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genesis: New package. (#21183)

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* genesis: New package.

* fujitsu-ssl2: fix unit test error

* genesis: Fix for comments and add test method

* genesis: Fix for comments

* genesis: Fix for comments
This commit is contained in:
takanori-ihara 2021-02-22 13:06:56 +09:00 committed by GitHub
parent 2d1fbddebe
commit 26d2356ad4
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GPG key ID: 4AEE18F83AFDEB23
3 changed files with 740 additions and 0 deletions
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342
var/spack/repos/builtin/packages/genesis/fj_compiler.patch Normal file
View file

@ -0,0 +1,342 @@
--- a/configure.ac
+++ b/configure.ac
@@ -124,11 +124,7 @@ AC_PROG_F77($genesis_default_fc)
# check actual compiler
AC_MSG_CHECKING([for actual compiler])
-if test x"${FC}" = x"mpifrtpx"; then
- VER_OPT="-V"
-else
- VER_OPT="--version"
-fi
+VER_OPT="--version"
fc_ver_info=$(${FC} -E ${VER_OPT})
for vtok in ${fc_ver_info} ; do
@@ -158,9 +154,13 @@ for vtok in ${fc_ver_info} ; do
done
if test -z "${FC_ACT}"; then
- FC_ACT=${FC}
+ FC_ACT=`basename ${FC}`
fi
+
+
+
+
AC_MSG_RESULT([$FC_ACT])
version_warning=yes
@@ -256,7 +256,7 @@ for vtok in ${cc_ver_info} ; do
done
if test -z "${CC_ACT}"; then
- CC_ACT=${CC}
+ CC_ACT=`basename ${CC}`
fi
AC_MSG_RESULT([$CC_ACT])
@@ -322,18 +322,12 @@ if test x"${enable_openmp}" = x"yes"; th
elif test x"${FC_ACT}" = x"pgf90"; then
OPT_OPENMP="-mp"
- elif test x"${FC_ACT}" = x"frtpx"; then
+ elif test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"frt"; then
OPT_OPENMP="-Kopenmp"
- elif test x"${FC_ACT}" = x"mpifrtpx"; then
+ elif test x"${FC_ACT}" = x"mpifrtpx" -o x"${FC_ACT}" = x"mpifrt"; then
OPT_OPENMP="-Kopenmp"
- elif test x"${FC_ACT}" = x"frt"; then
- OPT_OPENMP="-KOMP"
-
- elif test x"${FC_ACT}" = x"mpifrt"; then
- OPT_OPENMP="-KOMP"
-
fi
fi
@@ -439,7 +433,8 @@ fi
AC_ARG_ENABLE([parallel_IO],
[AS_HELP_STRING([--enable-parallel_IO], [enable parallel_IO (defalt: no)])],
[], [enable_parallel_IO=no])
-if test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"mpifrtpx"; then
+if test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"mpifrtpx" -o \
+ x"${FC_ACT}" = x"frt" -o x"${FC_ACT}" = x"mpifrt"; then
enable_parallel_IO=no
fi
#if test x"${mainly_single}" = x"yes"; then
@@ -742,22 +737,16 @@ else
elif test x"${FC_ACT}" = x"pgf90"; then
FCFLAGS="-O2 -fastsse -Mipa=fast,inline -m64 -Mflushz -pc 64 -mcmodel=medium -Msmartalloc=huge"
- elif test x"${FC_ACT}" = x"frtpx"; then
- FCFLAGS="-m -Kvisimpact -Kocl -Kswp"
-
- elif test x"${FC_ACT}" = x"mpifrtpx"; then
- FCFLAGS="-m -Kocl -Kfast,openmp,parallel,simd=2,noalias -Nlst=t -Koptmsg=2"
- FCFLAGS_FFTE_KERNEL_FPP__PGI__SP=" -m -Kocl -Kfast,openmp,parallel,simd=2,noalias -Nlst=t -Koptmsg=2"
- FCFLAGS_FPP__PGI_NOOPT="-m -Kocl -Kfast,openmp,parallel,simd=2,noalias -Nlst=t -Koptmsg=2"
- FCFLAGS_KERNELS_PAIRLIST="-m -Kocl -Kfast,openmp,parallel,simd=2,nounroll,swp_strong,noalias=s -Nlst=t -Koptmsg=2"
- FCFLAGS_DIHEDRAL="-m -xsp_energy_dihedrals_mod.calculate_dihedral_2 -Kocl -Kfast,openmp,parallel,simd=2,noalias -Nlst=t -Koptmsg=2"
- FCFLAGS_KERNELS=" -m -Kocl -Kfast,openmp,parallel,simd=2,swp_strong,noalias=s -Nlst=t -Koptmsg=2"
