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Merge pull request #12836 from boegel/20210510120257_new_pr_R-bundle-…
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…Bioconductor312

add patch for rhdf5filters extension in Bioconductor 3.12 bundle to fix installation on aarch64
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@Micket
Micket authored May 10, 2021
2 parents bb8a248 + cd2a572 commit ecb3507
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7 changes: 6 additions & 1 deletion ...uild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.12-foss-2020b-R-4.0.3.eb
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Original file line number Diff line number Diff line change
Expand Up @@ -328,7 +328,12 @@ exts_list = [
'checksums': ['48c81620346c1c652d15098d1c90df749a28ca747ade82d2a1e276191fc1d691'],
}),
('rhdf5filters', '1.2.0', {
'checksums': ['58df019a2c8626cc236ebe19d44b830a6c3b5f787ea4090d5b57454a88d676cb'],
'patches': ['rhdf5filters-1.2.0_fix-configure-aarch64.patch'],
'checksums': [
'58df019a2c8626cc236ebe19d44b830a6c3b5f787ea4090d5b57454a88d676cb', # rhdf5filters_1.2.0.tar.gz
# rhdf5filters-1.2.0_fix-configure-aarch64.patch
'01d00415dcf41d7ca331b69ef7b3d99834719474ef1da8f66a540d027e24da5b',
],
}),
('rhdf5', '2.34.0', {
'checksums': ['11d70b8d8284d4b7a6beb4c5b65abd42451e46d04f65dfc82bf265a677c8952a'],
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278 changes: 278 additions & 0 deletions easybuild/easyconfigs/r/R-bundle-Bioconductor/rhdf5filters-1.2.0_fix-configure-aarch64.patch
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Original file line number Diff line number Diff line change
@@ -0,0 +1,278 @@
fix configure script for aarch64 CPUs
see https://github.com/grimbough/rhdf5filters/pull/6

From 6e9bb1e1f6a32584d4acb3773b03f48811e504e5 Mon Sep 17 00:00:00 2001
From: Mike Smith <grimbough@gmail.com>
Date: Tue, 24 Nov 2020 15:51:57 +0100
Subject: [PATCH 01/45] Modifying configure to identify CPU architecture

---
configure | 179 ++++++++++++++++++++++++++++++++-------------------
configure.ac | 33 ++++++++--
2 files changed, 137 insertions(+), 75 deletions(-)

diff --git a/configure b/configure
index 144ffc7..e118c13 100755
--- a/configure
+++ b/configure
@@ -1992,6 +1992,17 @@ RHDF5_INCLUDE=`"${R_HOME}/bin${R_ARCH_BIN}/Rscript" -e 'cat(system.file("include

echo "configuring the BLOSC filter..."

+## check if we have an x86 CPU
+machine=`uname -m`
+case $machine in #(
+ *86*) :
+ x86_CPU=true ;; #(
+ *) :
+ x86_CPU=false
+ ;;
+esac
+echo x86_CPU="$x86_CPU"
+
## see if -msse2 is a supported flag
ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
@@ -2818,8 +2829,74 @@ else
MSSE2=false
fi

-## check CPU supports sse2
-ac_ext=c
+## see if -mavx2 is a supported flag
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts -mavx2" >&5
+$as_echo_n "checking whether C compiler accepts -mavx2... " >&6; }
+if ${ax_cv_check_cflags___mavx2+:} false; then :
+ $as_echo_n "(cached) " >&6
+else
+
+ ax_check_save_flags=$CFLAGS
+ CFLAGS="$CFLAGS -mavx2"
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+
+int
+main ()
+{
+
+ ;
+ return 0;
+}
+_ACEOF
+if ac_fn_c_try_compile "$LINENO"; then :
+ ax_cv_check_cflags___mavx2=yes
+else
+ ax_cv_check_cflags___mavx2=no
+fi
+rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
+ CFLAGS=$ax_check_save_flags
+fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_check_cflags___mavx2" >&5
+$as_echo "$ax_cv_check_cflags___mavx2" >&6; }
+if test "x$ax_cv_check_cflags___mavx2" = xyes; then :
+ MAVX2=true
+else
+ MAVX2=false
+fi
+
+
+if test "$cross_compiling" = yes; then :
+ { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5
+$as_echo "$as_me: error: in \`$ac_pwd':" >&2;}
+as_fn_error $? "cannot run test program while cross compiling
+See \`config.log' for more details" "$LINENO" 5; }
+else
+ cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h. */
+#include <stdlib.h>
+int
+main ()
+{
+__builtin_cpu_init ();
+ ;
+ return 0;
+}
+
+_ACEOF
+if ac_fn_c_try_run "$LINENO"; then :
+ ax_cv_gcc_check_x86_cpu_init=true
+else
+ ax_cv_gcc_check_x86_cpu_init=false
+fi
+rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \
+ conftest.$ac_objext conftest.beam conftest.$ac_ext
+fi
+
+
+## check CPU supports sse2 and avx2
+if "$x86_CPU" == true && "$ax_cv_gcc_check_x86_cpu_init" == true ; then
+ ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
@@ -2931,72 +3008,6 @@ fi



