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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Received on Fri Sep 23 2011 - 08:30:03 PDT
