VMD-L Mailing List

From: Christoph Willing (c.willing_at_uq.edu.au)
Date: Thu Mar 29 2012 - 07:30:12 CDT

I just rebuilt vmd 1.9.1 with MPI support (mpich2-1.2.1-p1). However
at startup, running a single instance of this build aborts, reporting
the error:

Info) Initializing parallel VMD instances via MPI...
Assertion failed in file helper_fns.c at line 337: 0
memcpy argument memory ranges overlap, dst_=0x9a4b80 src_=0-x9a4b80
len_=544
Internal ABORT - process 0

Googling for this sort of error turned up:
     http://trac.mcs.anl.gov/projects/mpich2/ticket/1006
where a fix is suggested.

I applied a similar fix (patch below) and the resulting build now runs
as expected i.e. without aborting at startup.

chris

--- src/VMDMPI.C.orig 2012-02-02 17:54:56.000000000 +1000
+++ src/VMDMPI.C 2012-03-29 21:56:58.756600825 +1000
@@ -95,7 +95,7 @@
    strncpy(nodename, namebuf,
      (((namelen + 1) < (maxnodenamelen-1)) ? (namelen+1) :
(maxnodenamelen-1)));

- MPI_Allgather(&nodes[mynode], sizeof(nodeinfo), MPI_BYTE,
+ MPI_Allgather(mynode ? &nodes[mynode] : MPI_IN_PLACE,
sizeof(nodeinfo), MPI_BYTE,
                  &nodes[ 0], sizeof(nodeinfo), MPI_BYTE,
                  MPI_COMM_WORLD);

Christoph Willing +61 7 3365 8316
Research Computing Centre
University of Queensland