Charm++: standalone mode (not using charmrun) Converse/Charm++ Commit ID: v6.4.0-beta1-0-g5776d21 CharmLB> Load balancer assumes all CPUs are same. Charm++> Running on 1 unique compute nodes (8-way SMP). Charm++> cpu topology info is gathered in 0.001 seconds. Info: NAMD CVS-2012-06-06 for Linux-x86_64-multicore-memopt Warning: Warning: *** EXPERIMENTAL MEMORY OPTIMIZED VERSION *** Warning: 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 60400 for multicore-linux64 Info: Built Thu Jun 7 13:16:22 CEST 2012 by cruzchue on Cyrus Info: 1 NAMD CVS-2012-06-06 Linux-x86_64-multicore-memopt 1 Cyrus cruzchue Info: Running on 1 processors, 1 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0857351 s ComputeMsmMgr: (constructor) PE 0 Info: 35.5078 MB of memory in use based on /proc/self/stat Info: Configuration file is eg07PSF4.namd Info: Working in the current directory /home/cruzchue/31_runGCCX/04_INTERfile/01_small TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 20 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: MIN ATOMS PER PATCH 40 Info: INITIAL TEMPERATURE 310 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 ./testPSF4.dcd Info: DCD FREQUENCY 100 Info: DCD FIRST STEP 100 Info: XST FILENAME testPSF4.xst Info: XST FREQUENCY 100 Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME ./testPSF4 Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME ./testPSF4.restart Info: RESTART FREQUENCY 100 Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 10 Info: SWITCHING OFF 12 Info: PAIRLIST DISTANCE 14 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 19.5 Info: ENERGY OUTPUT STEPS 100 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 1000 Info: PRESSURE OUTPUT STEPS 100 Info: LANGEVIN DYNAMICS ACTIVE Info: LANGEVIN TEMPERATURE 310 Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS Info: LANGEVIN DYNAMICS NOT 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 1339069947 Info: USE HYDROGEN BONDS? NO Info: STRUCTURE FILE RanEctGag.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS ../99_common/par_all22_prot_cmap.inp Info: PARAMETERS ../99_common/par_all36_carbMOD3.prm Info: PARAMETERS ../99_common/toppar_all36_glycopeptideMOD3.str Info: PARAMETERS ../99_common/parGCCXsulf.inp Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: BINARY COORDINATES meltEct.3C35.restart.coor In the memory optimized version, the compression of molecule information is not supported! Please use the non-memory optimized version. FATAL ERROR: MEMOPT: unsupported usage [0] Stack Traceback: [0:0] CmiAbort+0x70 [0xaf039f] [0:1] _Z8NAMD_diePKc+0x56 [0x541c26] [0:2] _ZN9NamdState24checkMemOptCompatibilityEv+0xc9 [0x97b6e9] [0:3] _ZN9NamdState14configListInitEP10ConfigList+0x3f1 [0x97bc01] [0:4] [0x9e83bb] [0:5] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x34 [0x9eb034] [0:6] TclInvokeStringCommand+0x88 [0xb1fd88] [0:7] [0xb228a0] [0:8] [0xb65683] [0:9] [0xb6b443] [0:10] TclEvalObjEx+0x86 [0xb244f6] [0:11] [0xb2d44d] [0:12] [0xb228a0] [0:13] [0xb23c86] [0:14] Tcl_EvalEx+0x16 [0xb24466] [0:15] Tcl_FSEvalFileEx+0x151 [0xb86271] [0:16] Tcl_EvalFile+0x2e [0xb8642e] [0:17] _ZN9ScriptTcl4loadEPc+0x1a [0x9ec00a] [0:18] _Z18after_backend_initiPPc+0x24a [0x54653a] [0:19] main+0x1a [0x50bb5a] [0:20] __libc_start_main+0xed [0x7fd0340c076d] [0:21] [0x50dd2d] [0] Stack Traceback: [0:0] [0xaef8cc] [0:1] CmiAbort+0xaa [0xaf03d9] [0:2] _Z8NAMD_diePKc+0x56 [0x541c26] [0:3] _ZN9NamdState24checkMemOptCompatibilityEv+0xc9 [0x97b6e9] [0:4] _ZN9NamdState14configListInitEP10ConfigList+0x3f1 [0x97bc01] [0:5] [0x9e83bb] [0:6] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x34 [0x9eb034] [0:7] TclInvokeStringCommand+0x88 [0xb1fd88] [0:8] [0xb228a0] [0:9] [0xb65683] [0:10] [0xb6b443] [0:11] TclEvalObjEx+0x86 [0xb244f6] [0:12] [0xb2d44d] [0:13] [0xb228a0] [0:14] [0xb23c86] [0:15] Tcl_EvalEx+0x16 [0xb24466] [0:16] Tcl_FSEvalFileEx+0x151 [0xb86271] [0:17] Tcl_EvalFile+0x2e [0xb8642e] [0:18] _ZN9ScriptTcl4loadEPc+0x1a [0x9ec00a] [0:19] _Z18after_backend_initiPPc+0x24a [0x54653a] [0:20] main+0x1a [0x50bb5a] [0:21] __libc_start_main+0xed [0x7fd0340c076d] [0:22] [0x50dd2d]