[CP2K-user] [CP2K:17883] Re: DBCSR error during build

[jerryt...@gmail.com]

Dear Alfio,
I downloaded CP2K via git as follows:

git clone -b support/v2022.2 https://github.com/cp2k/cp2k.git 
cp2k-2022.2_Intel

I then cd to cp2k-2022.2_Intel and ran:

"source arch/Linux-intel-x86_64-tanoury.psmp" using the arch file I 
attached previously.

Please see the attached log file for the compile details.

Kindest regards,
Jerry
On Monday, October 17, 2022 at 4:06:04 AM UTC-4 Alfio Lazzaro wrote:

> Dear Jerry,
> Could you confirm how you are downloading CP2K? From the message "fatal: 
> Not a git repository (or any parent up to mount point /cluster)" I assume 
> you are not using git. Please, check the instructions at:
>
> https://github.com/cp2k/cp2k#downloading-cp2k-source-code
> https://github.com/cp2k/cp2k/blob/master/INSTALL.md
>
> Basically, you can use the versioned tarballs, cp2k-X.Y.tar.bz2 or "git 
> clone --recursive".
>
> Alfio
>
> Il giorno domenica 16 ottobre 2022 alle 23:09:59 UTC+2 jerryt... at gmail.com 
> ha scritto:
>
>> Oops, here's the arch file that I sourced.
>>
>>
>>
>> On Sunday, October 16, 2022 at 4:50:19 PM UTC-4 jerryt... at gmail.com 
>> wrote:
>>
>>> Hi Alfio,
>>> I started over and compiled CP2K by sourcing the attached arch file, 
>>> slightly modified from the original.  However, I got a DBCSR error:
>>>
>>> $  make -j 8 ARCH=Linux-intel-x86_64-tanoury VERSION=psmp
>>> Discovering programs ...
>>> /cluster/home/tanoury/CP2K/cp2k-2022.1_Intel/exts/Makefile.inc:2: *** 
>>> "No DBCSR submodule available, please run '$  make -j 8 
>>> ARCH=Linux-intel-x86_64-tanoury VERSION=psmp
>>> Discovering programs ...
>>> /cluster/home/tanoury/CP2K/cp2k-2022.1_Intel/exts/Makefile.inc:2: *** 
>>> "No DBCSR submodule available, please run 'git submodule update --init 
>>> --recursive'".  Stop.
>>> make[1]: *** [psmp] Error 2
>>> make: *** [all] Error 2
>>> ".  Stop.
>>> make[1]: *** [psmp] Error 2
>>> make: *** [all] Error 2
>>>
>>> I ran 'git submodule update --init --recursive' from the cp2k home 
>>> directory and in the dbcsr directory, but got the same message shown below:
>>> cd
>>> fatal: Not a git repository (or any parent up to mount point /cluster)
>>> Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not 
>>> set).
>>>
>>> This was the reason why I was build DBCSR separately.  How do I fix this?
>>>
>>> Kind regards,
>>> Jerry
>>>
>>> On Saturday, October 8, 2022 at 10:22:52 AM UTC-4 jerryt... at gmail.com 
>>> wrote:
>>>
>>>> Hi Alfio,
>>>> Thank you.  I found the problem.
>>>>
>>>> Jerry
>>>>
>>>> On Thursday, September 29, 2022 at 5:26:06 AM UTC-4 Alfio Lazzaro wrote:
>>>>
>>>>> DBCSR is part of CP2K as a submodule and it is fully integrated in the 
>>>>> CP2K compilation. You don't need to build it separately. So just compile 
>>>>> CP2K and it will automatically compile DBCSR too.
>>>>>
>>>>> Alfio
>>>>>
>>>>>
>>>>>
>>>>> Il giorno mercoledì 28 settembre 2022 alle 19:29:25 UTC+2 
>>>>> jerryt... at gmail.com ha scritto:
>>>>>
>>>>>> Dear Forum,
>>>>>> I am building CP2K 2022.1 with Intel 2021.3 compilers and MKL using 
>>>>>> the toolchain.  After the toolchain built the arch files, I then went to 
>>>>>> build dbcsr following the directions on your website.  I used the following 
>>>>>> for cmake:
>>>>>>
>>>>>>
>>>>>> cmake -DUSE_SMM=libxsmm -DUSE_ACCEL=cuda -DWITH_GPU=V100 
>>>>>> -DCMAKE_HAVE_LIBC_PTHREAD=/usr/include -DBLA_VENDOR=Intel10_64lp_seq ..
>>>>>>
>>>>>> However, during I got the following error:
>>>>>> -- Performing Test f95-reshape-order-allocatable - Success
>>>>>> CMake Error at cmake/fypp-sources.cmake:9 (message):
>>>>>>   Failed to find the FYPP preprocessor.
>>>>>> Call Stack (most recent call first):
>>>>>>   src/CMakeLists.txt:3 (include)
>>>>>>
>>>>>>
>>>>>> -- Configuring incomplete, errors occurred!
>>>>>>
>>>>>> Please provide guidance on how to fix this.
>>>>>>
>>>>>> Best regards,
>>>>>> Jerry
>>>>>>
>>>>>>

