Some problem during compiling cp2k-4.1 using intel compiler

Tianshu Jiang in Beijing jts2t... at gmail.com
Sun Apr 8 07:59:04 UTC 2018
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I'm sorry for the unclear explanation above. I have been trying to compile 
CP2K with the two compiler(GNU and Intel) separately. But none of 
them make it. I'm using the cluster of our laboratory and some settings on 
it may lead to some problem. So I came here for some help.
I'll do as you suggested, thank you !

在 2018年4月8日星期日 UTC+8下午3:20:57，Alfio Lazzaro写道：
>
> I'm confused... You are not using Intel compiler, you are using GNU?
> Anyway, you should use the MPI wrapper for the compilation, i.e.
>
> FC = mpif90
> LD = mpif90
>
> Alfio
>
>
> Il giorno sabato 7 aprile 2018 13:52:30 UTC+2, Tianshu Jiang in Beijing ha 
> scritto:
>>
>> Hi, Alfio, 
>>
>> This error 
>>
>> ld: skipping incompatible /share/soft/intel_2017/
>> compilers_and_libraries_2017.1.132/linux/mpi/mic/lib/libmpifort.a when 
>> searching for -lmpifort
>> ld: cannot find -lmpifort
>> ld: skipping incompatible /share/soft/intel_2017/
>> compilers_and_libraries_2017.1.132/linux/mpi/mic/lib/debug_mt/libmpi.so 
>> when searching for -lmpi
>> ld: skipping incompatible /share/soft/intel_2017/
>> compilers_and_libraries_2017.1.132/linux/mpi/mic/lib/debug_mt/libmpi.a 
>> when searching for -lmpi
>> ld: skipping incompatible /share/soft/intel_2017/
>> compilers_and_libraries_2017.1.132/linux/mpi/mic/lib/libmpi.so when 
>> searching for -lmpi
>> ld: skipping incompatible /share/soft/intel_2017/
>> compilers_and_libraries_2017.1.132/linux/mpi/mic/lib/libmpi.a when 
>> searching for -lmpi
>> ld: cannot find -lmpi
>> ld: skipping incompatible /share/soft/intel_2017/
>> compilers_and_libraries_2017.1.132/linux/mpi/mic/lib/libmpigi.a when 
>> searching for -lmpigi
>> ld: cannot find -lmpigi
>> make[3]: *** [/share/home/tshjiang/intel_cp2k/exe/Linux-x86-64-gfortran/
>> graph.psmp] Error 1
>> make[3]: *** Waiting for unfinished jobs....
>> make[2]: *** [all] Error 2
>> make[1]: *** [psmp] Error 2
>> make: *** [all] Error 2
>>
>>
>> is related the version of Intel compiler ? The mismatching version of 
>> cp2k and Intel compiler lead  to the final incompatible error?
>> By the way, if I make cp2k using GNU's compiler, my arch file is as 
>> follows
>>
>> # Tested with: GFortran 4.9.2, MPICH 3.1, LAPACK 3.5.0, ScaLAPACK 2.0.2
>> CC         = /soft/gcc-6.4.0/bin/gcc
>> CPP        =
>> FC         = gfortran
>> LD         = gfortran
>> AR         = ar -r
>> ACML_INC   = /share/home/tshjiang/cp2k-4.1/tools/toolchain/install/
>> acml_install/gfortran64/include
>> ACML_LIB   = /share/home/tshjiang/cp2k-4.1/tools/toolchain/install/
>> acml_install/gfortran64/lib
>> FFTW_INC   = /share/home/tshjiang/cp2k-4.1/tools/toolchain/install/fftw-
>> 3.3.4/include
>> FFTW_LIB   = /share/home/tshjiang/cp2k-4.1/tools/toolchain/install/fftw-
>> 3.3.4/lib
>> LIBINT_INC = /share/home/tshjiang/cp2k-4.1/tools/toolchain/install/libint
>> -1.1.4/include
>> LIBINT_LIB = /share/home/tshjiang/cp2k-4.1/tools/toolchain/install/libint
>> -1.1.4/lib
>> LIBXC_INC  = /share/home/tshjiang/cp2k-4.1/tools/toolchain/install/libxc/
>> include
