AMBER Archive (2005)

Subject: Re: AMBER: REMD error!!!

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Thu Oct 20 2005 - 12:30:13 CDT

you can also delte lines up until the next frame, usually starting line
after a line that is not full length
(box size or partial line of coordinates)

Anthony Cruz wrote:

>Thank you to ALL for your answers.
>
>I think that is something wrong with the file because at frame 2300 the file
>have only 32M. I will truncate the file after this point.
>Thank you for all your help!
>
>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???
>>>>
>>>>-----------------------------------------------------------------------
>>>>The AMBER Mail Reflector
>>>>To post, send mail to amber_at_scripps.edu
>>>>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>>>>
>>>>
>
>-----------------------------------------------------------------------
>The AMBER Mail Reflector
>To post, send mail to amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>

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