Installation error GMX+CP2K on CRAY

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1

GROMACS version:
GROMACS modification: Yes/No
Here post your question

Dear Gromacs community

I tried to install GROMACS 2022.2 in combination with CP2K.2022.1 on our CRAY supercomputer.
From what I understand in a previous post (link reported at the end of this post) the
-DCP2K_LINKER_FLAGS is not needed anymore starting from cp2k.9.1

I successfully install cp2k.2022.1 and I tried to install gromacs

I got some mpi warning:

warning: use of old-style cast [-Wold-style-cast]
MPI_Comm libraryWorldCommunicator_ = MPI_COMM_NULL;

and at the end this error at the end:

…

[100%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/selection/sm_simple.cpp.o
[100%] Building CXX object src/gromacs/CMakeFiles/libgromacs.dir/selection/symrec.cpp.o
3 warnings generated.
7 warnings generated.
18 warnings generated.
[100%] Linking CXX static library …/…/lib/libgromacs_mpi_d.a
[100%] Built target libgromacs
[100%] Linking CXX executable …/…/bin/gmx_mpi_d
ld.lld: error: unable to find library -lsymspg
ld.lld: error: unable to find library -lplumed
ld.lld: error: unable to find library -lgsl
ld.lld: error: unable to find library -lxsmmf
ld.lld: error: unable to find library -lxsmm
ld.lld: error: unable to find library -lxcf03
ld.lld: error: unable to find library -lxc
ld.lld: error: unable to find library -lint2
ld.lld: error: unable to find library -lfftw3_mpi
ld.lld: error: unable to find library -lfftw3
ld.lld: error: unable to find library -lfftw3_omp
ld.lld: error: unable to find library -lvori
ld.lld: error: unable to find library -lsymspg
ld.lld: error: unable to find library -lplumed
ld.lld: error: unable to find library -lgsl
ld.lld: error: unable to find library -lxsmmf
ld.lld: error: unable to find library -lxsmm
ld.lld: error: unable to find library -lxcf03
ld.lld: error: unable to find library -lxc
ld.lld: error: unable to find library -lint2
ld.lld: error: too many errors emitted, stopping now (use -error-limit=0 to see all errors)
clang-11: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [src/programs/CMakeFiles/gmx.dir/build.make:97: bin/gmx_mpi_d] Error 1
make[1]: *** [CMakeFiles/Makefile2:6163: src/programs/CMakeFiles/gmx.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

Here my cmake file

#!/bin/bash
export DIR_LIB=/lustre/igladich/opt/cp2k-2022.1/tools/toolchain/install/
source ${DIR_LIB}/setup
export DIR_CP2K=/lustre/igladich/opt/cp2k-2022.1/
export DIR_GMX=/lustre/igladich/opt/gromacs-2022.2_wCP2K/

${DIR_LIB}/cmake-3.22.1/bin/cmake … -DGMX_MPI=ON
-DCMAKE_INSTALL_PREFIX=${DIR_GMX}/opt/ -DGMX_DOUBLE=ON
-DBUILD_SHARED_LIBS=OFF -DGMXAPI=OFF -DGMX_INSTALL_NBLIB_API=OFF
-DGMX_FFT_LIBRARY=fftw3
-DCMAKE_PREFIX_PATH=${DIR_LIB}/fftw-3.3.10
-DCP2K_DIR=${DIR_CP2K}/lib/local/psmp -DGMX_CP2K=ON

Please, let me know if you have any suggestions
Thank you very much for your help

Best

Ivan

PS:

2

Hi there should be file libcp2k.pc in the directory /lustre/igladich/opt/cp2k-2022.1//lib/local/psmp/pkgconfig could you share that?

