TCL/NAMD: FATAL ERROR: error reading output from command: interrupted system call

From: Corenflos, Steven Charles (
Date: Wed Mar 05 2008 - 15:03:47 CST

I'm getting an error message running a TCL script that's calling the namd. Trying to track down the source of the problem is frustrating me to no end. I know that these same scripts are working fine on a university-owned research server, but when we try to use them on our own server we run into this problem. The relevant portion of the output follows this message.

Originally I suspected the problem was occuring somewhere around vmd (which is also used), but John on the VMD list informed me that the stack trace shows the problem coming from somewhere around the charm library. When removing the charm usage so the script was executed on a single processor with the vanilla namd it worked flawlessly, which seems to confirm that the problem is something to do with the script attempting to parallelize namd with charm.

If anyone knows where to direct me for some help with this it would be greatly appreciated and I may yet keep some of my hair.


Info) VMD for LINUXAMD64, version 1.8.6 (April 6, 2007)
Info) Email questions and bug reports to
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 8 CPUs detected.
Info) Free system memory: 13051MB (81%)
AMA) ----------------------------ama_cycle.tcl---------------------------------
TCL: error reading output from command: interrupted system call
FATAL ERROR: error reading output from command: interrupted system call
    while executing
"exec vmd -dispdev text -e ${amadir}/ama_cycle.tcl | tee -a ${molname}.log"
    invoked from within
"time {exec vmd -dispdev text -e ${amadir}/ama_cycle.tcl | tee -a ${molname}.log}"
    invoked from within
"if {1} {

set t $t_start
set cycle 0
set fT [open $Tfile w]; puts "AMA) Open file ${Tfile} for saving OP timestep information..."
    (file "/home/long/AMA/ama_namd.tcl" line 40)
    invoked from within
"source ${amadir}/ama_namd.tcl"
    (file "1cwp-vmd-H.conf" line 169)
Stack Traceback:
  [0] CmiAbort+0x33 [0x7f17f5]
  [1] _Z8NAMD_diePKc+0x62 [0x4b2f62]
  [2] _ZN9ScriptTcl3runEPc+0x54 [0x6fb75e]
  [3] main+0x21b [0x4b6743]
  [4] __libc_start_main+0xf4 [0x2b6dd6cb4b44]
  [5] _ZNSt8ios_base4InitD1Ev+0x3a [0x4b28da]

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