CP2K installation error.

Alfio Lazzaro alfio.... at gmail.com
Mon Jul 27 14:15:40 CEST 2015


OK, we are making progress...
However, the problem is not MKL.
You need to have a compiler first (I assume gfortran) and then an MPI
implementation. Again, mpirun is not what we need for compiling.
Is there any other command inside:

/opt/sgi/mpt/mpt-2.01/bin/mpirun

?
We are looking for mpif90...

What I can suggest to you is to get everything from CP2K installation by
using the toolchain tool under

tools/toolchain

Just run the script install_cp2k_toolchain.sh.
It will take a while and it will install everything in your area.

Alfio



2015-07-27 14:09 GMT+02:00 Kalyanashis Jana <kalyan.... at gmail.com>:

> 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
>



-- 
Alfio Lazzaro
skype account: alfio.lazzaro
email: alfio.... at gmail.com (per messaggi a cui prometto di rispondere
in qualche giorno, ma rispondo! :) )
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