Ok, no intel compilers but with the same impi (3.2.2) set to use
gfortran, gcc and g++:
ambertools (serial - OK)
amber (serial - OK)
ambertools (parallel - ERROR)
and here will follow the error message.
Is it Debian so Bad?
BTW compiling openmpi 1.4.3 and using the very same gnu compilers
everything get compiled correctly... but there I have the problem
that infiniband becomes slow while with impi infiniband is just
right.
...
a - dsarpack.o
a - wallclock.o
ranlib arpack.a
mv arpack.a /software/amber11/lib
make[2]: Leaving directory
`/share/lcbc/software/amber11/AmberTools/src/arpack'
mpif90 -ffree-form -o pbsa.MPI dsvdc.o pbsa.o pb_read.o pb_write.o
getcoor.o runmd.o runmin.o force.o pb_init.o sa_driver.o np_force.o
pb_force.o pb_fddrv.o pb_iimdrv.o pb_nlsolver.o pb_exmol.o pb_mpfrc.o
pb_direct.o pb_list.o timer.o egb.o ene.o locmem.o myopen.o rdparm.o
pb_lsolver.o decomp.o rgroup.o rfree.o debug.o coed20.o indexg.o
irre32.o phidev.o project.o qld.o coed6.o irre31.o miniop.o
prodis.o qint.o wint.o transf.o curv.o GrToPr.o jumps.o problem.o
IIM.o regular.o ctime.o gmres.o daxpy.o ddot.o dheqr.o dpigmr.o
dscal.o dslui2.o dxlcal.o dchkw.o dgmres.o dnrm2.o drlcal.o
dsilus.o dslui.o isdgmr.o dcopy.o dhels.o dorth.o ds2y.o
dslugm.o dsmv.o qs2i1d.o d1mach.o fdump.o i1mach.o j4save.o
xercnt.o xerhlt.o xermsg.o xerprn.o xersve.o xgetua.o amg.o aux1r5.o
amg1r5.o bicg.o dbcg.o dslui4.o dsluti.o dsmtv.o dslubc.o isdbcg.o
pb_chkfrc.o svdcmp.o svbksb.o pythag.o \
../lib/nxtsec.o ../lib/random.o \
/software/amber11/lib/arpack.a /software/amber11/lib/lapack.a
/software/amber11/lib/blas.a
/bin/mv pbsa.MPI /software/amber11/bin
make[1]: Leaving directory
`/share/lcbc/software/amber11/AmberTools/src/pbsa'
(cd nab && make parallel )
make[1]: Entering directory
`/share/lcbc/software/amber11/AmberTools/src/nab'
mpicc -DBINDIR='"/software/amber11/bin"' \
-DINCDIR='"/software/amber11/include"' \
-DLIBDIR='"/software/amber11/lib"' \
-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
-lgfortran "' \
-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DMPI \
-o /software/amber11/bin/mpinab nab.c
gcc: ": No such file or directory
<command-line>: warning: missing terminating " character
<command-line>: warning: missing terminating " character
nab.c: In function 'n2c':
nab.c:159: error: missing terminating " character
nab.c:159: error: expected expression before ',' token
nab.c: In function 'cc':
nab.c:261: error: missing terminating " character
nab.c:261: error: expected expression before ')' token
make[1]: *** [mpinab] Error 1
make[1]: Leaving directory `/share/lcbc/software/amber11/AmberTools/src/nab'
make: *** [parallel] Error 2
On 09/23/11 17:24, Carlos Sosa wrote:
> 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
>>>>
>>>
>>>
>>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 23 2011 - 12:30:03 PDT
