Re: [AMBER] AMBER 10 serial compile problem

From: Jason Swails <>
Date: Tue, 15 Mar 2011 09:57:54 -0700


2011/3/15 Dmitry Osolodkin <>

> Hello list,
> I'm trying to compile serial 32-bit version of AMBER 10 with current
> version of Intel® Fortran Composer XE 2011 for Linux (2011.2.137). The
> compiler complains that:
> ifort -o addles lesmain.o addspace.o readprm.o writprm.o readcrd.o
> writcrd.o pick.o rline.o nxt.o intgr.o find.o of.o
> geti.o unit.o getc.o alert.o echo.o get4c.o getd.o
> wlesprm.o lesprm.o les2prm.o checksz.o addspace_atm1st.o ../lib/random.o
> ../lib/mexit.o ../lib/nxtsec.o -lsvml
> -L/opt/intel/composerxe/mkl/lib/32 -lmkl_lapack -lmkl -lguide -lpthread
> ld: cannot find -lmkl_lapack
> make[1]: *** [addles] Error 1

Intel changed their MKL libraries (and names) all around since the time that
Amber10 was released. Amber11 should be up-to-date as far as linking to the
MKL is concerned (though that may possibly change as well). You can choose
to skip using the MKL by unsetting MKL_HOME, and this error should go away.
Alternatively, you have to get rid of the MKL libraries that no longer exist
(like -lmkl_lapack) and substitute in libraries that *do* exist (and are
needed) in the config.h file.

Try putting the following libs on your line (replacing -lmkl_lapack):
-lmkl_core -lmkl_sequential

If you get complaints about missing functions, then you may need to link
other libraries (though I'm not sure which routines are in which libs in
your version of MKL). Look in your /opt/intel/composerxe/mkl/lib/32
directory for additional libs. In my version (10.0.something), I see
libmkl_ia32.a (-lmkl_ia32), and libmkl_intel.a (-lmkl_intel) that may
provide what you need.

Hope this helps,

> MKL is as provided inside the Fortran Composer XE suite. Option -lvml
> removed according to previous advices in the list. Option -w95 removed
> as deprecated for this version of compiler suite. OS is up-to-date
> OpenSUSE 11.3 if it is important.
> What should I do?
> With best regards,
> Dmitry.
> --
> Dmitry Osolodkin
> Researcher
> Group of Computational Molecular Design
> Department of Chemistry
> Moscow State University
> Moscow 119991 Russia
> e-mail:
> Phone: +7-495-9393557
> Fax: +7-495-9390290
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Tue Mar 15 2011 - 10:00:03 PDT
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