[Openmd-users] (no subject)

[Dan Gezelter]

David,

  It would be helpful if you could send a copy of the md and frc files that he is using so that we can attempt to recreate this.  Also, does the same job fail on a single processor?  (i.e. if the openmd  binary is run instead of  mpirun -np N openmd_MPI)?  If this is happening in the single processor version as well as under MPI, the debugging will be much easier.

The debugging flags can give you more of a verbose backtrace in idb or gdb, so it may help to reconfigure with "--enable-debug".  That said, debugging in openmpi is a bit of a challenge, but if you are adept at using CLI debuggers you can start up a parallel debugging job :   mpirun -np 4 xterm -e gdb openmd_MPI 

and then use "run file.md" in each of the windows to start up the parallel job.

On RHEL 5.5, we've built and tested with the pathscale compilers (version 3.2) and  openmpi (version 1.3.2), but I think I can do a test build with the intel compilers if necessary.

Best regards,

 --Dan Gezelter

On Jul 19, 2010, at 5:52 AM, Baker D.J. wrote:

> Hello,
> 
> We are new to OpenMD, and recently we installed Openmd 1.1 on our linux cluster at the request of one of our users. We don't, at this stage, have many details of what he's doing, however his job aborts with the trace back as shown below. We build Openmd 1.1 with the Intel compilers v11.1 and openmpi v1.3.3 on a rhel 5.3 machine. Do anyone have any advice for us please? 
> 
> Should we, for example, preferably build with the gnu compilers, and/or another MPI library? Alternatively should we rebuild OpenMP with debugger support?
> 
> Best regards -- David Baker.
> 
> terminate called after throwing an instance of 'std::bad_cast'
>  what():  St8bad_cast
> [red0576:07809] *** Process received signal ***
> [red0576:07809] Signal: Aborted (6)
> [red0576:07809] Signal code:  (-6)
> [red0576:07809] [ 0] /lib64/libpthread.so.0 [0x2b13b79684c0]
> [red0576:07809] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x2b13b88e5215]
> [red0576:07809] [ 2] /lib64/libc.so.6(abort+0x110) [0x2b13b88e6cc0]
> [red0576:07809] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x114) [0x2b13b8465c44]
> [red0576:07809] [ 4] /usr/lib64/libstdc++.so.6 [0x2b13b8463db6]
> [red0576:07809] [ 5] /usr/lib64/libstdc++.so.6 [0x2b13b8463de3]
> [red0576:07809] [ 6] /usr/lib64/libstdc++.so.6 [0x2b13b8463eca]
> [red0576:07809] [ 7] /usr/lib64/libstdc++.so.6 [0x2b13b8400142]
> [red0576:07809] [ 8] /usr/lib64/libstdc++.so.6 [0x2b13b8415e98]
> [red0576:07809] [ 9] /usr/lib64/libstdc++.so.6(_ZSt4endlIcSt11char_traitsIcEERSt13basic_ostreamIT_T0_ES6_+0x15) [0x2b13b8437005]
> [red0576:07809] [10] openmd_MPI(_ZN6OpenMD10StatWriter9writeStatERKNS_5StatsE+0x139) [0x60c8e9]
> [red0576:07809] [11] openmd_MPI(_ZN6OpenMD24VelocityVerletIntegrator8postStepEv+0x15c) [0x59e69c]
> [red0576:07809] [12] openmd_MPI(_ZN6OpenMD24VelocityVerletIntegrator11doIntegrateEv+0x43) [0x59e4a3]
> [red0576:07809] [13] openmd_MPI(main+0xa30) [0x474fd0]
> [red0576:07809] [14] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2b13b88d2974]
> [red0576:07809] [15] openmd_MPI(_ZNSt8ios_base4InitD1Ev+0x49) [0x4744e9]
> [red0576:07809] *** End of error message ***
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***********************************************
  J. Daniel Gezelter
  Associate Professor of Chemistry
  Director of Graduate Admissions
  Department of Chemistry and Biochemistry
  251 Nieuwland Science Hall
  University of Notre Dame
  Notre Dame, IN 46556-5670

  phone:  +1 (574) 631-7595
  fax:    +1 (574) 631-6652
  e-mail: gezelter at nd.edu
  web:    http://www.nd.edu/~gezelter
************************************************