Comments (1)
Fravadona
commented on July 26, 2024
Hi eric-jm-lang,
I successfully built and ran CHAP, linked to GROMACS 2018.8, with everything compiled with Intel Compilers 2018.3 and Intel MKL 2018.3.
First you would need to apply the patch file at the end of #22 that fixes a few bugs and compilation issues.
Then, if you want to be able to relocate CHAP after installation then you'll also need to apply the patch in #23 .
And if you want to compile CHAP with MKL's LAPACK/LAPACKE/BLAS/CBLAS then you should also change this:
--- chap-version_0_9_1/src/geometry/cubic_spline_interp_1D.cpp.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/src/geometry/cubic_spline_interp_1D.cpp 2019-12-06 16:47:52.052585866 +0100
@@ -26,7 +26,7 @@
#include <stdexcept>
#include <string>
-#include <lapacke.h>
+#include <mkl_lapacke.h>
#include "geometry/basis_spline.hpp"
#include "geometry/cubic_spline_interp_1D.hpp"
--- chap-version_0_9_1/src/geometry/cubic_spline_interp_3D.cpp.orig 2018-05-02 13:22:36.000000000 +0200
+++ chap-version_0_9_1/src/geometry/cubic_spline_interp_3D.cpp 2019-12-06 16:48:16.509297021 +0100
@@ -26,7 +26,7 @@
#include <stdexcept>
#include <string>
-#include <lapacke.h>
+#include <mkl_lapacke.h>
#include "geometry/basis_spline.hpp"
#include "geometry/cubic_spline_interp_3D.hpp"
For CHAP compilation with MKL there's a trick in the CMAKE command, which is to specify a dot for all related LAPACK and BLAS stuff.
So here's my CMAKE command, with AVX2 processor acceleration but you can change it. GROMACS and BOOST are supposed to be installed in a "3rdparty" directory inside the CHAP directory:
# First source the Intel environement (Compilers and MKL)
. /opt/intel/XXXXXX/compilervars.sh intel64
. /opt/intel/XXXXXX/mklvars intel64
CHAPDIR='/opt/chap-gmx2018.8-intel2018.3-avx2'
IFLAGS='-xCORE-AVX2 -mkl=sequential'
cmake3 \
-DCMAKE_INSTALL_PREFIX=${CHAPDIR} \
-DGROMACS_DIR=${CHAPDIR}/3rdparty/share/cmake/gromacs \
-DBOOST_ROOT=${CHAPDIR}/3rdparty \
-DCMAKE_VERBOSE_MAKEFILE=ON \
-DCMAKE_C_COMPILER="$(which icc)" \
-DCMAKE_C_FLAGS="${IFLAGS}" \
-DCMAKE_CXX_COMPILER="$(which icpc)" \
-DCMAKE_CXX_FLAGS="${IFLAGS}" \
-DLAPACKE_CBLAS_INCLUDE_DIR=. \
-DLAPACKE_LAPACKE_INCLUDE_DIR=. \
-DLAPACKE_LIB=. \
-DLAPACK_LIB=. \
-DBLAS_LIB=. \
-DCBLAS_LIB=. \
..
Remark: As GROMACS utilises MKL in sequential mode, it may be a good idea to specify it for CHAP also (I'm not very sure).
Remark: If BOOST isn't installed on a standard location then the BOOST_ROOT won't work unless it is installed in the same place than GROMACS.
Remark: If you want to statically link the Intel libraries to the binary, just add -static-intel after -mkl=sequential (though GROMACS would also need to be compiled this way because it doesn't make sense otherwise).
That's all, I hope this will prove useful to you.
Cheers.
PS: If you you to compile GROMACS with static Intel libraries I can provide the CMAKE command for it.
from chap.
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from chap.