AMBER Archive (2005)

Subject: Re: AMBER: REMD error!!!

From: Wei Zhang (zweig_at_scripps.edu)
Date: Thu Oct 20 2005 - 11:15:51 CDT

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???
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
> 

-- 
Wei Zhang <zweig_at_scripps.edu>
The Scripps Research Institute

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu