I've skipped parallel AmberTools15 and informed the users.
Anyway I'd appreciate any extra help from the mailing
list concerning this issue.
--matt
On 09/23/11 21:26, Ross Walker wrote:
> Hi Matteo,
>
> Do you really need AmberTools in parallel? - I would suggest just skipping
> AmberTools parallel and building AMBER in parallel instead.
>
> cd $AMBERHOME/AmberTools/src
> ./configure -mpi gnu
> make clean
> cd ../../
> ./AT15_Amber.py
> cd src
> make clean
> make parallel
>
> This will build you sander.MPI and pmemd.MPI which are the programs that
> most benefit from running in parallel and chances are they will be much
> easier to build than AMBERTools.
>
> It will also likely be much easier to debug compilation problems if there
> are failures here.
>
> All the best
> Ross
>
>> -----Original Message-----
>> From: Matteo Guglielmi [mailto:matteo.guglielmi.epfl.ch]
>> Sent: Friday, September 23, 2011 12:07 PM
>> To: amber.ambermd.org
>> Subject: Re: [AMBER] AmberTools Parallel Compilation Issue
>>
>> 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
>>>>
>>>
>>>
>>>
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Sat Sep 24 2011 - 08:30:02 PDT
