AMBER Archive (2008)

Subject: RE: AMBER: MKL libraries/Amber10

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Fri May 16 2008 - 11:31:17 CDT

If I understand the Amber10 manual, I should first compile AmberTools. In doing that in /usr/local/amber10 (set to me with chwon and chgrp) I have first (in my .bashrc) set the MKL_HOME env var and sourced as indicated below.

Then, after consulting the help, as user:

./configure_at icc

whereby all tests (icc g77 flex NETCDF) were OK

make -f Makefile_at

ended at Completed installation of AmberTools, vers 1.

Before performing tests, may I ask why during the compilation both g++ and g77 were used. In particular about g77, should I have indicated ifort as compiler (as I'll do for Amber10 and openmpi)? I was unable to see an option for ifort in place of g77 for the above compilation.

When all that is in order, I understand to unpack Amber10.tar.bz2 into /usr/local/amber10
and proceed to compile.

Incidentally (which I forgot to mention in my original post), are MKL libraries of help even for a NUMA-type machine with dual-opterons?

Thanks
francesco

--- On Thu, 5/15/08, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> From: Ross Walker <ross_at_rosswalker.co.uk>
> Subject: RE: AMBER: MKL libraries/Amber10
> To: amber_at_scripps.edu
> Date: Thursday, May 15, 2008, 7:59 PM
> Indeed, although as far as I can tell the following works
> just fine:
>
>
>
> /opt/intel/mkl/10.0.1.014//lib/em64t/libmkl_lapack.a
> /opt/intel/mkl/10.0.1.014//lib/em64t/libmkl_em64t.a
> -L/opt/intel/mkl/10.0.1.
> 014//lib/em64t -lguide –lpthread
>
>
>
> This is what the amber 10 configure script sets up and it
> compiles and links
> fine for me. Perhaps Intel will deprecate this interface in
> later versions
> but for the moment it works fine. Note you should also make
> sure you
> correctly source the MKL environment scripts in your
> bashrc. I.e.
>
>
>
> export MKL_HOME=/opt/intel/mkl/10.0.1.014/
>
> source $MKL_HOME/tools/environment/mklvarsem64t.sh
>
>
>
> All the best
>
> Ross
>
>
>
>
>
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of
> yongleli
> Sent: Thursday, May 15, 2008 7:04 PM
> To: amber_at_scripps.edu
> Subject: Re: AMBER: MKL libraries/Amber10
>
>
>
> There are many changes in the Intel compiler 10.x version,
> you will find the
> detailed instructions from
>
> the user guide pp. 5-5. A reasonable option list chosen on
> Intel Xeon 64 CPU
> is:
>
>
>
> LOADLIB= -L/usr/intel/mkl/10.0.1.014/lib/em64t
> -lmkl_vml_mc
> -lmkl_solver_lp64 -lmkl_em64t -lmkl_lappack95 -lmkl_core
> -lguide -lpthread
>
>
>
> The most different feature from early versions is the need
> of adding
> -lmkl_core, -lmkl_<CPU type>, and
> -lmkl_solver<_CPU type> options.
>
> _____
>
> yongleli
>
> 2008-05-16
>
> _____
>
> 发件人： Francesco Pietra
>
> 发送时间： 2008-05-16 02:06:59
>
> 收件人： Amber
>
> 抄送：
>
> 主题： AMBER: MKL libraries/Amber10
>
>
>
> Being in the process of installing Amber10, I also move
> from Intel compilers
> 9 to 10. What about the present prospects for the Intel MKL
> libraries
> (version 10 compilers) with respect to Amber10? Are there
> the same
> limitations as for Amber9?
>
> Thanks
>
> francesco pietra
>
>
>
>
>
>
>
>
>
>
>
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