Difference between revisions of "CP2K compiling with Intel"

From iRASPA
Jump to: navigation, search
(→‎CP2K)
(→‎CP2K basic openmpi)
 
(3 intermediate revisions by the same user not shown)
Line 99: Line 99:
 
==== CP2K ====
 
==== CP2K ====
  
−
<blockquote style="background-color: lightgrey; border: solid thin grey;">
 
 
<pre>
 
<pre>
 
# Tested with: intel 19.1.1.217, OPENMPICH 4.0.3, OpenBLAS 0.3.0, ScaLAPACK 2.1.0, FFTW 3.3.8, Libint 2.6.0, Libxc 4.3.4, libxsmm 1.15, SPGLIB 1.12.2
 
# Tested with: intel 19.1.1.217, OPENMPICH 4.0.3, OpenBLAS 0.3.0, ScaLAPACK 2.1.0, FFTW 3.3.8, Libint 2.6.0, Libxc 4.3.4, libxsmm 1.15, SPGLIB 1.12.2
Line 134: Line 133:
  
 
</pre>
 
</pre>
−
</blockquote>
 
  
 
Before running the test, raise the stack-limit to avoid segmentation faults.
 
Before running the test, raise the stack-limit to avoid segmentation faults.
Line 173: Line 171:
 
==== CP2K basic openmpi ====
 
==== CP2K basic openmpi ====
  
−
<blockquote style="background-color: lightgrey; border: solid thin grey;">
+
<pre>
−
# Tested with: intel 19.1.1.217, OPENMPICH 4.0.3, OpenBLAS 0.3.0, ScaLAPACK 2.1.0, FFTW 3.3.8, Libint 2.6.0, Libxc 4.3.4, libxsmm 1.15,SPGLIB 1.12.2<br>
+
# Tested with: Intel 19.1.1.217, OPENMPICH 4.0.3, OpenBLAS 0.3.0, ScaLAPACK 2.1.0, FFTW 3.3.8, Libint 2.6.0, Libxc 4.3.4, libxsmm 1.15,
−
# Author: David Dubbeldam (d.dubbeldam@uva.nl, University of Amsterdam, May 2020)<br>
+
#              ELPA 2019.11.001, PLUMED 2.6.0, SPGLIB 1.12.2, QUIP-2015, ParMETIS-4.0.3, Pexsi-1.2.0, SIRIUS 6.5.3, SpFFT 0.9.9, libvdw 0.4.0
−
<br>
+
# Author: David Dubbeldam (d.dubbeldam@uva.nl, University of Amsterdam, May 2020)
−
CC         = icc<br>
+
 
−
FC         = ifort<br>
+
CC           = /usr/lib64/openmpi4-intel/bin/mpicc
−
LD         = ifort<br>
+
FC           = /usr/lib64/openmpi4-intel/bin/mpifort
−
AR         = ar -r<br>
+
LD           = /usr/lib64/openmpi4-intel/bin/mpifort
−
<br>
+
AR           = ar -r
−
CFLAGS     = $(DFLAGS) -O2 -xcore-avx2 -fp-model precise -I/opt/include<br>
+
 
−
<br>
+
CFLAGS       = $(DFLAGS) -O2 -xcore-avx2 -fp-model precise -I/opt/include
−
DFLAGS     = -D__MKL -D__FFTW3 -D__LIBXC -D__LIBINT -D__LIBXSMM -D__SPGLIB<br>
+
 
−
<br>
+
DFLAGS       = -D__MPI_VERSION=4 -D__parallel -D__SCALAPACK
−
FCFLAGS     = $(DFLAGS) -O2 -funroll-loops -fpp -free -xcore-avx2 -I/opt/include<br>
+
DFLAGS      += -D__MKL -D__FFTW3 -D__LIBXC -D__LIBINT -D__LIBXSMM -D__SPGLIB
−
FCFLAGS   += -fp-model precise<br>
+
DFLAGS      += -D__SIRIUS -D__PLUMED2 -D__QUIP -D__LIBPEXSI -D__ELPA
−
FCFLAGS   += -g -traceback<br>
+
 
