[CP2K-user] Problems building cp2k with toolchain with elpa on intel KNL machine

Ronald Cohen reco... at gmail.com
Mon Jan 14 13:42:54 CET 2019


Hey! So I have a working version of cp2k.psmp on my KNL machine finally. 
Now I would like to build with elpa. 
However it fails. Any ideas would be greatly appreciated.

Ron

detail:


Simply using: 
./install_cp2k_toolchain.sh  --with-libint=install  --with-gcc=install 
--with-sirius=no --with-libxc=install --with-elpa=install
failed in the elpa build with no useful message.

So I configured elpa by hand for gnu and modified install_elpa.sh as 
follows:

lpa_ver=${elpa_ver:-2017.05.002} 
source "${SCRIPT_DIR}"/common_vars.sh 
source "${SCRIPT_DIR}"/tool_kit.sh 
source "${SCRIPT_DIR}"/signal_trap.sh 
SCALAPACK_LDFLAGS="-L$MKL_HOME/lib/intel64 -lmkl_scalapack_lp64 
-lmkl_gf_lp64 -lmkl_sequential \ 
                             -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread 
-lm -Wl,-rpath,$MKL_HOME/lib/intel64" 
SCALAPACK_FCFLAGS="-L$MKL_HOME/lib/intel64 -lmkl_scalapack_lp64 
-lmkl_gf_lp64 -lmkl_sequential \ 
                     -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread -lm 
-I$MKL_HOME/include/intel64/lp64" 

with_elpa=${1:-__INSTALL__} 

[ -f "${BUILDDIR}/setup_elpa" ] && rm "${BUILDDIR}/setup_elpa" 

ELPA_CFLAGS='-mavx512f -mavx512er -mavx512cd -mavx512pf ' 
ELPA_LDFLAGS='-L$MKL_HOME/lib/intel64 -lmkl_scalapack_lp64 -lmkl_gf_lp64 
-lmkl_sequential \ 
                             -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread 
-lm -Wl,-rpath,$MKL_HOME/lib/intel64' 
ELPA_LIBS='-L$MKL_HOME/lib/intel64 -lmkl_scalapack_lp64 -lmkl_gf_lp64 
-lmkl_sequential \ 
                     -lmkl_core -lmkl_blacs_intelmpi_lp64 -lpthread -lm 
-I$MKL_HOME/include/intel64/lp64' 
ELPA_CFLAGS_OMP='-fopenmp' 
ELPA_LIBS_OMP='' 
! [ -d "${BUILDDIR}" ] && mkdir -p "${BUILDDIR}" 
cd "${BUILDDIR}"

and then the toolchain ran and said it built elpa.




Then I tried the make of local.psmp and it makes it almost to the end, and 
fails on the link :


/usr/bin/ld: 
/home/rcohen/CP2K/cp2k/tools/toolchain/install/scalapack-2.0.2/lib/libscalapack.a(dgebs2d_.o)(.text+0xb7): 
unresolvable R_X86_64_32 relocation against symbol `BI_AuxBuff'
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status

or in detail ((I tried adding the -no-pie but it failed the same way as 
without):


