[CP2K-user] [CP2K:20623] Re: CP2k Installation Error

Sagnik Mukhopadhyay sagnikm2017 at gmail.com
Mon Aug 26 12:21:48 UTC 2024
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Dear Bharat, 

You can try the following in the linux terminal (or windows command prompt, 
if using windows)

1. Clone the master file
2. Go to /cp2k/tools/toolchain/ folder (from terminal)
3. Give the following command:   "./install_cp2k_toolchain.sh"  (this will 
take some time)
4. Go to folder /cp2k/tools/toolchain/install/arch/ and copy the arch files 
to /cp2k/arch/
5. In terminal write the command "source /cp2k/tools/toolchain/install/setup
6. Then go to cp2k folder and write the command "make -j n ARCH=local 
VERSION="ssmp psmp pdbg sdbg""
      (instead of "n" write how many number of cores you want to use for 
compilation)

Regards
Sagnik
On Saturday, August 24, 2024 at 5:36:15 PM UTC+5:30 Frederick Stein wrote:

> Dear Bharat,
> Two questions:
> 1) Which compiler do you want to use? First you write GCC14.1 but your 
> last post suggests IntelOneAPI. What compiler was OpenMPI compiled with? I 
> am not sure how compilation with different compiler systems is supported 
> within CP2K and DBCSR.
> 2) What was your workflow: How did you download CP2K/DBCSR? If you 
> upgraded CP2K from an existing distribution, have you also updated DBCSR 
> (directly or by configuring Git to update DBCSR automatically)?
> Best,
> Frederick
>
> bharat poudel schrieb am Freitag, 23. August 2024 um 20:30:07 UTC+2:
>
>> Sorry for the typo in earlier email.
>>
>> I got this error while installing dbcsr.
>>
>> [ 81%] Built target dbcsr
>>
>> [ 84%] Built target dbcsr_c
>>
>> [ 85%] Built target dbcsr_perf
>>
>> [ 86%] Built target dbcsr_unittest_common
>>
>> [ 88%] Built target dbcsr_unittest1
>>
>> [ 88%] Built target dbcsr_unittest2
>>
>> [ 89%] Built target dbcsr_unittest3
>>
>> [ 91%] Built target dbcsr_unittest4
>>
>> [ 91%] Built target dbcsr_tensor_unittest
>>
>> [ 92%] Built target dbcsr_tas_unittest
>>
>> [ 92%] Built target dbcsr_test_csr_conversions
>>
>> [ 94%] Built target dbcsr_test
>>
>> [ 95%] Built target dbcsr_tensor_test
>>
>> [ 97%] Built target dbcsr_example_1
>>
>> [ 97%] Built target dbcsr_example_2
>>
>> [ 98%] Built target dbcsr_example_3
>>
>> [ 98%] Built target dbcsr_tensor_example_1
>>
>> [ 98%] *Linking Fortran executable dbcsr_example_3_cpp*
>>
>> CMakeFiles/dbcsr_example_3_cpp.dir/dbcsr_example_3.cpp.o: In function 
>> `main':
>>
>> /qscratch/bpoudel/apps/dbcsr/examples/dbcsr_example_3.cpp:34: multiple 
>> definition of `main'
>>
>> /projects/global/toss4/compilers/intel/intel_2021/oneapi/compiler/2021.3.0/linux/bin/intel64/../../compiler/lib/intel64_lin/for_main.o:for_main.c:(.text+0x0): 
>> first defined here
>>
>> /projects/global/toss4/compilers/intel/intel_2021/oneapi/compiler/2021.3.0/linux/bin/intel64/../../compiler/lib/intel64_lin/for_main.o: 
>> In function `main':
>>
>> for_main.c:(.text+0x2e): undefined reference to `MAIN__'
>>
>> make[2]: *** [examples/CMakeFiles/dbcsr_example_3_cpp.dir/build.make:109: 
>> examples/dbcsr_example_3_cpp] Error 1
>>
>> make[1]: *** [CMakeFiles/Makefile2:1638: 
>> examples/CMakeFiles/dbcsr_example_3_cpp.dir/all] Error 2
>>
>> make: *** [Makefile:146: all] Error 2
>>
>>
>> Is it something relaetd to Fortran??
