From: Cesar Luis Avila (cavila_at_fbqf.unt.edu.ar)
Date: Thu Aug 10 2006 - 10:49:43 CDT
Dear all,
I have problems with Namd 2.6b1 on AMD64 architectures.
charmrun exits on random points during simulation with the message :
------------- Processor 2 Exiting: Caught Signal ------------
Signal: segmentation violation
Suggestion: Try running with '++debug', or linking with '-memory paranoid'.
Fatal error on PE 2> segmentation violation
When I run with ++debug I get the message:
Charmrun: error on request socket--
Socket closed before recv.
Which according to Charm++ FAQ means a Segmentation fault.
1. *When I run my program, it gives this error:*
Charmrun: error on request socket--
Socket closed before recv.
This means that the node program died without informing charmrun
about it, which typically means a segmentation fault while in the
interrupt handler or other critical communications code. This
indicates severe corruption in Charm++'s data structures, which is
likely the result of a heap corruption bug in your program.
Re-linking with "-memory paranoid" may clarify the true problem.
So running charmrun with ++debug did not clarify too much.
This takes me to the second option, ie, linking with -memory paranoid.
I suppose this message means: the problem is not in Charm++ itself but
in the program you have compiled, NAMD. So please recompile it again but
this time link with -memory paranoid.
The problem is that I don't know how to pass this option to the
compiler. Is it enough to write
./config debug tcl fftw Linux-amd64-g++
prior to NAMD compiling? Or do I have to pass the option somewhere else?
Regards
Cesar Avila
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