+ elif test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"frt"; then
+ FCFLAGS="-Kocl"
- elif test x"${FC_ACT}" = x"frt"; then
- FCFLAGS="-m -Am -Kfast"
-
- elif test x"${FC_ACT}" = x"mpifrt"; then
- FCFLAGS="-m -Am -Kfast"
+ elif test x"${FC_ACT}" = x"mpifrtpx" -o x"${FC_ACT}" = x"mpifrt"; then
+ FCFLAGS="-Kocl -Kfast,openmp,parallel,simd=2,noalias -Nlst=t -Koptmsg=2"
+ FCFLAGS_FFTE_KERNEL_FPP__PGI__SP="-Kocl -Kfast,openmp,parallel,simd=2,noalias -Nlst=t -Koptmsg=2"
+ FCFLAGS_FPP__PGI_NOOPT="-Kocl -Kfast,openmp,parallel,simd=2,noalias -Nlst=t -Koptmsg=2"
+ FCFLAGS_KERNELS_PAIRLIST="-Kocl -Kfast,openmp,parallel,simd=2,nounroll,swp_strong,noalias=s -Nlst=t -Koptmsg=2"
+ FCFLAGS_DIHEDRAL="-xsp_energy_dihedrals_mod.calculate_dihedral_2 -Kocl -Kfast,openmp,parallel,simd=2,noalias -Nlst=t -Koptmsg=2"
+ FCFLAGS_KERNELS="-Kocl -Kfast,openmp,parallel,simd=2,swp_strong,noalias=s -Nlst=t -Koptmsg=2"
fi
@@ -776,22 +765,16 @@ else
elif test x"${FC_ACT}" = x"pgf90"; then
FCFLAGS="-m64 -Mflushz -pc 64 -mcmodel=medium -Msmartalloc=huge"
- elif test x"${FC_ACT}" = x"frtpx"; then
- FCFLAGS="-m -Kocl "
-
- elif test x"${FC_ACT}" = x"mpifrtpx"; then
- FCFLAGS=" -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- FCFLAGS_KERNELS=" -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- FCFLAGS_KERNELS_PAIRLIST="-m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- FCFLAGS_FFTE_KERNEL_FPP__PGI__SP=" -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- FCFLAGS_FPP__PGI_NOOPT=" -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- FCFLAGS_DIHEDRAL=" -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
-
- elif test x"${FC_ACT}" = x"frt"; then
- FCFLAGS="-m "
+ elif test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"frt"; then
+ FCFLAGS="-Kocl "
- elif test x"${FC_ACT}" = x"mpifrt"; then
- FCFLAGS="-m "
+ elif test x"${FC_ACT}" = x"mpifrtpx" -o x"${FC_ACT}" = x"mpifrt"; then
+ FCFLAGS=" -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS_KERNELS="-Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS_KERNELS_PAIRLIST="-Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS_FFTE_KERNEL_FPP__PGI__SP="-Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS_FPP__PGI_NOOPT="-Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS_DIHEDRAL="-Kocl -Kopenmp -Nlst=t -Koptmsg=2"
fi
@@ -813,22 +796,16 @@ else
elif test x"${FC_ACT}" = x"pgf90"; then
FCFLAGS="-g -m64 -Mflushz -pc 64 -mcmodel=medium -Msmartalloc=huge"
- elif test x"${FC_ACT}" = x"frtpx"; then
- FCFLAGS="-g -m -Kocl -Kopenmp"
+ elif test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"frt"; then
+ FCFLAGS="-g -Kocl -Kopenmp"
- elif test x"${FC_ACT}" = x"mpifrtpx"; then
- FCFLAGS=" -g -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- FCFLAGS_KERNELS=" -g -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- FCFLAGS_KERNELS_PAIRLIST=" -g -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- FCFLAGS_FFTE_KERNEL_FPP__PGI__SP=" -g -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- FCFLAGS_FPP__PGI_NOOPT=" -g -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- FCFLAGS_DIHEDRAL=" -g -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
-