>>
>> Bharat
>> On Friday, August 23, 2024 at 12:21:28 PM UTC-6 bharat poudel wrote:
>>
>>> HI Johan,
>>>
>>> The openmpi versions openmpi-5.0.5
>>> The cp2k version is the latest one 2024.
>>>
>>> Even while installing discrete I got this error
>>>
>>> /qscratch/bpoudel/apps/dbcsr/examples/dbcsr_tensor_example_1.F(698): 
>>> remark #8291: Recommended relationship between field width 'W' and the 
>>> number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
>>>
>>>          write (io_unit, "(a,t73,es8.2)") "performance: total number of 
>>> flops:", real(nflop_sum*numnodes)
>>>
>>> -----------------------------------^
>>>
>>> /qscratch/bpoudel/apps/dbcsr/examples/dbcsr_tensor_example_1.F(834): 
>>> remark #8291: Recommended relationship between field width 'W' and the 
>>> number of fractional digits 'D' in this edit descriptor is 'W>=D+7'.
>>>
>>>          write (io_unit, "(a,t73,es8.2)") "performance (batched): total 
>>> number of flops:", real(nflop_sum*numnodes)
>>>
>>> -----------------------------------^
>>>
>>> [ 98%] *Linking Fortran executable dbcsr_tensor_example_1*
>>>
>>> [ 98%] Built target dbcsr_tensor_example_1
>>>
>>> [ 98%] Building CXX object 
>>> examples/CMakeFiles/dbcsr_example_3_cpp.dir/dbcsr_example_3.cpp.o
>>>
>>> [ 98%] *Linking Fortran executable dbcsr_example_3_cpp*
>>>
>>> CMakeFiles/dbcsr_example_3_cpp.dir/dbcsr_example_3.cpp.o: In function 
>>> `main':
>>>
>>> /qscratch/bpoudel/apps/dbcsr/examples/dbcsr_example_3.cpp:34: multiple 
>>> definition of `main'
>>>
>>> /projects/global/toss4/compilers/intel/intel_2021/oneapi/compiler/2021.3.0/linux/bin/intel64/../../compiler/lib/intel64_lin/for_main.o:for_main.c:(.text+0x0): 
>>> first defined here
>>>
>>> /projects/global/toss4/compilers/intel/intel_2021/oneapi/compiler/2021.3.0/linux/bin/intel64/../../compiler/lib/intel64_lin/for_main.o: 
>>> In function `main':
>>>
>>> for_main.c:(.text+0x2e): undefined reference to `MAIN__'
>>>
>>> make[2]: *** 
>>> [examples/CMakeFiles/dbcsr_example_3_cpp.dir/build.make:109: 
>>> examples/dbcsr_example_3_cpp] Error 1
>>>
>>> make[1]: *** [CMakeFiles/Makefile2:1638: 
>>> examples/CMakeFiles/dbcsr_example_3_cpp.dir/all] Error 2
>>>
>>> make: *** [Makefile:146: all] Error 2
>>>
>>>
>>>
>>> I do not know how to sort this out. 
>>>
>>>
>>> Please let me know what more information you want to know about the cp2k 
>>> installation.
>>>
>>>
>>> Thank You
>>>
>>> Bharat
>>>
>>>
>>>
>>>
>>> On Friday, August 23, 2024 at 2:14:13 AM UTC-6 Johann Pototschnig wrote:
>>>
>>>> Hi Bharart,
>>>>
>>>> This is an error related to the *dbcsr *module.
>>>>
>>>> Some additional information about your installation would be useful:
>>>>
>>>> - Which version of CP2K are you trying to install?
>>>> -What is the version of OpenMPI?
