CP2K installation error.

Alfio Lazzaro alfio.... at gmail.com
Mon Jul 27 10:46:23 CEST 2015


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! :) )
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