- elif test x"${FC_ACT}" = x"frt"; then
- FCFLAGS="-g -m "
-
- elif test x"${FC_ACT}" = x"mpifrt"; then
- FCFLAGS="-g -m "
+ elif test x"${FC_ACT}" = x"mpifrtpx" -o x"${FC_ACT}" = x"mpifrt"; then
+ FCFLAGS=" -g -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS_KERNELS=" -g -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS_KERNELS_PAIRLIST=" -g -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS_FFTE_KERNEL_FPP__PGI__SP=" -g -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS_FPP__PGI_NOOPT=" -g -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS_DIHEDRAL=" -g -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
fi
@@ -850,23 +827,23 @@ else
elif test x"${FC_ACT}" = x"pgf90"; then
FCFLAGS="-O0 -g -m64 -Msmartalloc=huge"
- elif test x"${FC_ACT}" = x"frtpx"; then
+ elif test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"frt"; then
# FCFLAGS="-O0 -g -Hs -Hu -Ha"
FCFLAGS="-O0 -g -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
- elif test x"${FC_ACT}" = x"mpifrtpx"; then
- FCFLAGS=" -O0 -g -m -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
- FCFLAGS_KERNELS=" -O0 -g -m -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
- FCFLAGS_KERNELS_PAIRLIST=" -O0 -g -m -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
- FCFLAGS_FFTE_KERNEL_FPP__PGI__SP=" -O0 -g -m -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
- FCFLAGS_FPP__PGI_NOOPT=" -O0 -g -m -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
- FCFLAGS_DIHEDRAL=" -O0 -g -m -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
+ elif test x"${FC_ACT}" = x"mpifrtpx" -o x"${FC_ACT}" = x"mpifrt"; then
+ FCFLAGS=" -O0 -g -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
+ FCFLAGS_KERNELS=" -O0 -g -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
+ FCFLAGS_KERNELS_PAIRLIST=" -O0 -g -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
+ FCFLAGS_FFTE_KERNEL_FPP__PGI__SP=" -O0 -g -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
+ FCFLAGS_FPP__PGI_NOOPT=" -O0 -g -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
+ FCFLAGS_DIHEDRAL=" -O0 -g -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
- elif test x"${FC_ACT}" = x"frt"; then
- FCFLAGS="-O0 -g"
+ #elif test x"${FC_ACT}" = x"frt"; then
+ # FCFLAGS="-O0 -g"
- elif test x"${FC_ACT}" = x"mpifrt"; then
- FCFLAGS="-O0 -g"
+ #elif test x"${FC_ACT}" = x"mpifrt"; then
+ # FCFLAGS="-O0 -g"
fi
else
@@ -930,17 +907,11 @@ else
elif test x"${CC_ACT}" = x"pgcc"; then
CFLAGS="-O3 -fastsse -Mipa=fast,inline -m64 -Mflushz -pc 64 -mcmodel=medium -Msmartalloc=huge"
- elif test x"${CC_ACT}" = x"fccpx"; then
- CFLAGS="-m -Kvisimpact -Kocl -Kswp"
-
- elif test x"${CC_ACT}" = x"mpifccpx"; then
- CFLAGS="-m -Kvisimpact -Kocl -Kswp"
+ elif test x"${CC_ACT}" = x"fccpx" -o x"${CC_ACT}" = x"fcc"; then
+ CFLAGS="-Kocl"
- elif test x"${CC_ACT}" = x"fcc"; then
- CFLAGS="-m -Am -Kfast"
-
- elif test x"${CC_ACT}" = x"mpifcc"; then
- CFLAGS="-m -Am -Kfast"
+ elif test x"${CC_ACT}" = x"mpifccpx" -o x"${CC_ACT}" = x"mpifcc"; then
+ CFLAGS="-Kocl"
fi
@@ -959,17 +930,11 @@ else
elif test x"${CC_ACT}" = x"pgcc"; then
CFLAGS="-fastsse -Mipa=fast,inline -m64 -Mflushz -pc 64 -mcmodel=medium -Msmartalloc=huge"
- elif test x"${CC_ACT}" = x"fccpx"; then
