CP2K installation error.

Kalyanashis Jana kalyan.... at gmail.com
Mon Jul 27 14:09:14 CEST 2015


Thank you so much Alfio. I have installed Intel MKL library in
/home1/bganguly/ directory. But "which mpi" could not find the 'mpi' and
showing 'mpi' command not found... The mpirun directory is
"/opt/sgi/mpt/mpt-2.01/bin/mpirun"
Thanks,
Kalyanashis Jana

On Mon, Jul 27, 2015 at 2:16 PM, Alfio Lazzaro <alfio.... at gmail.com>
wrote:

> I'm sorry, we are discussing two different problems.
> The mpirun command is just for "running" your executable, there is no
> relation with the current problem.
> First you need to compile CP2K and for that you need a proper version of
> the MPI distribution and compilers installed.
> Since you are using Linux-x86-64-intel.popt arch file, I'm assuming that
> you have the Intel compilers (the intel in the name refers to that). Do you
> have Intel compilers in your system? If not, you need to use another
> compiler, like GNU (arch file Linux-x86-64-gfortran.popt). But still you
> need a proper version of MPI installed.
>
> What does it mean "all these are installed in root"? I assume they are
> somewhere in /, therefore you can use them...
>
> Alfio
>
>
> 2015-07-27 8:00 GMT+02:00 Kalyanashis Jana <kalyan.... at gmail.com>:
>
>> Hi Alfio,
>> I have not compiled the MPI... It has been installed in our cluster...
>> When I have checked the directory with "which mpirun", it has given a
>> path.. But all these are installed in root. I am trying to install cp2k
>> from my user only.
>> Thanks with regards,
>> Kalyanashis
>>
>> On Mon, Jul 27, 2015 at 10:32 AM, Alfio Lazzaro <alfio.... at gmail.com>
>> wrote:
>>
>>> Dear Kalyanashis Jana,
>>> OK, if MPI is installed on your system, then probably it is not in your
>>> path, i.e. you cannot run mpif90 in your shell. The command mpirun is for
>>> running the job, while you still have to compile it, so it has nothing to
>>> do with your current problem.
>>> How do you compile a MPI Fortran source file in your cluster, which
>>> command you use? Probably you have mpiifort?
>>>
>>> Alfio
>>>
>>> 2015-07-27 6:55 GMT+02:00 Kalyanashis Jana <kalyan.... at gmail.com>:
>>>
>>>> Thank you very much Lazzaro. MPI is installed in our cluster. Should I
>>>>  mention the mpi or mpirun path? If so, where should I mention the path?
>>>> MKL library is installed in our cluster, but I have done anything with
>>>> lapack or blas. Will it make any problem? Please kindly reply me.
>>>> Thanks in advances,
>>>> Kalyanashis Jana
>>>>
>>>> On Sun, Jul 26, 2015 at 1:46 PM, Alfio Lazzaro <alfio.... at gmail.com
>>>> > wrote:
>>>>
>>>>> Dear Kalyyanashis Jana,
>>>>> the error is clear:
>>>>>
>>>>> /bin/sh: mpif90: command not found
>>>>>
>>>>> This command is used to compile CP2K and it is specified in the arch
>>>>> file (FC       = mpif90). therefore the question is: do you have MPI
>>>>> installed on your cluster?
>>>>>
>>>>> Alfio
>>>>>
>>>>>
>>>>>
>>>>> Il giorno sabato 25 luglio 2015 14:25:47 UTC+2, Kalyanashis Jana ha
>>>>> scritto:
>>>>>>
>>>>>> Hi,