−
FCFLAGS    += -I${MKLROOT}/include -I${MKLROOT}/include/fftw<br>
+
FCFLAGS       = $(DFLAGS) -O2 -funroll-loops -fpp -free -xcore-avx2 -I/opt/include
−
FCFLAGS   += -I/opt/include -I/opt/lib/libint2-intel-max6/include<br>
+
FCFLAGS     += -fp-model precise
−
<br>
+
FCFLAGS     += -I${MKLROOT}/include -I${MKLROOT}/include/fftw
−
LDFLAGS = $(FCFLAGS) -static-intel<br>
+
FCFLAGS     += -I/opt/include -I/opt/include/sirius/ -I/opt/lib/libint2-intel-max6/include
−
LDFLAGS_C = $(FCFLAGS) -static-intel -nofor_main<br>
+
FCFLAGS      += -I/opt/include/elpa-2019.11.001/elpa -I/opt/include/elpa-2019.11.001/modules
−
<br>
+
 
−
INTEL_MKL_LIB = ${MKLROOT}/lib/intel64<br>
+
LDFLAGS       = $(FCFLAGS) -static-intel
−
<br>
+
LDFLAGS_C     = $(FCFLAGS) -static-intel -nofor_main
−
LIBS       = /opt/lib/libgsl.a /opt/lib/libgslcblas.a<br>
+
 
−
LIBS       += /opt/lib/libxcf03.a /opt/lib/libxc.a<br>
+
INTEL_MKL_LIB = ${MKLROOT}/lib/intel64
−
LIBS       += /opt/lib/libxsmmf.a /opt/lib/libxsmm.a<br>
+
 
−
LIBS       += /opt/lib/libint2-intel-max6/lib/libint2.a<br>
+
LIBS         = $(PLUMED_DEPENDENCIES) -lplumed
−
LIBS       += -Wl,--start-group \<br>
+
LIBS        += /opt/lib/libint2-intel-max6/lib/libint2.a
−
              $(MKLROOT)/interfaces/fftw3xf/libfftw3xf_intel.a \<br>
+
LIBS        += /opt/lib/libelpa.a
−
              -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_lapack95_lp64 -lmkl_blas95_lp64 \<br>
+
LIBS        += /opt/lib64/libsirius.a
−
              -Wl,--end-group -lpthread -lm<br>
+
LIBS        += /opt/lib64/libpexsi.a
−
LIBS       += -lz -lsymspg -ldl -lpthread -lstdc++<br>
+
LIBS        += /opt/lib64/libsuperlu_dist.a
−
</blockquote>
+
LIBS        += /opt/lib/libspfft.a
 +
LIBS        += /opt/lib/libvdwxc.a
 +
LIBS        += /opt/lib/libquip_core.a /opt/lib/libatoms.a
 +
LIBS        += /opt/lib/libFoX_sax.a
 +
LIBS        += /opt/lib/libFoX_common.a
 +
LIBS        += /opt/lib/libFoX_utils.a
 +
LIBS        += /opt/lib/libFoX_fsys.a
 +
LIBS         += /opt/lib/libparmetis.a /opt/lib/libmetis.a
 +
LIBS         += /opt/lib/libgsl.a /opt/lib/libgslcblas.a
 +
LIBS         += /opt/lib/libxcf03.a /opt/lib/libxc.a
 +
LIBS         += /opt/lib/libxsmmf.a /opt/lib/libxsmm.a
 +
LIBS        += $(MKLROOT)/interfaces/fftw3xf/libfftw3xf_intel.a \
 +
                -Wl,--start-group \
 +
                -lmkl_scalapack_lp64 \
 +
                -lmkl_blacs_openmpi_lp64 \
 +
                -lmkl_intel_lp64 \
 +
                -lmkl_sequential \
 +
                -lmkl_core \
 +
                -Wl,--end-group
 +
LIBS         += -lnetcdf -lhdf5_hl -lhdf5 -lz -lsymspg -ldl -liomp5 -lpthread -lstdc++ -lmpi_mpifh -lmpi_cxx -lmpi
 +
</pre>
 +
 
 +
Prepare for the regression tests
 +
module load mpi/openmpi4-x86_64-intel
 +
ulimit -c unlimited
 +
export OMPI_ALLOW_RUN_AS_ROOT=1
 +
export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 +
export OMPI_MCA_btl_openib_allow_ib=1
 +
export OMPI_MCA_btl_vader_single_copy_mechanism=none
 +
export OMPI_MCA_btl=openib,self,vader
 +
export OMPI_MCA_pml=^ucx
 +
export FI_PROVIDER=ofi_rxm
 +
export FI_PROVIDER="verbs;ofi_rxm"
 +
 
