CP2K version 2023.2 compile error

Jin-Soo Kim

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Sep 21, 2023, 1:55:16 AM9/21/23

to cp2k

Dear users and developers,

I am trying to install CP2K version 2023.2 but continuosly failed.

According to the installation instruction (https://github.com/cp2k/cp2k/blob/master/INSTALL.md),

I acquired the code, and ran toolchain script. (I couldn't install Docker container on my Linux CentOS 8 system)

I typed below commands:

cd cp2k-2023.2/tools/toolchain
./install_cp2k_toolchain.sh

Then I got below message:

----------------------------------------------------------

Done!
Now copy:
cp /home/jinsookim/cp2k-2023.2/tools/toolchain/install/arch/* to the cp2k/arch/ directory
To use the installed tools and libraries and cp2k version
compiled with it you will first need to execute at the prompt:
source /home/jinsookim/cp2k-2023.2/tools/toolchain/install/setup
To build CP2K you should change directory:
cd cp2k/
make -j 64 ARCH=local VERSION="ssmp sdbg psmp pdbg"

arch files for GPU enabled CUDA versions are named "local_cuda.*"
arch files for GPU enabled HIP versions are named "local_hip.*"
arch files for OpenCL (GPU) versions are named "local_opencl.*"
arch files for coverage versions are named "local_coverage.*"

Note that these pre-built arch files are for the GNU compiler, users have to adapt them for other compilers.
It is possible to use the provided CP2K arch files as guidance.

-------------------------------------------------------------------------------------------------------------------

Then I followed the instructions.

However, when I type the command

make -j 64 ARCH=local VERSION="ssmp sdbg psmp pdbg"

it seems everything goes well at first, but soon I got error message below:

----------------------------------------------------------------------------------------------------------------------------------

