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sentieon-genomics(GENESIS): add 2.0.x, 2.1.x, tests, fix for A64FX #1891

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sentieon-genomics(GENESIS): add 2.0.x, 2.1.x, tests, fix for A64FX #1891

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8f9ef83
Update GENESIS recipe: add version 2.0.x, 2.1.x and update URL
chig Oct 8, 2025
58d261e
Update for 2.1.6
chig Apr 8, 2026
4f78ce2
Fix for autoreconf in genseis
chig Apr 8, 2026
aca0120
Update GENESIS package.py
chig Apr 8, 2026
510aad5
Update GENESIS packge.py
chig May 27, 2026
4771921
Fix formatting of GENESIS package.py
chig May 28, 2026
6a5d7d4
genesis: remove leftover conflict markers
chig Jun 26, 2026
fe97f74
genesis: clean up package after rebase
chig Jun 26, 2026
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23 changes: 23 additions & 0 deletions repos/spack_repo/builtin/packages/genesis/fix-nvtx-include.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
--- a/configure.ac 2026-03-26 10:19:00.000000000 +0900
+++ b/configure.ac 2026-03-26 10:19:50.000000000 +0900
@@ -761,6 +761,20 @@

# NVCCFLAG
NVCCFLAG="-c -g -O3 ${GENCODEFLAG} --ftz=false --prec-div=true --prec-sqrt=true --fmad=true"
+
+ if test "x${CUDA_HOME}" != x; then
+ if test -d "${CUDA_HOME}/targets/sbsa-linux/include/nvtx3"; then
+ NVCCFLAG="${NVCCFLAG} -I${CUDA_HOME}/targets/sbsa-linux/include/nvtx3"
+ elif test -d "${CUDA_HOME}/include/nvtx3"; then
+ NVCCFLAG="${NVCCFLAG} -I${CUDA_HOME}/include/nvtx3"
+ fi
+ elif test "x${CUDA_PATH}" != x; then
+ if test -d "${CUDA_PATH}/targets/sbsa-linux/include/nvtx3"; then
+ NVCCFLAG="${NVCCFLAG} -I${CUDA_PATH}/targets/sbsa-linux/include/nvtx3"
+ elif test -d "${CUDA_PATH}/include/nvtx3"; then
+ NVCCFLAG="${NVCCFLAG} -I${CUDA_PATH}/include/nvtx3"
+ fi
+ fi
AC_SUBST(NVCCFLAG)
fi

373 changes: 373 additions & 0 deletions repos/spack_repo/builtin/packages/genesis/fj_compiler_2.0.0.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,373 @@
--- a/configure.ac
+++ b/configure.ac
@@ -146,12 +146,7 @@ AC_PROG_CXX($qsimulate_default_cxx)
# 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="-V"

fc_ver_info=$(${FC} -E ${VER_OPT})
for vtok in ${fc_ver_info} ; do
@@ -181,7 +176,7 @@ for vtok in ${fc_ver_info} ; do
done

if test -z "${FC_ACT}"; then
- FC_ACT=${FC}
+ FC_ACT=`basename ${FC}`
fi
F77_ACT=FC_ACT

@@ -322,7 +317,7 @@ 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])
@@ -861,6 +856,7 @@ FARCFLAGS_NOOPT=""
FARCFLAGS_KERNELS=""
FARCFLAGS_KERNELS_PAIRLIST=""
FARCFLAGS_DIHEDRAL=""
+FARCFLAGS_NOKPARALLEL=""

# FFLAGS
if test x"${ac_test_FFLAGS}" = x"set"; then
@@ -917,22 +913,17 @@ else
elif test x"${FC_ACT}" = x"pgf90"; then
FCFLAGS="-O2 -fastsse -Mipa=fast,inline -m64 -Mflushz -pc 64 -mcmodel=medium -Msmartalloc=huge"

