Cluster compilations

Every time a member of the Rizzo Group compiles a program on Cluster we should write a README file that documents details about the compilation. The content of this README file should then be inserted into this wiki with the date of install and the path of the code and executable programs.

CODE TO BE COMPILED: NAMD

AMBER11

Compiled on 2010/09/14

Tested on 2010/09/14 and 2010/09/15

Path: /sbhome0/balius/programs/amber11.2010.09.14.openmpi.intel/amber11

executable: /sbhome0/balius/programs/amber11.2010.09.14.openmpi.intel/amber11/bin

## Decriptin of the compilation
## This was complied by Trent Balius and Sundipto Mukherjee on 2010/09/14
## Runing of the amber test and a rizzo lab bench mark imply that sander.MPI is working (2010/09/15).
##
## Because we want to run on our nodes we preform the comulation them, by doing the following:
##  qsub -I -l nodes=1:ppn=2 -l walltime=12:00:00
##
## ### MAKE SERIAL
##
## cd /sbhome0/balius/programs/amber11.2010.09.14.openmpi.intel/amber11
##
## cd AmberTools/src/
##
## ./configure --help
##
## ./configure -noX11 -nobintraj intel
##
## cd /sbhome0/balius/programs/amber11.2010.09.14.openmpi.intel/amber11
## cd src/
## make serial
##
## #### MAKE PARALLEL
##
## cd $AMBERHOME/AmberTools/src
## make clean
##
## ./configure -noX11 -nobintraj -mpi intel
##
## make parallel
##
## cd ../../src/
##
## pwd
## /sbhome0/balius/programs/amber11.2010.09.14.openmpi.intel/amber11/src
##
## make parallel
##
##
## While compiling amber 11 serial, /bin/cpp was used (gnu) instead of intel icpc, although we  used intel compilers for everything else.
##
## Warning while configuring parallel/mpi/intel ambertools
##
## Testing mixed C/Fortran compilation:
##      icc  -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
##      ifort -O0 -c -o testp.f.o testp.f
##      icc -o testp testp.c.o testp.f.o -L/software1/intel/Compiler/11.1/069/lib/intel64/  -lifport -lifcore -lsvml
## /software1/intel/Compiler/11.1/069/lib/intel64/libimf.so: warning: warning: feupdateenv is not  implemented and will always fail
## OK
##
##