/home/jinsookim/cp2k/src/csvr_system_types.F(42): error #6959: The array constructor must be a constant. [RNG_STREAM_TYPE]
TYPE(rng_stream_type) :: gaussian_rng_stream = rng_stream_type()
-----------------------------------------------------------------------^
/home/jinsookim/cp2k/tools/build_utils/fypp -n /home/jinsookim/cp2k/src/pao_ml_gaussprocess.F pao_ml_gaussprocess.F90
compilation aborted for csvr_system_types.F90 (code 1)
make[3]: *** [/home/jinsookim/cp2k/Makefile:515: csvr_system_types.o] Error 1
make[3]: *** Waiting for unfinished jobs....
/opt/intel/oneapi/mpi/2021.10.0/bin/mpiifort -fc=ifort -c -fPIC -fp-model=precise -g -qopenmp -traceback -xHost -O2 -funroll-loops -m64 -I/opt/intel/oneapi/mkl/2023.2.0/include -I'/home/jinsookim/cp2k/tools/toolchain/install/fftw-3.3.10/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/libxc-6.2.2/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/libxsmm-1.17/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/COSMA-2.6.6/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/elpa-2023.05.001/cpu/include/elpa_openmp-2023.05.001/modules' -I'/home/jinsookim/cp2k/tools/toolchain/install/elpa-2023.05.001/cpu/include/elpa_openmp-2023.05.001/elpa' -I'/home/jinsookim/cp2k/tools/toolchain/install/gsl-2.7/include' -I/home/jinsookim/cp2k/tools/toolchain/install/hdf5-1.12.0/include -I/home/jinsookim/cp2k/tools/toolchain/install/libvdwxc-0.4.0/include -I/home/jinsookim/cp2k/tools/toolchain/install/spglib-1.16.2/include -I'/home/jinsookim/cp2k/tools/toolchain/install/SpFFT-1.0.6/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/SpLA-1.5.5/include/spla' -I/home/jinsookim/cp2k/tools/toolchain/install/sirius-7.4.3/include -D__LIBXSMM -D__parallel -D__MPI_F08 -D__MKL -D__FFTW3 -D__SCALAPACK -D__FFTW3 -D__LIBINT -D__LIBXC -D__COSMA -D__ELPA -D__GSL -D__HDF5 -D__LIBVDWXC -D__SPGLIB -D__LIBVORI -D__SPFFT -D__SPLA -D__SIRIUS -diag-disable=8291 -diag-disable=8293 -fpp -fpscomp logicals -free -D__COMPILE_ARCH="\"local\"" -D__COMPILE_DATE="\"Thu Sep 21 14:40:36 KST 2023\"" -D__COMPILE_HOST="\"master\"" -D__COMPILE_REVISION="\"git:6a2264c\"" -D__DATA_DIR="\"/home/jinsookim/cp2k/data\"" -D__SHORT_FILE__="\"pao_ml_neuralnet.F\"" -I'/home/jinsookim/cp2k/src/' -I'/home/jinsookim/cp2k/obj/local/psmp/exts/dbcsr' pao_ml_neuralnet.F90
/opt/intel/oneapi/mpi/2021.10.0/bin/mpiifort -fc=ifort -c -fPIC -fp-model=precise -g -qopenmp -traceback -xHost -O2 -funroll-loops -m64 -I/opt/intel/oneapi/mkl/2023.2.0/include -I'/home/jinsookim/cp2k/tools/toolchain/install/fftw-3.3.10/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/libxc-6.2.2/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/libxsmm-1.17/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/COSMA-2.6.6/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/elpa-2023.05.001/cpu/include/elpa_openmp-2023.05.001/modules' -I'/home/jinsookim/cp2k/tools/toolchain/install/elpa-2023.05.001/cpu/include/elpa_openmp-2023.05.001/elpa' -I'/home/jinsookim/cp2k/tools/toolchain/install/gsl-2.7/include' -I/home/jinsookim/cp2k/tools/toolchain/install/hdf5-1.12.0/include -I/home/jinsookim/cp2k/tools/toolchain/install/libvdwxc-0.4.0/include -I/home/jinsookim/cp2k/tools/toolchain/install/spglib-1.16.2/include -I'/home/jinsookim/cp2k/tools/toolchain/install/SpFFT-1.0.6/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/SpLA-1.5.5/include/spla' -I/home/jinsookim/cp2k/tools/toolchain/install/sirius-7.4.3/include -D__LIBXSMM -D__parallel -D__MPI_F08 -D__MKL -D__FFTW3 -D__SCALAPACK -D__FFTW3 -D__LIBINT -D__LIBXC -D__COSMA -D__ELPA -D__GSL -D__HDF5 -D__LIBVDWXC -D__SPGLIB -D__LIBVORI -D__SPFFT -D__SPLA -D__SIRIUS -diag-disable=8291 -diag-disable=8293 -fpp -fpscomp logicals -free -D__COMPILE_ARCH="\"local\"" -D__COMPILE_DATE="\"Thu Sep 21 14:40:36 KST 2023\"" -D__COMPILE_HOST="\"master\"" -D__COMPILE_REVISION="\"git:6a2264c\"" -D__DATA_DIR="\"/home/jinsookim/cp2k/data\"" -D__SHORT_FILE__="\"pao_ml_gaussprocess.F\"" -I'/home/jinsookim/cp2k/src/' -I'/home/jinsookim/cp2k/obj/local/psmp/exts/dbcsr' pao_ml_gaussprocess.F90
/opt/intel/oneapi/mpi/2021.10.0/bin/mpiifort -fc=ifort -c -fPIC -fp-model=precise -g -qopenmp -traceback -xHost -O2 -funroll-loops -m64 -I/opt/intel/oneapi/mkl/2023.2.0/include -I'/home/jinsookim/cp2k/tools/toolchain/install/fftw-3.3.10/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/libxc-6.2.2/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/libxsmm-1.17/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/COSMA-2.6.6/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/elpa-2023.05.001/cpu/include/elpa_openmp-2023.05.001/modules' -I'/home/jinsookim/cp2k/tools/toolchain/install/elpa-2023.05.001/cpu/include/elpa_openmp-2023.05.001/elpa' -I'/home/jinsookim/cp2k/tools/toolchain/install/gsl-2.7/include' -I/home/jinsookim/cp2k/tools/toolchain/install/hdf5-1.12.0/include -I/home/jinsookim/cp2k/tools/toolchain/install/libvdwxc-0.4.0/include -I/home/jinsookim/cp2k/tools/toolchain/install/spglib-1.16.2/include -I'/home/jinsookim/cp2k/tools/toolchain/install/SpFFT-1.0.6/include' -I'/home/jinsookim/cp2k/tools/toolchain/install/SpLA-1.5.5/include/spla' -I/home/jinsookim/cp2k/tools/toolchain/install/sirius-7.4.3/include -D__LIBXSMM -D__parallel -D__MPI_F08 -D__MKL -D__FFTW3 -D__SCALAPACK -D__FFTW3 -D__LIBINT -D__LIBXC -D__COSMA -D__ELPA -D__GSL -D__HDF5 -D__LIBVDWXC -D__SPGLIB -D__LIBVORI -D__SPFFT -D__SPLA -D__SIRIUS -diag-disable=8291 -diag-disable=8293 -fpp -fpscomp logicals -free -D__COMPILE_ARCH="\"local\"" -D__COMPILE_DATE="\"Thu Sep 21 14:40:36 KST 2023\"" -D__COMPILE_HOST="\"master\"" -D__COMPILE_REVISION="\"git:6a2264c\"" -D__DATA_DIR="\"/home/jinsookim/cp2k/data\"" -D__SHORT_FILE__="\"pao_input.F\"" -I'/home/jinsookim/cp2k/src/' -I'/home/jinsookim/cp2k/obj/local/psmp/exts/dbcsr' pao_input.F90
make[2]: *** [/home/jinsookim/cp2k/Makefile:146: all] Error 2
make[1]: *** [/home/jinsookim/cp2k/Makefile:128: sdbg] Error 2
make[1]: *** Waiting for unfinished jobs....
make[2]: *** [/home/jinsookim/cp2k/Makefile:146: all] Error 2
make[1]: *** [/home/jinsookim/cp2k/Makefile:128: pdbg] Error 2
make[2]: *** [/home/jinsookim/cp2k/Makefile:146: all] Error 2
make[1]: *** [/home/jinsookim/cp2k/Makefile:128: ssmp] Error 2
make[2]: *** [/home/jinsookim/cp2k/Makefile:146: all] Error 2
make[1]: *** [/home/jinsookim/cp2k/Makefile:128: psmp] Error 2
make: *** [Makefile:123: all] Error 2

