AMBER Archive (2005)

Subject: AMBER: REMD trajectory error!!!

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Fri Oct 28 2005 - 13:10:18 CDT

Hi user:

From 16 replicas 6 are corrupted in different parts
How I can identify the start and the end of a frame??
Each frame will have all the coordinates for all the atoms???

Thanks

Anthony

On Thursday 20 October 2005 10:28 am, Carlos Simmerling wrote:
> would the 2GB limit really cause it to stop at frame 2300?
> maybe- that's why I suggested manual inspection.
> Still, it seems like it should read the first 2GB and
> unless his system is huge that should be more than 2300 frames.
> carlos
>
> Wei Zhang wrote:
> >Hi Anthony:
> >
> >The ptraj error is because your trajectory file exceed 2G limit which is
> >beyond the limitation of ptraj. To fix this you need to manually change
> >the makefile add
> >
> >-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE
> >
> >to CFLAG and recompile ptraj, this may solve your problem
> >
> >On Thu, 2005-10-20 at 07:53 -0600, Anthony Cruz wrote:
> >>Hi User:
> >>
> >>I was doing a Replica exchange dynamics simulation of a small peptide
> >> with 16 temperature. The simulation stop before it ends. I have the
> >> following information from PBS:
> >>
> >>***************
> >>logfile (*.log)
> >>***************
> >> RUNNING MULTISANDER VERSION OF SANDER AMBER8
> >> Total processors = 16
> >> Number of groups = 16
> >>
> >> Looping over processors:
> >> WorldRank is the global PE rank
> >> NodeID is the local PE rank in current group
> >>
> >> Group = 0
> >> WorldRank = 0
> >> NodeID = 0
> >>
> >> Group = 1
> >> WorldRank = 1
> >> NodeID = 0
> >>
> >> Group = 2
> >> WorldRank = 2
> >> NodeID = 0
> >>
> >> Group = 3
> >> WorldRank = 3
> >> NodeID = 0
> >>
> >> Group = 4
> >> WorldRank = 4
> >> NodeID = 0
> >>
> >> Group = 5
> >> WorldRank = 5
> >> NodeID = 0
> >>
> >> Group = 6
> >> WorldRank = 6
> >> NodeID = 0
> >>
> >> Group = 7
> >> WorldRank = 7
> >> NodeID = 0
> >>
> >> Group = 8
> >> WorldRank = 8
> >> NodeID = 0
> >>
> >> Group = 9
> >> WorldRank = 9
> >> NodeID = 0
> >>
> >> Group = 10
> >> WorldRank = 10
> >> NodeID = 0
> >>
> >> Group = 11
> >> WorldRank = 11
> >> NodeID = 0
> >>
> >> Group = 12
> >> WorldRank = 12
> >> NodeID = 0
> >>
> >> Group = 13
> >> WorldRank = 13
> >> NodeID = 0
> >>
> >> Group = 14
> >> WorldRank = 14
> >> NodeID = 0
> >>
> >> Group = 15
> >> WorldRank = 15
> >> NodeID = 0
> >>
> >>getRegFromUnwindContext: Can't get Gr0 from UnwindContext, using 0
> >>
> >>
> >>************
> >>error (*.e)
> >>************
> >>forrtl: severe (24): end-of-file during read, unit 9,
> >>file /home/asantana/asv.299/spcrem_REP.rst.006
> >>Image PC Routine Line
> >> Source sander.REM 400000000049E880 Unknown
> >> Unknown Unknown sander.REM 400000000049D990 Unknown
> >> Unknown Unknown sander.REM 4000000000455EE0 Unknown
> >> Unknown Unknown sander.REM 40000000003C5140 Unknown
> >> Unknown Unknown sander.REM 40000000003C60B0 Unknown
> >> Unknown Unknown sander.REM 40000000003F7220
> >> Unknown Unknown Unknown sander.REM
> >> 400000000011CA70 Unknown Unknown Unknown sander.REM
> >> 400000000007DD60 Unknown Unknown Unknown sander.REM
> >> 4000000000078AC0 Unknown Unknown Unknown
> >> sander.REM 40000000000052D0 Unknown Unknown
> >> Unknown libc.so.6.1 2000000000666990 Unknown
> >> Unknown Unknown sander.REM 4000000000004CC0 Unknown
> >> Unknown Unknown MPI: MPI_COMM_WORLD rank 6 has terminated without
> >> calling MPI_Finalize() MPI: aborting job
> >>
> >>What could be the problem???
> >>Can I restart this simulation?
> >>
> >>Also when I try to truncate the trajectory the process stop with the
> >> following error:
> >>
> >>Amber8 Module: ptraj
> >>
> >>Read in control variables
> >>Read in atom names...
> >>Read in charges...
> >>Read in masses...
> >>Read in IAC (atoms involved in L-J)...
> >>Read in NUMEX (index to excl atom list)...
> >>Read in NNO (index for nonbond of @type)...
> >>Read in residue labels...
> >> LEU ARG ILE PRO CYS CYS PRO VAL ASN LEU
> >> LYS ARG LEU LEU VAL VAL VAL VAL VAL VAL
> >> VAL LEU VAL VAL VAL VAL ILE VAL GLY ALA
> >> LEU LEU MET GLY LEU
> >>Read in the residue to atom pointer list...
> >>Read in bond parameters RK and REQ...
> >>Read in angle parameters TK and TEQ...
> >>Read in dihedral parameters PK, PN and PHASE...
> >>Read in SOLTY...
> >>Read in L-J parameters CN1 and CN2...
> >>Read in info for bonds w/ hydrogen...
> >>Read in info for bonds w/out hydrogen...
> >>Read in info for angles w/ hydrogen...
> >>Read in info for angles w/out hydrogen...
> >>Read in info for dihedrals w/ hydrogen...
