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
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>
>
>
>
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Received on Fri Mar 16 2012 - 17:30:03 PDT