---------------------------------------------------------------------------------------------------------------------------------------

I don't know what to do next. Please help me~~~

Akash Mishra

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Sep 21, 2023, 1:57:09 AM9/21/23

to cp...@googlegroups.com

You can use spack to install cp2k along with its dependencies.

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Jin-Soo Kim

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Sep 21, 2023, 3:13:14 AM9/21/23

to cp2k

Thank you for anwering my question, Mishra.

But how can I use spack to install cp2k along with its dependencies?
First, I installed spack by typing

git clone https://github.com/spack/spack.git

. spack/share/spack/setup-env.sh

and then I setup compilers by typing

spack compiler find

spack compilers

Then I got below message:

-----------------------------------------------------------------------------------------------------------

==> Available compilers
-- dpcpp centos8-x86_64 -----------------------------------------
dp...@2023.2.0

-- gcc centos8-x86_64 -------------------------------------------
g...@8.3.1

-- intel centos8-x86_64 -----------------------------------------
in...@19.0.4.243

-- oneapi centos8-x86_64 ----------------------------------------
one...@2023.2.0

------------------------------------------------------------------------------------------------------------------

I don't know what to do next. How can I use spack to install cp2k along with its dependencies?

edf

T

Akash Mishra

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Sep 21, 2023, 3:22:01 AM9/21/23

to cp...@googlegroups.com

Hi I am sharing install script for g...@13.1.0

“spack -d install cp2k@2023.1+elpa %g...@13.1.0 target=zen4 ^amdfftw@4.1 ^amdscalapack@4.1 ^amdblis@4.1 ^amdlibflame@4.1 ^elpa+openmp ^ope...@4.1.4 fabrics=auto"

And if you want default dependencies just use below

"spack -d install cp2k@2023.1+elpa %g...@13.1.0 target=zen4 ^elpa+openmp ^ope...@4.1.4 fabrics=auto"

Please note the above script is for running on AMD genoa architecture , you can modify accordingly.

you can also check what all components getting installed using below command

"spack spec cp2k@2023.1+elpa %g...@13.1.0 target=zen4 ^amdfftw@4.1 ^amdscalapack@4.1 ^amdblis@4.1 ^amdlibflame@4.1 ^elpa+openmp ^ope...@4.1.4 fabrics=auto"

Regards

Akash Mishra

To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/3abebf4b-a429-4fb9-8339-8a2c36f589a9n%40googlegroups.com.