- CFLAGS="-m -Kocl"
-
- elif test x"${CC_ACT}" = x"mpifccpx"; then
- CFLAGS="-m -Kocl"
-
- elif test x"${CC_ACT}" = x"fcc"; then
- CFLAGS="-m -Am -Kfast"
+ elif test x"${CC_ACT}" = x"fccpx" -o x"${CC_ACT}" = x"fcc"; then
+ CFLAGS="-Kocl"
- elif test x"${CC_ACT}" = x"mpifcc"; then
- CFLAGS="-m -Am -Kfast"
+ elif test x"${CC_ACT}" = x"mpifccpx" -o x"${CC_ACT}" = x"mpifcc"; then
+ CFLAGS="-Kocl"
fi
@@ -991,17 +956,11 @@ else
elif test x"${CC_ACT}" = x"pgcc"; then
CFLAGS="-g -fastsse -Mipa=fast,inline -m64 -Mflushz -pc 64 -mcmodel=medium -Msmartalloc=huge"
- elif test x"${CC_ACT}" = x"fccpx"; then
- CFLAGS="-g -m -Kocl"
+ elif test x"${CC_ACT}" = x"fccpx" -o x"${CC_ACT}" = x"fcc"; then
+ CFLAGS="-g -Kocl"
- elif test x"${CC_ACT}" = x"mpifccpx"; then
- CFLAGS="-g -m -Kocl"
-
- elif test x"${CC_ACT}" = x"fcc"; then
- CFLAGS="-g -m -Am -Kfast"
-
- elif test x"${CC_ACT}" = x"mpifcc"; then
- CFLAGS="-g -m -Am -Kfast"
+ elif test x"${CC_ACT}" = x"mpifccpx" -o x"${CC_ACT}" = x"mpifcc"; then
+ CFLAGS="-g -Kocl"
fi
@@ -1023,19 +982,13 @@ else
elif test x"${CC_ACT}" = x"pgcc"; then
CFLAGS="-O0 -g -m64 -Msmartalloc=huge"
- elif test x"${CC_ACT}" = x"fccpx"; then
+ elif test x"${CC_ACT}" = x"fccpx" -o x"${CC_ACT}" = x"fcc"; then
# CFLAGS="-O0 -g -Hs -Hu -Ha"
CFLAGS="-O0 -g -Kocl"
- elif test x"${CC_ACT}" = x"mpifccpx"; then
+ elif test x"${CC_ACT}" = x"mpifccpx" -o x"${CC_ACT}" = x"mpifcc"; then
CFLAGS="-O0 -g -Kocl"
- elif test x"${CC_ACT}" = x"fcc"; then
- CFLAGS="-O0 -g"
-
- elif test x"${CC_ACT}" = x"mpifcc"; then
- CFLAGS="-O0 -g"
-
fi
fi
@@ -1056,17 +1009,11 @@ if test -z "${LDFLAGS}"; then
LDFLAGS=""
#LDFLAGS="-march=native -fuse-linker-plugin"
- elif test x"${FC_ACT}" = x"frtpx"; then
- LDFLAGS="-SSL2 -Kparallel -Nfjomplib"
-
- elif test x"${FC_ACT}" = x"mpifrtpx"; then
- LDFLAGS="-SSL2BLAMP -Kparallel -Nfjomplib"
-
- elif test x"${FC_ACT}" = x"frt"; then
- LDFLAGS="-KSPARC64VII,V9FMADD -SSL2"
+ elif test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"frt"; then
+ LDFLAGS="-Kparallel -Kopenmp -Nlibomp"
- elif test x"${FC_ACT}" = x"mpifrt"; then
- LDFLAGS="-KSPARC64VII,V9FMADD -SSL2"
+ elif test x"${FC_ACT}" = x"mpifrtpx" -o x"${FC_ACT}" = x"mpifrt"; then
+ LDFLAGS="-Kparallel -Kopenmp -Nlibomp"
fi
fi
@@ -1101,7 +1048,9 @@ AC_SUBST(PPFLAGS)
# USEKCOMP
AM_CONDITIONAL(USEKCOMP, test x"${FC_ACT}" = x"frtpx" -o \
- x"${FC_ACT}" = x"mpifrtpx")
+ x"${FC_ACT}" = x"mpifrtpx" -o \
+ x"${FC_ACT}" = x"frt" -o \
+ x"${FC_ACT}" = x"mpifrt")
# KCOMP preprocess macro
AC_ARG_ENABLE([pktimer],
@@ -1130,7 +1079,8 @@ AC_ARG_WITH([fj_timer_2],
[use FJ-timer in main loop (default: not use)])],
[], [with_fj_timer_2=no])
-if test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"mpifrtpx"; then
+if test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"mpifrtpx" -o \
+ x"${FC_ACT}" = x"frt" -o x"${FC_ACT}" = x"mpifrt"; then
AC_DEFINE(KCOMP, 1, [defined if K-computer compiler is used.])
DEFINED_VARIABLES+=" -DKCOMP"
@@ -1148,7 +1098,7 @@ if test x"${FC_ACT}" = x"frtpx" -o x"${F
mainly_pktimer=no
if test x"${enable_pktimer}" = x"yes"; then
- if test x"${FC_ACT}" = x"mpifrtpx"; then
+ if test x"${FC_ACT}" = x"mpifrtpx" -o x"${FC_ACT}" = x"mpifrt"; then
AC_DEFINE(PKTIMER, 1, [defined if PKTIMER is used.])
