[CP2K-user] [CP2K:13029] toolchain script can't find system libraries

zineb kerrami zz.k... at gmail.com
Fri Mar 27 03:58:34 UTC 2020


I'm not sure, but I think that you have to check if the libraries paths in
the files (Linux-x86-64-gfortran.sopt,popt.....) are corrects, if not you
can edit them and remake the compilation, I think that you can find the
include and lib folders for all the packages in tools/toolchain/install
folder.
I which that it could help

On Thu, 26 Mar 2020, 5:25 pm Ryan Kingsbury, <RKing... at lbl.gov> wrote:

> I'm trying to compile cp2k on Ubuntu (under Windows10 WSL) using the
> toolchain script, and I've run into several problems in which it seems the
> toolchain script and build system don'tt recognize system installed
> libraries.
>
> For example, when running the toolchain script, building fftw3 fails
> because it can't find the MPI library:
>
> ==================== Installing FFTW ====================
> fftw-3.3.8.tar.gz is found
> Installing from scratch into /home/ryan/anaconda3/envs/cp2k-2/code/cp2k-
> 7.1/tools/toolchain/install/fftw-3.3.8
> ERROR: (./scripts/install_fftw.sh, line 45) Non-zero exit code detected.
>
> examining the FFTW3 log shows:
>
> checking for ranlib... (cached) /home/ryan/anaconda3/envs/cp2k-2/bin/
> x86_64-conda_cos6-linux-gnu-ranlib
> checking for ocamlbuild... no
> checking for mpicc... mpicc
> checking for MPI_Init... no
> checking for MPI_Init in -lmpi... no
> checking for MPI_Init in -lmpich... no
> configure: error: could not find mpi library for --enable-mpi
>
> but I know that the toolchain script detected my (system-installed) MPI
> because I see the following in stdout:
>
> >>> ./install_cp2k_toolchain.sh --gpu-ver=P100 --with-openblas=no
> MPI is detected and it appears to be OpenMPI
> nvcc found, enabling CUDA by default
> Compiling with 4 processes.
> ==================== Finding GCC from system paths ====================
> path to gcc is  /home/ryan/anaconda3/envs/cp2k-2/bin/gcc
> path to g++ is  /usr/bin/g++
> path to gfortran is  /home/ryan/anaconda3/envs/cp2k-2/bin/gfortran
> Found include directory /usr/include
> Step gcc took 0.00 seconds.
> ==================== Getting proc arch info using OpenBLAS tools
> ====================
> OpenBLAS detected LIBCORE = haswell
> OpenBLAS detected ARCH    = x86_64
> ==================== Installing CMake ====================
> cmake-3.15.1 is already installed, skipping it.
> Step cmake took 0.00 seconds.
> Step valgrind took 0.00 seconds.
> ==================== Finding OpenMPI from system paths
> ====================
> path to mpirun is  /usr/bin/mpirun
> path to mpicc is  /usr/bin/mpicc
> path to mpif90 is  /usr/bin/mpif90
> path to mpic++ is  /usr/bin/mpic++
> Step openmpi took 0.00 seconds.
> Step reflapack took 0.00 seconds.
> Step openblas took 0.00 seconds.
>
>
> To circumvent the build problems, I tried installing binary packages for
> fftw3, libxc, libint, etc. from the Ubuntu repositories. But if I run make
> it seems that the /include directories are not set properly:
>
> >> make ARCH=Linux-x86-64-gfortran version='sopt ssmp popt'
> Discovering programs ...
> Removing stale archives for sopt ...
> Resolving dependencies for sopt ...
> make -C /home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/exts/dbcsr \
>    INCLUDEMAKE=/home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/arch/Linux-
> x86-64-gfortran.sopt \
>    LIBDIR=/home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/lib/Linux-x86-64-
> gfortran/sopt/exts/dbcsr \
>    OBJDIR=/home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/obj/Linux-x86-64-
> gfortran/sopt/exts/dbcsr \
>    FYPPEXE=/home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/tools/
> build_utils/fypp
> Removing stale archives ...
> Resolving dependencies ...
> /home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/tools/build_utils/fypp -n /
> home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/exts/dbcsr/src/base/
> dbcsr_kinds.F dbcsr_kinds.F90
> gfortran -c -O2 -g -mtune=native -D__FFTW3 -D__LIBINT -D__LIBXC -D__LIBXSMM