Jin-Soo Kim

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Sep 21, 2023, 10:27:50 PM9/21/23

to cp2k

Thank you for helping me, Mishra.

However, I still got problems.

I modified the script according to my architecture, as below:
"spack -d install cp2k@2023.1+elpa %g...@8.3.1 target=icelake ^elpa+openmp ^ope...@4.1.4 fabrics=auto"
Then I got very, very long error message below and I dont' know what is the reason.

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

==> [2023-09-22-11:22:05.969419] Error: ProcessError: Command exited with status 2:
'make' '-j16' 'ARCH=linux-centos8-icelake-gcc' 'VERSION=psmp'

7 errors found in build log:
285 /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/openmpi-4.1.4-x2zlwc4kg7zinapxtgbumkws3nbxeqsy/bin/mpicc -c -O2 -funroll-loops -ftree-vectorize -std=c99 -fopenmp -D__FFTW3 -
I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/fftw-3.3.10-2hpr2p625gonzgytdjctpjwbmigjofnv/include -D__parallel -D__SCALAPACK -D__LIBINT -D__LIBXC -D__ELPA=202305 -D__LIB
XSMM /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/src/pw/fpga/fft_fpga.c
286 /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/openmpi-4.1.4-x2zlwc4kg7zinapxtgbumkws3nbxeqsy/bin/mpicc -c -O2 -funroll-loops -ftree-vectorize -std=c99 -fopenmp -D__FFTW3 -
I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/fftw-3.3.10-2hpr2p625gonzgytdjctpjwbmigjofnv/include -D__parallel -D__SCALAPACK -D__LIBINT -D__LIBXC -D__ELPA=202305 -D__LIB
XSMM /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/src/pw/fpga/opencl_utils.c
287 /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/openmpi-4.1.4-x2zlwc4kg7zinapxtgbumkws3nbxeqsy/bin/mpicc -c -O2 -funroll-loops -ftree-vectorize -std=c99 -fopenmp -D__FFTW3 -
I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/fftw-3.3.10-2hpr2p625gonzgytdjctpjwbmigjofnv/include -D__parallel -D__SCALAPACK -D__LIBINT -D__LIBXC -D__ELPA=202305 -D__LIB
XSMM /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/src/grid/grid_unittest.c
288 /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/tools/build_utils/fypp -n /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jl
r5tzdtflpir7b4/spack-src/src/motion/dumpdcd.F dumpdcd.F90
289 /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/tools/build_utils/fypp -n /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jl
r5tzdtflpir7b4/spack-src/src/xc/xc_input_constants.F xc_input_constants.F90
290 echo git:b888bd8 > "/tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/obj/git-ref.tmp"
>> 291 cmp: /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/obj/git-ref: No such file or directory
292 /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/tools/build_utils/fypp -n /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jl
r5tzdtflpir7b4/spack-src/src/shg_int/constants_operator.F constants_operator.F90
293 /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/tools/build_utils/fypp -n /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jl
r5tzdtflpir7b4/spack-src/src/pilaenv_hack.F pilaenv_hack.F90
294 /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/openmpi-4.1.4-x2zlwc4kg7zinapxtgbumkws3nbxeqsy/bin/mpicc -c -O2 -funroll-loops -ftree-vectorize -std=c99 -fopenmp -D__FFTW3 -
I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/fftw-3.3.10-2hpr2p625gonzgytdjctpjwbmigjofnv/include -D__parallel -D__SCALAPACK -D__LIBINT -D__LIBXC -D__ELPA=202305 -D__LIB
XSMM /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/src/sockets.c
295 /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/openmpi-4.1.4-x2zlwc4kg7zinapxtgbumkws3nbxeqsy/bin/mpic++ -c -O2 -funroll-loops -ftree-vectorize -fopenmp -std=c++14 -D__FFTW
3 -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/fftw-3.3.10-2hpr2p625gonzgytdjctpjwbmigjofnv/include -D__parallel -D__SCALAPACK -D__LIBINT -D__LIBXC -D__ELPA=202305 -D__
LIBXSMM /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/src/torch_c_api.cpp
296 /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/tools/build_utils/fypp -n /tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jl
r5tzdtflpir7b4/spack-src/src/motion/xyz2dcd.F xyz2dcd.F90
297 /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/openmpi-4.1.4-x2zlwc4kg7zinapxtgbumkws3nbxeqsy/bin/mpif90 -c -O2 -funroll-loops -ftree-vectorize -ffree-form -ffree-line-leng
th-none -ggdb -fopenmp -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/libint-2.6.0-shapdij3gtg76l247st25r52d6bc5z3a/include -I/home/jinsookim/spack/opt/spack/linux-centos
8-icelake/gcc-8.3.1/libint-2.6.0-shapdij3gtg76l247st25r52d6bc5z3a/include/libint2 -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/boost-1.83.0-54x73sz6kfsr3v5nbj6toxhd7kpn
2ca2/include -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/libxc-6.2.2-s6ohccoi6hfgttsr2gz33cvvnginqb26/include -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/g
cc-8.3.1/elpa-2023.05.001-5y43sykgnczw5witjkbugfvssy2zspyl/include/elpa_openmp-2023.05.001/modules -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/elpa-2023.05.001-5y43syk
gnczw5witjkbugfvssy2zspyl/include/elpa_openmp-2023.05.001/elpa -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/libxsmm-1.17-ism3t6ngf365gk5vs7wc5wmcdml2jfoc/include -D__FF
TW3 -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/fftw-3.3.10-2hpr2p625gonzgytdjctpjwbmigjofnv/include -D__parallel -D__SCALAPACK -D__LIBINT -D__LIBXC -D__ELPA=202305 -D
__LIBXSMM -D__COMPILE_ARCH="\"linux-centos8-icelake-gcc\"" -D__COMPILE_DATE="\"Fri Sep 22 11:21:07 KST 2023\"" -D__COMPILE_HOST="\"master\"" -D__COMPILE_REVISION="\"git:b888bd8\"" -D__DATA_
DIR="\"/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/share/data\"" -D__SHORT_FILE__="\"motion/dumpdcd.F\"" -I'/tmp/jinsookim/s
pack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/src/motion/' -I'/tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/o
bj/linux-centos8-icelake-gcc/psmp/exts/dbcsr' dumpdcd.F90