DEFINED_VARIABLES+=" -DPKTIMER"
mainly_pktimer=yes

286
var/spack/repos/builtin/packages/genesis/fj_compiler_1.5.1.patch Normal file
View file

@ -0,0 +1,286 @@
--- a/configure.ac
+++ b/configure.ac
@@ -90,11 +90,7 @@ AC_PROG_F77($genesis_default_fc)
# check actual compiler
AC_MSG_CHECKING([for actual compiler])
-if test x"${FC}" = x"mpifrtpx"; then
- VER_OPT="-V"
-else
- VER_OPT="--version"
-fi
+VER_OPT="--version"
fc_ver_info=$(${FC} -E ${VER_OPT})
for vtok in ${fc_ver_info} ; do
@@ -124,7 +120,7 @@ for vtok in ${fc_ver_info} ; do
done
if test -z "${FC_ACT}"; then
- FC_ACT=${FC}
+ FC_ACT=`basename ${FC}`
fi
AC_MSG_RESULT([$FC_ACT])
@@ -228,7 +224,7 @@ for vtok in ${cc_ver_info} ; do
done
if test -z "${CC_ACT}"; then
- CC_ACT=${CC}
+ CC_ACT=`basename ${CC}`
fi
AC_MSG_RESULT([$CC_ACT])
@@ -294,18 +290,12 @@ if test x"${enable_openmp}" = x"yes"; th
elif test x"${FC_ACT}" = x"pgf90"; then
OPT_OPENMP="-mp"
- elif test x"${FC_ACT}" = x"frtpx"; then
+ elif test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"frt"; then
OPT_OPENMP="-Kopenmp"
- elif test x"${FC_ACT}" = x"mpifrtpx"; then
+ elif test x"${FC_ACT}" = x"mpifrtpx" -o x"${FC_ACT}" = x"mpifrt"; then
OPT_OPENMP="-Kopenmp"
- elif test x"${FC_ACT}" = x"frt"; then
- OPT_OPENMP="-KOMP"
-
- elif test x"${FC_ACT}" = x"mpifrt"; then
- OPT_OPENMP="-KOMP"
-
fi
fi
@@ -411,7 +401,8 @@ fi
AC_ARG_ENABLE([parallel_IO],
[AS_HELP_STRING([--enable-parallel_IO], [enable parallel_IO (defalt: yes(intel)/no(fujitsu))])],
[], [enable_parallel_IO=yes])
-if test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"mpifrtpx"; then
+if test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"mpifrtpx" -o \
+ x"${FC_ACT}" = x"frt" -o x"${FC_ACT}" = x"mpifrt"; then
enable_parallel_IO=no
fi
if test x"${enable_single}" = x"yes"; then
@@ -639,19 +630,13 @@ else
elif test x"${FC_ACT}" = x"pgf90"; then
FCFLAGS="-O2 -fastsse -m64 -Mflushz -pc 64 -mcmodel=medium -Msmartalloc=huge -Mbackslash"
- elif test x"${FC_ACT}" = x"frtpx"; then
- FCFLAGS="-m -Kocl -Kfast,openmp,parallel,simd=2,noalias -Nlst=t -Koptmsg=2"
- FCFLAGS_KERNELS_NONBOND="-m -O3 -Kocl -Kfsimple,noreduction,fp_contract,fp_relaxed,fz,ilfunc,mfunc,omitfp,simd_packed_promotion,openmp,parallel,simd=2 -Nlst=t -Koptmsg=2"
-
- elif test x"${FC_ACT}" = x"mpifrtpx"; then
- FCFLAGS="-m -Kocl -Kfast,openmp,parallel,simd=2,noalias -Nlst=t -Koptmsg=2"
- FCFLAGS_KERNELS_NONBOND="-m -O3 -Kocl -Kfsimple,noreduction,fp_contract,fp_relaxed,fz,ilfunc,mfunc,omitfp,simd_packed_promotion,openmp,parallel,simd=2 -Nlst=t -Koptmsg=2"
-
- elif test x"${FC_ACT}" = x"frt"; then
- FCFLAGS="-m -Am -Kfast"
-
- elif test x"${FC_ACT}" = x"mpifrt"; then
- FCFLAGS="-m -Am -Kfast"
+ elif test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"frt"; then
+ FCFLAGS="-Kocl -Kfast,openmp,parallel,simd=2,noalias -Nlst=t -Koptmsg=2"
+ FCFLAGS_KERNELS_NONBOND="-O3 -Kocl -Kfsimple,noreduction,fp_contract,fp_relaxed,fz,ilfunc,mfunc,omitfp,simd_packed_promotion,openmp,parallel,simd=2 -Nlst=t -Koptmsg=2"
+
