Re: Has NAMD been ported to Itanium2 + Linux?

From: Shantenu Jha (s.jha_at_ucl.ac.uk)
Date: Tue Aug 10 2004 - 16:25:28 CDT

> Does anyone know if NAMD runs on Itanium2 Linux clusters?

Yes.

I've pasted some notes and the build commands used to compile NAMD
(with the assistance of Matt Harvey, UCL) on the NCSA teragrid Itanium
cluster below, but please note, before using the pasted build commands
locally, that in all probability they'll need some tweaking to deal
with your specific platform.

[I'd have posted these on the NamdWiki as well, but it isn't accepting
edits, which maybe related to recent web server problems at
ks.uiuc.edu].

> I've looked at the FAQ, which almost implies that NCSA has ported
> NAMD to their Itanium cluster. But there are no details. Has that
> happened? Who might I contact to learn more about how it was done?

The NCSA Itanium cluster is part of the teragrid and has a prescribed
software environment, called the common-teragrid-software stack
(CTSS). There probably isn't much point going into the details of
CTSS, as the default environment (accessed via "softenv") is
documented else where, but it is useful to mention that the default
compiler is the intel 8.0.

I personally had lots of difficulty getting the compiler to use the
right version of mpich and maybe something to watch for. Also, the
teragrid IA64 cluster has myrinet interconnects and I had to
explicitly load the GM libraries (myricom's addon to mpich) , though I
got away with GM and not GM2.

I used charm 5.8 eventually, although later I was able to get the
default charm++ version that ships with NAMD 2.5 working as well.

To build charm++, on the teragrid IA64 use "mpi-linux-ia64 ecc gm"
platform option. The full command used was:

 ./build charm++ mpi-linux-ia64 ecc gm --no-shared -DCMK_OPTIMIZE=1
-I/usr/local/mpich/mpich-gm-1.2.5..10-intel-r2/include
-L/usr/local/mpich/mpich-gm-1.2.5..10- intel-r2/lib/
-L/opt/gm/lib/ -lgm -lpthread -lmpich -lpmpich
-lpthread

There is at least one other subtelty: either tweak the Makefiles to
reflect a problem with directory naming; easier to make a softlink to
  mpi-linux-ia64-gm -> mpi-linux-ia64-gm-ecc/

Regarding the simplearrayhello validation program (in pgms) , although
charm++ compiled, the validation program still required the following:

make OPTS="-L/usr/local/mpich/mpich-gm-1.2.5..10-intel-r2/lib/ -L/opt/gm/lib/ -lmpich
  -lpmpich -lgm -lpthread"

With charm++ built and the validation programs running, you're almost there.

For NAMD I used the Linux-ia64-MPI-GM-ecc option to config (the ecc stands
for the Intel 64bit compiler, GM for Myrinet specific stuff). I didn't try
the net-linux version, as we'll be using it on 100's of px , rather than
10's.

The Makearch file in the directory Linux-ia64-MPI-GM-ecc is,

include .rootdir/Make.charm
include .rootdir/arch/Linux-ia64-MPI-GM-ecc.arch
CHARM = $(CHARMBASE)/$(CHARMARCH)
NAMD_PLATFORM = $(NAMD_ARCH)-MPI-GM
include .rootdir/arch/$(NAMD_ARCH).base
include .rootdir/arch/$(NAMD_ARCH).tcl
include .rootdir/arch/$(NAMD_ARCH).fftw
include .rootdir/arch/$(NAMD_ARCH).plugins

and you can get the required 64 bit tcl,fftw and plugins from the
ks.uiuc.edu website (as mentioned in the notes.txt file).

Finally I had to add the following for the generated Makefile:

MPICHLIB=-L/usr/local/mpich/mpich-gm-1.2.5..10-intel-r2/lib/
-L/opt/gm/lib/ -lmpich -lpmpich -lgm -lpthread

and introduce a $(MPICHLIB) in the dependency list of namd2 target.

Don't know if that helps, but good luck!

Yes, I too had hell getting all this working, but thanks to great
support locally (Matt Harvey), we was able to get there.. I'm sure the
charm++/NAMD developers know this, but currently the barrier to
deployment of source code is almost prohibitively high.

Shantenu

-- 
--Shantenu Jha,  Research Fellow
Centre for Computational Science
University College London  (UCL)	http://www.realitygrid.org
s.jha_at_ucl.ac.uk    020-7679-5300        PGP Key ID 0x78F823E6

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