Re: [AMBER] A possible pmemd bug

From: Scott Brozell <>
Date: Thu, 22 Apr 2010 17:19:58 -0400


The bugfix.all corrections were made by Ross on Apr 16.
I just double checked the web, and they have been posted.


On Thu, Apr 22, 2010 at 10:01:24AM -0400, Robert Duke wrote:
> Ross,
> I don't know if Dave is still stuck in Germany by the volcano, but if you
> have time to fix the patchfile, that would be great. I don't have access
> to the web files and am traveling today myself in any case (hopefully not
> toward any soon-to-be active volcanoes). Lijiang, thank much for the
> report and correct analysis.

> From: "Lijiang Yang" <>
> > After I applied bugfix 31, the parallel version pmemd always crashes
> >and the error message is like: MPI_BCAST: Message truncated ... . Through
> >debugging, I found that the variable 'next_mult_fac' which is introduced
> >in bugfix 31 is not declared in the 'prmtop_int' common block. Therefore,
> >it always equals to 0 and thus induces the message buffer error at line
> >#1405 'call mpi_bcast(gbl_natex, next * next_mult_fac, mpi_integer, 0,
> >mpi_comm_world, err_code_mpi)'. Adding the variable 'next_mult_fac' to the
> >common block solved the problem. I don't know whether it happens to anyone
> >else.
> > BTW, my system is CentOS 5.4 x86_64, kernel 2.6.18-164.15.1.el5, the
> >compiler is intel compiler 11.1.056 and the parallel library is mpich
> >1.2.7p1. The configure command I used: ./configure linux_em64t ifort mpich
> >pubfft bintraj.

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Received on Thu Apr 22 2010 - 14:30:02 PDT
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