3

Hi Dmitry

thank you for your reply and help

We had some adjustments on our CRAY machine and now I am trying to install GROMACS 2022.3 in combination with CP2K.9.1 (right now I have some trouble installing the last version of cp2k).The error that I get is, anyway, very similar

[100%] Linking CXX executable …/…/bin/gmx_mpi_d
No supported cpu target is set, CRAY_CPU_TARGET=x86-64 will be used.
Load a valid targeting module or set CRAY_CPU_TARGET
/usr/bin/ld: cannot find -lplumed
/usr/bin/ld: cannot find -lgsl
/usr/bin/ld: cannot find -lgslcblas
/usr/bin/ld: cannot find -lxsmmf
/usr/bin/ld: cannot find -lxsmm
collect2: error: ld returned 1 exit status
make[2]: *** [src/programs/CMakeFiles/gmx.dir/build.make:97: bin/gmx_mpi_d] Error 1
make[1]: *** [CMakeFiles/Makefile2:6163: src/programs/CMakeFiles/gmx.dir/all] Error 2
make: *** [Makefile:166: all] Error 2

Below my libcp2k.pc

Name: libcp2k
Description: CP2K as a library
URL: https://www.cp2k.org
Version: git:d8d7100
includedir=/ddn/home/ivgladi48/opt/cp2k-9.1/src/start
Cflags: -I${includedir}
libdir=/ddn/home/ivgladi48/opt/cp2k-9.1/lib/local/psmp
Libs: -L${libdir} -Wl,-rpath=${libdir} -lcp2k -march=native -mtune=native -fno-omit-frame-pointer -g -O3 -funroll-loops -fopenmp -I’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/fftw-3.3.10/include’ -I’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/include’ -I’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/libxc-5.1.7/include’ -I’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/libxsmm-1.17/include’ -I’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/elpa-2021.11.001/cpu/include/elpa_openmp-2021.11.001/modules’ -I’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/elpa-2021.11.001/cpu/include/elpa_openmp-2021.11.001/elpa’ -I’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/gsl-2.7/include’ -fbacktrace -ffree-form -fimplicit-none -std=f2008 -Werror=aliasing -Werror=ampersand -Werror=c-binding-type -Werror=intrinsic-shadow -Werror=intrinsics-std -Werror=line-truncation -Werror=tabs -Werror=target-lifetime -Werror=underflow -Werror=unused-but-set-variable -Werror=unused-variable -Werror=unused-dummy-argument -Werror=conversion -Werror=zerotrip -Wno-maybe-uninitialized -Wuninitialized -Wuse-without-only -D__LIBXSMM -D__SCALAPACK -D__parallel -D__MPI_VERSION=3 -D__FFTW3 -D__LIBINT -D__LIBXC -D__ELPA -D__GSL -D__PLUMED2 -D__LIBVORI -D__COMPILE_ARCH=“local” -D__COMPILE_DATE=“Thu Oct 27 10:55:50 +03 2022” -D__COMPILE_HOST=“raad2a” -D__COMPILE_REVISION=“git:d8d7100” -D__DATA_DIR=“/ddn/home/ivgladi48/opt/cp2k-9.1/data” -Wl,–enable-new-dtags -L’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/fftw-3.3.10/lib’ -Wl,-rpath=‘/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/fftw-3.3.10/lib’ -L’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/libint-v2.6.0-cp2k-lmax-5/lib’ -L’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/libxc-5.1.7/lib’ -Wl,-rpath=‘/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/libxc-5.1.7/lib’ -L’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/libxsmm-1.17/lib’ -Wl,-rpath=‘/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/libxsmm-1.17/lib’ -L’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/elpa-2021.11.001/cpu/lib’ -Wl,-rpath=‘/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/elpa-2021.11.001/cpu/lib’ -L’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/gsl-2.7/lib’ -Wl,-rpath=‘/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/gsl-2.7/lib’ -L’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/plumed-2.7.3/lib’ -Wl,-rpath=‘/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/plumed-2.7.3/lib’ -L’/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/libvori-210412/lib’ -Wl,-rpath=‘/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/libvori-210412/lib’ -L/ddn/home/ivgladi48/opt/cp2k-9.1/lib/local/psmp/exts/dbcsr -ldbcsr -lplumed -ldl -lstdc++ -lz -ldl -lgsl -lgslcblas -lelpa_openmp -lxsmmf -lxsmm -ldl -lpthread -lxcf03 -lxc -lint2 -lfftw3_mpi -lfftw3 -lfftw3_omp -lz -ldl -lvori -lstdc++ -lstdc++

