diff options
3 files changed, 740 insertions, 0 deletions
diff --git a/var/spack/repos/builtin/packages/genesis/fj_compiler.patch b/var/spack/repos/builtin/packages/genesis/fj_compiler.patch new file mode 100644 index 0000000000..e71fc33855 --- /dev/null +++ b/var/spack/repos/builtin/packages/genesis/fj_compiler.patch @@ -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"${FC_ACT}" = x"mpifrt"; then + AC_DEFINE(PKTIMER, 1, [defined if PKTIMER is used.]) + DEFINED_VARIABLES+=" -DPKTIMER" + mainly_pktimer=yes diff --git a/var/spack/repos/builtin/packages/genesis/fj_compiler_1.5.1.patch b/var/spack/repos/builtin/packages/genesis/fj_compiler_1.5.1.patch new file mode 100644 index 0000000000..0bdbd4f58e --- /dev/null +++ b/var/spack/repos/builtin/packages/genesis/fj_compiler_1.5.1.patch @@ -0,0 +1,286 @@ +--- a/configure.ac ++++ b/configure.ac +@@ -90,11 +90,7 @@ AC_PROG_F77($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 diff --git a/var/spack/repos/builtin/packages/genesis/package.py b/var/spack/repos/builtin/packages/genesis/package.py new file mode 100644 index 0000000000..3711fa4e9f --- /dev/null +++ b/var/spack/repos/builtin/packages/genesis/package.py @@ -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") |