VASP stands for Vienna Ab-initio Simulation Package and is a code written in FORTRAN 90 with MPI support that performs quantum-mechanical molecular dynamics (MD). This benchmark requires low latency networks to scale (Infiband over GbE). A free software stack (Open64/MVAPICH2/ACML/ScaLAPACK) performs comparably to the Intel stack.
| Version | Date | Notes |
|---|---|---|
| 0.1.3 | 2022-06-14 | Shell->bash, changes->history, typos |
| 0.1.2 | 2020-12-27 | Improve link section, line length |
| 0.1.1 | 2020-05-03 | Typos |
| 0.1.0 | 2016-08-27 | Initial release |
As root
cd /root/ckuelker/bm/bin
./speedup
./init-intel-license
./init-intel-compiler
cd /home/hpc/bm-vasp/src/Benchmarks
tar xvzf vasp.tar.gz
mv vasp vasp-007
chown -R hpc:hpc vasp-007As user hpc:
source /cm/shared/apps/intel-ics-2013/bin/compilervars.sh intel64
source /cm/shared/apps/intel-ics-2013/bin/iccvars.sh intel64
source /cm/shared/apps/intel-ics-2013/bin/ifortvars.sh intel64
source /cm/shared/apps/intel-ics-2013/impi/4.1.0.024/intel64/bin/mpivars.sh intel64
source /cm/shared/apps/intel-ics-2013/composer_xe_2013.1.117/mkl/bin/mklvars.sh intel64cd /home/hpc/bm-vasp/src/Benchmarks/vasp-007
./build.shcd /home/hpc/bm-vasp/src/Benchmarks/vasp-007
./run.shEventually edit run.sh and change core number to be used.
Optimization (changing compiler flags) in the make files:
Benchmarks/vasp/src/vasp.5.lib/Makefile
Benchmarks/vasp/src/wannier90-1.2/Makefile
Benchmarks/vasp/src/vasp.5.2.12/makefileThe Intel cluster has 12 core per CPU, Intel(R) Xeon(R) CPU E5645 @ 2.40GHz. Assuming the source is in ~/bm/src/vasp.tar.gz
tar xvzf bm/src/vasp.tar.gz
cd bm/src/vasp-5.2.12
module load intel/cs-xe-2013--binary
module load intelmpi/4.1.1--binary
module load blas/2011--intel--cs-xe-2013--binary
#module load boost/1.53.0--intel--cs-xe-2013--binaryOne problem is that the Intel wrapper is not made available for VASP. The file /lib/intel64/libfftw3xf_intel.a do not exists. Which will be announced like this:
make: *** No rule to make target `/lib/intel64/libfftw3xf_intel.a', needed by
`vasp'. Stop.
mkdir -p ~/bm/build/intel/fftw3xf
cd /prod/compilers/intel/cs-xe-2013/binary/composer_xe_2013.1.117/mkl/\
interfaces/fftw3xf
make libem64t compiler=intel install_to=~/bm/build/intel/fftw3xf
echo "export LD_LIBRARY_PATH=/new/prod/compilers/intel/cs-xe-2013/binary/impi\
/4.1.1.036/lib64/:/new/prod/compilers/intel/cs-xe-2013/binary/lib/intel64/:~/\
bm/build/intel/fftw3xf" > env
source envThat do not work, try this
cp src/vasp.5.2.12/makefile src/vasp.5.2.12/makefile.original
sed -i -e 's%\$(MKL_PATH)/libfftw3xf_intel.a%~/bm/build/intel/fftw3xf/\
libfftw3xf_intel.a%' src/vasp.5.2.12/makefile
diff src/vasp.5.2.12/makefile.original src/vasp.5.2.12/makefile
73c73
< FFT3D = fftmpi.o fftmpi_map.o fftw3d.o fft3dlib.o $(MKL_PATH)/libfftw3xf_intel.a
---
> FFT3D = fftmpi.o fftmpi_map.o fftw3d.o fft3dlib.o ~/bm/build/intel/fftw3xf/libfftw3xf_intel.aThen an other error occurs
ifort: error #10236: File not found: '/opt/intel/mkl/lib/intel64/libmkl_scalapack_lp64.a'
ifort: error #10236: File not found: '/opt/intel/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a'They can be found at:
/prod/compilers/intel/cs-xe-2013/binary/composer_xe_2013.1.117/mkl/lib/intel64/
sed -i -e 's%/opt/intel/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.a%/prod/\
compilers/intel/cs-xe-2013/binary/composer_xe_2013.1.117/mkl/lib/intel64/\
libmkl_blacs_intelmpi_lp64.a%' src/vasp.5.2.12/makefile
sed -i -e 's%/opt/intel/mkl/lib/intel64/libmkl_scalapack_lp64.a%/eurora_old/\
prod/compilers/intel/cs-xe-2013/binary/composer_xe_2013.1.117/mkl/lib/intel64/\
libmkl_scalapack_lp64.a%' src/vasp.5.2.12/makefileSuppressing warning and remarks:
Option -diag-disable warn (Linux and Mac OS X) and /Qdiag-disable:warn (Windows) disable all Source Checker diagnostics except those that have an “error” severity level. They suppress all Source Checker warnings, cautions, and remarks.
The original link to a PDF from slides of 2013 should be available. However sometimes (2020-10-21) are not. In this case the document is available via archive.org