AMBER Archive (2004)

Subject: AMBER: AMBER 5 (sander) Parallel PME on IBM p630

From: uddhavesh bhaskar sonavane (ubs3_at_rediffmail.com)
Date: Fri Feb 06 2004 - 02:01:24 CST

Dear Sir, I am facing problem running parallel sander (of AMBER 5.0) with PME. The job is terminated with segmentation fault. No error has been seen in output file. Below is given last part of o/p file. Kindly help me to solve error. However, -DMEM_ALLOC flag is not used in the sander compilation (Compilation fails with this flag). Other flags like -DMPI -DPOE used in the compilation. With regards uddhav OUTPUT FILE ----------- NATOM = 9245 NTYPES = 18 NBONH = 8823 MBONA = 452 NTHETH = 554 MTHETA = 694 NPHIH = 946 MPHIA = 972 NHPARM = 0 NPARM = 0 NNB = 15014 NRES = 2901 NBONA = 452 NTHETA = 694 NPHIA = 972 NUMBND = 50 NUMANG = 113 NPTRA = 68 NATYP = 27 NPHB = 1 IFBOX = 1 NMXRS = 33 IFCAP = 0 EWALD MEMORY USE: | Total heap storage needed = 980 | Total stack storage needed = 273796 | Adjacent nonbond minimum mask = 15014 | Max number of pointers = 25 | List build maxmask = 30028 | Maximage = 35888 EWALD LOCMEM POINTER OFFSETS | Real memory needed by PME = 274776 | Size of ERFTABLE = 47092 | Real memory needed by ERFTABLE = 235460 | Integer memory needed by ADJ = 30028 | Integer memory used by local nonb= 404807 | Real memory used by local nonb = 260612 | MAX NONBOND PAIRS = 25000000 | Memory Use Allocated Used | Real 2300000 1103734 | Hollerith 25000000 76863 | Integer 1000000 701507 (static) | Max Nonbonded Pairs:50000000 BOX TYPE: RECTILINEAR 2. CONTROL DATA FOR THE RUN PDB 10mer AT TIMLIM= 999999. IREST = 0 IBELLY= 0 KFORM = 1 ICHDNA= 0 IMIN = 0 IPOL = 0 IEWALD= 1 NTX = 1 NTXO = 1 IG = 71277 TEMPI = 0.00 HEAT = 0.000 NTB = 2 IFTRES= 1 BOXX = 61.318 BOXY = 41.857 BOXZ = 41.857 NRUN = 1 NTT = 1 TEMP0 = 300.000 DTEMP = 0.000 TAUTP = 0.200 TAUTS = 0.200 ISOLVP= 0 VLIMIT= 0.000 NTP = 2 PRES0 = 1.000 COMP = 44.600 TAUP = 0.200 NPSCAL= 0 NTCM = 0 NSCM = 9999999 NSTLIM= 100 INIT = 3 NTU = 1 T = 0.000 DT = 0.00100 NTC = 4 TOL = 0.00050 JFASTW = 0 NTF = 2 NTID = 0 NTNB = 1 NSNB = 25 IDIEL = 1 IMGSLT= 0 IPRR = 0 IPRW = 0 ITRSLU= 1 CUT = 9.000 SCNB = 2.000 SCEE = 1.200 DIELC = 1.000 CUT2ND= 0.00000 NTPR = 50 NTWR = 50 NTWX = 0 NTWV = 0 NTWE = 0 NTWXM = 999999 NTWVM = 999999 NTWEM = 999999 IOUTFM= 0 NTWPRT= 0 NTWPR0= 0 NTR = 0 NTRX = 1 TAUR = 0.00000 NMROPT= 0 ISFTRP= 0 RWELL = 1.00000 PENCUT= 0.10000 IVCAP = 0 MATCAP= 0 FCAP = 1.500 OTHER DATA: IFCAP = 0 NATCAP= 0 CUTCAP= 0.000 XCAP = 0.000 YCAP = 0.000 ZCAP = 0.000 NATOM = 9245 NRES = 2901 Water definition for fast triangulated model: Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2 | PLEVEL = 1: runmd parallelization, no EKCMR | ILBNOB = 0 | ILBOPT = 0 | No special load balancing optimizations ************************************************** * * * EXPERIMENTAL EWALD OPTION REQUESTED * * * * Note that this option is new and not * * tested as extensively on as many * * machines as the rest of this code * * * ************************************************** 3. ATOMIC COORDINATES AND VELOCITIES PDB 10mer AT begin time read from input coords = 0.200 ps Number of triangulated 3-point waters found: 2863 Using 2863 waters for fast wat-wat Solute/solvent pointers: IPTSOL= 38 NATRCM= 656 IPTRES= 0 IPTATM= 0 NSPSOL= 3 NSPSTR= 638 NSOLUT= 9245 NATOM = 9245 | Running AMBER/MPI version on 8 nodes | Atom division among processors

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