  
  

Latest revision as of 14:12, 11 June 2020

Compiling

Compiling subpackages

Serial

preparation

source /opt/intel/compilers_and_libraries_2020/linux/bin/compilervars.sh intel64
source /opt/intel/compilers_and_libraries_2020/linux/mkl/bin/mklvars.sh intel64
export AR="xiar"
export FC="ifort"
export CC="icc"
export CXX="icpc"
export F77=${FC}
export F90=${FC}

Gsl

Reduced optimization to "-O1", but with intel-compiler still fails LinAlg-unit test 

wget http://gnu.askapache.com/gsl/gsl-2.6.tar.gz
tar -zxvf gsl-2.6.tar.gz
 ./configure --prefix=/usr/local CC=icc FC=ifort CXX=icpc FCFLAGS="-O1 -xcore-avx2" CFLAGS="-O1 -xcore-avx2" CXXFLAGS="-O1 -xcore-avx2" --enable-shared=no
make -j 16
make check

Libint2

Reduced optimization to "-O2" 

wget https://github.com/cp2k/libint-cp2k/releases/download/v2.6.0/libint-v2.6.0-cp2k-lmax-4.tgz
wget https://github.com/cp2k/libint-cp2k/releases/download/v2.6.0/libint-v2.6.0-cp2k-lmax-5.tgz
wget https://github.com/cp2k/libint-cp2k/releases/download/v2.6.0/libint-v2.6.0-cp2k-lmax-6.tgz
wget https://github.com/cp2k/libint-cp2k/releases/download/v2.6.0/libint-v2.6.0-cp2k-lmax-7.tgz
tar -zxvf libint-v2.6.0-cp2k-lmax-5.tgz
cd libint-v2.6.0-cp2k-lmax-5
./configure --prefix=/usr/local CC=icc FC=ifort CXX=icpc FCFLAGS="-O2 -xcore-avx2" CFLAGS="-O2 -xcore-avx2" CXXFLAGS="-O2 -xcore-avx2" --enable-shared=no --enable-fortran --with-cxx-optflags="-O2 -xcore-avx2"
make -j 24
make -j 24 check

all tests ok

edit Makefile in directory fortran line 12 should read (-lstdc++ added) 

COMPUTE_LIB = -L../lib -lint2 -lstdc++

line 37 change CXX to FC 

 $(LTLINK) $(FC) $(CXXFLAGS) $(LDFLAGS) $(COMPUTE_LIB) $(SYSLIBS) $(FCLIBS) -o $@ $^

sudo make install
sudo make install_fortran

/usr/local/lib/libint2.a

Libxsmm

A library for improved performance for matrix multiplication and deep learning primitives 

wget https://www.cp2k.org/static/downloads/libxsmm-1.15.tar.gz
tar -zxvf libxsmm-1.15.tar.gz
sudo make PREFIX=/usr/local FC=/opt/intel/compilers_and_libraries_2020.1.217/linux/bin/intel64/ifort CC=/opt/intel/compilers_and_libraries_2020.1.217/linux/bin/intel64/icc CXX=/opt/intel/compilers_and_libraries_2020.1.217/linux/bin/intel64/icpc FCFLAGS="-O2 -xcore-avx2" CFLAGS="-O2 -xcore-avx2" CXXFLAGS="-O2 -xcore-avx2" STATIC=1 NO_SHARED=1 MALLOC=0  -j 24 install

all 16 test okay 

make PREFIX=/usr/local STATIC=1 NO_SHARED=1 install

/usr/local/lib/libxsmm.a
/usr/local/lib/libxsmmext.a
/usr/local/lib/libxsmmf.a
/usr/local/lib/libxsmmgen.a
/usr/local/lib/libxsmmnoblas.a

Libxc

wget https://www.cp2k.org/static/downloads/libxc-4.3.4.tar.gz
tar -zxvf libxc-4.3.4.tar.gz
cd libxc-4.3.4
./configure --prefix=/usr/local CC=icc FC=ifort CXX=icpc FCFLAGS="-O2 -xcore-avx2" CFLAGS="-O2 -xcore-avx2" CXXFLAGS="-O2 -xcore-avx2" --enable-shared=no --enable-static=yes --enable-fortran
make -j 24
make check

