MacOSX net version segmentation fault

From: Joshua Adelman (jadelman_at_berkeley.edu)
Date: Mon Mar 31 2008 - 18:25:29 CDT

I am attempting to compile namd from source to do some testing and
development on my quadcore G5 workstation and have run into some
problems. I get a segmentation fault at launch which I believe is
some sort of problem with the communication between the processors.
I've tested the charm++ build and all of the tests passed ok. I've
also done a similar compilation and build on my powerbook G4 without
any issue.

The exact error is:

$ ./charmrun ++local ++verbose +p4 ./namd2
Charmrun> charmrun started...
Charmrun> adding client 0: "127.0.0.1", IP:127.0.0.1
Charmrun> adding client 1: "127.0.0.1", IP:127.0.0.1
Charmrun> adding client 2: "127.0.0.1", IP:127.0.0.1
Charmrun> adding client 3: "127.0.0.1", IP:127.0.0.1
Charmrun> Charmrun = 127.0.0.1, port = 55862
Charmrun> start 0 node program on localhost.
Charmrun> start 1 node program on localhost.
Charmrun> start 2 node program on localhost.
Charmrun> start 3 node program on localhost.
Charmrun> node programs all started
Charmrun> Waiting for 0-th client to connect.
Charmrun> client 0 connected (IP=127.0.0.1 data_port=54398)
Charmrun> Waiting for 1-th client to connect.
Charmrun> client 1 connected (IP=127.0.0.1 data_port=54399)
Charmrun> Waiting for 2-th client to connect.
Charmrun> client 3 connected (IP=127.0.0.1 data_port=54400)
Charmrun> Waiting for 3-th client to connect.
Charmrun> client 2 connected (IP=127.0.0.1 data_port=54401)
Charmrun> All clients connected.
Charmrun> IP tables sent.
Charmrun> node programs all connected
Charm++: scheduler running in netpoll mode.
Info: NAMD 2.6 for MacOSX-PPC
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 Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 50900 for net-ppc-darwin
Info: Built Mon Mar 31 16:01:35 PDT 2008 by lev on
wh212-1.espm.berkeley.edu
------------- Processor 0 Exiting: Caught Signal ------------
Signal: segmentation violation
Suggestion: Try running with '++debug', or linking with '-memory
paranoid'.
Fatal error on PE 0> segmentation violation

The culprit line of code from the source is in main.C in the call to
tbsoft_sendusage. I believe the offending call is the argument of the
if-statement.
pw = getpwuid(getuid());
if ( pw && pw->pw_name ) {
     strncpy(user, pw->pw_name, 127); user[127] = 0;
  } else {
     sprintf(user,"%d",getuid());
  }

I'm guessing this has something to do with my system's configuration,
but I'm not exactly sure. Any suggestions would be appreciated.

Josh

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