[CP2K-user] issues installing cp2k v.7.1 on a Beowulf cluster with CentOS 7.6

[Sergey Chulkov]

Hi Katharina,

You can compile CP2K 7.1 on CentOS 7.6 with the system-default compiler 
(gcc 4.8.5) using the following toolchain options:

./install_cp2k_toolchain.sh -j 16 --with-gcc=system --with-cmake=install 
--with-openmpi=system --with-libxc=install --with-libint=no 
--with-fftw=install --with-openblas=install --with-scalapack=install 
--with-libxsmm=install --with-elpa=no --with-sirius=no --with-gsl=install 
--with-libvdwxc=no --with-spglib=install --with-hdf5=no --with-spfft=no

Please notice that gcc 4.8.5 has a limited support of C++11 standard, hence 
you will not be able to compile some vital libraries (e.g. libint2). If gcc 
4.8.5 is the only compiler available on your cluster (try to run 'module 
avail' first), you can still build a recent gnu compiler manually. In case 
of a CentOS 7.6 cluster with Infiniband interconnect, gcc 9.2.0 along with 
openucx 1.6.1 and openmpi 4.0.2 works without any issues. In order to 
compile openucx with Infiniband support, the package 'rdma-core-devel' from 
the CentOS 'base' repository needs to be installed.

Best wishes,
Sergey

On Wednesday, February 12, 2020 at 9:35:47 AM UTC, Katharina Doblhoff-Dier 
wrote:
>
> Dear CP2K community,
> I am having some issues getting cp2k to work on a Beowulf cluster running 
> CentOS 7.6 using gcc 4.8.5 
>
> The first issue that I ran into was that toolchain had problems with 
> spfft. Looking into that, it seems spfft can only be compiled with gcc >=6 
> (a warining instead of a weird error message for the toolchain would be 
> nice!). Since I am not in dire need of plane waves, I kicked sirius and 
> spfft out of the toolchain via with-sirius=no and with-spfft=no. I did the 
> smae with libint and elpa, because I had issues with them too and 
> proceeded, just to get another rather weird error message from toolchain:
>
>
> >./install_cp2k_toolchain.sh --with-openmpi=system --with-sirius=no --with-spfft=no --with-libint=no --with-elpa=no
> MPI is detected and it appears to be OpenMPI
> nvcc not found, disabling CUDA by default
> Compiling with 64 processes.
> ==================== Finding GCC from system paths ====================
> path to gcc is  /usr/bin/gcc
> path to g++ is  /usr/bin/g++
> path to gfortran is  /usr/bin/gfortran
> Found include directory /usr/include
> Found lib directory /usr/lib64
> Step gcc took 0.00 seconds.
> ==================== Getting proc arch info using OpenBLAS tools ====================
> OpenBLAS-0.3.6.tar.gz: OK
> Checksum of OpenBLAS-0.3.6.tar.gz Ok
> OpenBLAS detected LIBCORE = zen
> OpenBLAS detected ARCH    = x86_64
> ==================== Installing CMake ====================
> cmake-3.15.1.tar.gz: OK
> Checksum of cmake-3.15.1.tar.gz Ok
> Installing from scratch into /home/mark/CP2K/cp2k-7.1/tools/toolchain/install/cmake-3.15.1
> Step cmake took 231.00 seconds.
> Step valgrind took 0.00 seconds.
> ==================== Finding OpenMPI from system paths ====================
> path to mpirun is  /usr/local/openmpi/bin/mpirun
> path to mpicc is  /usr/local/openmpi/bin/mpicc
> path to mpif90 is  /usr/local/openmpi/bin/mpif90
> path to mpic++ is  /usr/local/openmpi/bin/mpic++
> Step openmpi took 0.00 seconds.
> Step reflapack took 0.00 seconds.
> ==================== Installing OpenBLAS ====================
> OpenBLAS-0.3.6.tar.gz is found
> Installing from scratch into /home/mark/CP2K/cp2k-7.1/tools/toolchain/install/openblas-0.3.6
> patching file kernel/x86_64/KERNEL.SKYLAKEX
> Step openblas took 86.00 seconds.
> ==================== Installing FFTW ====================
> fftw-3.3.8.tar.gz: OK
> Checksum of fftw-3.3.8.tar.gz Ok
> Installing from scratch into /home/mark/CP2K/cp2k-7.1/tools/toolchain/install/fftw-3.3.8
> Step fftw took 49.00 seconds.
> Step spfft took 0.00 seconds.
> Step libint took 0.00 seconds.
> ==================== Installing LIBXC ====================
> libxc-4.3.4.tar.gz: OK
> Checksum of libxc-4.3.4.tar.gz Ok
> Installing from scratch into /home/mark/CP2K/cp2k-7.1/tools/toolchain/install/libxc-4.3.4
> Step libxc took 244.00 seconds.
> Step libsmm took 0.00 seconds.
> ==================== Installing Libxsmm ====================
> libxsmm-1.14.tar.gz: OK
> Checksum of libxsmm-1.14.tar.gz Ok
> Installing from scratch into /home/mark/CP2K/cp2k-7.1/tools/toolchain/install/libxsmm-1.14
> Step libxsmm took 13.00 seconds.
> ==================== Installing ScaLAPACK ====================
> scalapack-2.0.2.tgz: OK
> Checksum of scalapack-2.0.2.tgz Ok
> Installing from scratch into /home/mark/CP2K/cp2k-7.1/tools/toolchain/install/scalapack-2.0.2
> Step scalapack took 35.00 seconds.
> Step elpa took 0.00 seconds.
> Step ptscotch took 0.00 seconds.
> Step parmetis took 0.00 seconds.
> /home/mark/CP2K/cp2k-7.1/tools/toolchain/scripts/tool_kit.sh: line 12: /usr/bin/date: Argument list too long   <<<<<====== ?!?
>
> The problem seems to be a call to time, but this is weird, because the command itself works and has obviously been used before. So now I am confused. Any help is appreciated!
> Thank you and best regards,
> Katharina
>  
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20200212/3dae13c8/attachment.htm>