+ elif test x"${FC_ACT}" = x"mpifrtpx" -o x"${FC_ACT}" = x"mpifrt"; then
+ FCFLAGS="-Kocl -Kfast,openmp,parallel,simd=2,noalias -Nlst=t -Koptmsg=2"
+ FCFLAGS_KERNELS_NONBOND="-O3 -Kocl -Kfsimple,noreduction,fp_contract,fp_relaxed,fz,ilfunc,mfunc,omitfp,simd_packed_promotion,openmp,parallel,simd=2 -Nlst=t -Koptmsg=2"
fi
@@ -670,20 +655,14 @@ else
elif test x"${FC_ACT}" = x"pgf90"; then
FCFLAGS="-m64 -Mflushz -pc 64 -mcmodel=medium -Msmartalloc=huge -Mbackslash"
- elif test x"${FC_ACT}" = x"frtpx"; then
- FCFLAGS="-m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- FCFLAGS_KERNELS_NONBOND="-m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
-
+ elif test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"frt"; then
+ FCFLAGS="-Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS_KERNELS_NONBOND="-Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- elif test x"${FC_ACT}" = x"mpifrtpx"; then
- FCFLAGS="-m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- FCFLAGS_KERNELS_NONBOND="-m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- elif test x"${FC_ACT}" = x"frt"; then
- FCFLAGS="-m "
-
- elif test x"${FC_ACT}" = x"mpifrt"; then
- FCFLAGS="-m "
+ elif test x"${FC_ACT}" = x"mpifrtpx" -o x"${FC_ACT}" = x"mpifrt"; then
+ FCFLAGS="-Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS_KERNELS_NONBOND="-Kocl -Kopenmp -Nlst=t -Koptmsg=2"
fi
@@ -705,19 +684,13 @@ else
elif test x"${FC_ACT}" = x"pgf90"; then
FCFLAGS="-g -m64 -Mflushz -pc 64 -mcmodel=medium -Msmartalloc=huge -Mbackslash"
- elif test x"${FC_ACT}" = x"frtpx"; then
- FCFLAGS="-g -m -Kocl -Kopenmp"
- FCFLAGS_KERNELS_NONBOND=" -g -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
-
- elif test x"${FC_ACT}" = x"mpifrtpx"; then
- FCFLAGS=" -g -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
- FCFLAGS_KERNELS_NONBOND=" -g -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
-
- elif test x"${FC_ACT}" = x"frt"; then
- FCFLAGS="-g -m "
-
- elif test x"${FC_ACT}" = x"mpifrt"; then
- FCFLAGS="-g -m "
+ elif test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"frt"; then
+ FCFLAGS="-g -Kocl -Kopenmp"
+ FCFLAGS_KERNELS_NONBOND=" -g -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+
+ elif test x"${FC_ACT}" = x"mpifrtpx" -o x"${FC_ACT}" = x"mpifrt"; then
+ FCFLAGS=" -g -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS_KERNELS_NONBOND=" -g -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
fi
@@ -739,18 +712,12 @@ else
elif test x"${FC_ACT}" = x"pgf90"; then
FCFLAGS="-O0 -g -m64 -Msmartalloc=huge"
- elif test x"${FC_ACT}" = x"frtpx"; then
- FCFLAGS=" -O0 -g -m -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
- FCFLAGS_KERNELS_NONBOND=" -O0 -g -m -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
-
- elif test x"${FC_ACT}" = x"mpifrtpx"; then
- FCFLAGS_KERNELS_NONBOND=" -O0 -g -m -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
+ elif test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"frt"; then
+ FCFLAGS=" -O0 -g -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