> -D__SPGLIB -ffree-form -ffree-line-length-none -ftree-vectorize -funroll-loops
> -std=f2008 -I/fftw/3.3/include -I/libint/2.6.0-lmax-6/include -I/libxc/4.3
> .4/include -I/libxsmm/1.14/include -D__SHORT_FILE__="\"dbcsr_kinds.F\"" -I
> '/home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/exts/dbcsr/src/base/' -I
> '/home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/exts/dbcsr/src'
> dbcsr_kinds.F90
> f951: Warning: Nonexistent include directory '/fftw/3.3/include' [-
> Wmissing-include-dirs]
> f951: Warning: Nonexistent include directory
> '/libint/2.6.0-lmax-6/include' [-Wmissing-include-dirs]
> f951: Warning: Nonexistent include directory '/libxc/4.3.4/include' [-
> Wmissing-include-dirs]
> f951: Warning: Nonexistent include directory '/libxsmm/1.14/include' [-
> Wmissing-include-dirs]
> /home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/tools/build_utils/fypp -n /
> home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/exts/dbcsr/src/base/
> dbcsr_machine_internal.F dbcsr_machine_internal.F90
> gfortran -c -O2 -g -mtune=native -D__FFTW3 -D__LIBINT -D__LIBXC -D__LIBXSMM
> -D__SPGLIB -ffree-form -ffree-line-length-none -ftree-vectorize -funroll-loops
> -std=f2008 -I/fftw/3.3/include -I/libint/2.6.0-lmax-6/include -I/libxc/4.3
> .4/include -I/libxsmm/1.14/include -D__SHORT_FILE__=
> "\"dbcsr_machine_internal.F\"" -I
> '/home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/exts/dbcsr/src/base/' -I
> '/home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/exts/dbcsr/src'
> dbcsr_machine_internal.F90
> f951: Warning: Nonexistent include directory '/fftw/3.3/include' [-
> Wmissing-include-dirs]
> f951: Warning: Nonexistent include directory
> '/libint/2.6.0-lmax-6/include' [-Wmissing-include-dirs]
> f951: Warning: Nonexistent include directory '/libxc/4.3.4/include' [-
> Wmissing-include-dirs]
> f951: Warning: Nonexistent include directory '/libxsmm/1.14/include' [-
> Wmissing-include-dirs]
> /home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/tools/build_utils/fypp -n /
> home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/exts/dbcsr/src/base/
> dbcsr_machine.F dbcsr_machine.F90
> gfortran -c -O2 -g -mtune=native -D__FFTW3 -D__LIBINT -D__LIBXC -D__LIBXSMM
> -D__SPGLIB -ffree-form -ffree-line-length-none -ftree-vectorize -funroll-loops
> -std=f2008 -I/fftw/3.3/include -I/libint/2.6.0-lmax-6/include -I/libxc/4.3
> .4/include -I/libxsmm/1.14/include -D__SHORT_FILE__="\"dbcsr_machine.F\""
> -I'/home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/exts/dbcsr/src/base/' -I
> '/home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/exts/dbcsr/src'
> dbcsr_machine.F90
> f951: Warning: Nonexistent include directory '/fftw/3.3/include' [-
> Wmissing-include-dirs]
> f951: Warning: Nonexistent include directory
> '/libint/2.6.0-lmax-6/include' [-Wmissing-include-dirs]
> f951: Warning: Nonexistent include directory '/libxc/4.3.4/include' [-
> Wmissing-include-dirs]
> f951: Warning: Nonexistent include directory '/libxsmm/1.14/include' [-
> Wmissing-include-dirs]
> dbcsr_machine.F90:62:10:
>
>  #if defined(__LIBXSMM)
>           1
> Fatal Error: Can't open module file 'libxsmm.mod' for reading at (1): No
> such file or directory
> compilation terminated.
> /home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/exts/dbcsr/Makefile:428:
> recipe for target 'dbcsr_machine.o' failed
> make[4]: *** [dbcsr_machine.o] Error 1
> Makefile:129: recipe for target 'libdbcsr' failed
> make[3]: *** [libdbcsr] Error 2
> /home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/exts/Makefile.inc:16:
> recipe for target 'dbcsr' failed
> make[2]: *** [dbcsr] Error 2
> /home/ryan/anaconda3/envs/cp2k-2/code/cp2k-7.1/Makefile:123: recipe for
> target 'sopt' failed
> make[1]: *** [sopt] Error 2
> Makefile:118: recipe for target 'all' failed
> make: *** [all] Error 2
>
> How can I make sure the toolchain script and/or build system recognize
> system-installed libraries? Thanks in advance for your assistance!
>
>
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