Charm++ parallel programming system

[Jim Phillips <jim AT ks.uiuc.edu>]

Try --with-debug when you configure the NAMD build directory.

-Jim


On Wed, 21 Jul 2010, Jaime Gonzalez wrote:

> Hello,
>
> Thanks for your help. I had already tried this but GDB does not show
> me the code. When I start "gdb namd2" and run "(gdb) list," gdb can
> not find the file:
>
>  ../sysdeps/i386/elf/start.S
>
> This happens because the compiler has not generated properly debugging 
> symbols.
>
> If I try to establish a breackpoint in a particular line tells me that
> the file is not xxxxxxx.C.
>
> I set the source directories in GDB, but still can not find the code.
> I changed the Makefile to compile NAMD on debug trying various things
> $ (CHARMC)-ggdb-O0-verbose-ld + +-option
> $ (CHARMC)-g-O-verbose-ld + +-option
>
> but none of these solve the problem.
> Someone has debugged NAMD with GDB or CharmDebug ?
>
> Thanks you.
>
>      Jaime
>
> On Tue, Jul 20, 2010 at 7:52 PM, Jim Phillips 
> <jim AT ks.uiuc.edu>
>  wrote:
> > You can run NAMD in standalone mode (no charmrun) inside gdb:
> >
> > jim@lisboa>gdb
> >  namd2
> > GNU gdb Red Hat Linux (6.3.0.0-1.153.el4rh)
> > ...
> > (gdb) run apoa1.namd
> > Starting program: namd2 apoa1.namd
> >
> > -Jim
> >
> >
> > On Tue, 20 Jul 2010, Jaime Gonzalez wrote:
> >
> > > 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@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@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!*