mpif90 -no-pie -mavx512f -mavx512er -mavx512cd -mavx512pf -march=native 
-fno-omit-frame-pointer -g  -O3 -funroll-loops -ffast-math  -fopenmp 
-I/home/rcohen/CP2K/cp2k/tools/toolchain/build  
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/mpich-3.2.1/include'  
-m64 
-I/mnt/beegfs/intel/compilers_and_libraries_2018.5.274/linux/mkl/include 
-I/mnt/beegfs/intel/compilers_and_libraries_2018.5.274/linux/mkl/include/fftw 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/fftw-3.3.7/include' 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/libint-1.1.6/include' 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/libxc-4.0.3/include' 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/libxsmm-1.10.0/include' 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/elpa-2017.05.002/include/elpa_openmp-2017.05.002/modules' 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/elpa-2017.05.002/include/elpa_openmp-2017.05.002/elpa' 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/gsl-2.5/include' 
-I/home/rcohen/CP2K/cp2k/tools/toolchain/install/spglib-1.10.4/include 
-I/home/rcohen/CP2K/cp2k/tools/toolchain/install/hdf5-1.10.4/include 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/json_fortran-6.9.0/include' 
-ffree-form -std=f2003 -fimplicit-none  -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 
-Werror=uninitialized -Wno-maybe-uninitialized -Wuse-without-only  
-D__LIBXSMM  -D__parallel  -D__FFTW3  -D__LIBINT -D__LIBINT_MAX_AM=6 
-D__LIBDERIV_MAX_AM1=5 -D__LIBXC -D__SCALAPACK -D__ELPA=201705 -D__GSL 
-D__SPGLIB -D__HDF5 -D__JSON   -D__COMPILE_ARCH="\"local\"" 
-D__COMPILE_DATE="\"Mon Jan 14 14:15:43 CET 2019\"" 
-D__COMPILE_HOST="\"tomcat3\"" -D__COMPILE_REVISION="\"git:89b110c40\"" 
-D__DATA_DIR="\"/home/rcohen/CP2K/cp2k/data\"" -no-pie 
-Wl,--enable-new-dtags 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/mpich-3.2.1/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/mpich-3.2.1/lib'  
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/fftw-3.3.7/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/fftw-3.3.7/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/libint-1.1.6/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/libint-1.1.6/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/libxc-4.0.3/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/libxc-4.0.3/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/libxsmm-1.10.0/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/libxsmm-1.10.0/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/scalapack-2.0.2/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/scalapack-2.0.2/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/elpa-2017.05.002/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/elpa-2017.05.002/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/gsl-2.5/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/gsl-2.5/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/spglib-1.10.4/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/spglib-1.10.4/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/hdf5-1.10.4/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/hdf5-1.10.4/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/json_fortran-6.9.0/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/json_fortran-6.9.0/lib' 
-L/home/rcohen/CP2K/cp2k/lib/local/psmp -o 
/home/rcohen/CP2K/cp2k/exe/local/cp2k_shell.psmp cp2k_shell.o  -lcp2kstart 
-lcp2kmc -lcp2kswarm -lcp2kmotion -lcp2kthermostat -lcp2kemd -lcp2ktmc 
-lcp2kmain -lcp2kgrid -ldbcsrarnoldi -ldbcsrx -lcp2kshg_int -lcp2keri_mme 
-lcp2kminimax -lcp2khfxbase -lcp2ksubsys -lcp2kxc -lcp2kao -lcp2kinput 
-lcp2kpw -lcp2kfft -lcp2kfm -lcp2kcommon -lcp2kmpiwrap -lcp2kbase 
-L/home/rcohen/CP2K/cp2k/lib/local/psmp/exts/dbcsr -ldbcsr -ljsonfortran 
-lhdf5 -lsymspg -lgsl -lgslcblas -lelpa_openmp -lscalapack -lxsmmf -lxsmm 
-ldl -lpthread -lxcf03 -lxc -Wl,-Bstatic -lderiv -lint -Wl,-Bdynamic 
-lfftw3 -lfftw3_omp  -lmpi -lmpicxx  -Wl,--start-group 
/mnt/beegfs/intel/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64/libmkl_gf_lp64.a 
/mnt/beegfs/intel/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64/libmkl_core.a 
/mnt/beegfs/intel/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64/libmkl_sequential.a 
-Wl,--end-group -lpthread -lm -ldl -lstdc++
mpif90 -no-pie -mavx512f -mavx512er -mavx512cd -mavx512pf -march=native 
-fno-omit-frame-pointer -g  -O3 -funroll-loops -ffast-math  -fopenmp 
-I/home/rcohen/CP2K/cp2k/tools/toolchain/build  
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/mpich-3.2.1/include'  
-m64 
-I/mnt/beegfs/intel/compilers_and_libraries_2018.5.274/linux/mkl/include 
-I/mnt/beegfs/intel/compilers_and_libraries_2018.5.274/linux/mkl/include/fftw 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/fftw-3.3.7/include' 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/libint-1.1.6/include' 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/libxc-4.0.3/include' 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/libxsmm-1.10.0/include' 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/elpa-2017.05.002/include/elpa_openmp-2017.05.002/modules' 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/elpa-2017.05.002/include/elpa_openmp-2017.05.002/elpa' 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/gsl-2.5/include' 
