Charm++ parallel programming system

[Jaime Gonzalez <jim.jaime AT gmail.com>]

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!*
>>