Debug NAMD with CharmDebug

From: Jaime Gonzalez (jim.jaime_at_gmail.com)
Date: Tue Jul 20 2010 - 03:41:45 CDT

Hello,

I am a researcher at the University of Rey Juan Carlos (Spain). We are
trying to perform a dynamic molecular simulation on GPU with CUDA using
force models offering NAMD. For this we need to understand the code of NAMD
almost to perfection.
So far we have studied the code without the debugger, but now we need to use
a debugger that allows us to follow step by step implementation of NAMD.
We have tried to run NAMD CharmDebug but errors occur when running and the
program aborts unexpectedly.

We are using NAMD_2.7b3 with Charm++ 6.2.1.
Charm++ is built with net-linux -g options.
CharmDebug works perfectly with simple examples.
We just want to run only on a single processor in local mode.

If there was any other way to debug runtime NAMD, I would greatly appreciate
your help.

Thank you very much.
Regards,

Jaime

The trace of errors when I press 'Start' is:

*jaime_at_plebiotic:~/Documentos/NAMD_2.7b3_Source/Linux-x86-g++$ sudo
./charmdebug
DISPLAY variable = 127.0.1.1:0.0
ParDebug> /home/jaime/Documentos/NAMD_2.7b3_Source/Linux-x86-g++/charmrun
+p1 /home/jaime/Documentos/NAMD_2.7b3_Source/Linux-x86-g++/namd2 input +cpd
+DebugSuspend +DebugDisplay 127.0.1.1:0.0 ++server
ServThread started
Parallel program printed: ccs: 2
ccs: Server IP = 127.0.1.1, Server port = 60908 $

ParDebug> Charmrun started (CCS IP 127.0.1.1, port 60908)
Connecting to: 127.0.1.1:60908
root_at_localhost's password:
Parallel program printed: Charm++: scheduler running in netpoll mode.
Charm++> Running on 1 unique compute nodes (8-way SMP).
Charm++> Cpu topology info:
PE to node map: 0
Node to PE map:
Chip #0: 0
Charm++> cpu topology info is gathered in 0.002 seconds.
Info: NAMD 2.7b3 for Linux-x86
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 60200 for net-linux
Info: Built lun jul 19 11:23:39 CEST 2010 by jaime on plebiotic
Info: 1 NAMD 2.7b3 Linux-x86 1 plebiotic root
Info: Running on 1 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 2537.6 s

Machine is 32 bit, little endian
size -A /home/jaime/Documentos/NAMD_2.7b3_Source/Linux-x86-g++/namd2
string1: |85472 141934592| 85472 141934592
string1: |135144 142020064| 135144 142020064
byteList: 0 80 0

list is null!
Error while starting the application (error: java.lang.NullPointerException.
Aborting...
java.lang.NullPointerException
    at charm.debug.pdata.ChareTypePList.load(ChareTypePList.java:22)
    at charm.debug.ParDebug.startProgram(ParDebug.java:1738)
    at charm.debug.ParDebug.actionPerformed(ParDebug.java:1020)
    at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
    at
javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
    at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
    at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
    at
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
    at
java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
..
..
..
    at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
ServThread terminated
Finished running parallel program
java.net.ConnectException: Connection refused
    at sun.nio.ch.Net.connect(Native Method)
    at sun.nio.ch.SocketChannelImpl.connect(SocketChannelImpl.java:507)
    at java.nio.channels.SocketChannel.open(SocketChannel.java:146)
    at charm.ccs.CcsServer.sendRequest(CcsServer.java:194)
    at charm.ccs.CcsServer.sendRequest(CcsServer.java:160)
    at charm.debug.CpdUtil.getListLength(CpdUtil.java:39)
    at charm.debug.ParDebug.populateNewList(ParDebug.java:495)
..
..
..

    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Network error connecting to PE 0 to access list converse/localqueue
byteList: 0 0 0

java.net.ConnectException: Connection refused
    at sun.nio.ch.Net.connect(Native Method)
    at sun.nio.ch.SocketChannelImpl.connect(SocketChannelImpl.java:507)
    at java.nio.channels.SocketChannel.open(SocketChannel.java:146)
    at charm.ccs.CcsServer.sendRequest(CcsServer.java:194)
    at charm.ccs.CcsServer.sendRequest(CcsServer.java:160)
    at charm.debug.CpdUtil.byteList(CpdUtil.java:70)
    at charm.debug.CpdUtil.getPList(CpdUtil.java:116)
    at charm.debug.CpdUtil.getPList(CpdUtil.java:124)
..
..
..
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Network error connecting to PE 0 to access list converse/localqueue
Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
    at charm.debug.fmt.Consumer.decode(Consumer.java:78)
    at charm.debug.CpdUtil.getPList(CpdUtil.java:118)
    at charm.debug.CpdUtil.getPList(CpdUtil.java:124)
    at charm.debug.ParDebug.populateNewList(ParDebug.java:496)
    at charm.debug.ParDebug.actionPerformed(ParDebug.java:1361)
..
..
..

    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
notifyFreeze: 2648 pe=0
Error: processor 0 already frozen!*

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