Re: [ESPResSo] how to use nemd

[Guillaume Larsen]

Hello Torsten,

Thank you for your comment!
There is still a problem when i execute ESPResSo with one CPU. Running ESPResSo with one CPU of my procedure (including the initialization of nemd), ESPResSo returns the following error messages at the beginning of warm-up:
[MECA-MEFSTATIONO1:23217] *** Process received signal ***
[MECA-MEFSTATIONO1:23217] Signal: Bus error (7)
[MECA-MEFSTATIONO1:23217] Signal code:  (128)
[MECA-MEFSTATIONO1:23217] Failing at address: (nil)
[MECA-MEFSTATIONO1:23217] [ 0] /lib64/libpthread.so.0 [0x3c2240e930]
[MECA-MEFSTATIONO1:23217] [ 1] /home/guillaume.larsen/espresso/Espresso_bin(calculate_verlet_ia+0x2c7) [0x43090a]
[MECA-MEFSTATIONO1:23217] [ 2] /home/guillaume.larsen/espresso/Espresso_bin(force_calc+0x2d42) [0x446e90]
[MECA-MEFSTATIONO1:23217] [ 3] /home/guillaume.larsen/espresso/Espresso_bin(integrate_vv+0x1fc) [0x43aa17]
[MECA-MEFSTATIONO1:23217] [ 4] /home/guillaume.larsen/espresso/Espresso_bin(mpi_integrate+0x40) [0x415549]
[MECA-MEFSTATIONO1:23217] [ 5] /home/guillaume.larsen/espresso/Espresso_bin(integrate+0x226) [0x43d24b]
[MECA-MEFSTATIONO1:23217] [ 6] /usr/lib64/libtcl8.4.so(TclInvokeStringCommand+0x69) [0x3c2382c589]
[MECA-MEFSTATIONO1:23217] [ 7] /usr/lib64/libtcl8.4.so(TclEvalObjvInternal+0x2f3) [0x3c2382dc73]
[MECA-MEFSTATIONO1:23217] [ 8] /usr/lib64/libtcl8.4.so [0x3c23856c21]
[MECA-MEFSTATIONO1:23217] [ 9] /usr/lib64/libtcl8.4.so(TclCompEvalObj+0x9e) [0x3c2385a07e]
[MECA-MEFSTATIONO1:23217] [10] /usr/lib64/libtcl8.4.so(Tcl_EvalObjEx+0x70) [0x3c2382eb70]
[MECA-MEFSTATIONO1:23217] [11] /usr/lib64/libtcl8.4.so(Tcl_ForeachObjCmd+0x4b0) [0x3c23833700]
[MECA-MEFSTATIONO1:23217] [12] /usr/lib64/libtcl8.4.so(TclEvalObjvInternal+0x2f3) [0x3c2382dc73]
[MECA-MEFSTATIONO1:23217] [13] /usr/lib64/libtcl8.4.so(Tcl_EvalEx+0x38b) [0x3c2382e16b]
[MECA-MEFSTATIONO1:23217] [14] /usr/lib64/libtcl8.4.so(Tcl_FSEvalFile+0x217) [0x3c23871167]
[MECA-MEFSTATIONO1:23217] [15] /usr/lib64/libtcl8.4.so(Tcl_EvalFile+0x2f) [0x3c2387124f]
[MECA-MEFSTATIONO1:23217] [16] /usr/lib64/libtk8.4.so(Tk_MainEx+0x2e6) [0x3c20a47816]
[MECA-MEFSTATIONO1:23217] [17] /home/guillaume.larsen/espresso/Espresso_bin(main+0x64) [0x410083]
[MECA-MEFSTATIONO1:23217] [18] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3c2181d994]
[MECA-MEFSTATIONO1:23217] [19] /home/guillaume.larsen/espresso/Espresso_bin [0x40ff69]
[MECA-MEFSTATIONO1:23217] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 23217 on node MECA-MEFSTATIONO1 exited on signal 7 (Bus error).

Note that if I remove the initialization of nemd from the procedure, the program runs well even with one CPU.
Do you know what kind of problem is that?

Best regards,

Guillaume


> Date: Tue, 23 Mar 2010 12:23:57 +0100
> From: address@hidden
> To: address@hidden
> Subject: Re: [ESPResSo] how to use nemd
>
> Dear Guillaume,
>
> the NEMD feature does only work, if you start ESPResSo with one CPU only.
> It does not run in parallel. The number of CPUs can be given to the
> ESPResSo start script as a second parameter:
>
> # Espresso <your-tcl-script> 1
>
> Greetings,
> Torsten
>
> Guillaume Larsen wrote:
> > dear all,
> >
> > i am experiencing difficulties using the non-equilibrium MD (NEMD)
> > feature of ESPResSo.
> > Trying to initialize the feature with the command "nemd shearrate
> > $n_slabs $shearrate", the following message is returned: {037 NEMD is a
> > single node feature}
> > does anyone know what is problem?
> > Thanks in advance,
> >
> > Regards
> >
> > Guillaume
> >
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>
> --
> Dr. Torsten Stühn
> MPI für Polymerforschung
> Ackermannweg 10
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>
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