.4637 5.4654 6.0739 -189.3057 -5.8334 0.0000 0.0000 69.4996 -76.0677 353.2705 -145.5673 -75.4692 310.1775 ENERGY: 900 13.4527 29.5527 6.5362 8.2731 -192.4573 -6.4756 0.0000 0.0000 66.1702 -74.9481 336.3472 -141.1183 -74.4365 316.1995 LDB: ============= START OF LOAD BALANCING ============== 1.76551 LDB: TIME 1.76627 LOAD: AVG 0.0136733 MAX 0.0677331 PROXIES: TOTAL 7 MAXPE 1 MAXPATCH 7 None 0.00855855 LDB: TIME 1.76631 LOAD: AVG 0.0136733 MAX 0.0327058 PROXIES: TOTAL 7 MAXPE 1 MAXPATCH 7 TorusLB 0.00855855 LDB: TIME 1.76636 LOAD: AVG 0.0136733 MAX 0.0327058 PROXIES: TOTAL 7 MAXPE 1 MAXPATCH 7 TorusLB 0.00855855 LDB: ============== END OF LOAD BALANCING =============== 1.76682 Info: Initial time: 8 CPUs 0.000143468 s/step 0.00166051 days/ns 85.5039 MB memory TIMING: 1000 CPU: 0.138979, 0.000135979/step Wall: 0.222306, 0.000135888/step, 0 hours remaining, 85.503906 MB of memory in use. ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG ENERGY: 1000 15.2553 23.5997 6.4436 10.6106 -187.5762 -9.5104 0.0000 0.0000 60.6439 -80.5335 308.2566 -141.1774 -80.3138 297.6666 TCL: CLIENT: