compiling namd on SGI Altix

From: Blake Mertz (jbmertz_at_email.arizona.edu)
Date: Tue Dec 23 2008 - 11:09:10 CST

Hi,

I'm trying to compile an mpi-enabled version of namd on the two SGI altix
machines here at the U. of Arizona. My query is concerning compiling namd on
the SGI Altix 4700 (
http://anise.u.arizona.edu/HPC2/02_hpc/03_hpc_systems/02_hpc_shared_memory.shtml),
which has an Itanium2 architecture and intel c compilers (I believe it's
version 10).

I've downloaded the code for tcl and fftw for ia64 and set them up in the
appropriate directories. I'm also able to successfully compile charm5.9
(./build charm++ mpi-linux-ia64 mpt icc), confirmed by running
simplearrayhello and megatest, but when I go to the directory created by the
config script for compiling namd (Linux-ia64-MPT-icc) and type make, I get
the following error message:

[marin][~/bin/NAMD_2.6_Source/Linux-ia64-MPT-icc]> make
icpc -D_IA64 -I/usr/local/gnu/include
-I~/bin/NAMD_2.6_Source/charm5.9/mpi-linux-ia64-mpt-icc/~/bin/NAMD_2.6_Source/charm5.9/mpi-linux-ia64-mpt-icc/include
-DCMK_OPTIMIZE=1 -Isrc -Iinc -Iplugins/include
-I~/bin/tcl-linux-ia64/include -I/home/u11/jbmertz/tcl/include -DNAMD_TCL
-DUSE_NON_CONST -I~/bin/fftw-linux-ia64/include
-I/home/u11/jbmertz/fftw/include -DNAMD_FFTW -DNAMD_VERSION=\"2.6\"
-DNAMD_PLATFORM=\"Linux-ia64-MPT\" -static-libcxa -cxxlib-icc -O2 -ftz
-IPF_fma -IPF_fltacc -IPF_flt_eval_method0 -IPF_fp_speculationfast -o
obj/common.o -c src/common.C
src/common.C(22): catastrophic error: could not open source file "charm++.h"
  #include "charm++.h"
                      ^

compilation aborted for src/common.C (code 4)
make: *** [obj/common.o] Error 4

I've searched through the namd-l archive, and found a couple of references
to compiling on an sgi altix. Jim Phillips' reply to Alessandro (
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4648.html) seems to
indicate that charm++.h may be missing, but it's actually in my
charm-5.9/mpi-linux-ia64-mpt-icc/include directory. Based on the thread
started by Michel Espinoza-Fonseca (
http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/1854.html), I've
changed Make.charm to point to my compiled charm5.9 directory. At this
point, I'm not sure what to do to point the compiler towards the charm++.h
file, because nothing obvious is popping up at me in the Makefile, Makearch,
or Make.depends files. Has anyone else run into this issue when setting up
namd on an SGI altix? Thanks!

Blake

-- 
Research Assistant
Department of Chemistry
University of Arizona
"Life is not easy for any of us. But what of that? We must have perseverance
and above all confidence in ourselves. We must believe that we are gifted
for something and that this thing must be attained." Marie Curie
"Start by doing what's necessary; then do what's possible; and suddenly you
are doing the impossible." St. Francis of Assissi

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