CP2K installation error.

Alfio Lazzaro alfio.... at gmail.com
Thu Jul 30 09:58:22 CEST 2015


Hi Kalyanashis Jana,
OK, I assume that everything was correctly installed.
The next step is to set the environment variables to use what you have 
installed.

Have you done source of the setup files under the install directory in the 
toolchain installation?
You have to do that for every shell you open (probably you can put in some 
shell startup file). Just type:

source <path-to-setup>/setup

Then you can check the MPI version by typing:

mpif90 -v
mpifort for MPICH version 3.1.2
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/data/vjoost/toolchain-gcc492/install/libexec/gcc/x86_64-unknown-linux-gnu/4.9.2/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: /data/vjoost/toolchain-gcc492/build/gcc-4.9.2/configure 
--prefix=/data/vjoost/toolchain-gcc492/install 
--enable-languages=c,c++,fortran --disable-multilib --disable-bootstrap 
--enable-lto --enable-plugins
Thread model: posix
gcc version 4.9.2 (GCC) 


After that you can move to compile CP2K....

Alfio


Il giorno giovedì 30 luglio 2015 09:32:53 UTC+2, Kalyanashis Jana ha 
scritto:
>
> Hi Alfio,
> I have downloaded cp2k-2.6.1 version and run the install_cp2k_toolchain.sh. 
> It has downloaded required softwares and generated local.popt, sopt etc 
> file. After that, I have copied them to arch folder and run make command 
> what I was instructed.
> But I got the following error
> "make[3]: *** [ma_config.o] Error 1
> cc1: error: unrecognized command line option "-Wc-binding-type"
> cc1: error: unrecognized command line option "-Wintrinsic-shadow"
> cc1: error: unrecognized command line option "-Wintrinsics-std"
> cc1: error: unrecognized command line option "-Wno-tabs"
> cc1: error: unrecognized command line option "-Wrealloc-lhs-all"
> cc1: error: unrecognized command line option "-Wtarget-lifetime"
> cc1: error: unrecognized command line option "-Wunused-but-set-variable"
> /soft/bishwajit/cp2k-2.6.1/src/ma/ma_config.F:0: error: bad value (native) 
> for -march= switch
> /soft/bishwajit/cp2k-2.6.1/src/ma/ma_config.F:0: error: bad value (native) 
> for -mtune= switch
> make[3]: *** [ma_config.o] Error 1
> cc1: error: unrecognized command line option "-Wc-binding-type"
> cc1: error: unrecognized command line option "-Wintrinsic-shadow"
> cc1: error: unrecognized command line option "-Wintrinsics-std"
> cc1: error: unrecognized command line option "-Wno-tabs"
> cc1: error: unrecognized command line option "-Wrealloc-lhs-all"
> cc1: error: unrecognized command line option "-Wtarget-lifetime"
> cc1: error: unrecognized command line option "-Wunused-but-set-variable"
> /soft/bishwajit/cp2k-2.6.1/src/ma/ma_kinds.F:0: error: bad value (native) 
> for -march= switch
> /soft/bishwajit/cp2k-2.6.1/src/ma/ma_kinds.F:0: error: bad value (native) 
> for -mtune= switch
> make[3]: *** [ma_kinds.o] Error 1
> make[2]: *** [all] Error 2
> make[1]: *** [popt] Error 2
> cc1: error: unrecognized command line option "-Wc-binding-type"
> cc1: error: unrecognized command line option "-Wintrinsic-shadow"
> cc1: error: unrecognized command line option "-Wintrinsics-std"
> cc1: error: unrecognized command line option "-Wno-tabs"
> cc1: error: unrecognized command line option "-Wrealloc-lhs-all"
> cc1: error: unrecognized command line option "-Wtarget-lifetime"
> cc1: error: unrecognized command line option "-Wc-binding-type"
> cc1: error: unrecognized command line option "-Wunused-but-set-variable"
> cc1: error: unrecognized command line option "-Wintrinsic-shadow"
> cc1: error: unrecognized command line option "-Wintrinsics-std"
> cc1: error: unrecognized command line option "-Wno-tabs"
> cc1: error: unrecognized command line option "-Wrealloc-lhs-all"
> cc1: error: unrecognized command line option "-Wtarget-lifetime"
> cc1: error: unrecognized command line option "-Wunused-but-set-variable"
> /soft/bishwajit/cp2k-2.6.1/src/ma/ma_kinds.F:0: error: bad value (native) 
> for -march= switch
> /soft/bishwajit/cp2k-2.6.1/src/ma/ma_kinds.F:0: error: bad value (native) 
> for -mtune= switch
> make[3]: /soft/bishwajit/cp2k-2.6.1/src/ma/machine_architecture_types.F:0: 
> error: bad value (native) for -march= switch
> *** [ma_kinds.o] Error 
> 1/soft/bishwajit/cp2k-2.6.1/src/ma/machine_architecture_types.F:0: error: 
> bad value (native) for -mtune= switch
>
> make[3]: *** [machine_architecture_types.o] Error 1
> make[2]: *** [all] Error 2
> make[1]: *** [psmp] Error 2
> make: *** [all] Error 2"
>
>
>
>
>
>
> AND THE LOCAL.POPT file is here
>
> "CC       = gcc
> CPP      =
> FC       = mpif90
> LD       = mpif90
> AR       = ar -r
