The 4.1.2 compatibility problems with sander were fixed. This was in NCSU. A
workaround was found for that and all was good but it looks like there is
now a load of issues with other things needing rism and fftw3 even though
the configure script says it turned that off.
It seems that even disabling nab doesn't work since mmpbsa_py tries to build
a bunch of nabstuff that looks for libsff which in turn needs rism and
fftw3.
Sigh...
> -----Original Message-----
> From: B. Lachele Foley [mailto:lfoley.uga.edu]
> Sent: Friday, March 16, 2012 5:07 PM
> To: AMBER Developers Mailing List
> Subject: Re: [AMBER-Developers] Builds of AMBER 12 with gcc 4.1.2
> failing
>
> If so, then it wasn't before I had to find a way to use gcc44 on about
> a dozen RHEL 5 installations. At that time Amber would not run
> properly on 4.1.x -- even if you got it to compile, basic (non-rism)
> tests could fail. If support for 4.1.x was written in, it was done
> recently. I do recall discussion in the last few months about it. I
> just don't recall if it happened, 4.1 being pretty old by now and all
> of us being busier than any human needs to be, I expect.
>
> Here is the workaround I posted for using gcc44 on RHEL 5 without
> screwing up things for the rest of the OS:
> http://archive.ambermd.org/201006/0196.html
>
> My only change now would be not to put the links in /usr/local because
> that is very deeply coded into root's path on many linuxes -- hard to
> make /usr/local invisible to root. Use /opt or /programs or something
> instead.
>
> :-) Lachele
>
> Dr. B. Lachele Foley
> Complex Carbohydrate Research Center
> The University of Georgia
> Athens, GA USA
> lfoley.uga.edu
> http://glycam.ccrc.uga.edu
>
> ________________________________________
> From: Ross Walker [ross.rosswalker.co.uk]
> Sent: Friday, March 16, 2012 7:57 PM
> To: 'AMBER Developers Mailing List'
> Subject: Re: [AMBER-Developers] Builds of AMBER 12 with gcc 4.1.2
> failing
>
> I am assuming we did because Redhat 5.0 is prevalent 'EVERYWHERE' - I
> thought this was why RISM building was supposed to be skipped if the
> configure script detected gcc 4.1.2.
>
> > -----Original Message-----
> > From: B. Lachele Foley [mailto:lfoley.uga.edu]
> > Sent: Friday, March 16, 2012 4:54 PM
> > To: AMBER Developers Mailing List
> > Subject: Re: [AMBER-Developers] Builds of AMBER 12 with gcc 4.1.2
> > failing
> >
> > Did you guys write in support for 4.1.x? I recall gcc having
> bugginess
> > that was bad for Amber in that series.
> >
> > :-) Lachele
> >
> > Dr. B. Lachele Foley
> > Complex Carbohydrate Research Center
> > The University of Georgia
> > Athens, GA USA
> > lfoley.uga.edu
> > http://glycam.ccrc.uga.edu
> >
> > ________________________________________
> > From: Ross Walker [ross.rosswalker.co.uk]
> > Sent: Friday, March 16, 2012 7:24 PM
> > To: AMBER Developers Mailing List
> > Subject: [AMBER-Developers] Builds of AMBER 12 with gcc 4.1.2 failing
> >
> > Hi All,
> >
> > There seem to be issues compiling AMBER 12 on Redhat 5 which has gcc
> > 4.1.2.
> > The configure suggests it is working fine:
> >
> > ./configure gnu
> >
> > ....
> > Obtaining the gnu suite version:
> > gcc -v
> > The version is 4.1.2
> > Skipping the parts of AmberTools that depend on fftw3
> > ....
> >
> >
> > But then running make gives:
> >
> > make[3]: Entering directory `/server-
> > home/rcw/amber/AmberTools/src/rism'
> > gfortran -c -DBINTRAJ \
> > \
> > -O3 -ffree-form -I/server-home/rcw//amber/include
> > -I/server-home/rcw//amber/include \
> > -o rism_report_c.o rism_report_c.F90
> > gfortran -c -DBINTRAJ \
> > \
> > -O0 -ffree-form -I/server-home/rcw//amber/include
> > -I/server-home/rcw//amber/include \
> > -o fftw3.o fftw3.F90
> > In file fftw3.F90:33
> >
> > use, intrinsic :: iso_c_binding
> > 1
> > Error: Unclassifiable statement at (1)
> > In file fftw3.f03:3
> >
> > Included at fftw3.F90:37
> >
> > integer, parameter :: C_FFTW_R2R_KIND = C_INT32_T
> > 1
> > Error: Parameter 'c_int32_t' at (1) has not been declared or is a
> > variable,
> > which does not reduce to a constant expression
> > In file fftw3.f03:5
> >
> > So it still tries to build rism.
> >
> > but config.h in $AMBERHOME looks good:
> >
> > #1D-RISM
> > RISM=no
> >
> > #3D-RISM NAB
> > RISMSFF=
> > TESTRISMSFF=
> >
> > #3D-RISM SANDER
> > RISMSANDER=
> > SANDER_RISM_INTERFACE=
> > FLIBS_RISMSANDER=
> > TESTRISMSANDER=
> >
> > but it looks like in $AMBERHOME/AmberTools/src/Makefile it still
> tries
> > to
> > build RISM for NAB
> >
> > # nab:
> > (cd cifparse && $(MAKE) install )
> > (cd sff && $(MAKE) install )
> > (cd pbsa && $(MAKE) libinstall )
> > (cd rism && $(MAKE) $(RISM) )
> > (cd nab && $(MAKE) install )
> > (cd nss && $(MAKE) install )
> >
> > so it calls the RISM makefile with $1 as 'no' but then the RISM
> > Makefile
> > does not seem to know how to process that:
> >
> > .PHONY: yes no \
> > librism librism_mpi rism1d$(SFX) \
> > rism3d.snglpnt$(SFX) rism3d.snglpnt.MPI$(SFX) \
> > install install_mpi uninstall clean
> >
> > ...
> > ...
> > yes: install
> >
> > no:
> >
> > install: librism rism1d$(SFX)
> > /bin/mv rism1d$(SFX) $(BINDIR)
> > ...
> > ...
> >
> > So 'make no' still leads to it being built.
> >
> > Any ideas? - maybe the order needs changing here?
> >
> > All the best
> > Ross
> >
> > /\
> > \/
> > |\oss Walker
> >
> > ---------------------------------------------------------
> > | Assistant Research Professor |
> > | San Diego Supercomputer Center |
> > | Adjunct Assistant Professor |
> > | Dept. of Chemistry and Biochemistry |
> > | University of California San Diego |
> > | NVIDIA Fellow |
> > | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> > | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> > ---------------------------------------------------------
> >
> > Note: Electronic Mail is not secure, has no guarantee of delivery,
> may
> > not
> > be read every day, and should not be used for urgent or sensitive
> > issues.
> >
> >
> >
> >
> > _______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> >
> >
> >
> > _______________________________________________
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> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
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Received on Fri Mar 16 2012 - 17:30:04 PDT
