From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Mon Oct 22 2007 - 09:13:08 CDT
Ah, the solution to this is very simple, use the latest version of NAMD!
It's also covered in a previous post to the list:
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4978.html
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Karol Kaszuba
Sent: Monday, October 22, 2007 6:16 AM
To: namd-l_at_ks.uiuc.edu
Subject: RE: namd-l: Itanium_and_CMAP
Hello,
I am very sorry for my late reply.
1) Which version of NAMD are you using?
I am using NAMD 2.6b1 for Linux-amd64-TCP
2) Is it the precompiled binary?
I am not a person responsible for compilation but
based on the first lines of the error message (shown below) I guess
that it is a precompiled binary - if it is necessary I can ask about it.
3) What error do you get when it crashes?
Charm++: scheduler running in netpoll mode.
Info: NAMD 2.6b1 for Linux-amd64-TCP
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 50900 for net-linux-amd64-tcp-iccstatic
Info: Built Fri Jul 29 11:32:31 CDT 2005 by jim on tijuana.ks.uiuc.edu
Info: Sending usage information to NAMD developers via UDP. Sent data is:
Info: 1 NAMD 2.6b1 Linux-amd64-TCP 4 n96 karol
Info: Running on 4 processors.
Info: 8360 kB of memory in use.
Info: Configuration file is but.namd
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 2000 steps
Info: FIRST LDB TIMESTEP 50
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
Info: MIN ATOMS PER PATCH 100
Info: INITIAL TEMPERATURE 310
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME optimized.dcd
Info: DCD FREQUENCY 1000
Info: DCD FIRST STEP 1000
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME optimized
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME optimized.restart
Info: RESTART FREQUENCY 1000
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 10
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 14
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 0
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 16.5
Info: ENERGY OUTPUT STEPS 100
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RANDOM NUMBER SEED 1193050715
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB cmap.pdb
Info: STRUCTURE FILE cmap.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS par_all27_prot_lipid_BUT.prm
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
FATAL ERROR: BAD IMPROPER FORMAT IN CHARMM PARAMETER FILE
LINE=*CMAP*
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: BAD IMPROPER FORMAT IN CHARMM PARAMETER FILE
LINE=*CMAP*
Stack Traceback:
[0] CmiAbort+0x35 [0x73428d]
[1] _Z8NAMD_diePKc+0x63 [0x49a8e3]
[2] _ZN10Parameters18add_improper_paramEPcP8_IO_FILE+0x3e9 [0x620d49]
[3] _ZN10Parameters26read_charmm_parameter_fileEPc+0xa82 [0x61ff42]
[4] _ZN10ParametersC1EP13SimParametersP10StringList+0x23f [0x623d6f]
[5] _ZN9NamdState14configListInitEP10ConfigList+0x5fc [0x613de4]
[6] _ZN9ScriptTcl9initcheckEv+0x73 [0x65a3d3]
[7] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x2b [0x656c13]
[8] TclInvokeStringCommand+0x91 [0x755f18]
[9] /opt/namd/namd2.6/namd2 [0x78bd68]
[10] Tcl_EvalEx+0x176 [0x78c3ab]
[11] Tcl_EvalFile+0x134 [0x783db4]
[12] _ZN9ScriptTcl3runEPc+0x1c [0x656014]
[13] main+0x222 [0x49d862]
[14] __libc_start_main+0xf6 [0x2b6ddb8a0136]
[15] _ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_c+0x52
[0x49a22a]
Fatal error on PE 0> FATAL ERROR: BAD IMPROPER FORMAT IN CHARMM PARAMETER
FILE
LINE=*CMAP*
4) Does it work if you don't use CMAP?
It works when I do not use CMAP forcefield.
Karol
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