>>>>>>  I have tried to install cp2k software in a cluster machine. I could
>>>>>> not install it. I got the following error
>>>>>>
>>>>>> "make LDFLAGS= -C
>>>>>> /home1/bganguly/cp2k-2.5.0/makefiles/../obj/Linux-x86-64-intel/tools -f
>>>>>> /home1/bganguly/cp2k-2.5.0/makefiles/../makefiles/Makefile makedepf90
>>>>>> make[1]: Entering directory
>>>>>> `/home1/bganguly/cp2k-2.5.0/obj/Linux-x86-64-intel/tools'
>>>>>> make[1]: `makedepf90' is up to date.
>>>>>> make[1]: Leaving directory
>>>>>> `/home1/bganguly/cp2k-2.5.0/obj/Linux-x86-64-intel/tools'
>>>>>> make -C /home1/bganguly/cp2k-2.5.0/makefiles/../src -f
>>>>>> /home1/bganguly/cp2k-2.5.0/makefiles/../makefiles/Makefile all.dep
>>>>>> make[1]: Entering directory `/home1/bganguly/cp2k-2.5.0/src'
>>>>>> make[1]:
>>>>>> `/home1/bganguly/cp2k-2.5.0/makefiles/../obj/Linux-x86-64-intel/popt/all.dep'
>>>>>> is up to date.
>>>>>> make[1]: Leaving directory `/home1/bganguly/cp2k-2.5.0/src'
>>>>>> cp
>>>>>> /home1/bganguly/cp2k-2.5.0/makefiles/../src/cuda/LIBCUDA_DEPENDENCIES
>>>>>> /home1/bganguly/cp2k-2.5.0/makefiles/../obj/Linux-x86-64-intel/popt/libc_cuda.dep
>>>>>> if [ -e
>>>>>> /home1/bganguly/cp2k-2.5.0/makefiles/../src/dbcsr_lib/cuda/libcusmm/LIBCUSMM_DEPENDENCIES
>>>>>> ]; then \
>>>>>>           cp
>>>>>> /home1/bganguly/cp2k-2.5.0/makefiles/../src/dbcsr_lib/cuda/libcusmm/LIBCUSMM_DEPENDENCIES
>>>>>> /home1/bganguly/cp2k-2.5.0/makefiles/../obj/Linux-x86-64-intel/popt/libc_cusmm.dep;
>>>>>> \
>>>>>>         fi
>>>>>> cp
>>>>>> /home1/bganguly/cp2k-2.5.0/makefiles/../src/machine/LIBMA_DEPENDENCIES
>>>>>> /home1/bganguly/cp2k-2.5.0/makefiles/../obj/Linux-x86-64-intel/popt/libc_ma.dep
>>>>>> make -C
>>>>>> /home1/bganguly/cp2k-2.5.0/makefiles/../obj/Linux-x86-64-intel/popt -f
>>>>>> /home1/bganguly/cp2k-2.5.0/makefiles/../makefiles/Makefile _progr
>>>>>> make[1]: Entering directory
>>>>>> `/home1/bganguly/cp2k-2.5.0/obj/Linux-x86-64-intel/popt'
>>>>>> mpif90 -c -D__INTEL -D__FFTSG -D__parallel -D__BLACS -D__SCALAPACK
>>>>>> -D__FFTW3 -D__LIBXC2 -I/home1/bganguly/intel/mkl/include
>>>>>> -I/home1/bganguly/intel/mkl/include/fftw -I/opt/sgi/mpt/mpt-2.05/include
>>>>>> -I/home1/bganguly/libxc-2.2.2/include -O3 -msse2 -heap-arrays 64
>>>>>> -funroll-loops -fpp -free -D__COMPILE_ARCH="\"Linux-x86-64-intel\""
>>>>>> -D__COMPILE_DATE="\"Sat Jul 25 16:52:12 IST 2015\""
>>>>>> -D__COMPILE_HOST="\"service0\"" -D__COMPILE_REVISION="\"svn:13632\""
>>>>>> -D__SHORT_FILE__="\"f77_blas_poison.F\""
>>>>>> /home1/bganguly/cp2k-2.5.0/makefiles/../src/f77_blas_poison.F
>>>>>> /bin/sh: mpif90: command not found
>>>>>> make[1]: *** [f77_blas_poison.o] Error 127
>>>>>> make[1]: Leaving directory
>>>>>> `/home1/bganguly/cp2k-2.5.0/obj/Linux-x86-64-intel/popt'
>>>>>> make: *** [build] Error 2"
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> I have pasted the Linux-x86-64-intel.popt
>>>>>>
>>>>>>
>>>>>> # by default some intel compilers put temporaries on the stack
>>>>>> # this might lead to segmentation faults is the stack limit is set to
>>>>>> low