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[tanoury at hpchead:CP2K]$ git clone -b support/v2022.2 https://github.com/cp2k/cp2k.git cp2k-2022.2_Intel
Cloning into 'cp2k-2022.2_Intel'...
remote: Enumerating objects: 229793, done.
remote: Counting objects: 100% (72/72), done.
remote: Compressing objects: 100% (53/53), done.
remote: Total 229793 (delta 32), reused 45 (delta 19), pack-reused 229721
Receiving objects: 100% (229793/229793), 215.29 MiB | 572.00 KiB/s, done.
Resolving deltas: 100% (194612/194612), done.
Checking out files: 100% (6760/6760), done.

[tanoury at hpchead:cp2k-2022.2_Intel]$ source arch/Linux-intel-x86_64-tanoury.psmp 
MPI is detected and it appears to be Intel MPI
You have chosen to use the Intel compiler, therefore the installation of the GCC compiler will be skipped.
Compiling with 8 processes.
==================== Finding GCC from system paths ====================
path to gcc is /cluster/app/gcc/8.4.0/bin/gcc
path to g++ is /cluster/app/gcc/8.4.0/bin/g++
path to gfortran is /cluster/app/gcc/8.4.0/bin/gfortran
Found include directory /usr/include
Found lib directory /cluster/app/gcc/8.4.0/lib64
Step gcc took 1.00 seconds.
==================== Finding Intel compiler from system paths ====================
path to icc is /cluster/home/tanoury/intel/2021.3_gnu8.4.0/compiler/2021.3.0/linux/bin/intel64/icc
path to icpc is /cluster/home/tanoury/intel/2021.3_gnu8.4.0/compiler/2021.3.0/linux/bin/intel64/icpc
path to ifort is /cluster/home/tanoury/intel/2021.3_gnu8.4.0/compiler/2021.3.0/linux/bin/intel64/ifort
Step intel took 0.00 seconds.
==================== Getting proc arch info using OpenBLAS tools ====================
OpenBLAS detected LIBCORE = skylakex
OpenBLAS detected ARCH    = x86_64
==================== Finding CMake from system paths ====================
path to cmake is /cluster/app/cmake/3.24.1/bin/cmake
Step cmake took 0.00 seconds.
==================== Finding Intel MPI from system paths ====================
path to mpirun is /cluster/home/tanoury/intel/2021.3_gnu8.4.0/mpi/2021.3.0//bin/mpirun
path to mpiicc is /cluster/home/tanoury/intel/2021.3_gnu8.4.0/mpi/2021.3.0//bin/mpiicc
path to mpiicpc is /cluster/home/tanoury/intel/2021.3_gnu8.4.0/mpi/2021.3.0//bin/mpiicpc
path to mpiifort is /cluster/home/tanoury/intel/2021.3_gnu8.4.0/mpi/2021.3.0//bin/mpiifort
Found lib directory /cluster/home/tanoury/intel/2021.3_gnu8.4.0/mpi/2021.3.0/lib/release
libmpi is found in ld search path
libmpicxx is found in ld search path
Step intelmpi took 1.00 seconds.
WARNING: (/cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/scripts/stage2/install_mkl.sh, line 23) MKL FFTW3 interface is present, but FFTW library is needed for FFTW-MPI wrappers.
==================== Finding MKL from system paths ====================
MKLROOT is found to be /cluster/home/tanoury/intel/2021.3_gnu8.4.0/mkl/2021.3.0
libm is found in ld search path
libdl is found in ld search path
Step mkl took 0.00 seconds.
==================== Installing FFTW ====================
fftw-3.3.10.tar.gz is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/fftw-3.3.10
Step fftw took 821.00 seconds.
==================== Installing LIBINT ====================
libint-v2.6.0-cp2k-lmax-5.tgz is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5
Step libint took 3129.00 seconds.
==================== Installing LIBXC ====================
libxc-5.2.3.tar.gz is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/libxc-5.2.3
Step libxc took 215.00 seconds.
==================== Installing Libxsmm ====================
libxsmm-1.17.tar.gz is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/libxsmm-1.17
