GENESIS 1.6.0 with GPU support
ウェブページ
https://www.r-ccs.riken.jp/labs/cbrt/バージョン
1.6.0ビルド環境
- Intel Parallel Studio XE 2018 Update 4
- CUDA 11.1 Update 1
ビルドに必要なファイル
- genesis-1.6.0.tar.bz2
- tests-1.6.0.tar.bz2
- fortdep.py.patch
--- fortdep.py.org 2020-12-28 14:05:33.000000000 +0900
+++ fortdep.py 2020-12-28 14:39:43.000000000 +0900
@@ -24,6 +24,7 @@
re_fcomment = re.compile( "(^[^!]*)!(.*$)" )
re_module = re.compile( "^(.*;+|\s*)\s*module\s*([^\s,]*)\s*", re.I )
re_use = re.compile( "^(.*;+\s*|\s*)use\s+([^\s,]*)\s*", re.I )
+ re_include = re.compile( "^(\s*)#include\s+['\"]([^'\"]+)['\"]\s*" )
mod_ext = ".mod"
def __init__( self, fname = "", ext = ".o" ):
@@ -31,6 +32,7 @@
self.filename = fname
self.modules = []
self.depmods = []
+ self.includes = []
def setFilename( self, fname, ext = ".o" ):
if len(fname) == 0:
@@ -54,6 +56,14 @@
if ( ma ):
modname = ma.group(2).lower()
self.appendDependMods( modname )
+ mi = FortranFile.re_include.search( line )
+ if ( mi ):
+ srcname = mi.group(2)
+ if re.search( r".h$", srcname, re.I ):
+ #self.includes.append( srcname )
+ pass
+ else:
+ self.includes.append( re.sub( r'\.[a-zA-Z0-9]+$', ".o", srcname ) )
myf.close()
self.makeUniqList()
@@ -64,8 +74,9 @@
self.depmods.append( modname + FortranFile.mod_ext )
def makeUniqList( self ):
- self.modules = list(set(self.modules))
- self.depmods = list(set(self.depmods))
+ self.modules = list(set(self.modules))
+ self.depmods = list(set(self.depmods))
+ self.includes = list(set(self.includes))
def getMyModuleFilenames( self ):
return self.modules
@@ -87,7 +98,8 @@
if m.lower() in mods_avail or not mods_avail:
depmods.append(m)
ret = ""
- ret += self.objname + ": " + self.filename + " " + " ".join(depmods) + " " + static_deps
+ ret += self.objname + ": " + self.filename + " " + " ".join(depmods) + \
+ " " + " ".join(self.includes) + " " + static_deps
if len(self.modules) > 0:
ret += "\n"
ret += " ".join(self.modules) + ": " + self.filename + " " + self.objname
ビルド手順
#!/bin/sh
VERSION=1.6.0
BASEDIR=/home/users/${USER}/Software/GENESIS/${VERSION}
SRC_TARBALL=${BASEDIR}/genesis-${VERSION}.tar.bz2
TESTS_TARBALL=${BASEDIR}/tests-${VERSION}.tar.bz2
FORTDEP_PATCH=${BASEDIR}/fortdep.py.patch
INSTALLDIR=/local/apl/lx/genesis160-CUDA
WORKDIR=/work/users/${USER}
BUILDDIR=${WORKDIR}/genesis-${VERSION}
TESTSDIR=${WORKDIR}/tests-${VERSION}
PARALLEL=12
PARALLEL_TESTS=8
# ----------------------------------------------------------------------------
umask 0022
module purge
module load intel_parallelstudio/2018update4
module load cuda/11.1
export LANG=C
export LC_ALL=C
export OMP_NUM_THREADS=1
cd ${WORKDIR}
if [ -d genesis-${VERSION} ]; then
mv genesis-${VERSION} genesis-erase
rm -rf genesis-erase &
fi
if [ -d tests-${VERSION} ]; then
mv tests-${VERSION} tests-erase
rm -rf tests-erase &
fi
tar jxf ${SRC_TARBALL}
tar jxf ${TESTS_TARBALL}
cd ${BUILDDIR}
patch -p0 < ${FORTDEP_PATCH}
FC=mpiifort CC=mpiicc ./configure --prefix=${INSTALLDIR} \
--enable-gpu \
--enable-single \
--with-cuda=/local/apl/lx/cuda-11.1
make depend
make -j ${PARALLEL} && make install
SPDYN=${INSTALLDIR}/bin/spdyn
cd ${TESTSDIR}/regression_test
# spdyn tests
./test.py "mpirun -np ${PARALLEL_TESTS} $SPDYN" gpu
./test_remd.py "mpirun -np ${PARALLEL_TESTS} $SPDYN" gpu
./test_rpath.py "mpirun -np ${PARALLEL_TESTS} $SPDYN" gpu
./test_gamd.py "mpirun -np ${PARALLEL_TESTS} $SPDYN" gpu
./test_fep.py "mpirun -np ${PARALLEL_TESTS} $SPDYN" gpu
メモ
- テストは全て通過(仕様上動作しない test_remd の 9 個のテストを除く)
- バイナリ(spdyn)は P100, V100 のどちらでも動作します(ccgpup, ccgpuv で確認)。ただし、ネイティブサポートにはなっていない可能性があります。