- elif test x"${FC_ACT}" = x"frtpx"; then
- FCFLAGS="-m -Kocl -Kfast,openmp,parallel,simd=2,noalias -Nlst=t -Koptmsg=2"
-
- elif test x"${FC_ACT}" = x"mpifrtpx"; then
- FCFLAGS="-m -Kocl -Kfast,openmp,parallel,simd=2,noalias -Nlst=t -Koptmsg=2"
- FCFLAGS_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"${FC_ACT}" = x"frt"; then
- FCFLAGS="-m -Am -Kfast"
+ elif test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"frt"; then
+ FCFLAGS="-Kocl"

- elif test x"${FC_ACT}" = x"mpifrt"; then
- FCFLAGS="-m -Am -Kfast"
+ elif test x"${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"
+ FCFLAGS_NOKPARALLEL=" -Kocl -Kfast,openmp,simd=2,noalias -Nlst=t -Koptmsg=2"

fi

@@ -956,16 +947,16 @@ else
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=" -Kocl -Kopenmp -Nlst=t -Koptmsg=2"

elif test x"${FC_ACT}" = x"mpifrtpx"; then
- FCFLAGS="-m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS=" -Kocl -Kopenmp -Nlst=t -Koptmsg=2"

elif test x"${FC_ACT}" = x"frt"; then
- FCFLAGS="-m "
+ FCFLAGS=" -Kocl -Kopenmp -Nlst=t -Koptmsg=2"

elif test x"${FC_ACT}" = x"mpifrt"; then
- FCFLAGS="-m "
+ FCFLAGS=" -Kocl -Kopenmp -Nlst=t -Koptmsg=2"

fi

@@ -992,16 +983,16 @@ else
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="-g -Kocl -Kopenmp"

elif test x"${FC_ACT}" = x"mpifrtpx"; then
- FCFLAGS=" -g -m -Kocl -Kopenmp -Nlst=t -Koptmsg=2"
+ FCFLAGS=" -g -Kocl -Kopenmp -Nlst=t -Koptmsg=2"

elif test x"${FC_ACT}" = x"frt"; then
- FCFLAGS="-g -m "
+ FCFLAGS="-g -Kocl -Kopenmp"

elif test x"${FC_ACT}" = x"mpifrt"; then
- FCFLAGS="-g -m "
+ FCFLAGS=" -g -Kocl -Kopenmp -Nlst=t -Koptmsg=2"

fi

@@ -1028,7 +1019,7 @@ else
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=" -O0 -g -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"

elif test x"${FC_ACT}" = x"mpifrtpx"; then
FCFLAGS="-O0 -g -Hs -Hu -Ha"
@@ -1037,12 +1028,19 @@ else
FCFLAGS_FFTE_KERNEL_FPP__PGI__SP="-O0 -g -Hs -Hu -Ha -Kopenmp"
FCFLAGS_FPP__PGI_NOOPT="-O0 -g -Hs -Hu -Ha -Kopenmp"
FCFLAGS_DIHEDRAL="-O0 -g -Hs -Hu -Ha -Kopenmp"
+ FCFLAGS_NOKPARALLEL="-O0 -g -Hs -Hu -Ha -Kopenmp"

elif test x"${FC_ACT}" = x"frt"; then
- FCFLAGS="-O0 -g"
+ FCFLAGS=" -O0 -g -Kocl -Kopenmp -Hs -Hu -Ha -Nlst=t -Koptmsg=2"

elif test x"${FC_ACT}" = x"mpifrt"; then
- FCFLAGS="-O0 -g"
+ FCFLAGS="-O0 -g -Hs -Hu -Ha"
+ FCFLAGS_KERNELS="-O0 -g -Hs -Hu -Ha -Kopenmp"
+ FCFLAGS_KERNELS_PAIRLIST="-O0 -g -Hs -Hu -Ha -Kopenmp"
+ FCFLAGS_FFTE_KERNEL_FPP__PGI__SP="-O0 -g -Hs -Hu -Ha -Kopenmp"
+ FCFLAGS_FPP__PGI_NOOPT="-O0 -g -Hs -Hu -Ha -Kopenmp"
+ FCFLAGS_DIHEDRAL="-O0 -g -Hs -Hu -Ha -Kopenmp"
+ FCFLAGS_NOKPARALLEL="-O0 -g -Hs -Hu -Ha -Kopenmp"