>> LIBXC_LIB  = /share/home/tshjiang/cp2k-4.1/tools/toolchain/install/libxc/
>> lib
>> DFLAGS     = -D__FFTW3 -D__LIBINT -D__LIBXC2 -D__MPI_VERSION=3\
>>              -D__LIBINT_MAX_AM=7 -D__LIBDERIV_MAX_AM1=6 -D__MAX_CONTR=4\
>>              -D__parallel -D__SCALAPACK
>> CPPFLAGS   =
>> FCFLAGS    = $(DFLAGS) -O2 -ffast-math -ffree-form -ffree-line-length-
>> none\
>>              -fopenmp -ftree-vectorize -funroll-loops\
>>              -mtune=native\
>>              -I$(ACML_INC) -I$(FFTW_INC) -I$(LIBINT_INC) -I$(LIBXC_INC)
>> LDFLAGS    = $(FCFLAGS) -static-libgfortran
>> LIBS       = /share/home/tshjiang/cp2k-4.1/tools/toolchain/install/
>> libscalapack.a\
>>              /share/home/tshjiang/cp2k-4.1/tools/toolchain/install/acml-
>> 5.3.1/gfortran64/lib/libacml.a\
>>              $(FFTW_LIB)/libfftw3.a\
>>              $(FFTW_LIB)/libfftw3_threads.a\
>>              $(LIBXC_LIB)/libxcf90.a\
>>              $(LIBXC_LIB)/libxc.a\
>>
>>              $(LIBINT_LIB)/libderiv.a\
>>              $(LIBINT_LIB)/libint.a
>>
>> The version of my GNU compiler is 6.4.0.
>> Does there exists some obvious error in this arch file ?
>> Thanks for your patience!
>>
>> 在 2018年4月7日星期六 UTC+8下午2:06:17，Alfio Lazzaro写道：
>>>
>>> Note that Intel 17.0.1 is not supported (see 
>>> https://www.cp2k.org/dev:compiler_support ). Make sure that your CP2K 
>>> installation goes through the regtest (
>>> https://www.cp2k.org/dev:regtesting ).
>>>
>>> Alfio
>>>
>>>
>>>
>>> Il giorno venerdì 6 aprile 2018 14:11:57 UTC+2, Tianshu Jiang in Beijing 
>>> ha scritto:
>>>>
>>>> Dear all, 
>>>>
>>>> I have been compiling cp2k-4.1 using intel compiler for several days 
>>>> but there is always problems.
>>>> I edit both Linux-x86-64-gfortran.psmp and Linux-x86-64-intel-mic.psmp 
>>>> file according to the tutorial searched from the internet.
>>>> But in my latest trial, the beginning is OK, then the error emerge. 
>>>> The compiling environment is on our cluster, the version of Intel 
>>>> compiler is 17.0.1, libint 1.1.4 and libxc 2.2.2.
>>>> The error information is as follows
>>>>
>>>>
>>>> mpiifort -c -D__MKL -D__FFTW3 -D__LIBINT -D__LIBXC2 -D__MPI_VERSION=3 -
>>>> D__LIBINT_MAX_AM=7 -D__LIBDERIV_MAX_AM1=6 -D__MAX_CONTR=4 -D__parallel 
>>>> -D__SCALAPACK -O2 -g -traceback -fpp -free -I/soft/intel_2017/
>>>> compilers_and_libraries_2017/linux/mkl/include -I/soft/intel_2017/
>>>> compilers_and_libraries_2017/linux/mkl/include/fftw -I/share/home/
>>>> tshjiang/intel_cp2k/tools/toolchain/install/libint-1.1.4/include -I/
>>>> share/home/tshjiang/intel_cp2k/tools/toolchain/install/libxc-2.2.2/include 
>>>> -D__COMPILE_ARCH="\"Linux-x86-64-gfortran\"" -D__COMPILE_DATE="\"Fri 
>>>> Apr  6 19:45:36 CST 2018\"" -D__COMPILE_HOST="\"ln02\"" -
>>>> D__COMPILE_REVISION="\"svn:17462\"" -D__DATA_DIR=
>>>> "\"/share/home/tshjiang/intel_cp2k/data\"" -D__SHORT_FILE__=
>>>> "\"eri_mme/eri_mme_lattice_summation.F\"" /share/home/tshjiang/
>>>> intel_cp2k/src/eri_mme/eri_mme_lattice_summation.F
>>>> ld: group ended before it began (--help for usage)
>>>> make[3]: *** [/share/home/tshjiang/intel_cp2k/exe/Linux-x86-64-gfortran
>>>> /graph.psmp] Error 1
>>>> make[3]: *** Waiting for unfinished jobs....
