Hi Matteo,
Since potentially the issue is with the compiler I only suggested GNU, not
the OS.
On Fri, Sep 23, 2011 at 10:21 AM, Matteo Guglielmi <matteo.guglielmi.epfl.ch
> wrote:
> Carlos)
>
> Unfortunately I cannot move to RedHat, the cluster is already up and
> running with lots of codes installed.
>
> DAC)
>
> Just changing the compilers to 11.1 (fresh installation from .tgz files)
> makes ambertools (serial) basically not compilable at all (it crashes
> right after the compilation of python):
>
> ### ERRORS with intel 11.1, impi 3.2.2, ambertools serial ###
> ...
> changing mode of /software/amber11/lib/python2.6/lib-dynload/audioop.so
> to 755
> changing mode of /software/amber11/lib/python2.6/lib-dynload/ to 755
> running install_scripts
> copying build/scripts-2.6/idle -> /software/amber11/bin
> copying build/scripts-2.6/pydoc -> /software/amber11/bin
> copying build/scripts-2.6/2to3 -> /software/amber11/bin
> copying build/scripts-2.6/smtpd.py -> /software/amber11/bin
> changing mode of /software/amber11/bin/idle to 755
> changing mode of /software/amber11/bin/pydoc to 755
> changing mode of /software/amber11/bin/2to3 to 755
> changing mode of /software/amber11/bin/smtpd.py to 755
> running install_egg_info
> Writing
> /software/amber11/lib/python2.6/lib-dynload/Python-2.6.6-py2.6.egg-info
> if test -f /software/amber11/bin/python -o -h
> /software/amber11/bin/python; \
> then rm -f /software/amber11/bin/python; \
> else true; \
> fi
> (cd /software/amber11/bin; ln python2.6 python)
> rm -f /software/amber11/bin/python-config
> (cd /software/amber11/bin; ln -s python2.6-config python-config)
> /usr/bin/install -c -m 644 ./Misc/python.man \
> /software/amber11/share/man/man1/python.1
> make[1]: Leaving directory
> `/share/lcbc/software/amber11/AmberTools/src/etc/Python-2.6.6'
> Starting installation of MTK++ at Fri Sep 23 16:17:02 CEST 2011.
> (cd mtkpp && make install )
> make[1]: Entering directory
> `/share/lcbc/software/amber11/AmberTools/src/mtkpp'
> Making install in src
> make[2]: Entering directory
> `/share/lcbc/software/amber11/AmberTools/src/mtkpp/src'
> Making install in Diagnostics
> make[3]: Entering directory
> `/share/lcbc/software/amber11/AmberTools/src/mtkpp/src/Diagnostics'
> /bin/bash ../../libtool --tag=CXX --mode=compile icpc -DHAVE_CONFIG_H
> -I. -I../.. -I/software/amber11/AmberTools/src/boost-1.38.0 -I./..
> -std=c++0x -DNDEBUG -DUSE_TINYXML -DTIXML_USE_STL -DC99_OK -O2 -fPIC
> -DHAVE_ZLIB -DHAVE_ZLIB -MT MTKException.lo -MD -MP -MF
> .deps/MTKException.Tpo -c -o MTKException.lo MTKException.cpp
> libtool: compile: icpc -DHAVE_CONFIG_H -I. -I../..
> -I/software/amber11/AmberTools/src/boost-1.38.0 -I./.. -std=c++0x
> -DNDEBUG -DUSE_TINYXML -DTIXML_USE_STL -DC99_OK -O2 -fPIC -DHAVE_ZLIB
> -DHAVE_ZLIB -MT MTKException.lo -MD -MP -MF .deps/MTKException.Tpo -c
> MTKException.cpp -o MTKException.o
> /usr/include/c++/4.4.5/bits/stringfwd.h(67): error: identifier
> "char16_t" is undefined
> template<> struct char_traits<char16_t>;
> ^
>
> /usr/include/c++/4.4.5/bits/stringfwd.h(68): error: identifier
> "char32_t" is undefined
> template<> struct char_traits<char32_t>;
> ...