PASS: xc-run_testsuite
============================================================================
Testsuite summary for libxc 4.3.4
============================================================================
# TOTAL: 1
# PASS: 1

sudo make install
sudo cp src/*.mod /usr/local/include/

/usr/local/lib/libxc.a
/usr/local/lib/libxcf03.a
/usr/local/lib/libxcf90.a

CP2K

# Tested with: intel 19.1.1.217, OPENMPICH 4.0.3, OpenBLAS 0.3.0, ScaLAPACK 2.1.0, FFTW 3.3.8, Libint 2.6.0, Libxc 4.3.4, libxsmm 1.15, SPGLIB 1.12.2
# Author: David Dubbeldam (d.dubbeldam@uva.nl, University of Amsterdam, May 2020)

CC            = icc
FC            = ifort
LD            = ifort
AR            = ar -r

CFLAGS        = $(DFLAGS) -O2 -xcore-avx2 -fp-model precise -I/opt/include

DFLAGS        = -D__MKL -D__FFTW3 -D__LIBXC -D__LIBINT -D__LIBXSMM -D__SPGLIB

FCFLAGS       = $(DFLAGS) -O2 -funroll-loops -fpp -free -xcore-avx2 -I/opt/include
FCFLAGS      += -fp-model precise
FCFLAGS      += -I${MKLROOT}/include -I${MKLROOT}/include/fftw
FCFLAGS      += -I/opt/include -I/opt/lib/libint2-intel-max6/include

LDFLAGS       = $(FCFLAGS) -static-intel
LDFLAGS_C     = $(FCFLAGS) -static-intel -nofor_main

INTEL_MKL_LIB = ${MKLROOT}/lib/intel64

LIBS          = /opt/lib/libgsl.a /opt/lib/libgslcblas.a
LIBS         += /opt/lib/libxcf03.a /opt/lib/libxc.a
LIBS         += /opt/lib/libxsmmf.a /opt/lib/libxsmm.a
LIBS         += /opt/lib/libint2-intel-max6/lib/libint2.a
LIBS         += -Wl,--start-group \
                $(MKLROOT)/interfaces/fftw3xf/libfftw3xf_intel.a \
                -lmkl_intel_lp64 -lmkl_sequential -lmkl_core -lmkl_lapack95_lp64 -lmkl_blas95_lp64 \
                -Wl,--end-group -lpthread -lm
LIBS         += -lz -lsymspg -ldl -lpthread -lstdc++

Before running the test, raise the stack-limit to avoid segmentation faults. 

ulimit -s unlimited

Summary --------------------------------
Number of FAILED tests 0
Number of WRONG tests 4
Number of CORRECT tests 3197
Number of NEW tests 3
Total number of tests 3204
GREPME 0 4 3197 3 3204 X

Summary: correct: 3197 / 3204; new: 3; wrong: 4; 50min
Status: FAILED

MPI

preparation

source /opt/intel/compilers_and_libraries_2020/linux/bin/compilervars.sh intel64
source /opt/intel/compilers_and_libraries_2020/linux/mkl/bin/mklvars.sh intel64
export AR="xiar"
export FC="/usr/lib64/openmpi4-intel/bin/mpifort"
export CC="/usr/lib64/openmpi4-intel/bin/mpicc"
export CXX="/usr/lib64/openmpi4-intel/bin/mpicxx"
export F77=${FC}
export F90=${FC}
module load mpi/openmpi4-x86_64-intel
export OMPI_MCA_pml=^ucx
export OMPI_MCA_btl=self,tcp
export OMPI_MCA_btl_openib_allow_ib=1
export OMPI_MCA_btl_vader_single_copy_mechanism=none
ulimit -s unlimited

CP2K basic openmpi

# Tested with: Intel 19.1.1.217, OPENMPICH 4.0.3, OpenBLAS 0.3.0, ScaLAPACK 2.1.0, FFTW 3.3.8, Libint 2.6.0, Libxc 4.3.4, libxsmm 1.15,
#              ELPA 2019.11.001, PLUMED 2.6.0, SPGLIB 1.12.2, QUIP-2015, ParMETIS-4.0.3, Pexsi-1.2.0, SIRIUS 6.5.3, SpFFT 0.9.9, libvdw 0.4.0
# Author: David Dubbeldam (d.dubbeldam@uva.nl, University of Amsterdam, May 2020)