fi
else
@@ -1090,6 +1088,7 @@ AC_SUBST(FCFLAGS_KERNELS)
AC_SUBST(FCFLAGS_KERNELS_PAIRLIST)
AC_SUBST(FCFLAGS_DIHEDRAL)
AC_SUBST(FCFLAGS_DISABLEFARC)
+AC_SUBST(FCFLAGS_NOKPARALLEL)

# CFLAGS
if test x"${ac_test_CFLAGS}" = x"set"; then
@@ -1117,16 +1116,16 @@ 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 -Kfast"
+ CFLAGS=" -Kfast -Kocl -Kswp"

elif test x"${CC_ACT}" = x"mpifcc"; then
- CFLAGS="-m -Kfast"
+ CFLAGS=" -Kfast -Kocl -Kswp"

fi

@@ -1150,16 +1149,16 @@ 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 -Kfast"
+ CFLAGS=" -Kocl"

elif test x"${CC_ACT}" = x"mpifcc"; then
- CFLAGS="-m -Kfast"
+ CFLAGS=" -Kocl"

fi

@@ -1186,16 +1185,16 @@ 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 -Kfast"
+ CFLAGS="-g -Kocl"

elif test x"${CC_ACT}" = x"mpifcc"; then
- CFLAGS="-g -m -Kfast"
+ CFLAGS="-g -Kocl"

fi

@@ -1228,10 +1227,10 @@ else
CFLAGS="-O0 -g -Kocl"

elif test x"${CC_ACT}" = x"fcc"; then
- CFLAGS="-O0 -g"
+ CFLAGS="-O0 -g -Kocl"

elif test x"${CC_ACT}" = x"mpifcc"; then
- CFLAGS="-O0 -g"
+ CFLAGS="-O0 -g -Kocl"

fi
else
@@ -1277,17 +1276,11 @@ 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"${FC_ACT}" = x"frt"; then
- LDFLAGS="-SSL2 -Kparallel -Nfjomplib"
+ elif test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"frt"; then
+ LDFLAGS="-SSL2 -Kparallel -Kopenmp -Nlibomp"

- elif test x"${FC_ACT}" = x"mpifrt"; then
- LDFLAGS="-SSL2BLAMP -Kparallel -Nfjomplib"
+ elif test x"${FC_ACT}" = x"mpifrtpx" -o x"${FC_ACT}" = x"mpifrt"; then
+ LDFLAGS="-SSL2BLAMP -Kparallel -Kopenmp -Nlibomp"

fi
fi
@@ -1357,7 +1350,8 @@ 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"

@@ -1375,7 +1369,7 @@ if test x"${FC_ACT}" = x"frtpx" -o x"${FC_ACT}" = x"mpifrtpx"; then
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
--- a/src/lib/Makefile.am
+++ b/src/lib/Makefile.am
@@ -120,6 +120,28 @@ else
$(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I. $(FCFLAGS_FFTE_KERNEL_FPP__PGI__SP) -c $*.f90
endif

