AMBER Archive (2004)

Subject: RE: AMBER: Amber7 bugfix1

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jul 06 2004 - 13:17:49 CDT

Dear Sachin

The bugfixes are not designed to be applied manually but instead are
interpreted by the program patch.

Ensure that you have patch installed, replace your modified makefile with
the original one and then do:

cd $AMBERHOME
patch -p0 <bugfix.1

When prompted supply the path to the relevant files, namely:

src/lapack/Makefile

and

src/Machines/Machine.ifc

All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of sachin patil
> Sent: 06 July 2004 10:48
> To: amber_at_scripps.edu
> Subject: AMBER: Amber7 bugfix1
>
> Hi,
> I am trying to apply Bugfix1 for Amber7. I have
> modified my amber7/src/lapack/Makefile: which
> initially looked like
> --------------------------------------------------------
> SHELL=/bin/sh
> SRCDIR=..
> VPATH=
>
> install:
> ./Makelapack
>
> # if you have vendor-supplied or otherwise optimized
> LAPACK libraries,
> # use the following:
>
> DUMMYLIB= xerbla.o
> dummy: $(DUMMYLIB)
> ar r lapack.a $(DUMMYLIB)
>
>
> # otherwise, to compile the subset of LAPACK need for
> amber, use the
> # following definition:
>
> LAPACKLIB= dsyev.o dlansy.o dsytrd.o dorgtr.o dsteqr.o
> \
> dsterf.o dlascl.o dlamch.o xerbla.o ilaenv.o dlassq.o
> dsytd2.o \
> dlatrd.o dorgql.o dorgqr.o dlasrt.o dlaset.o dlanst.o
> dlaev2.o \
> dlasr.o dlapy2.o dlartg.o dlae2.o dorg2r.o dlarft.o
> dlarfb.o \
> dorg2l.o dlarfg.o dlarf.o dspev.o dlansp.o dsptrd.o
> dopgtr.o \
> dppsv.o dspsv.o dgeev.o dsptrs.o dsptrf.o dpptrs.o
> dpptrf.o \
> dgebak.o dtrevc.o dlacpy.o dhseqr.o dorghr.o dgehrd.o
> dgebal.o \
> dlange.o dlabad.o dlahqr.o dlarfx.o dlanhs.o dlaln2.o
> dgehd2.o \
> dlahrd.o dlanv2.o dladiv.o dgerq2.o dorm2r.o dlarnv.o
> dgeqr2.o \
> dlaruv.o
>
> lapack.a: $(LAPACKLIB)
> ar r lapack.a $(LAPACKLIB)
> ../Compile RANLIB lapack.a
>
> clean:
> -/bin/rm -f *.o lapac
> --------------------------------------------------------
>
> After adding the patch it looks like this-
>
> --------------------------------------------------------
> SHELL=/bin/sh
> SRCDIR=..
> VPATH=
>
> install:
> ./Makelapack
>
> # if you have vendor-supplied or otherwise optimized
> LAPACK libraries,
> # use the following:
>
> DUMMYLIB= xerbla.o
> dummy: $(DUMMYLIB)
> ar r lapack.a $(DUMMYLIB)
>
>
> # otherwise, to compile the subset of LAPACK need for
> amber, use the
> # following definition:
>
> LAPACKLIB= dsyev.o dlansy.o dsytrd.o dorgtr.o dsteqr.o
> \
> dsterf.o dlascl.o dlamch.o xerbla.o ilaenv.o dlassq.o
> dsytd2.o \
> dlatrd.o dorgql.o dorgqr.o dlasrt.o dlaset.o dlanst.o
> dlaev2.o \
> dlasr.o dlapy2.o dlartg.o dlae2.o dorg2r.o dlarft.o
> dlarfb.o \
> dorg2l.o dlarfg.o dlarf.o dspev.o dlansp.o dsptrd.o
> dopgtr.o \
> dppsv.o dspsv.o dgeev.o dsptrs.o dsptrf.o dpptrs.o
> dpptrf.o \
> dgebak.o dtrevc.o dlacpy.o dhseqr.o dorghr.o dgehrd.o
> dgebal.o \
> dlange.o dlabad.o dlahqr.o dlarfx.o dlanhs.o dlaln2.o
> dgehd2.o \
> dlahrd.o dlanv2.o dladiv.o dgerq2.o dorm2r.o dlarnv.o
> dgeqr2.o \
> dlaruv.o
>
>
> lapack.a: $(LAPACKLIB)
> ar r lapack.a $(LAPACKLIB)
> ../Compile RANLIB lapack.a
>
> clean:
> -/bin/rm -f *.o lapack.a
>
> *** Makefile 2000/02/23 04:01:11 1.6
> --- Makefile 2002/03/06 17:47:43
> ***************
> *** 37,39 ****
> --- 37,41 ----
> .f.o: $<
> $(SRCDIR)/Compile L3 $<
>
> + dlamch.o: dlamch.f
> + ../Compile L0 dlamch.f
> --------------------------------------------------------
> when I type
> % ./Makelapack
> It gives error message-
>
> Makefile:38: *** target pattern contains no `%'.
> Stop.
>
> Any help & suggestions are highly appreciated.
>
> Thank you
>
> Sachin Patil
> =============
> Dept. of Medicinal & Biological Cheistry
> University of Toledo
> Toledo, Ohio 43606
>
>
>
>
>
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