I had explicitly tested this before it seems something has changed.
To be clear, are you building from the Git repo or from the tar ball?
configure should have died with an error message and explicit instructions on how to configure without RISM. From your message it sounds like this is not happening. Can you confirm that there is no error message?
If you have not done so, can you try
./configure -norism gnu
If that still doesn't work, please let me know. Either way, I should have a fix out for tomorrow morning if it can wait that long.
Tyler
On 2012-03-16, at 8:08 PM, Ross Walker wrote:
> Ok - the problem is that 'sff' tries to build an amber rism module even if
> $RISM = no.
>
> However, disabling the building of sff leads to problems building nss in NAB
> which needs libsff. I can disable nss as well but other parts of nab need it
> as well. The only solution I could find was to disable building nab
> completely.
>
> Any better ideas for fixing?
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: Ross Walker [mailto:ross.rosswalker.co.uk]
>> Sent: Friday, March 16, 2012 4:24 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.
>>
>>
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber-developers
________________________________________________________________
Tyler Luchko
Postdoctoral Associate
Case Group
BioMaPS Institute
Rutgers University
Piscataway, New Jersey
tluchko.rutgers.edu
848-445-5239
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Received on Fri Mar 16 2012 - 17:30:05 PDT
