AMBER Archive (2008)

Subject: RE: AMBER: Amber10 testing problem

From: Cenk \(Jenk\) Andac (cenk_andac_at_yahoo.com)
Date: Wed May 14 2008 - 04:13:13 CDT


Hi Ross,

the "-static" flag worked out OK. Thanks.

jenk

--- On Tue, 5/13/08, Ross Walker <ross_at_rosswalker.co.uk> wrote:

> From: Ross Walker <ross_at_rosswalker.co.uk>
> Subject: RE: AMBER: Amber10 testing problem
> To: amber_at_scripps.edu
> Date: Tuesday, May 13, 2008, 4:20 PM
> Hi Jenk,
>
> Are you sure the environment is the same on the machine you
> are running the test on and the one you compiled on? This
> looks to me like the LD_LIBRARY_PATH could be different in
> some way between compilation and testing. Such that sander
> then looks in the wrong place or at a different MKL
> version.
>
> You could also try compiling statically and see if that
> fixes the problem.
>
> You may also simply have not had the MKL library paths
> added to LD_LIBRARY_PATH. Make sure you source the mkl
> environment setup scripts in your bashrc / cshrc. E.g. on
> my machine in /etc/bashrc I have:
>
> source
> /opt/intel/mkl/10.0.1.014/tools/environment/mklvarsem64t.sh
> export MKL_HOME=/opt/intel/mkl/10.0.1.014/
>
> Good luck,
> Ross
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf
> > Of Cenk (Jenk) Andac
> > Sent: Tuesday, May 13, 2008 12:46 PM
> > To: amber_at_scripps.edu
> > Subject: AMBER: Amber10 testing problem
> >
> > Dear Amber Community,
> >
> > I have just installed Amber10.serial on a Linux
> system. The installation
> > went fine with ifort10 and MKL libraries. However, I
> am having some
> > problems testing the sander module of Amber10. As far
> as I understand the
> > MKL library I use seems to act weird or it just could
> be another bug that
> > I am not aware of.
> >
> >
> > Here are the error messages I get when I type
> "make test"
> >
> > cd circ_dna && ./Run.circdna
> > MKL func load error:
> /home_palamut2/software/library/intel-
> > mkl/lib/em64t/libmkl_vml_mc.so: undefined symbol:
> vmlGetErrorCallBack
> > ./Run.circdna: Program error
> > make: *** [test.sander.GB] Error 1
> >
> > and "make test.serial.QMMM"
> >
> > cd qmmm2/1NLN_test_diagonalizers &&
> ./Run.1NLN_internal
> > MKL func load error:
> /home_palamut2/software/library/intel-
> > mkl/lib/em64t/libmkl_vml_mc.so: undefined symbol:
> vmlGetErrorCallBack
> > ./Run.1NLN_internal: Program error
> > make: *** [test.sander.QMMM] Error 1
> >
> > I would apprec─▒ate it if an AMBER professional could
> let me know whether
> > there is a workaround for the error messages I am
> getting.
> >
> >
> > regards,
> >
> > jenk
> >
> >
> >
> >
> >
> >
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