[CP2K-user] [CP2K:20616] Re: CP2k Installation Error

Frederick Stein f.stein at hzdr.de
Sat Aug 24 12:06:15 UTC 2024
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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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