>>>>
>>>> You can also try to installing DBCSR(https://github.com/cp2k/dbcsr) 
>>>> separately and provide the path via --with-dbcsr=/path/ 
>>>>
>>>>
>>>> On Thursday, August 22, 2024 at 9:53:26 PM UTC+2 bharat poudel wrote:
>>>>
>>>>>
>>>>> Here is more info:
>>>>>
>>>>> /usr/bin/env python3 
>>>>> /qscratch/bpoudel/apps/cp2k/exts/dbcsr/tools/build_utils/fypp/bin/fypp -n 
>>>>> --line-marker-format=gfortran5 
>>>>> /qscratch/bpoudel/apps/cp2k/exts/dbcsr/src/base/dbcsr_machine.F 
>>>>> dbcsr_machine.F90
>>>>>
>>>>> /usr/bin/env python3 
>>>>> /qscratch/bpoudel/apps/cp2k/exts/dbcsr/tools/build_utils/fypp/bin/fypp -n 
>>>>> --line-marker-format=gfortran5 
>>>>> /qscratch/bpoudel/apps/cp2k/exts/dbcsr/src/base/dbcsr_machine.F 
>>>>> dbcsr_machine.F90
>>>>>
>>>>> /qscratch/bpoudel/apps/cp2k/tools/toolchain/install/openmpi-5.0.5/bin/mpifort 
>>>>> -c -fno-omit-frame-pointer -fopenmp -g -march=native -mtune=native  -O1   
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/openmpi-5.0.5/include'  
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/openblas-0.3.28/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/fftw-3.3.10/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/libxc-6.2.2/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/libgrpp-main-20231225/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/libxsmm-1.17/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/COSMA-2.6.6/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/scotch-6.0.0/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/superlu_dist-6.1.0/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/pexsi-1.2.0/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/gsl-2.7/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/libdeepmd_c-2.2.7/include' 
>>>>> -I/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/hdf5-1.14.2/include 
>>>>> -I/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/libvdwxc-0.4.0/include 
>>>>> -I/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/spglib-2.3.1/include 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/SpFFT-1.1.0/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/SpLA-1.6.1/include/spla' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/dftd4-3.6.0/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/dftd4-3.6.0/include/dftd4/GNU-14.1.0' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/dftd4-3.6.0/include/mctc-lib/GNU-14.1.0' 
>>>>> -fbacktrace -ffree-form -fimplicit-none -std=f2008 -fsanitize=leak 
>>>>> -fcheck=all,no-array-temps -ffpe-trap=invalid,zero,overflow -finit-derived 
>>>>> -finit-real=snan -finit-integer=-42 -Werror=realloc-lhs 
>>>>> -finline-matmul-limit=0 -Werror=aliasing -Werror=ampersand 
>>>>> -Werror=c-binding-type -Werror=intrinsic-shadow -Werror=intrinsics-std 
>>>>> -Werror=line-truncation -Werror=tabs -Werror=target-lifetime 
>>>>> -Werror=underflow -Werror=unused-but-set-variable -Werror=unused-variable 
>>>>> -Werror=unused-dummy-argument -Werror=unused-parameter -Werror=unused-label 
>>>>> -Werror=conversion -Werror=zerotrip -Wno-maybe-uninitialized 
>>>>> -Wuninitialized -Wuse-without-only  -D__LIBXSMM  -D__parallel -D__MPI_F08 
>>>>> -D__FFTW3  -D__LIBINT -D__LIBXC -D__LIBGRPP -D__parallel -D__COSMA 
>>>>> -D__LIBPEXSI -D__GSL -D__PLUMED2 -D__DEEPMD -D__HDF5 -D__LIBVDWXC 
>>>>> -D__SPGLIB -D__LIBVORI -D__LIBTORCH -D__SPFFT    -D__SPLA -D__DFTD4 
>>>>> -D__HAS_IEEE_EXCEPTIONS -D__CHECK_DIAG  -fallow-argument-mismatch 
>>>>> -D__SHORT_FILE__="\"dbcsr_machine.F\"" 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/exts/dbcsr/src/base/' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/exts/dbcsr/src' dbcsr_machine.F90 
>>>>>
>>>>> /qscratch/bpoudel/apps/cp2k/tools/toolchain/install/openmpi-5.0.5/bin/mpifort 