+ FCFLAGS_KERNELS_NONBOND=" -O0 -g -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
- elif test x"${FC_ACT}" = x"frt"; then
- FCFLAGS="-O0 -g"
-
- elif test x"${FC_ACT}" = x"mpifrt"; then
- FCFLAGS="-O0 -g"
+ elif test x"${FC_ACT}" = x"mpifrtpx" -o x"${FC_ACT}" = x"mpifrt"; then
+ FCFLAGS_KERNELS_NONBOND=" -O0 -g -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"
fi
else
@@ -804,16 +771,16 @@ else
CFLAGS="-O3 -fastsse -m64 -Mflushz -pc 64 -mcmodel=medium -Msmartalloc=huge"
elif test x"${CC_ACT}" = x"fccpx"; then
- CFLAGS="-m -Kvisimpact -Kocl -Kswp"
+ CFLAGS="-Kvisimpact -Kocl -Kswp"
elif test x"${CC_ACT}" = x"mpifccpx"; then
- CFLAGS="-m -Kvisimpact -Kocl -Kswp"
+ CFLAGS="-Kvisimpact -Kocl -Kswp"
elif test x"${CC_ACT}" = x"fcc"; then
- CFLAGS="-m -Am -Kfast"
+ CFLAGS="-Am -Kfast"
elif test x"${CC_ACT}" = x"mpifcc"; then
- CFLAGS="-m -Am -Kfast"
+ CFLAGS="-Am -Kfast"
fi
@@ -833,16 +800,16 @@ else
CFLAGS="-fastsse -m64 -Mflushz -pc 64 -mcmodel=medium -Msmartalloc=huge"
elif test x"${CC_ACT}" = x"fccpx"; then
- CFLAGS="-m -Kocl"
+ CFLAGS=" -Kocl"
elif test x"${CC_ACT}" = x"mpifccpx"; then
- CFLAGS="-m -Kocl"
+ CFLAGS=" -Kocl"
elif test x"${CC_ACT}" = x"fcc"; then
- CFLAGS="-m -Am -Kfast"
+ CFLAGS=" -Am -Kfast"
elif test x"${CC_ACT}" = x"mpifcc"; then
- CFLAGS="-m -Am -Kfast"
+ CFLAGS=" -Am -Kfast"
fi
@@ -865,16 +832,16 @@ else
CFLAGS="-g -fastsse -m64 -Mflushz -pc 64 -mcmodel=medium -Msmartalloc=huge"
elif test x"${CC_ACT}" = x"fccpx"; then
- CFLAGS="-g -m -Kocl"
+ CFLAGS="-g -Kocl"
elif test x"${CC_ACT}" = x"mpifccpx"; then
- CFLAGS="-g -m -Kocl"
+ CFLAGS="-g -Kocl"
elif test x"${CC_ACT}" = x"fcc"; then
- CFLAGS="-g -m -Am -Kfast"
+ CFLAGS="-g -Am -Kfast"
elif test x"${CC_ACT}" = x"mpifcc"; then
- CFLAGS="-g -m -Am -Kfast"
+ CFLAGS="-g -Am -Kfast"
fi
@@ -928,17 +895,11 @@ if test -z "${LDFLAGS}"; then
LDFLAGS=""
#LDFLAGS="-march=native -fuse-linker-plugin"
- elif test x"${FC_ACT}" = x"frtpx"; then
- LDFLAGS="-SSL2 -Kparallel -Nfjomplib"
-
- elif test x"${FC_ACT}" = x"mpifrtpx"; then
- LDFLAGS="-SSL2BLAMP -Kparallel -Nfjomplib"
-
- elif test x"${FC_ACT}" = x"frt"; then
- LDFLAGS="-KSPARC64VII,V9FMADD -SSL2"
+ elif test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"frt"; then
+ LDFLAGS="-Kparallel -Nfjomplib -Nlibomp"
- elif test x"${FC_ACT}" = x"mpifrt"; then
- LDFLAGS="-KSPARC64VII,V9FMADD -SSL2"
+ elif test x"${FC_ACT}" = x"mpifrtpx" -o x"${FC_ACT}" = x"mpifrt"; then
+ LDFLAGS="-Kparallel -Nfjomplib -Nlibomp"
fi
fi
@@ -973,10 +934,13 @@ AC_SUBST(PPFLAGS)
# USEKCOMP
AM_CONDITIONAL(USEKCOMP, test x"${FC_ACT}" = x"frtpx" -o \
- x"${FC_ACT}" = x"mpifrtpx")
+ x"${FC_ACT}" = x"mpifrtpx" -o \
+ x"${FC_ACT}" = x"frt" -o \
+ x"${FC_ACT}" = x"mpifrt")
# KCOMP preprocess macro
-if test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"mpifrtpx"; then
+if test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"mpifrtpx" -o \
+ x"${FC_ACT}" = x"frt" -o x"${FC_ACT}" = x"mpifrt"; then
AC_DEFINE(KCOMP, 1, [defined if K-computer compiler is used.])
