Hello,
On Sun, Apr 24, 2011 at 9:13 PM, Dean Cuebas
<deancuebas.missouristate.edu>wrote:
> Dear all,
>
> I followed amberonmac.blogspot.com instructions for building AT 1.5
>
> The only hiccups were as follows:
>
>
> At the end of the make:
> +++++++++++++++++++++++++++
> .
> .
> .
> (cd mmpbsa_py && make install)
> /bin/bash setup.sh
> AMBERHOME is not set. Assuming it is /opt/amber11/AmberTools
>
In this case, AMBERHOME is not set. This is tested for by "if [ -z
$AMBERHOME ]; then"..., which will only be entered if AMBERHOME is really
not set. Make sure that when you run
echo $AMBERHOME
you see /opt/amber11. This is a bug in the setup script that was caused
when mmpbsa_py was moved from Amber to AmberTools, and I'll work on a patch
for this. However, this should work just fine if AMBERHOME is actually set
as an environment variable.
> Also,
>
> During tests:
>
> Several messages as follows, other than that, no fails,:
>
> ++++++++++++++++++++++++++++++
> .
> .
> .
> .
> Running test to do simple minimization
> (this tests the molecular mechanics interface)
>
> ld: warning: alignment lost in merging tentative definition _tconjgrad
> ld: warning: alignment lost in merging tentative definition _tconjgradMME
> ld: warning: alignment lost in merging tentative definition _tconjgradOther
> ld: warning: alignment lost in merging tentative definition _tgb2
> ld: warning: alignment lost in merging tentative definition _tgb2Other
> ld: warning: alignment lost in merging tentative definition _tgb2dgemm1
> ld: warning: alignment lost in merging tentative definition _tgb2dgemm2
> ld: warning: alignment lost in merging tentative definition _tgb2dgemm3
> ld: warning: alignment lost in merging tentative definition _tinit
> ld: warning: alignment lost in merging tentative definition _tmd
> ld: warning: alignment lost in merging tentative definition _tmdIO
> ld: warning: alignment lost in merging tentative definition _tmdOther
> ld: warning: alignment lost in merging tentative definition _tmme
> ld: warning: alignment lost in merging tentative definition _tmme2
> ld: warning: alignment lost in merging tentative definition _tmme2Angl
> ld: warning: alignment lost in merging tentative definition _tmme2Bond
> ld: warning: alignment lost in merging tentative definition _tmme2Born
> ld: warning: alignment lost in merging tentative definition _tmme2Cons
> ld: warning: alignment lost in merging tentative definition _tmme2Nonb
> ld: warning: alignment lost in merging tentative definition _tmme2Other
> ld: warning: alignment lost in merging tentative definition _tmme2Pair
> ld: warning: alignment lost in merging tentative definition _tmme2Phi
> ld: warning: alignment lost in merging tentative definition _tmmeAngl
> ld: warning: alignment lost in merging tentative definition _tmmeBond
> ld: warning: alignment lost in merging tentative definition _tmmeBorn
> ld: warning: alignment lost in merging tentative definition _tmmeCons
> ld: warning: alignment lost in merging tentative definition _tmmeNonb
> ld: warning: alignment lost in merging tentative definition _tmmeOther
> ld: warning: alignment lost in merging tentative definition _tmmePB
> ld: warning: alignment lost in merging tentative definition _tmmePair
> ld: warning: alignment lost in merging tentative definition _tmmePhi
> ld: warning: alignment lost in merging tentative definition _tmmeRism
> ld: warning: alignment lost in merging tentative definition _tnewton
> ld: warning: alignment lost in merging tentative definition
> _tnewtonCholesky
> ld: warning: alignment lost in merging tentative definition _tnewtonDSYEV
> ld: warning: alignment lost in merging tentative definition _tnewtonLevel
> ld: warning: alignment lost in merging tentative definition _tnewtonMME
> ld: warning: alignment lost in merging tentative definition _tnewtonMME2
> ld: warning: alignment lost in merging tentative definition _tnewtonOther
> ld: warning: alignment lost in merging tentative definition _tnmode
> ld: warning: alignment lost in merging tentative definition _tnmodeAmat
> ld: warning: alignment lost in merging tentative definition _tnmodeDSYEV
> ld: warning: alignment lost in merging tentative definition _tnmodeDSYEVD
> ld: warning: alignment lost in merging tentative definition _tnmodeDiagA
> ld: warning: alignment lost in merging tentative definition _tnmodeEigenvec
> ld: warning: alignment lost in merging tentative definition _tnmodeFact
> ld: warning: alignment lost in merging tentative definition _tnmodeHessian
> ld: warning: alignment lost in merging tentative definition _tnmodeInvdiag
> ld: warning: alignment lost in merging tentative definition _tnmodeLan
> ld: warning: alignment lost in merging tentative definition _tnmodeNorm
> ld: warning: alignment lost in merging tentative definition _tnmodeOther
> ld: warning: alignment lost in merging tentative definition _tnmodeSort
> ld: warning: alignment lost in merging tentative definition _treduceegb
> ld: warning: alignment lost in merging tentative definition _treducemme
> diffing ltest.out.check with ltest.out
> PASSED
>
These messages are weird. How did you install everything? With MacPorts?
Or did you just install the GCC binaries?
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 25 2011 - 00:00:04 PDT