>>>>> -c -fno-omit-frame-pointer -fopenmp -g -march=native -mtune=native  -O3 
>>>>> -funroll-loops   
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/openmpi-5.0.5/include'  
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/openblas-0.3.28/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/fftw-3.3.10/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/libxc-6.2.2/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/libgrpp-main-20231225/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/libxsmm-1.17/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/COSMA-2.6.6/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/scotch-6.0.0/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/superlu_dist-6.1.0/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/pexsi-1.2.0/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/gsl-2.7/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/libdeepmd_c-2.2.7/include' 
>>>>> -I/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/hdf5-1.14.2/include 
>>>>> -I/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/libvdwxc-0.4.0/include 
>>>>> -I/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/spglib-2.3.1/include 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/SpFFT-1.1.0/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/SpLA-1.6.1/include/spla' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/dftd4-3.6.0/include' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/dftd4-3.6.0/include/dftd4/GNU-14.1.0' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/tools/toolchain/install/dftd4-3.6.0/include/mctc-lib/GNU-14.1.0' 
>>>>> -fbacktrace -ffree-form -fimplicit-none -std=f2008  -Werror=aliasing 
>>>>> -Werror=ampersand -Werror=c-binding-type -Werror=intrinsic-shadow 
>>>>> -Werror=intrinsics-std -Werror=line-truncation -Werror=tabs 
>>>>> -Werror=target-lifetime -Werror=underflow -Werror=unused-but-set-variable 
>>>>> -Werror=unused-variable -Werror=unused-dummy-argument 
>>>>> -Werror=unused-parameter -Werror=unused-label -Werror=conversion 
>>>>> -Werror=zerotrip -Wno-maybe-uninitialized -Wuninitialized 
>>>>> -Wuse-without-only  -D__LIBXSMM  -D__parallel -D__MPI_F08 -D__FFTW3  
>>>>> -D__LIBINT -D__LIBXC -D__LIBGRPP -D__parallel -D__COSMA -D__LIBPEXSI 
>>>>> -D__GSL -D__PLUMED2 -D__DEEPMD -D__HDF5 -D__LIBVDWXC -D__SPGLIB -D__LIBVORI 
>>>>> -D__LIBTORCH -D__SPFFT    -D__SPLA -D__DFTD4   -fallow-argument-mismatch 
>>>>> -D__SHORT_FILE__="\"dbcsr_machine.F\"" 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/exts/dbcsr/src/base/' 
>>>>> -I'/qscratch/bpoudel/apps/cp2k/exts/dbcsr/src' dbcsr_machine.F90 
>>>>>
>>>>>
>>>>> my gcc version is 14.1.0
>>>>> On Thursday, August 22, 2024 at 1:44:42 PM UTC-6 bharat poudel wrote:
>>>>>
>>>>>> Hi There
>>>>>>
>>>>>> I encountered this error while installing CP2K.
>>>>>>
>>>>>> *f951:* *Fatal Error:* Reading module ‘*dbcsr_kinds.mod*’ at line 1 
>>>>>> column 2: Unexpected EOF
>>>>>>
>>>>>> compilation terminated.
>>>>>>
>>>>>> make[4]: *** 
>>>>>> [/qscratch/bpoudel/apps/cp2k/exts/build_dbcsr//Makefile:266: 
>>>>>> dbcsr_machine.o] Error 1
>>>>>>
>>>>>> make[3]: *** 
>>>>>> [/qscratch/bpoudel/apps/cp2k/exts/build_dbcsr/Makefile:187: libdbcsr] Error 
>>>>>> 2
>>>>>>
>>>>>> make[2]: *** [/qscratch/bpoudel/apps/cp2k/exts/Makefile.inc:38: 
>>>>>> dbcsr] Error 2
>>>>>>
>>>>>> make[2]: *** Waiting for unfinished jobs....
>>>>>>
>>>>>> *f951:* *Fatal Error:* Reading module ‘*dbcsr_kinds.mod*’ at line 1 
>>>>>> column 2: Unexpected EOF
>>>>>>
>>>>>> compilation terminated.
>>>>>>
>>>>>>
>>>>>> It looks like this one is related to fortran. I am installing it on 
>>>>>> the cluster with openmpi and plumed.
>>>>>>
>>>>>>
>>>>>> Really looking forward for the help.
>>>>>>
>>>>>>
>>>>>> Bharat
>>>>>>
>>>>>

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