Step libxsmm took 220.00 seconds.
Step scalapack took 0.00 seconds.
==================== Installing COSMA ====================
COSMA-v2.5.1.tar.gz is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/COSMA-2.5.1
Step cosma took 52.00 seconds.
==================== Installing ELPA ====================
elpa-2021.11.002.tar.gz is found
patching file nvcc_wrap
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/elpa-2021.11.002/cpu
Step elpa took 1337.00 seconds.
==================== Installing PT-Scotch ====================
scotch_6.0.0.tar.gz is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/scotch-6.0.0
Step ptscotch took 54.00 seconds.
==================== Installing SuperLU_DIST ====================
superlu_dist_6.1.0.tar.gz is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/superlu_dist-6.1.0
Step superlu took 86.00 seconds.
==================== Installing PEXSI ====================
pexsi_v1.2.0.tar.gz is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/pexsi-1.2.0
Step pexsi took 138.00 seconds.
WARNING: (./scripts/stage6/install_quip.sh) A QUIP installation using the Intel compiler is currently not supported. The QUIP package will not be installed.
==================== Installing gsl ====================
gsl-2.7.tar.gz is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/gsl-2.7
Step gsl took 533.00 seconds.
==================== Installing PLUMED ====================
plumed-src-2.8.0.tgz is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/plumed-2.8.0
Step plumed took 708.00 seconds.
==================== Installing hdf5 ====================
hdf5-1.12.0.tar.bz2 is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/hdf5-1.12.0
^[[1;3BStep hdf5 took 641.00 seconds.
==================== Installing libvdwxc ====================
libvdwxc-0.4.0.tar.gz is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/libvdwxc-0.4.0
Step libvdwxc took 129.00 seconds.
==================== Installing spglib ====================
spglib-1.16.2.tar.gz is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/spglib-1.16.2
Step spglib took 30.00 seconds.
==================== Installing libvori ====================
libvori-220621.tar.gz is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/libvori-220621
Step libvori took 30.00 seconds.
Step spfft took 0.00 seconds.
==================== Installing spla ====================
SpLA-1.5.4.tar.gz is found
Installing from scratch into /cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/tools/toolchain/install/SpLA-1.5.4
Step spla took 46.00 seconds.
Step sirius took 0.00 seconds.

Check the output above for error messages and consistency!
If everything is OK, you can build a CP2K production binary with
   make -j ARCH=Linux-intel-x86_64-tanoury VERSION=psmp
Alternatively, you can add further checks, e.g. for regression testing, with
   make -j ARCH=Linux-intel-x86_64-tanoury VERSION=psmp DO_CHECKS=yes
or build CP2K only with shared libraries using
   make -j ARCH=Linux-intel-x86_64-tanoury VERSION=psmp SHARED=yes
or build CP2K as a library with
   make -j ARCH=Linux-intel-x86_64-tanoury VERSION=psmp libcp2k
[tanoury at hpchead:cp2k-2022.2_Intel]$
[tanoury at hpchead:cp2k-2022.2_Intel]$ source tools/toolchain/install/setup 
[tanoury at hpchead:cp2k-2022.2_Intel]$ make -j8 ARCH=Linux-intel-x86_64-tanoury VERSION=psmp
Discovering programs ...
/cluster/home/tanoury/CP2K/cp2k-2022.2_Intel/exts/Makefile.inc:2: *** "No DBCSR submodule available, please run 'git submodule update --init --recursive'".  Stop.
make[1]: *** [psmp] Error 2
make: *** [all] Error 2