Re: [AMBER] A possible pmemd bug

From: Robert Duke <>
Date: Thu, 22 Apr 2010 10:01:24 -0400

HI Lijiang,
I am guessing that you got burned by some munging of the bugfix file 31, and
your fix is correct. The problem does not exist in my original fixed
source, but looking again at bugfix 31, next_mult_fac is declared but not
defined in the common block. SO everyone, for now, if you use extra points,
you may want to hand patch prmtop_dat.fpp to include next_mult_fac in the
prmtop_int common block. My apologies to all on this. I did the bugfix
independent of work going on for adding charmm to pmemd in another group; I
did not have the charmm code (if available, not updated); the original fix
was correct. A generous third party did a hand merge of my source after I
submitted working code for the extra points fix, but it clearly was a
complicated-enough blending to get things screwed up. 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.
Best Regards - Bob Duke
----- Original Message -----
From: "Lijiang Yang" <>
To: <>
Sent: Thursday, April 22, 2010 7:59 AM
Subject: [AMBER] A possible pmemd bug

> Hi Dr. Duke,
> 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.
> Best,
> Lijiang Yang
> Department of Chemistry
> Peking University
> _______________________________________________
> AMBER mailing list

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Received on Thu Apr 22 2010 - 07:30:02 PDT
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