From: Wei Huang (whuang_at_cct.lsu.edu)
Date: Fri Apr 16 2010 - 15:41:25 CDT
Dear NAMD experts,
I am trying to set up REMD simulation with the tcl scripts come with NAMD2.7b2. I am able to run REMD simulation using the input files in the example directory with 8 CPU cores in the PBS queue. However, when I run 16 replicas (1 replica/core), the PBS job seems to be running but no outputs are generated except the log files and nrc files. After the PBS job finishes, I get the following error message in every log files:
FATAL ERROR: disconnect server
while executing
"error "disconnect server""
("while" body line 9)
invoked from within
"while { 1 } {
while [catch {gets $server_channel cmd} rval] {
puts $errorCode
if {![string match "POSIX EINTR*" $errorCode]} {
..."
(file "fold_alanin.job0.0.log.nrc" line 11)
[0] Stack Traceback:
[0] CmiAbort+0x5f [0xabcdf3]
[1] _Z8NAMD_diePKc+0x62 [0x509172]
[2] _ZN9ScriptTcl3runEPc+0x54 [0x97142a]
[3] _Z18after_backend_initiPPc+0x22b [0x50d98b]
[4] main+0x3a [0x50d72a]
[5] __libc_start_main+0xdb [0x345b61c3fb]
[6] _ZNSt8ios_base4InitD1Ev+0x52 [0x508ada]
Could some one help me figure out what the problem could be? Thanks! Please let me know if I didn't provide enough information for troubleshooting.
Best,
Wei
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