CP2K installation error.

Kalyanashis Jana kalyan.... at gmail.com
Thu Jul 30 09:25:06 CEST 2015


Hi David,
Thank you so much for the arch. But could not installed properly. I have
requested our cluster administrator for the MPI path.. And I will try to
compile it. However, I have successfully installed cp2k-2.5. in our native
cluster. Mkl and MPI libraries are installed properly in the native
cluster. Still there is a problem of MPI. When I have tried to run a test
file I got the following error
"********************************************
 *** ERROR in open_file (MODULE cp_files) ***
 ********************************************

 *** The specified OLD file <H2O-3x3.inp> cannot be opened. It does not ***
 *** exist.                                                             ***

 *** Program stopped at line number 375 of MODULE cp_files ***

 ===== Routine Calling Stack =====

            1 create_cp2k_input_reading
 CP2K| Abnormal program termination, stopped by process number 0
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them."

Can you kindly tell me why did I get such error?
Thank you very much,
Kalyanashis Jana

On Tue, Jul 28, 2015 at 3:05 PM, Rolf David <rolf.d... at gmail.com> wrote:

> I don't know how to proper compile those two. But if you have
> mpiicc/mpiicpc/mpiifort  in
>  /home1/bganguly/intel/compilers_and_libraries_2016.0.079/linux/mpi/intel64/bin
> directory.
>
>
> Try this arch file (hoping the arrangement of folder didn't change much
> fro 11 to 14)
>
>
> INTEL_DIR=Where icc is probably: /opt/intel/Compiler/11.1/073/ (find /
>> -name "icc")
>> INTEL_INC=$(INTEL_DIR)/include
>> INTEL_LIB=$(INTEL_DIR)/lib/intel64
>> MKL_DIR=/home1/bganguly/intel/mkl (or where mkl is, even in opt try find
>> / -name "libfftw3xf_intel.a" you'll find the FFTW_LIB dir and you can go
>> back to the mkl root)
>> MKL_INC=$(MKL_DIR)/include
>> MKL_LIB=$(MKL_DIR)/lib/intel64
>> FFTW_INC=$(MKL_INC)/fftw
>> FFTW_LIB=$(MKL_DIR)/interfaces/fftw3xf
>> LIBXC_DIR=/home1/bganguly/libxc-2.2.2
>> LIBXC_INC=$(LIBXC_DIR)/include
>> LIBXC_LIB=$(LIBXC_DIR)/lib
>> INC=-I$(INTEL_INC) -I$(MKL_INC) -I$(FFTW_INC) -I$(LIBXC_INC)
>>
>> CC       = icc
>> CPP      =
>> FC       = mpiifort
>> LD       = mpiifort
>> AR       = ar -r
>> DFLAGS   = -D__INTEL -D__FFTSG -D__parallel -D__BLACS -D__SCALAPACK
>> -D__FFTW3 -D__LIBXC2
>> CPPFLAGS =
>> FCFLAGS   =  $(DFLAGS) $(INC) -O3 -msse2 -heap-arrays 64 -funroll-loops
>> -fpp -free
>> FCFLAGS2 = $(DFLAGS) $(INC) -O1 -msse2 -heap-arrays 64 -fpp -free
>> LDFLAGS   = $(FCFLAGS)
>>
>> LIBS = -L$(MKL_LIB) -Wl,-rpath,$(MKL_LIB) \
>>         -lmkl_scalapack_lp64 \
>>         -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 \
>>         -lmkl_sequential -lmkl_core \
>>         -lstdc++ \
>>         $(FFTW_LIB)/libfftw3xf_intel.a \
>>         $(LIBXC_LIB)/libxcf90.a $(LIBXC_LIB)/libxc.a \
>>         -lpthread -lm
>> graphcon.o: graphcon.F
>>         $(FC) -c $(FCFLAGS2) $<"
>
>
>
>
> Of course I don't know how the O3/O1 on files for the intel 11.
> But for the 14, it's (and it's with libint so the qs_vxc behave
> differently without I guess) :
>
> FCFLAGS  = $(DFLAGS) $(INC) -O2 -heap-arrays 64 -funroll-loops -fpp -free
>> (+ specific processor vectorisation/opt like your -msse2)
>> FCFLAGS2 = $(DFLAGS) $(INC) -O1 -heap-arrays 64 -fpp -free (+ specific
>> processor vectorisation/opt like your -msse2)
>> FCFLAGS3 = $(DFLAGS) $(INC) -O0 -heap-arrays 64 -fpp -free (+ specific
>> processor vectorisation/opt like your -msse2)
>> # In order to avoid segv when HF exchange for example
>> qs_vxc_atom.o: qs_vxc_atom.F
>>         $(FC) -c $(FCFLAGS2) $<
>> # https://groups.google.com/forum/#!topic/cp2k/G67XV-dyk5E
>> # -O1 on Intel Compiler
>> external_potential_types.o: external_potential_types.F
>>         $(FC) -c $(FCFLAGS2) $<
>> qs_linres_current.o: qs_linres_current.F
>>         $(FC) -c $(FCFLAGS2) $<
>> # https://groups.google.com/forum/#!topic/cp2k/G67XV-dyk5E
>> # -O0 on Intel Compiler
>> mp2_optimize_ri_basis.o: mp2_optimize_ri_basis.F
>>         $(FC) -c $(FCFLAGS3) $<
>
>
> Rolf
>
> On Tuesday, July 28, 2015 at 10:59:38 AM UTC+2, Kalyanashis Jana wrote:
>>
>>
>> Hi David,
>>
>> If you have installed Intel MPI somewhere in /home1/bganguly/intel, there
>>> should be a impi folder (like there is a mkl folder).
>>> It's by default like
>>>
>>> intel/impi/$IMPI_VERSION/intel64/bin
>>>
>>>
>>> Yeah, I have installed the MPI library in /home1/bganguly/intel
>> directory...
>>
>>
>>> And you have here: mpirun/mpiexec/mpiicc/mpiicpc/mpiifort.
>>>
>>>
>>> These commands are there in
>>  /home1/bganguly/intel/compilers_and_libraries_2016.0.079/linux/mpi/intel64/bin
>> directory.
>>
>>> The mpi you have (sgi/mpt/mpt-2.01/) is the SGI Message Passing Toolkit
>>> (SGI MPI if i'm correct)
>>>
>>>
>>> Which version on Intel MPI did you installed ? Part of a package (like
>>> intel parallel studio XE cluster) or as a seperate bundle ? What are your
>>> version of intel compilers (11 ? 12 ? 14 ? 15 ?).
>>>
>>> Or you're trying to use a MPI (SGI or other) with intel compilers ?
>>>
>>
>> I have installed mkl library as a separate bundle and the version was 11.
>> But I have installed the mkl library and the MPI library in the same
>> directory. After that, I do not find out mkl library related folder such as
>> mkl or other folder are not   Can you please tell me the proper way to
>> compile these two library?
>>
>> Thanks with regards,
>> Kalyanashis Jana
>>
>


-- 
Thanks with regards
Kalyanashis Jana
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