[gmx-users] error on compilation on BlueGene/P

[Fabio Affinito]

Thank you, Mark and Berk!
your suggestion was helpful and I successfully compiled on the frontend.
Now I have a problem when I compile on the compute nodes.
Configure was fine with these parameters:

../configure --prefix=/bgp/userinternal/cin0644a/gromacs \
              --host=ppc --build=ppc64 --enable-ppc-sqrt=1 \
              --disable-ppc-altivec \
              --enable-bluegene --enable-fortran --enable-mpi \
              --with-fft=fftw3 \
              --program-suffix=_mpi_bg \
              --without-x \
             CC=mpixlc_r \
             CFLAGS="-O3 -qarch=450d -qtune=450" \
             MPICC=mpixlc_r CXX=mpixlC_r \
             CXXFLAGS="-O3 -qarch=450d -qtune=450" \
             CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \
             F77=mpixlf77_r FFLAGS="-O3 -qarch=auto -qtune=auto" \
             LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib" \
             LIBS="-lmass"

But when I compile using "make mdrun" the compilation stops in this way.

creating libgmxpreprocess_mpi.la
(cd .libs && rm -f libgmxpreprocess_mpi.la && ln -s
../libgmxpreprocess_mpi.la libgmxpreprocess_mpi.la)
make[1]: *** No rule to make target `../mdlib/libmd_mpi.la', needed by
`mdrun'.  Stop.
make[1]: Leaving directory `/bgp/userinternal/cin0644a/gmx/bgp/src/kernel'

Any suggestion? Thanks!

Fabio


On 09/21/2010 12:03 AM, Mark Abraham wrote:
> Hi,
> 
> IIRC GROMACS has done something radical to FORTRAN inner loops (like
> removing them) since those instructions were written. Removing
> --enable-fortran will make your symptoms go away. The C inner loops will
> be fine, should you ever be running mdrun on the front end nodes.
> 
>> ... and if I add the --enable-bluegene flag :
>>
>>
> "../../../../../src/gmxlib/nonbonded/nb_kernel_bluegene/nb_kernel_gen_bluegene.h",
>> line 163.21: 1506-1231 (S) The built-in function "__fpsub" is
>> not valid
>> for the target architecture.
>>
>> and more similar errors.
> 
> Sure. --enable-bluegene is only useful for the mdrun binary for the
> compute system.
> 
> Mark
> 
>> On 09/20/2010 05:35 PM, Fabio Affinito wrote:
>> > Hi all,
>> > I'm trying to install Gromacs on BG/P following the
>> instruction reported
>> > here:
>> >
>>
> http://www.gromacs.org/Downloads/Installation_Instructions/GROMACS_on_BlueGene>
> 
>> > I ran configure:
>> > ../configure --prefix=/bgp/userinternal/cin0644a/gromacs \
>> >              --enable-ppc-sqrt \
>> >              --disable-ppc-altivec \
>> >              --enable-fortran \
>> >              --with-fft=fftw3 \
>> >              --without-x \
>> >              CFLAGS="-O3 -qarch=auto -qtune=auto" \
>> >              CC="xlc_r -q64" \
>> >              CXX="xlC_r -q64" \
>> >              CXXFLAGS="-O3 -qarch=auto -qtune=auto" \
>> >              CPPFLAGS="-I/bgp/userinternal/cin0644a/fftwlibs/include" \
>> >              F77="xlf_r -q64" \
>> >              FFLAGS="-O3 -qnoprefetch -qarch=auto -qtune=auto" \
>> >              LDFLAGS="-L/bgp/userinternal/cin0644a/fftwlibs/lib"
>> >
>> > But when I compile with make I get this error:
>> >
>> >
>>
> "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",>
> line 42.10: 1506-296 (S) #include file "nbkernel010_f77_single.h" not found.
>> >
>>
> "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",>
> line 43.10: 1506-296 (S) #include file "nbkernel020_f77_single.h" not found.
>> >
>>
> "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",>
> line 44.10: 1506-296 (S) #include file "nbkernel030_f77_single.h" not found.
>> >
>>
> "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",>
> line 45.10: 1506-296 (S) #include file "nbkernel100_f77_single.h" not found.
>> > [...]
>> >
>>
> "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",>
> line 114.5: 1506-045 (S) Undeclared identifier nbkernel010_f77_single.
>> >
>>
> "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",>
> line 115.5: 1506-045 (S) Undeclared identifier nbkernel020_f77_single.
>> >
>>
> "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",>
> line 116.5: 1506-045 (S) Undeclared identifier nbkernel030_f77_single.
>> >
>>
> "../../../../../src/gmxlib/nonbonded/nb_kernel_f77_single/nb_kernel_f77_single.c",>
> line 117.5: 1506-045 (S) Undeclared identifier nbkernel100_f77_single.
>> >
>> >
>> > Do you have any hint about that?
>> >
>> > Thanks in advance!
>> >
>> > F.
>> >
>> >
>>
>>
>> --
>> *********************************************
>> Fabio Affinito, PhD
>> CINECA
>> InterUniversity Computer Center
>> Via Magnanelli, 6/3
>> Casalecchio di Reno (Bologna) ITALY
>> +39/051/6171794 (Phone)
>> e-mail: f.affinito at cineca.it
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> 


-- 
*********************************************
Fabio Affinito, PhD
CINECA
InterUniversity Computer Center
Via Magnanelli, 6/3
Casalecchio di Reno (Bologna) ITALY
+39/051/6171794 (Phone)
e-mail: f.affinito at cineca.it