+fft3d_1dalltoall.o : fft3d_1dalltoall.fpp
+if USEKCOMP
+ cp $*.fpp $*.f90
+ $(FPP) $(PPFLAGS) $(DEFS) $*.f90
+ mv $*.cpp.f90 $*.f90
+ $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I. $(FCFLAGS_NOKPARALLEL) -c $*.f90
+else
+ $(FPP) $(PPFLAGS) $(DEFS) $*.fpp $*.f90
+ $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I. $(FCFLAGS) -c $*.f90
+endif
+
+fft3d_2dalltoall.o : fft3d_2dalltoall.fpp
+if USEKCOMP
+ cp $*.fpp $*.f90
+ $(FPP) $(PPFLAGS) $(DEFS) $*.f90
+ mv $*.cpp.f90 $*.f90
+ $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I. $(FCFLAGS_NOKPARALLEL) -c $*.f90
+else
+ $(FPP) $(PPFLAGS) $(DEFS) $*.fpp $*.f90
+ $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I. $(FCFLAGS) -c $*.f90
+endif
+
.fpp.o:
if USEKCOMP
cp $*.fpp $*.f90

--- a/src/spdyn/Makefile.am
+++ b/src/spdyn/Makefile.am
@@ -277,12 +277,46 @@ else
$(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS) -c $*.f90
endif

+sp_energy_pme_opt_1dalltoall.o : sp_energy_pme_opt_1dalltoall.fpp
+if USEKCOMP
+ cp $*.fpp $*.f90
+ $(FPP) $(PPFLAGS) $(DEFS) $*.f90
+ mv $*.cpp.f90 $*.f90
+ $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS_NOKPARALLEL) -c $*.f90
+else
+ $(FPP) $(PPFLAGS) $(DEFS) $*.fpp $*.f90
+ $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS_NOOPT) -c $*.f90
+endif
+
+sp_energy_pme_opt_2dalltoall.o : sp_energy_pme_opt_2dalltoall.fpp
+if USEKCOMP
+ cp $*.fpp $*.f90
+ $(FPP) $(PPFLAGS) $(DEFS) $*.f90
+ mv $*.cpp.f90 $*.f90
+ $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS_NOKPARALLEL) -c $*.f90
+else
+ $(FPP) $(PPFLAGS) $(DEFS) $*.fpp $*.f90
+ $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS_NOOPT) -c $*.f90
+endif
+
+sp_energy_pme_opt_slab.o : sp_energy_pme_opt_slab.fpp
+if USEKCOMP
+ cp $*.fpp $*.f90
+ $(FPP) $(PPFLAGS) $(DEFS) $*.f90
+ mv $*.cpp.f90 $*.f90
+ $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS_NOKPARALLEL) -c $*.f90
+else
+ $(FPP) $(PPFLAGS) $(DEFS) $*.fpp $*.f90
+ $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS_NOOPT) -c $*.f90
+endif
+
+
sp_energy_pme_noopt_1dalltoall.o : sp_energy_pme_noopt_1dalltoall.fpp
if USEKCOMP
cp $*.fpp $*.f90
$(FPP) $(PPFLAGS) $(DEFS) $*.f90
mv $*.cpp.f90 $*.f90
- $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS) -c $*.f90
+ $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS_NOKPARALLEL) -c $*.f90
else
$(FPP) $(PPFLAGS) $(DEFS) $*.fpp $*.f90
$(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS_NOOPT) -c $*.f90
@@ -293,7 +327,7 @@ if USEKCOMP
cp $*.fpp $*.f90
$(FPP) $(PPFLAGS) $(DEFS) $*.f90
mv $*.cpp.f90 $*.f90
- $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS) -c $*.f90
+ $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS_NOKPARALLEL) -c $*.f90
else
$(FPP) $(PPFLAGS) $(DEFS) $*.fpp $*.f90
$(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS_NOOPT) -c $*.f90
@@ -304,7 +338,7 @@ if USEKCOMP
cp $*.fpp $*.f90
$(FPP) $(PPFLAGS) $(DEFS) $*.f90
mv $*.cpp.f90 $*.f90
- $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS) -c $*.f90
+ $(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS_NOKPARALLEL) -c $*.f90
else
$(FPP) $(PPFLAGS) $(DEFS) $*.fpp $*.f90
$(FC) $(DEFAULT_INCLUDES) $(INCLUDES) -I../lib $(FCFLAGS_NOOPT) -c $*.f90
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