>>>> make[2]: *** [all] Error 2
>>>> make[1]: *** [psmp] Error 2
>>>> make: *** [all] Error 
>>>>
>>>>
>>>>
>>>> I even can not figure out where is the error. The command of make is:
>>>>
>>>> make -j 8 ARCH=Linux-x86-64-gfortran VERSION=psmp
>>>>
>>>> the arch file looks like
>>>>
>>>> # Tested with: GFortran 4.9.2, MPICH 3.1, LAPACK 3.5.0, ScaLAPACK 2.0.2
>>>> CC         = icc
>>>> CPP        =
>>>> FC         = mpiifort
>>>> LD         = mpiifort
>>>> AR         = ar -r
>>>>
>>>> LIBINT_INC = /share/home/tshjiang/intel_cp2k/tools/toolchain/install/
>>>> libint-1.1.4/include
>>>>
>>>> LIBINT_LIB = /share/home/tshjiang/intel_cp2k/tools/toolchain/install/
>>>> libint-1.1.4/lib
>>>> LIBXC_INC  = /share/home/tshjiang/intel_cp2k/tools/toolchain/install/
>>>> libxc-2.2.2/include
>>>> LIBXC_LIB  = /share/home/tshjiang/intel_cp2k/tools/toolchain/install/
>>>> libxc-2.2.2/lib
>>>> DFLAGS     = -D__MKL -D__FFTW3 -D__LIBINT -D__LIBXC2 -D__MPI_VERSION=3\
>>>>              -D__LIBINT_MAX_AM=7 -D__LIBDERIV_MAX_AM1=6 -D__MAX_CONTR=4
>>>> \
>>>>              -D__parallel -D__SCALAPACK
>>>> CFLAGS     = $(DFLAGS)
>>>> CPPFLAGS   =
>>>> MKLROOT    = /soft/intel_2017/compilers_and_libraries_2017/linux/mkl
>>>> FCFLAGS    = $(DFLAGS) -O2 -g -traceback -fpp -free \
>>>>              -I$(MKLROOT)/include -I$(MKLROOT)/include/fftw -I$(
>>>> LIBINT_INC) -I$(LIBXC_INC)
>>>> FCFLAGS2   = $(DFLAGS) -O0 -g -traceback -fpp -free \
>>>>              -I$(MKLROOT)/include -I$(MKLROOT)/include/fftw -I$(
>>>> LIBINT_INC) -I$(LIBXC_INC)
>>>> LDFLAGS    = $(FCFLAGS) -static-intel
>>>> LDFLAGS_C  = $(FCFLAGS) -static-intel -nofor_main
>>>> LIBS       = $(MKLROOT)/lib/intel64/libmkl_scalapack_lp64.a \
>>>>              -WI,--start-group $(MKLROOT)/lib/intel64/libmkl_intel_lp64
>>>> .a \
>>>>              $(MKLROOT)/lib/intel64/libmkl_sequential.a \
>>>>              $(MKLROOT)/lib/intel64/libmkl_core.a \
>>>>              $(MKLROOT)/lib/intel64/libmkl_blacs_intelmpi_lp64.a -Wl,--
>>>> end-group \
>>>>              -lpthread -lm \
>>>>              -L$(LIBXC_LIB) -lxcf90 -lxc \
>>>>              $(LIBINT_LIB)/libderiv.a \
>>>>              $(LIBINT_LIB)/libint.a -lstdc++
>>>> mp2_optimize_ri_basis.o:mp2_optimize_ri_basis.F
>>>>         $(FC) -c $(FCFLAGS2) $<
>>>> hfx_contraction_methods.o:hfx_contraction_methods.F
>>>>         $(FC) -c $(FCFLAGS2) $<
>>>>
>>>> Can anyone encounter the similar situation and give some advice. 
>>>> I will be appreciated for your suggestion.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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