> #### END ####
>
> Now fresh installation again from .tgz files, same setup but
> using intel compilers 11.0:
>
> FLIBS= -L$(LIBDIR) -lsff -lpbsa -lrism -ldrfftw -ldfftw
> $(LIBDIR)/arpack.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a
> $(LIBDIR)/libnetcdf.a -L/software/intel/Compiler/11.0/084/lib/intel64/
> -lifport -lifcore -lsvml
>
> ambertools (serial - OK)
> amber (serial - OK)
> ambertools (parallel with "make nabonly" - ERROR)
>
> I get exactly the same error message (what to do next then?):
>
> ....
> a - amber_rism_interface.o
> ranlib /software/amber11/lib/libsff.a
> mpicc -o /software/amber11/bin/hcp_getpdb hcp_getpdb.c
> make[1]: Leaving directory
> `/share/lcbc/software/amber11/AmberTools/src/sff'
> (cd nab && make install )
> make[1]: Entering directory
> `/share/lcbc/software/amber11/AmberTools/src/nab'
> mpicc -shared-intel -DBINDIR='"."' -DINCDIR='"."' -DLIBDIR='"."' \
> -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI
> \
> -DCC='"mpicc"' -DCPP='"/software/amber11/bin/ucpp -l"'
> -DFLIBS='"-L/software/amber11/lib -lsff_mpi -lpbsa
> /software/amber11/lib/arpack.a /software/amber11/lib/lapack.a
> /software/amber11/lib/blas.a /software/amber11/lib/libnetcdf.a
> -L/software/intel/Compiler/11.0/084/lib/intel64/ -lifport -lifcore
> -lsvml "' -o nab nab.c
> nab.c(159): error: missing closing quote
> CPP, cppstring, INCDIR,
> ^
>
> nab.c(261): error: missing closing quote
> sprintf( word, " %s ", FLIBS );
> ^
>
> compilation aborted for nab.c (code 2)
> make[1]: *** [nab] Error 2
> make[1]: Leaving directory
> `/share/lcbc/software/amber11/AmberTools/src/nab'
> make: *** [nabonly] Error 2
>
>
>
>
>
> On 09/23/11 15:51, Carlos Sosa wrote:
> > This is not a solution but a workaround. I used Intel MPI and the GNU
> > compiler on RedHat and did not encounter any problems.
> >
> > On Fri, Sep 23, 2011 at 8:15 AM, David A Case<case.biomaps.rutgers.edu
> >wrote:
> >
> >> On Fri, Sep 23, 2011, Matteo Guglielmi wrote:
> >>
> >>> ### ERROR MESSAGE ###
> >>>
> >>> nab.c(261): error: missing closing quote
> >>> sprintf( word, " %s ", FLIBS );
> >>> ^
> >>
> >> This sort of error has been reported several times before. As far as I
> can
> >> see, no one has ever found anything wrong with the Amber codes, and it
> is
> >> frustrating, since the code itself above looks fine. You might play
> with
> >> the
> >> FLIBS variable in config.h (is it perhaps empty?), to see if anything
> pops
> >> out.
> >>
> >>> PS: using the intel compilers 11.1 insead of 11.0 I cannot even
> >>> compile the serial version of ambertools... I get very similar
> >>> error messages which I'm not reporting here.
> >>
> >> Can you do a fresh reinstall, configure (serial) and "make nabonly",
> then
> >> report the exact error results (and complete version information on the
> >> compiler and OS)?
> >>
> >> ...thx...dac
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Carlos P Sosa, Ph.D.
Adjunct Assistant Professor
*Biomedical Informatics and Computational Biology* (BICB)
University of Minnesota Rochester
300 University Square<http://www1.umn.edu/twincities/maps/UniversitySquare/>
R0869A
111 S Broadway
Rochester, MN 55904
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Received on Fri Sep 23 2011 - 08:30:04 PDT