> >>Read in info for dihedrals w/out hydrogen...
> >>Read in excluded atom list...
> >>Read in h-bond parameters: AG, BG, and HBCUT...
> >>Read in atomic symbols (types)...
> >>Read in tree information...
> >>Read in the JOIN info...
> >>Read in the IROTAT info...
> >>Successfully completed readParm.
> >>
> >>PTRAJ: Processing input file...
> >> Input is from standard input
> >>
> >>PTRAJ: trajin spcrem_REP.mdcrd.001 1 167675
> >>Checking coordinates: spcrem_REP.mdcrd.001
> >>FYI ptraj(): trajin stop value (167675) is greater than the number of
> >> sets read in
> >>FYI ptraj(): Setting stop to the maximum value (167673)
> >>
> >>PTRAJ: trjout spcrem_REP.mdcrd.001c
> >>
> >>ERROR in dispatchToken: Token string "trjout" not found in tokenlist
> >>
> >>
> >>ERROR in dispatchToken: Token string "spcrem_rep.mdcrd.001c" not found in
> >>tokenlist
> >>
> >>FYI: No output trajectory specified (trajout), none will be saved.
> >>
> >>PTRAJ: Successfully read the input file.
> >> Coordinate processing will occur on 167673 frames.
> >> Summary of I/O and actions follows:
> >>
> >>INPUT COORDINATE FILES
> >> File (spcrem_REP.mdcrd.001) is an AMBER trajectory with 167673 sets
> >>
> >>OUTPUT COORDINATE FILE
> >> NULL entry
> >>
> >>ACTIONS
> >> Stack is NULL
> >>
> >>Processing AMBER trajectory file spcrem_REP.mdcrd.001
> >>
> >>Set 1 .................................................
> >>Set 50 .................................................
> >>Set 100 .................................................
> >>Set 150 .................................................
> >>Set 200 .................................................
> >>Set 250 .................................................
> >>Set 300 .................................................
> >>Set 350 .................................................
> >>Set 400 .................................................
> >>Set 450 .................................................
> >>Set 500 .................................................
> >>Set 550 .................................................
> >>Set 600 .................................................
> >>Set 650 .................................................
> >>Set 700 .................................................
> >>Set 750 .................................................
> >>Set 800 .................................................
> >>Set 850 .................................................
> >>Set 900 .................................................
> >>Set 950 .................................................
> >>Set 1000 .................................................
> >>Set 1050 .................................................
> >>Set 1100 .................................................
> >>Set 1150 .................................................
> >>Set 1200 .................................................
> >>Set 1250 .................................................
> >>Set 1300 .................................................
> >>Set 1350 .................................................
> >>Set 1400 .................................................
> >>Set 1450 .................................................
> >>Set 1500 .................................................
> >>Set 1550 .................................................
> >>Set 1600 .................................................
> >>Set 1650 .................................................
> >>Set 1700 .................................................
> >>Set 1750 .................................................
> >>Set 1800 .................................................
> >>Set 1850 .................................................
> >>Set 1900 .................................................
> >>Set 1950 .................................................
> >>Set 2000 .................................................
> >>Set 2050 .................................................
> >>Set 2100 .................................................
> >>Set 2150 .................................................
> >>Set 2200 .................................................
> >>Set 2250 .................................................
> >>Set 2300 .................................................
> >>Set 2350 ...................................
> >>ERROR in readAmberTrajectory(): Set #2386 is corrupted ( 4.066 2)...
> >>
> >>
> >>
> >>PTRAJ: Successfully read in 2385 sets and processed 2385 sets.
> >> Dumping accumulated results (if any)
> >>
> >>How I can repair the data???
> >>I going to loose all the work???
> >>
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