...

827 /usr/bin/ld: /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/libxsmm-1.17-ism3t6ngf365gk5vs7wc5wmcdml2jfoc/lib/libxsmmf.a(libxsmm-mod.o): unable to initialize decompress sta
tus for section .debug_info
828 /usr/bin/ld: /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/libxsmm-1.17-ism3t6ngf365gk5vs7wc5wmcdml2jfoc/lib/libxsmmf.a(libxsmm-mod.o): unable to initialize decompress sta
tus for section .debug_info
829 /usr/bin/ld: /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/libxsmm-1.17-ism3t6ngf365gk5vs7wc5wmcdml2jfoc/lib/libxsmm.a(libxsmm_main.o): unable to initialize decompress sta
tus for section .debug_info
830 /usr/bin/ld: /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/libxsmm-1.17-ism3t6ngf365gk5vs7wc5wmcdml2jfoc/lib/libxsmm.a(libxsmm_main.o): unable to initialize decompress sta
tus for section .debug_info
831 /usr/bin/ld: /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/libxsmm-1.17-ism3t6ngf365gk5vs7wc5wmcdml2jfoc/lib/libxsmm.a(libxsmm_main.o): unable to initialize decompress sta
tus for section .debug_info
832 /usr/bin/ld: /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/libxsmm-1.17-ism3t6ngf365gk5vs7wc5wmcdml2jfoc/lib/libxsmm.a(libxsmm_main.o): unable to initialize decompress sta
tus for section .debug_info
>> 833 /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/libxsmm-1.17-ism3t6ngf365gk5vs7wc5wmcdml2jfoc/lib/libxsmm.a: error adding symbols: File format not recognized
>> 834 collect2: error: ld returned 1 exit status
>> 835 make[3]: *** [/tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/obj/linux-centos8-icelake-gcc/psmp/all.dep:156: /tmp/jinsookim/spack-stage/spack-
stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/exe/linux-centos8-icelake-gcc/graph.psmp] Error 1
836 make[3]: *** Waiting for unfinished jobs....
837 /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/openmpi-4.1.4-x2zlwc4kg7zinapxtgbumkws3nbxeqsy/bin/mpif90 -c -O2 -funroll-loops -ftree-vectorize -ffree-form -ffree-line-leng
th-none -ggdb -fopenmp -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/libint-2.6.0-shapdij3gtg76l247st25r52d6bc5z3a/include -I/home/jinsookim/spack/opt/spack/linux-centos
8-icelake/gcc-8.3.1/libint-2.6.0-shapdij3gtg76l247st25r52d6bc5z3a/include/libint2 -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/boost-1.83.0-54x73sz6kfsr3v5nbj6toxhd7kpn
2ca2/include -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/libxc-6.2.2-s6ohccoi6hfgttsr2gz33cvvnginqb26/include -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/g
cc-8.3.1/elpa-2023.05.001-5y43sykgnczw5witjkbugfvssy2zspyl/include/elpa_openmp-2023.05.001/modules -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/elpa-2023.05.001-5y43syk
gnczw5witjkbugfvssy2zspyl/include/elpa_openmp-2023.05.001/elpa -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/libxsmm-1.17-ism3t6ngf365gk5vs7wc5wmcdml2jfoc/include -D__FF
TW3 -I/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/fftw-3.3.10-2hpr2p625gonzgytdjctpjwbmigjofnv/include -D__parallel -D__SCALAPACK -D__LIBINT -D__LIBXC -D__ELPA=202305 -D
__LIBXSMM -D__COMPILE_ARCH="\"linux-centos8-icelake-gcc\"" -D__COMPILE_DATE="\"Fri Sep 22 11:21:18 KST 2023\"" -D__COMPILE_HOST="\"master\"" -D__COMPILE_REVISION="\"git:b888bd8\"" -D__DATA_
DIR="\"/home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/share/data\"" -D__SHORT_FILE__="\"eri_mme/eri_mme_lattice_summation.F\""
-I'/tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/src/eri_mme/' -I'/tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdt
flpir7b4/spack-src/obj/linux-centos8-icelake-gcc/psmp/exts/dbcsr' eri_mme_lattice_summation.F90
>> 838 make[2]: *** [/tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/Makefile:146: all] Error 2
>> 839 make[1]: *** [/tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-src/Makefile:128: psmp] Error 2
>> 840 make: *** [Makefile:123: all] Error 2

See build log for details:
/tmp/jinsookim/spack-stage/spack-stage-cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4/spack-build-out.txt

Traceback (most recent call last):
File "/home/jinsookim/spack/lib/spack/spack/build_environment.py", line 1017, in _setup_pkg_and_run
return_value = function(pkg, kwargs)
File "/home/jinsookim/spack/lib/spack/spack/installer.py", line 2512, in build_process
return installer.run()
File "/home/jinsookim/spack/lib/spack/spack/installer.py", line 2376, in run
self._real_install()
File "/home/jinsookim/spack/lib/spack/spack/installer.py", line 2472, in _real_install
phase_fn.execute()
File "/home/jinsookim/spack/lib/spack/spack/builder.py", line 433, in execute
self.phase_fn(pkg, pkg.spec, pkg.prefix)
File "/home/jinsookim/spack/lib/spack/spack/builder.py", line 309, in _adapter
return phase_fn(spec, prefix)
File "/home/jinsookim/spack/var/spack/repos/builtin/packages/cp2k/package.py", line 835, in build
File "/home/jinsookim/spack/lib/spack/spack/builder.py", line 152, in __forward
return self.__getattr__(fn_name)(*args, **kwargs)
File "/home/jinsookim/spack/lib/spack/spack/builder.py", line 72, in __call__
return self.phase_fn(self.builder.pkg, spec, prefix)
File "/home/jinsookim/spack/lib/spack/spack/build_systems/makefile.py", line 102, in build
inspect.getmodule(self.pkg).make(*self.build_targets)
File "/home/jinsookim/spack/lib/spack/spack/build_environment.py", line 178, in __call__
return super().__call__(*args, **kwargs)
File "/home/jinsookim/spack/lib/spack/spack/util/executable.py", line 231, in __call__
raise ProcessError("Command exited with status %d:" % proc.returncode, long_msg)
spack.util.executable.ProcessError: Command exited with status 2:
'make' '-j16' 'ARCH=linux-centos8-icelake-gcc' 'VERSION=psmp'
==> [2023-09-22-11:22:06.898531] Flagging cp2k-2023.1-jblwsfketn2lmlt3jlr5tzdtflpir7b4 as failed: ProcessError: Command exited with status 2:
'make' '-j16' 'ARCH=linux-centos8-icelake-gcc' 'VERSION=psmp'
==> [2023-09-22-11:22:06.909504] ChildError: ProcessError: Command exited with status 2:
'make' '-j16' 'ARCH=linux-centos8-icelake-gcc' 'VERSION=psmp'

