Compiling and running NAMD on multiple nodes of SDSC Trestles

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Tue Jul 03 2012 - 13:28:36 CDT

Hi!

I am trying to run NAMD 2.9 on multiple nodes of SDSC Trestles. It runs
fine on all 32 cores of the same node. However, if more than 1 node is
specified I get the error message:

mpiexec_trestles-3-17.local: cannot connect to local mpd
(/tmp/mpd2.console_gianluca); possible causes:
   1. no mpd is running on this host
   2. an mpd is running but was started without a "console" (-n option)
In case 1, you can start an mpd on this host with:
     mpd &
and you will be able to run jobs just on this host.

I e-mailed the administrators for help and I got the following answer:

"did you compile with the mvapich_ib mpi stack?"

I tried then to compile charm++ with:

./build charm++ net-linux-x86_64 ibverbs iccstatic --mvapich_ib
--no-build-shared --with-production

But I get the warning messages:

./bin/charmc --mvapich_ib --no-build-shared --with-production -c -I.
pipelinestrategy.C
icpc: command line warning #10006: ignoring unknown option '-fmvapich_ib'
icpc: command line warning #10006: ignoring unknown option
'-fno-build-shared'
icpc: command line warning #10006: ignoring unknown option
'-fwith-production'

and I am still not able to run on multiple nodes.

Any help would be appreciated,

Thanks,

      Gianluca

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Research Scientist at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------

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