AMBER Archive (2004)

Subject: AMBER: installing amber8 on a dual processor single box

From: Carsten Detering (detering_at_u.washington.edu)
Date: Fri Apr 02 2004 - 12:37:46 CST

Dear all,

after a more or less troublesome set-up (thanks to Bob Duke from UNC at this
point), I would like to share the experience of setting up Amber8 on a dual
processor machine (Redhat 8) using MPICH-1.2.5.2 and the new Intel fortran
90 compiler. I guess this works for Redhat releases down to 7.2. Correct me
if I am wrong.

1. Download the compiler from http://premier.intel.com. You have to create
an account beforehand on www.intel.com; you will get password and login by
email. THey said these would work for the premier site as well, but at the
time I was doing it there was something wrong with their web site and I was
not able to log in. Contact quadsupport if it does not work.
After having successfully logged in to the premier site, download the
l_fc_pc_7[2].1.038.tar file. According to Bob Duke, this compiler supports
glib2.2.5, 2.2.93, and 2.3.2 (see the mail reflector for his detailed email
to me about this). After you downloaded the file and untared, copy the
license file you have gotten from intel by mail in the same directory as the
compiler (I don't know if that's really necessary for installation, though).
Then install the compiler. The location of the compiler should be
/opt/intel/compiler70/ia32/bin, unless you specified something else. Make
sure this is in your path.
2.Download and install MPICH. The latest version is 1.2.5.2. For
installation, set the following environment variables (this is taken from
Bob Dukes pmemd3.00 release notes with a little adjustment for single box
dual processor machine - thanks)
setenv FC ifc
setenv F90 ifc
setenv FLIB_LIST -lPEPCF90
setenv FFLAGS "-auto -tpp6 -mp1" (works for Athlon)
setenv RSHCOMMAND /usr/bin/rsh (depends on your installation)
 ./configure --disable-devdebug \
                  -prefix=/install-directory-for-mpich -optf77=-O2 -optcc=-O
2 \
                  --with-device=ch_shmem \
                  --disable-c++
THis should work. If you had MPICH before and used it with amber7, it
depends which compiler you compiled it with. Compilation of AMber8 in
parallel would not work if you had compiled MPICH with a g77. In case of
doubt re-install MPICH clean (this is what I did), and recompile it using
the settings above.
3. Go to the /amber8/src directory. You should have installed amber8 in
serial mode first, according to the manual (I used './configure -p4 ifc(or
ifc7)' and then 'make serial'). THis worked flawlessly for me. Possible
failures were in marginal rounding errors. Before compiling for parallel,
make sure you have set the MPICH_HOME dir to the MPICH-installation-dir, and
the DO_PARALLEL to 'mpirun -np 2', if you have two processors. THen do as
described in the manual: make clean, ./configure -mpich ifc, make parallel.
Now for the test, just type 'make test' ('make test.parallel' does not
work). Look up the *.dif files if you get possible failures, the error
should be in the third digit after the komma.

I hope this will be useful for some people.

Cheers,
Carsten

--------------------------------------------
Carsten Detering
University of Washington
Department of Chemistry
Seattle, WA 98195
Fon 206.543.5081
Fax 206.685.8665

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