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Akash Mishra

unread,

Sep 25, 2023, 2:30:08 AM9/25/23

to cp...@googlegroups.com

Can you upgrade the compiler like g...@13.1.0 and check.

To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/1e2abf57-f4cc-4e67-ae0b-6bc2722da394n%40googlegroups.com.

Mario A Bianchet

unread,

Oct 20, 2023, 3:22:05 PM10/20/23

to cp2k

Hi

Have the same problem in gcc@12.3. Any solution to it?

Thanks

Message has been deleted

Matthias Heyden

unread,

Nov 11, 2023, 9:09:41 AM11/11/23

to cp2k

Hi,
The error described above:

>> 833 /home/jinsookim/spack/opt/spack/linux-centos8-icelake/gcc-8.3.1/libxsmm-1.17-ism3t6ngf365gk5vs7wc5wmcdml2jfoc/lib/libxsmm.a: error adding symbols: File format not recognized

is caused by a broken build of the libxsmm library for small matrix multiplications. The build for libxsmm by spack breaks, because it is not using the right binutils.
See also:
https://github.com/libxsmm/libxsmm/issues/652
https://github.com/spack/spack/issues/28404

There are two workarounds to this:
1. install cp2k without libxsmm (using blas instead)
spack install cp2k smm=blas (add any other specification details and options)
Note, that this will likely cost you significant performance (depending on what you do with cp2k). In my case, compute times increase by a factor of 4.

2. Build with functional libxsmm (not fully successful, see below)
First, uninstall the broken libxsmm library built by spack
spack uninstall libxsmm
Now built binutils as specified in the link above (https://github.com/libxsmm/libxsmm/issues/652)
spack install binutils+ld+gas
Now make sure that these bintutils are used by your system in your next attempt to build libxsmm and cp2k.
A simple solution is to add the corresponding bin directory to the start of your PATH environment variable to make sure they are used. (this can be achieved in many other ways, too).
In my case:
export PATH=/home/mheyden/src/spack/opt/spack/linux-ubuntu18.04-zen/gcc-13.1.0/binutils-2.41-lm4zu5gvi5uj2kodjfrvwtmzadyaczq3/bin:$PATH
Now built a functional libxsmm library:
spack install libxsmm blas=0
Note: cp2k would not compile without the added blas=0 option. libxsmm seems to include fallback calls to blas otherwise, but this dependency doesn't seem to have been included in the spack package (speculation).
Now install cp2k:
spack install cp2k (add any other specification details and options)
Unsolved problem:
During execution of cp2k this results in almost immediate crashes in my case (aiMD). If you are only using the classical MD part of cp2k, I suspect you'll be fine, but I did not test it.

Solution:
I could not get the spack package for cp2k to work with libxsmm and gave up on it. I went on to compile cp2k using cp2k's own install_cp2k_toolchain. (cp2k-2023.2/tools/toolchain/install_cp2k_toolchain.sh). The latter is essentially doing what spack is supposed to do, but with a curated list of libraries and working compiler instructions (thanks cp2k). There a few minor dependencies I needed to take care of:
sudo apt-get install pkg-config
sudo apt-get install zlib1g-dev

but everything else went smoothly and the resulting cp2k binaries are working and fast.

Hope this is useful.

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