CP2k Installation Error

bharat poudel

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Aug 22, 2024, 3:44:42 PM8/22/24

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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

bharat poudel

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Aug 22, 2024, 3:53:26 PM8/22/24

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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

/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

Johann Pototschnig

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Aug 23, 2024, 4:14:13 AM8/23/24

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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/

bharat poudel

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Aug 23, 2024, 2:21:28 PM8/23/24

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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

bharat poudel

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Aug 23, 2024, 2:30:07 PM8/23/24

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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

Frederick Stein

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Aug 24, 2024, 8:06:15 AM8/24/24

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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

Sagnik Mukhopadhyay

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Aug 26, 2024, 8:21:48 AM8/26/24

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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

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