[CP2K-user] [CP2K:20491] Re: Issues Compiling CP2K on HPC

[Frederick Stein]

COSMA and HDF5 (both written in C++) are also used by CP2K but can be 
turned off to build the toolchain.

Johann Pototschnig schrieb am Donnerstag, 25. Juli 2024 um 11:00:07 UTC+2:

> stdio.h is a basic header, since it cannot be found it indicates a problem 
> with the paths of C/C++. 
> With "which gcc" you can check the location of the compiler and then you 
> can check that the include directory is visible. 
>
> The script get_openblas_arch.sh uses openblas routines to identify the 
> architecture of the system, so it would be good if it is excused on the 
> compute nodes. 
>
> There are some dependencies the install script checks and it then 
> activates certain modules. 
> In your case it is probably the sirius module that requires cosma, gsl , 
> hdf5, and activates them. 
> So you should add --with-sirius=no to deactivate the modules. 
> On Wednesday, July 24, 2024 at 5:55:40 PM UTC+2 Lenard Carroll wrote:
>
>> Hi there, I am trying to compile CP2K on an HPC. First, I am loading the 
>> following modules:
>>
>> module load GCC/11.2.0 OpenMPI/4.1.1 FFTW/3.3.10 ELPA/2021.05.001 
>> ScaLAPACK/2.1.0-fb OpenBLAS/0.3.20 imkl/2022.0.1 CMake/3.26.4
>>
>> GCC
>> OpenMPI
>> FFTW
>> ELPA
>> Scalapack
>> Openblas
>> MKL
>> CMake
>>
>> Then I am running the following script with toolchain:
>> bash install_cp2k_toolchain.sh -j 48 --mpi-mode=openmpi --math-mode=mkl 
>> --with-gcc=system --with-libint=no --with-libxsmm=no --with-hdf5=no 
>> --with-spfft=no --with-spla=no --with-cosma=no --with-gsl=no 
>> --with-intel=no --with-cmake=system --with-openmpi=system 
>> --with-fftw=system --with-mkl=system --with-openblas=system 
>> --with-elpa=system --with-scalapack=system > output.log
>>
>> This gives me errors in:
>> getarch.c:80:10: fatal error: stdio.h: No such file or directory
>>    80 | #include <stdio.h>
>>       |          ^~~~~~~~~
>> compilation terminated.
>> make: *** [Makefile.prebuild:100: getarch] Error 1
>> Makefile.system:1546: Makefile.: No such file or directory
>> make: *** No rule to make target 'Makefile.'.  Stop.
>> ERROR: 
>> (/lustre/home/iff/lcarroll/CP2K/cp2k/tools/toolchain/scripts/get_openblas_arch.sh, 
>> line 50) Non-zero exit code detected.
>> ERROR: (./scripts/stage0/setup_buildtools.sh, line 67) Non-zero exit code 
>> detected.
>> /lustre/home/iff/lcarroll/CP2K/cp2k/tools/toolchain/scripts/tool_kit.sh: 
>> line 663: 
>> /lustre/home/iff/lcarroll/CP2K/cp2k/tools/toolchain/install/libxc-6.2.2/install_successful: 
>> No such file or directory
>> /lustre/home/iff/lcarroll/CP2K/cp2k/tools/toolchain/scripts/tool_kit.sh: 
>> line 663: 
>> /lustre/home/iff/lcarroll/CP2K/cp2k/tools/toolchain/install/COSMA-2.6.6/install_successful: 
>> No such file or directory
>> /lustre/home/iff/lcarroll/CP2K/cp2k/tools/toolchain/scripts/tool_kit.sh: 
>> line 663: 
>> /lustre/home/iff/lcarroll/CP2K/cp2k/tools/toolchain/install/gsl-2.7/install_successful: 
>> No such file or directory
>> /lustre/home/iff/lcarroll/CP2K/cp2k/tools/toolchain/scripts/tool_kit.sh: 
>> line 663: 
>> /lustre/home/iff/lcarroll/CP2K/cp2k/tools/toolchain/install/hdf5-1.14.2/install_successful: 
>> No such file or directory
>> /lustre/home/iff/lcarroll/CP2K/cp2k/tools/toolchain/scripts/tool_kit.sh: 
>> line 663: 
>> /lustre/home/iff/lcarroll/CP2K/cp2k/tools/toolchain/install/SpFFT-1.1.0/install_successful: 
>> No such file or directory
>>
>> It then fails to install libxc, cosma, gsl, hdf5, spfft.
>>
>> Why is it even trying to install these when I stated not to use it? or 
>> does --with-cosma=no mean something else?
>>
>> I can imagine that these errors alone is what's causing the make of 
>> local.psmp to fail.
>
>

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