AMBER Archive (2005)

Subject: Re: AMBER: REMD error!!!

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Oct 20 2005 - 11:28:15 CDT

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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