CC            = /usr/lib64/openmpi4-intel/bin/mpicc
FC            = /usr/lib64/openmpi4-intel/bin/mpifort
LD            = /usr/lib64/openmpi4-intel/bin/mpifort
AR            = ar -r

CFLAGS        = $(DFLAGS) -O2 -xcore-avx2 -fp-model precise -I/opt/include

DFLAGS        = -D__MPI_VERSION=4 -D__parallel -D__SCALAPACK
DFLAGS       += -D__MKL -D__FFTW3 -D__LIBXC -D__LIBINT -D__LIBXSMM -D__SPGLIB
DFLAGS       += -D__SIRIUS -D__PLUMED2 -D__QUIP -D__LIBPEXSI -D__ELPA

FCFLAGS       = $(DFLAGS) -O2 -funroll-loops -fpp -free -xcore-avx2 -I/opt/include
FCFLAGS      += -fp-model precise
FCFLAGS      += -I${MKLROOT}/include -I${MKLROOT}/include/fftw
FCFLAGS      += -I/opt/include -I/opt/include/sirius/ -I/opt/lib/libint2-intel-max6/include
FCFLAGS      += -I/opt/include/elpa-2019.11.001/elpa -I/opt/include/elpa-2019.11.001/modules

LDFLAGS       = $(FCFLAGS) -static-intel
LDFLAGS_C     = $(FCFLAGS) -static-intel -nofor_main

INTEL_MKL_LIB = ${MKLROOT}/lib/intel64

LIBS          = $(PLUMED_DEPENDENCIES) -lplumed
LIBS         += /opt/lib/libint2-intel-max6/lib/libint2.a
LIBS         += /opt/lib/libelpa.a
LIBS         += /opt/lib64/libsirius.a
LIBS         += /opt/lib64/libpexsi.a
LIBS         += /opt/lib64/libsuperlu_dist.a
LIBS         += /opt/lib/libspfft.a
LIBS         += /opt/lib/libvdwxc.a
LIBS         += /opt/lib/libquip_core.a /opt/lib/libatoms.a
LIBS         += /opt/lib/libFoX_sax.a
LIBS         += /opt/lib/libFoX_common.a
LIBS         += /opt/lib/libFoX_utils.a
LIBS         += /opt/lib/libFoX_fsys.a
LIBS         += /opt/lib/libparmetis.a /opt/lib/libmetis.a
LIBS         += /opt/lib/libgsl.a /opt/lib/libgslcblas.a
LIBS         += /opt/lib/libxcf03.a /opt/lib/libxc.a
LIBS         += /opt/lib/libxsmmf.a /opt/lib/libxsmm.a
LIBS         += $(MKLROOT)/interfaces/fftw3xf/libfftw3xf_intel.a \
                -Wl,--start-group \
                -lmkl_scalapack_lp64 \
                -lmkl_blacs_openmpi_lp64 \
                -lmkl_intel_lp64 \
                -lmkl_sequential \
                -lmkl_core \
                -Wl,--end-group
LIBS         += -lnetcdf -lhdf5_hl -lhdf5 -lz -lsymspg -ldl -liomp5 -lpthread -lstdc++ -lmpi_mpifh -lmpi_cxx -lmpi

Prepare for the regression tests 

module load mpi/openmpi4-x86_64-intel
ulimit -c unlimited
export OMPI_ALLOW_RUN_AS_ROOT=1
export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
export OMPI_MCA_btl_openib_allow_ib=1
export OMPI_MCA_btl_vader_single_copy_mechanism=none
export OMPI_MCA_btl=openib,self,vader
export OMPI_MCA_pml=^ucx
export FI_PROVIDER=ofi_rxm
export FI_PROVIDER="verbs;ofi_rxm"


Summary --------------------------------

Number of FAILED tests 0
Number of WRONG tests 3
Number of CORRECT tests 3198
Number of NEW tests 3
Total number of tests 3204
GREPME 0 3 3198 3 3204 X

Summary: correct: 3198 / 3204; new: 3; wrong: 3; 8min
Status: FAILED

Retrieved from "https://wiki.iraspa.org/index.php?title=CP2K_compiling_with_Intel&oldid=1280"