Error in compilation of PETSC
Posted: Sun Apr 14, 2019 7:46 pm
Hello!
I've recently tried to recompile Yambo v4.4. I had a working compilation of the same exact branch before, but perhaps some of the compilers changed since I last did it, and now I am having issues when compiling PETSc, getting the following error:
===============================================================================
Configuring PETSc to compile on your system
===============================================================================
===============================================================================
***** WARNING: MAKEFLAGS (set to w -- VPATH=/global/homes/v/vatsal/codes/yambo-devel/compile_devel-excitonlifetimes/../lib/petsc) found in environment variables
use ./configure MAKEFLAGS=$MAKEFLAGS if you really want to use that value ****** =============================================================================== ===============================================================================
It appears you do not have valgrind installed on your system.
We HIGHLY recommend you install it from http://www.valgrind.org
Or install valgrind-devel or equivalent using your package manager.
Then rerun ./configure ===============================================================================
TESTING: checkLib from config.packages.BlasLapack(config/BuildSystem/config/packages/BlasLapack.py:106) *******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
-------------------------------------------------------------------------------
You set a value for --with-blas-lapack-lib=<lib>, but ['/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a', '-Wl,--start-group', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_intel_lp64.a', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_intel_thread.a', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_core.a', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a', '-Wl,-zmuldefs,--end-group', '-lpthread', '-lm', '-ldl', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a', '-Wl,--start-group', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_intel_lp64.a', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_intel_thread.a', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_core.a', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a', '-Wl,-zmuldefs,--end-group', '-lpthread', '-lm', '-ldl'] cannot be used
*******************************************************************************
Here are the options I am using for the configure:
export MKLLIBS="$MKLROOT/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group $MKLROOT/lib/intel64/libmkl_intel_lp64.a $MKLROOT/lib/intel64/libmkl_intel_thread.a $MKLROOT/lib/intel64/libmkl_core.a $MKLROOT/lib/intel64/libmkl_blacs_intelmpi_lp64.a -Wl,-zmuldefs,--end-group -lpthread -lm -ldl"
../configure \
--enable-dp \
--enable-msgs-comps \
--enable-memory-profile \
--enable-open-mp \
--enable-iotk \
--enable-slepc-linalg \
--with-extlibs-path="/global/homes/v/vatsal/codes/yambo-libs/" \
--with-blas-libs="$MKLLIBS" \
--with-lapack-libs="$MKLLIBS" \
--with-blacs-libs="$MKLLIBS" \
--with-scalapack-libs="$MKLLIBS" \
--with-fft-libs="/usr/common/software/mkl/2017.up2/interfaces/hsw/intel/libfftw3xf_intel.a" \
--with-fft-includedir="-I${MKLROOT}/include/fftw" \
--with-libxc-path="/global/common/sw/cray/cnl6/haswell/libxc/3.0.0/intel/17.0.2.174/uff3mhq" \
--with-netcdf-path="/opt/cray/pe/netcdf/4.4.1.1.3/INTEL/16.0" \
--with-hdf5-path="/opt/cray/pe/hdf5/1.10.0.3/INTEL/16.0" \
--with-mpi-path="/opt/cray/pe/mpt/7.6.2/gni/mpich-intel/16.0/" \
MPIFC=ftn FCFLAGS="-O3 -qopenmp" MPICC=cc CC=icc FC=ifort CPP="cpp -P"
I've also attached the config.log if that can provide any information.
Thanks so much!
I've recently tried to recompile Yambo v4.4. I had a working compilation of the same exact branch before, but perhaps some of the compilers changed since I last did it, and now I am having issues when compiling PETSc, getting the following error:
===============================================================================
Configuring PETSc to compile on your system
===============================================================================
===============================================================================
***** WARNING: MAKEFLAGS (set to w -- VPATH=/global/homes/v/vatsal/codes/yambo-devel/compile_devel-excitonlifetimes/../lib/petsc) found in environment variables
use ./configure MAKEFLAGS=$MAKEFLAGS if you really want to use that value ****** =============================================================================== ===============================================================================
It appears you do not have valgrind installed on your system.
We HIGHLY recommend you install it from http://www.valgrind.org
Or install valgrind-devel or equivalent using your package manager.
Then rerun ./configure ===============================================================================
TESTING: checkLib from config.packages.BlasLapack(config/BuildSystem/config/packages/BlasLapack.py:106) *******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
-------------------------------------------------------------------------------
You set a value for --with-blas-lapack-lib=<lib>, but ['/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a', '-Wl,--start-group', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_intel_lp64.a', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_intel_thread.a', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_core.a', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a', '-Wl,-zmuldefs,--end-group', '-lpthread', '-lm', '-ldl', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_scalapack_lp64.a', '-Wl,--start-group', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_intel_lp64.a', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_intel_thread.a', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_core.a', '/opt/intel/compilers_and_libraries_2018.1.163/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a', '-Wl,-zmuldefs,--end-group', '-lpthread', '-lm', '-ldl'] cannot be used
*******************************************************************************
Here are the options I am using for the configure:
export MKLLIBS="$MKLROOT/lib/intel64/libmkl_scalapack_lp64.a -Wl,--start-group $MKLROOT/lib/intel64/libmkl_intel_lp64.a $MKLROOT/lib/intel64/libmkl_intel_thread.a $MKLROOT/lib/intel64/libmkl_core.a $MKLROOT/lib/intel64/libmkl_blacs_intelmpi_lp64.a -Wl,-zmuldefs,--end-group -lpthread -lm -ldl"
../configure \
--enable-dp \
--enable-msgs-comps \
--enable-memory-profile \
--enable-open-mp \
--enable-iotk \
--enable-slepc-linalg \
--with-extlibs-path="/global/homes/v/vatsal/codes/yambo-libs/" \
--with-blas-libs="$MKLLIBS" \
--with-lapack-libs="$MKLLIBS" \
--with-blacs-libs="$MKLLIBS" \
--with-scalapack-libs="$MKLLIBS" \
--with-fft-libs="/usr/common/software/mkl/2017.up2/interfaces/hsw/intel/libfftw3xf_intel.a" \
--with-fft-includedir="-I${MKLROOT}/include/fftw" \
--with-libxc-path="/global/common/sw/cray/cnl6/haswell/libxc/3.0.0/intel/17.0.2.174/uff3mhq" \
--with-netcdf-path="/opt/cray/pe/netcdf/4.4.1.1.3/INTEL/16.0" \
--with-hdf5-path="/opt/cray/pe/hdf5/1.10.0.3/INTEL/16.0" \
--with-mpi-path="/opt/cray/pe/mpt/7.6.2/gni/mpich-intel/16.0/" \
MPIFC=ftn FCFLAGS="-O3 -qopenmp" MPICC=cc CC=icc FC=ifort CPP="cpp -P"
I've also attached the config.log if that can provide any information.
Thanks so much!