>>>>>> # stack limits can be increased by sysadmins or e.g with ulimit -s
>>>>>> 256000
>>>>>> # furthermore new ifort (10.0?) compilers support the option
>>>>>> # -heap-arrays 64
>>>>>> # add this to the compilation flags is the other options do not work
>>>>>> # The following settings worked for:
>>>>>> # - AMD64 Opteron
>>>>>> # - SUSE Linux Enterprise Server 10.0 (x86_64)
>>>>>> # - Intel(R) Fortran Compiler for Intel(R) EM64T-based applications,
>>>>>> Version 10.0.025
>>>>>> # - AMD acml library version 3.6.0
>>>>>> # - MPICH2-1.0.5p4
>>>>>> # - SCALAPACK library          1.8.0
>>>>>> #
>>>>>> INTEL_INC=/home1/bganguly/intel/mkl/include
>>>>>> INTEL_LIB=/home1/bganguly/intel/mkl/lib/intel64
>>>>>> FFT_INC=/home1/bganguly/intel/mkl/include/fftw
>>>>>> MKLROOT=/home1/bganguly/intel/mkl
>>>>>>
>>>>>>
>>>>>> CC       = icc
>>>>>> CPP      =
>>>>>> FC       = mpif90
>>>>>> LD       = mpif90
>>>>>> AR       = ar -r
>>>>>> DFLAGS   = -D__INTEL -D__FFTSG -D__parallel -D__BLACS -D__SCALAPACK
>>>>>> -D__FFTW3 -D__LIBXC2
>>>>>> CPPFLAGS =
>>>>>> FCFLAGS  = $(DFLAGS) -I$(INTEL_INC) -I$(FFT_INC)
>>>>>> -I/opt/sgi/mpt/mpt-2.05/include -I/home1/bganguly/libxc-2.2.2/include -O3
>>>>>> -msse2 -heap-arrays 64 -funroll-loops -fpp -free
>>>>>> FCFLAGS2 = $(DFLAGS) -I$(INTEL_INC) -I$(FFT_INC)
>>>>>> -I/opt/sgi/mpt/mpt-2.05/include -I/home1/bganguly/libxc-2.2.2/include -O1
>>>>>> -msse2 -heap-arrays 64 -fpp -free
>>>>>> LDFLAGS  = $(FCFLAGS) -I$(INTEL_INC) -I/opt/sgi/mpt/mpt-2.05/include
>>>>>> -I/home1/bganguly/libxc-2.2.2/include
>>>>>> LIBS =  -L$(MKLROOT)/lib/intel64
>>>>>>  $(MKLROOT)/lib/intel64/libmkl_blas95_lp64.a
>>>>>>  $(MKLROOT)/lib/intel64/libmkl_lapack95_lp64.a
>>>>>> /lhome1/bganguly/libxc-2.2.2/lib/libxc.a \
>>>>>>          -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_sequential
>>>>>> -lmkl_core -lmkl_blacs_sgimpt_lp64   -lpthread -lm
>>>>>> $(INTEL_LIB)/libfftw3xf_intel.a
>>>>>>
>>>>>>
>>>>>> #LIBS     = $(INTEL_LIB)/libscalapack.a \
>>>>>> #           $(INTEL_LIB)/libblacs_init.a \
>>>>>> #           $(INTEL_LIB)/libblacs.a \
>>>>>> #           $(INTEL_LIB)/libacml.a\
>>>>>> #           $(INTEL_LIB)/libacml_mv.a \
>>>>>> #           $(INTEL_LIB)/libfftw3.a
>>>>>>
>>>>>> OBJECTS_ARCHITECTURE = machine_intel.o
>>>>>>
>>>>>>
>>>>>>
>>>>>> graphcon.o: graphcon.F
>>>>>>         $(FC) -c $(FCFLAGS2) $<"
>>>>>>
>>>>>> Please kindly tell me, what is the problem?
>>>>>> Thanks in advance,
>>>>>> Kalyanashis Jana
>>>>>>
>>>>>>
>>>>
>>>>
>>>> --
>>>> Thanks with regards
>>>> Kalyanashis Jana
>>>>
>>>
>>>
>>>
>>> --
>>> Alfio Lazzaro
>>> skype account: alfio.lazzaro
>>> email: alfio.... at gmail.com (per messaggi a cui prometto di
>>> rispondere in qualche giorno, ma rispondo! :) )
>>>
>>
>>
>>
>> --
>> Thanks with regards
>> Kalyanashis Jana
>>
>
>
>
> --
> Alfio Lazzaro
> skype account: alfio.lazzaro
> email: alfio.... at gmail.com (per messaggi a cui prometto di rispondere
> in qualche giorno, ma rispondo! :) )
>



-- 
Thanks with regards
Kalyanashis Jana
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