Re: AMBER: AMBER10 compiling SANDER parallel problem

From: David A. Case <>
Date: Tue, 18 Nov 2008 16:25:23 -0500

On Tue, Nov 18, 2008, Hazard, E. Starr wrote:
> ./configure_amber -lam g95

Was lam compiled with g95?

> The mpif77 does exist where the error above says it does not.

The error message (from lam, not from Amber!) is very misleading here. It
actually has nothing to do with mpif77 not being present...

> When I build with the lamsource option
> make clean
> ./configure_amber -lamsource g95
> ./configure_lam
> make parallel
> ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a \
> ../lib/nxtsec.o ../lib/sys.a mt19937.o ncsu-abmd-hooks.o ncsu-bbmd-ctxt.o ncsu-bbmd-hooks.o ncsu-cftree.o ncsu-colvar-math.o ncsu-colvar-type.o ncsu-colvar-utils.o ncsu-colvar.o ncsu-constants.o ncsu-cv-ANGLE.o ncsu-cv-DISTANCE.o ncsu-cv-HANDEDNESS.o ncsu-cv-MULTI_RMSD.o ncsu-cv-N_OF_BONDS.o ncsu-cv-N_OF_STRUCTURES.o ncsu-cv-R_OF_GYRATION.o ncsu-cv-TORSION.o ncsu-lexer.o ncsu-parser.o ncsu-pmd-hooks.o ncsu-rmsd.o ncsu-sander-hooks.o ncsu-sander-proxy.o ncsu-smd-hooks.o ncsu-umbrella.o ncsu-utils.o ncsu-value.o ../netcdf/lib/libnetcdf.a -L/opt/intel/mkl/10.0.011/lib/em64t -lvml -lmkl_lapack -lmkl -lguide -lpthread
> ld: cannot find -lvml

Try leaving out the -lvml. This was put in based on earlier versions of MKL,
and might not be appropriate for MKL version 10. Note that most people who
have MKL also have the Intel compilers, so that the g95/MKL combination is
probably not very well tested. If you continue to have problems, certainly try
leaving out MKL...its presence or absence doesn't really make a big
difference, except maybe for some GB simulations.

[And, if you have the ifort compilers licensed, consider using them. They will
certainly provide a performance improvement over g95.]


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
Received on Fri Dec 05 2008 - 15:56:26 PST
Custom Search