> WFLAGS   = -Waliasing -Wampersand -Wc-binding-type -Wintrinsic-shadow 
> -Wintrinsics-std -Wline-truncation -Wno-tabs -Wrealloc-lhs-all 
> -Wtarget-lifetime -Wunderflow -Wunused-but-set-variable -Wunused-variable 
> -Wconversion -Werror
> DFLAGS   = -D__LIBINT -D__FFTW3 -D__LIBXC2 -D__LIBINT_MAX_AM=6 
> -D__LIBDERIV_MAX_AM1=5 -D__parallel -D__SCALAPACK
> FCFLAGS  = -I$(CP2KINSTALLDIR)/include -std=f2003 -fimplicit-none 
> -ffree-form -fno-omit-frame-pointer -g -O1 -O3 -march=native -ffast-math 
> $(DFLAGS) $(WFLAGS)
> LDFLAGS  = -L$(CP2KINSTALLDIR)/lib $(FCFLAGS)
> CFLAGS   = $(DFLAGS) -I$(CP2KINSTALLDIR)/include -fno-omit-frame-pointer 
> -g -O1
> LIBS     = -lxc -lderiv -lint  -lscalapack -lreflapack -lrefblas -lstdc++ 
> -lfftw3"
>
> Please kindly help me...
>
> On Mon, Jul 27, 2015 at 7:34 PM, Alfio Lazzaro <alfi... at gmail.com 
> <javascript:>> wrote:
>
>> I'm sorry, I don't have experience with Intel MPI... Is there any reason 
>> why you are using Intel tools? Anyway, probably someone else can answer 
>> better to your question.
>> BTW, you can find the toolchain script here:
>>
>> http://svn.code.sf.net/p/cp2k/code/trunk/cp2k/tools/toolchain/
>>
>> You can probably move to a new CP2K version and use the toolchain to 
>> compile everything.
>>
>> Alfio
>>
>>
>>
>> 2015-07-27 15:29 GMT+02:00 Kalyanashis Jana <kalya... at gmail.com 
>> <javascript:>>:
>>
>>> Okay. I have compiled the intel MPI in /home1/bganguly/intel directory. 
>>> During installtion, it has asked whether I would like to install in 
>>> /home1/bganguly/intel directory. After that, I could not find out the mkl 
>>> and other directories in the intel directory. But MPI command did not find 
>>> out 'mpi' path also.. Is there any other way to compile MPI and MKL 
>>> library? 
>>> Thanks in advance,
>>> Kalyan
>>>
>>> On Mon, Jul 27, 2015 at 6:18 PM, Alfio Lazzaro <alfi... at gmail.com 
>>> <javascript:>> wrote:
>>>
>>>> OK, then you don't have MPI installed on your system. Could you ask to 
>>>> your system administrator where are the MPI wrappers for compilation?
>>>>
>>>> Alfio
>>>>
>>>> 2015-07-27 14:43 GMT+02:00 Kalyanashis Jana <kalya... at gmail.com 
>>>> <javascript:>>:
>>>>
>>>>> Hello Alfio,
>>>>>
>>>>>
>>>>> Is there any other command inside:
>>>>>>
>>>>>> /opt/sgi/mpt/mpt-2.01/bin/mpirun
>>>>>>
>>>>>> ?
>>>>>>
>>>>>
>>>>>  
>>>>> Other command are:
>>>>> mpiexec_mpt  mpiexec_my_mpt  mpirun  mpt_forward  omplace  rail-config 
>>>>>
>>>>>
>>>>> We are looking for mpif90...
>>>>>>
>>>>>
>>>>> But 'mpif90' is not there...
>>>>>
>>>>>  
>>>>>
>>>>>> 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.
>>>>>>
>>>>> Sorry, but there is no install_cp2k_toolchain.sh file in the tools 
>>>>> directory. Even there is no "toolchain" directory
>>>>> Available files in tools directory are 
>>>>> "addSynopsis.py           cp2kController           Fun2D               
>>>>>      make_reference.py        replacer.py
>>>>> analyze_gfortran_ast.py  cp2k-wisdom              get_arch_code       
>>>>>      manual                   RestartTools
>>>>> ASE                      cubecruncher             get_revision_number 
>>>>>      maple2f90.py             robo2doxy.py
>>>>> autotune_grid            dbcsr_test               hfx_tools           
>>>>>      normalizeFortranFile.py  scriptmini
>>>>> base64                   diffEpsilon.py           input_converter.py   
>>>>>     plot_mem_from_trace.py   svn2cl
>>>>> build_libsmm             dist_mat.f90             input_editing       
>>>>>      prepare_ci.py            testUtils.py
>>>>> buildUtils.py            do_replace_wp            input_parser.py     
>>>>>      prepareDoxy.py           trajana.f90
>>>>> checkRet.py              f77_interface           
>>>>>  instantiateTemplates.py  prettify.py
>>>>> clean_cwd.sh             find_bitrot_code.py      lowerPrecision.py   
>>>>>      QS
>>>>> convert_to_dp.py         find_openmp_mistakes.py  makedepf90           
>>>>>     regtesting"
>>>>>
>>>>>  
>>>>> Thank you so much,
>>>>> Kalyanashis Jana
>>>>>  
>>>>
>>>>
>>>>
>>>> -- 
>>>> Alfio Lazzaro
>>>> skype account: alfio.lazzaro
>>>> email: alfi... at gmail.com <javascript:> (per messaggi a cui prometto 
>>>> di rispondere in qualche giorno, ma rispondo! :) )
>>>>  
>>>
>>>
>>>
>>> -- 
>>> Thanks with regards
>>> Kalyanashis Jana
>>>  
>>
>>
>>
>> -- 
>> Alfio Lazzaro
>> skype account: alfio.lazzaro
>> email: alfi... at gmail.com <javascript:> (per messaggi a cui prometto di 
>> rispondere in qualche giorno, ma rispondo! :) )
>>  
>
>
>
> -- 
> Thanks with regards
> Kalyanashis Jana
>  
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