Here the script that I used for the gromacs installation

#!/bin/bash
cd build
rm -rf *
export DIR_LIB=/ddn/home/ivgladi48/opt/cp2k-9.1/tools/toolchain/install/
source ${DIR_LIB}/setup
export DIR_CP2K=/ddn/home/ivgladi48/opt/cp2k-9.1/
export DIR_GMX=/ddn/home/ivgladi48/opt/gromacs-2022.3/
${DIR_LIB}/cmake-3.22.1/bin/cmake … -DGMX_MPI=ON
-DCMAKE_INSTALL_PREFIX=${DIR_GMX}/opt/ -DGMX_DOUBLE=ON
-DBUILD_SHARED_LIBS=OFF -DGMXAPI=OFF -DGMX_INSTALL_NBLIB_API=OFF
-DGMX_FFT_LIBRARY=fftw3 -DCMAKE_PREFIX_PATH=${DIR_LIB}/fftw-3.3.10
-DCP2K_DIR=${DIR_CP2K}/lib/local/psmp -DGMX_CP2K=ON

Thank you very much for any possible help

Best
Ivan

4

Hi, Could you try compile CP2K without GSL and without PLUMED and then link to GROMACS?

5

Hi

removing gsl and plumed I was able to compile.
The code runs a simple test case, but now I am going to do more performance tests
(it looks a bit slow, also for a simple classical MD, but I want to be more precise…)
Thank you very much

PS: below the installation note for cp2k and gromacs used on my CRAY machine, in case someone needs

CP2K

!/bin/bash
rm -rf cp2k-9.1
tar -xvf cp2k-9.1.tar.bz2
module switch PrgEnv-cray/6.0.10 PrgEnv-gnu/6.0.9
module switch gcc/10.3.0 gcc/9.3.0
cd cp2k-9.1/tools/toolchain/
./install_cp2k_toolchain.sh --libint-lmax=5 --with-fftw=install --with-plumed=no --with-sirius=no --with-spfft=no --with-cosma=no --with-gsl=no --with-spglib=no --with-plumed=no
cp /ddn/home/ivgladi48/opt/New/cp2k-9.1/tools/toolchain/install/arch/* …/…/arch/
cd …/…/
source /ddn/home/ivgladi48/opt/New/cp2k-9.1/tools/toolchain/install/setup
make -j 24 ARCH=local VERSION=“ssmp sdbg psmp pdbg” libcp2k

GMX

#!/bin/bash
module switch PrgEnv-cray/6.0.10 PrgEnv-gnu/6.0.9
module switch gcc/10.3.0 gcc/9.3.0
cd build
rm -rf *
export DIR_LIB=/ddn/home/ivgladi48/opt/New/cp2k-9.1/tools/toolchain/install/
source ${DIR_LIB}/setup
export DIR_CP2K=/ddn/home/ivgladi48/opt/New/cp2k-9.1/
export DIR_GMX=/ddn/home/ivgladi48/opt/gromacs-2022.3/
${DIR_LIB}/cmake-3.22.1/bin/cmake … -DGMX_MPI=ON -DCMAKE_INSTALL_PREFIX=${DIR_GMX}/opt/ -DGMX_DOUBLE=ON -DBUILD_SHARED_LIBS=OFF -DGMXAPI=OFF -DGMX_INSTALL_NBLIB_API=OFF -DGMX_FFT_LIBRARY=fftw3 -DCMAKE_PREFIX_PATH=${DIR_LIB}/fftw-3.3.10 -DCP2K_DIR=${DIR_CP2K}/lib/local/psmp -DGMX_CP2K=ON
make -j 24
make install

6

good that its now working!