DEFINED_VARIABLES+=" -DKCOMP"
fi
@@ -1049,13 +1013,13 @@ if test x"${IS_RICC}" == x"yes"; then
if test -n "${RICC_FCFLAGS}"; then
FCFLAGS=${RICC_FCFLAGS}
else
- FCFLAGS="-pc -m -omp"
+ FCFLAGS="-pc -omp"
fi
if test -n "${RICC_CFLAGS}"; then
CFLAGS=${RICC_CFLAGS}
else
- CFLAGS="-pc -m -omp"
+ CFLAGS="-pc -omp"
fi
if test -n "${RICC_PPFLAGS}"; then

112
var/spack/repos/builtin/packages/genesis/package.py Normal file
View file

@ -0,0 +1,112 @@
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Genesis(AutotoolsPackage, CudaPackage):
"""GENESIS is a Molecular dynamics and modeling software
for bimolecular systems such as proteins, lipids, glycans,
and their complexes.
"""
homepage = "https://www.r-ccs.riken.jp/labs/cbrt/"
url = "https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2020/09/genesis-1.5.1.tar.bz2"
git = "https://github.com/genesis-release-r-ccs/genesis-2.0.git"
version("master", branch="master")
version(
"1.5.1",
sha256="62a453a573c36779484b4ffed2dfa56ea03dfe1308d631b33ef03f733259b3ac",
url="https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2020/09/genesis-1.5.1.tar.bz2",
)
resource(
when="@1.5.1",
name="user_guide",
url="https://www.r-ccs.riken.jp/labs/cbrt/wp-content/uploads/2019/10/GENESIS-1.4.0.pdf",
sha256="da2c3f8bfa1e93adb992d3cfce09fb45d8d447a94f9a4f884ac834ea7279b9c7",
expand=False,
placement="doc",
)
variant("openmp", default=True, description="Enable OpenMP.")
variant("single", default=False, description="Enable single precision.")
variant("hmdisk", default=False, description="Enable huge molecule on hard disk.")
conflicts("%apple-clang", when="+openmp")
depends_on("autoconf", type="build", when="@1.5.1 %fj")
depends_on("autoconf", type="build", when="@master")
depends_on("automake", type="build", when="@1.5.1 %fj")
depends_on("automake", type="build", when="@master")
depends_on("libtool", type="build", when="@1.5.1 %fj")
depends_on("libtool", type="build", when="@master")
depends_on("m4", type="build", when="@1.5.1 %fj")
depends_on("m4", type="build", when="@master")
depends_on("mpi", type=("build", "run"))
depends_on("lapack")
depends_on("python@2.6.9:2.8.0", type=("build", "run"), when="@master")
patch("fj_compiler.patch", when="@master %fj")
patch("fj_compiler_1.5.1.patch", when="@1.5.1 %fj")
parallel = False
@property
def force_autoreconf(self):
# Run autoreconf due to build system patch
return self.spec.satisfies("@1.5.1 %fj")
def configure_args(self):
spec = self.spec
options = []
options.extend(self.enable_or_disable("openmp"))
options.extend(self.enable_or_disable("single"))
options.extend(self.enable_or_disable("hmdisk"))
if "+cuda" in spec:
options.append("--enable-gpu")
options.append("--with-cuda=%s" % spec["cuda"].prefix)
else:
options.append("--disable-gpu")
if spec.target == "a64fx" and self.spec.satisfies("@master %fj"):
options.append("--host=Fugaku")
return options
def setup_build_environment(self, env):
env.set("FC", self.spec["mpi"].mpifc, force=True)
env.set("F77", self.spec["mpi"].mpif77, force=True)
env.set("CC", self.spec["mpi"].mpicc, force=True)
env.set("CXX", self.spec["mpi"].mpicxx, force=True)
env.set("LAPACK_LIBS", self.spec["lapack"].libs.ld_flags)
if "+cuda" in self.spec:
cuda_arch = self.spec.variants["cuda_arch"].value
cuda_gencode = " ".join(self.cuda_flags(cuda_arch))
env.set("NVCCFLAGS", cuda_gencode)
def install(self, spec, prefix):
make("install")
install_tree("doc", prefix.share.doc)
@run_after("install")
def cache_test_sources(self):
if self.spec.satisfies("@master"):
self.cache_extra_test_sources(["tests"])
def test(self):
if self.spec.satisfies("@master"):
exe_name = self.spec["python"].command.path
test_name = join_path(
self.install_test_root, "tests", "regression_test", "test.py"
)
bin_name = join_path(self.prefix.bin, "spdyn")
opts = [
test_name,
self.spec["mpi"].prefix.bin.mpirun + " -np 8 " + bin_name,
]
env["OMP_NUM_THREADS"] = "1"
self.run_test(exe_name, options=opts, expected="Passed 53 / 53")