-I/home/rcohen/CP2K/cp2k/tools/toolchain/install/spglib-1.10.4/include 
-I/home/rcohen/CP2K/cp2k/tools/toolchain/install/hdf5-1.10.4/include 
-I'/home/rcohen/CP2K/cp2k/tools/toolchain/install/json_fortran-6.9.0/include' 
-ffree-form -std=f2003 -fimplicit-none  -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 
-Werror=uninitialized -Wno-maybe-uninitialized -Wuse-without-only  
-D__LIBXSMM  -D__parallel  -D__FFTW3  -D__LIBINT -D__LIBINT_MAX_AM=6 
-D__LIBDERIV_MAX_AM1=5 -D__LIBXC -D__SCALAPACK -D__ELPA=201705 -D__GSL 
-D__SPGLIB -D__HDF5 -D__JSON   -D__COMPILE_ARCH="\"local\"" 
-D__COMPILE_DATE="\"Mon Jan 14 14:15:43 CET 2019\"" 
-D__COMPILE_HOST="\"tomcat3\"" -D__COMPILE_REVISION="\"git:89b110c40\"" 
-D__DATA_DIR="\"/home/rcohen/CP2K/cp2k/data\"" -no-pie 
-Wl,--enable-new-dtags 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/mpich-3.2.1/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/mpich-3.2.1/lib'  
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/fftw-3.3.7/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/fftw-3.3.7/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/libint-1.1.6/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/libint-1.1.6/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/libxc-4.0.3/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/libxc-4.0.3/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/libxsmm-1.10.0/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/libxsmm-1.10.0/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/scalapack-2.0.2/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/scalapack-2.0.2/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/elpa-2017.05.002/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/elpa-2017.05.002/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/gsl-2.5/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/gsl-2.5/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/spglib-1.10.4/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/spglib-1.10.4/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/hdf5-1.10.4/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/hdf5-1.10.4/lib' 
-L'/home/rcohen/CP2K/cp2k/tools/toolchain/install/json_fortran-6.9.0/lib' 
-Wl,-rpath='/home/rcohen/CP2K/cp2k/tools/toolchain/install/json_fortran-6.9.0/lib'  
-L/home/rcohen/CP2K/cp2k/lib/local/psmp -o 
/home/rcohen/CP2K/cp2k/exe/local/libcp2k_unittest.psmp libcp2k_unittest.o  
-lcp2kstart -lcp2kmc -lcp2kswarm -lcp2kmotion -lcp2kthermostat -lcp2kemd 
-lcp2ktmc -lcp2kmain -lcp2kgrid -ldbcsrarnoldi -ldbcsrx -lcp2kshg_int 
-lcp2keri_mme -lcp2kminimax -lcp2khfxbase -lcp2ksubsys -lcp2kxc -lcp2kao 
-lcp2kinput -lcp2kpw -lcp2kfft -lcp2kfm -lcp2kcommon -lcp2kmpiwrap 
-lcp2kbase -L/home/rcohen/CP2K/cp2k/lib/local/psmp/exts/dbcsr -ldbcsr 
-ljsonfortran -lhdf5 -lsymspg -lgsl -lgslcblas -lelpa_openmp -lscalapack 
-lxsmmf -lxsmm -ldl -lpthread -lxcf03 -lxc -Wl,-Bstatic -lderiv -lint 
-Wl,-Bdynamic -lfftw3 -lfftw3_omp  -lmpi -lmpicxx  -Wl,--start-group 
/mnt/beegfs/intel/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64/libmkl_gf_lp64.a 
/mnt/beegfs/intel/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64/libmkl_core.a 
/mnt/beegfs/intel/compilers_and_libraries_2018.5.274/linux/mkl/lib/intel64/libmkl_sequential.a 
-Wl,--end-group -lpthread -lm -ldl -lstdc++
/usr/bin/ld: 
/home/rcohen/CP2K/cp2k/tools/toolchain/install/scalapack-2.0.2/lib/libscalapack.a(dgebs2d_.o)(.text+0xb7): 
unresolvable R_X86_64_32 relocation against symbol `BI_AuxBuff'
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
/home/rcohen/CP2K/cp2k/obj/local/psmp/all.dep:94: recipe for target 
'/home/rcohen/CP2K/cp2k/exe/local/cp2k_shell.psmp' failed
make[3]: *** [/home/rcohen/CP2K/cp2k/exe/local/cp2k_shell.psmp] Error 1
make[3]: *** Waiting for unfinished jobs....
/usr/bin/ld: 
/home/rcohen/CP2K/cp2k/tools/toolchain/install/scalapack-2.0.2/lib/libscalapack.a(dgebs2d_.o)(.text+0xb7): 
unresolvable R_X86_64_32 relocation against symbol `BI_AuxBuff'
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
/home/rcohen/CP2K/cp2k/obj/local/psmp/all.dep:98: recipe for target 
'/home/rcohen/CP2K/cp2k/exe/local/libcp2k_unittest.psmp' failed
make[3]: *** [/home/rcohen/CP2K/cp2k/exe/local/libcp2k_unittest.psmp] Error 
1
/usr/bin/ld: 
/home/rcohen/CP2K/cp2k/tools/toolchain/install/scalapack-2.0.2/lib/libscalapack.a(dgebs2d_.o)(.text+0xb7): 
unresolvable R_X86_64_32 relocation against symbol `BI_AuxBuff'
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
/home/rcohen/CP2K/cp2k/obj/local/psmp/all.dep:90: recipe for target 
'/home/rcohen/CP2K/cp2k/exe/local/cp2k.psmp' failed
make[3]: *** [/home/rcohen/CP2K/cp2k/exe/local/cp2k.psmp] Error 1
/home/rcohen/CP2K/cp2k/Makefile:132: recipe for target 'all' failed
make[2]: *** [all] Error 2
/home/rcohen/CP2K/cp2k/Makefile:121: recipe for target 'psmp' failed
make[1]: *** [psmp] Error 2
Makefile:116: recipe for target 'all' failed
make: *** [all] Error 2



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