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Amber 12 Installation

posted Jan 15, 2013, 12:48 PM by Danny Xu   [ updated Jan 17, 2013, 12:12 PM ]

must run $AMBERHOME/ --update-tree at least several times to get all file patched up before installation.

also, install    flex tcsh zlib-devel bzip2-devel  libXt-devel libXext-devel libXdmcp-devel

may have to break dependency...

gcc-4.4 (opensuse 11.2) and its gfortran work find with GNU install in serial mode.

One problem encountered with leap code, missing -lSM

workaround: cd /usr/lib64
cp -s

export CC=icc
export F77=ifort
export FC=ifort
export CXX=icpc

For mpi, used mpich2-1.3.2p1 compiled with intel

INL installation

module load ...
Compilation will fail because of ./configure somehow addes incorrect path to mkl libs
don't know why, it didn't happen on desktop because there was no mkl to use, I guess

To fix it, vi config.h and manually replace "/lib/intel64" to ""


Currently Loaded Modulefiles:
  1) pbs                   3) intel-mkl/11.1.046
  2) intel/11.1.046        4) openmpi-intel/1.2.6

Note, need to unload intel 10.1 module after loading openmpi-intel/1.2.6. This works for parallel installation, at least "make test" run fine.

module load intel/11.1.046 intel-mkl/11.1.046 mvapich2-intel/1.0.2
also works, but "make test" parallel did not go through, this may be mvapich restrctions.