-if "$MSSE2" = true && "$SSE2_SUPPORTED" = true ; then
- SSE2="-DSHUFFLE_SSE2_ENABLED"
- MSSE2="-msse2"
- SSE2_BITSHUFFLE='bitshuffle-sse2.o: bitshuffle-sse2.c
- $(CC) $(FLAGS) -c bitshuffle-sse2.c'
- SSE2_BITSHUFFLE_OBJ='bitshuffle-sse2.o'
- SSE2_SHUFFLE='shuffle-sse2.o: shuffle-sse2.c
- $(CC) $(FLAGS) -c shuffle-sse2.c'
- SSE2_SHUFFLE_OBJ='shuffle-sse2.o'
- SSE2_OBJ_PATH='lib/blosc-1.16.3/'
-else
- SSE2=""
- MSSE2=""
- SSE2_BITSHUFFLE=""
- SSE2_SHUFFLE=""
- SSE2_BITSHUFFLE_OBJ=""
- SSE2_SHUFFLE_OBJ=""
- SSE2_OBJ_PATH=""
-fi
-
-
-
-
-
-
-
-
-
-## see if -mavx2 is a supported flag
-{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether C compiler accepts -mavx2" >&5
-$as_echo_n "checking whether C compiler accepts -mavx2... " >&6; }
-if ${ax_cv_check_cflags___mavx2+:} false; then :
- $as_echo_n "(cached) " >&6
-else
-
- ax_check_save_flags=$CFLAGS
- CFLAGS="$CFLAGS -mavx2"
- cat confdefs.h - <<_ACEOF >conftest.$ac_ext
-/* end confdefs.h. */
-
-int
-main ()
-{
-
- ;
- return 0;
-}
-_ACEOF
-if ac_fn_c_try_compile "$LINENO"; then :
- ax_cv_check_cflags___mavx2=yes
-else
- ax_cv_check_cflags___mavx2=no
-fi
-rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext
- CFLAGS=$ax_check_save_flags
-fi
-{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ax_cv_check_cflags___mavx2" >&5
-$as_echo "$ax_cv_check_cflags___mavx2" >&6; }
-if test "x$ax_cv_check_cflags___mavx2" = xyes; then :
- MAVX2=true
-else
- MAVX2=false
-fi
-
-## check CPU supports avx2
-

ac_ext=c
ac_cpp='$CPP $CPPFLAGS'
@@ -3062,6 +3073,38 @@ else
fi


+else
+ SSE2_SUPPORTED=false
+ AVX2_SUPPORTED=false
+fi
+
+if "$MSSE2" = true && "$SSE2_SUPPORTED" = true ; then
+ SSE2="-DSHUFFLE_SSE2_ENABLED"
+ MSSE2="-msse2"
+ SSE2_BITSHUFFLE='bitshuffle-sse2.o: bitshuffle-sse2.c
+ $(CC) $(FLAGS) -c bitshuffle-sse2.c'
+ SSE2_BITSHUFFLE_OBJ='bitshuffle-sse2.o'
+ SSE2_SHUFFLE='shuffle-sse2.o: shuffle-sse2.c
+ $(CC) $(FLAGS) -c shuffle-sse2.c'
+ SSE2_SHUFFLE_OBJ='shuffle-sse2.o'
+ SSE2_OBJ_PATH='lib/blosc-1.16.3/'
+else
+ SSE2=""
+ MSSE2=""
+ SSE2_BITSHUFFLE=""
+ SSE2_SHUFFLE=""
+ SSE2_BITSHUFFLE_OBJ=""
+ SSE2_SHUFFLE_OBJ=""
+ SSE2_OBJ_PATH=""
+fi
+
+
+
+
+
+
+
+

if "$MAVX2" = true && "$AVX2_SUPPORTED" = true ; then
AVX2="-DSHUFFLE_AVX2_ENABLED"
diff --git a/configure.ac b/configure.ac
index bce61de..3edd950 100644
--- a/configure.ac
+++ b/configure.ac
@@ -36,10 +36,34 @@ AC_SUBST(RHDF5_INCLUDE)

echo "configuring the BLOSC filter..."

+## check if we have an x86 CPU
+machine=`uname -m`
+AS_CASE([$machine],
+ [*86*], [x86_CPU=true],
+ [x86_CPU=false]
+)
+echo x86_CPU="$x86_CPU"
+
## see if -msse2 is a supported flag
AX_CHECK_COMPILE_FLAG([-msse2], [MSSE2=true], [MSSE2=false])
-## check CPU supports sse2
-AX_GCC_X86_CPU_SUPPORTS(sse2, [SSE2_SUPPORTED=true], [SSE2_SUPPORTED=false])
+## see if -mavx2 is a supported flag
+AX_CHECK_COMPILE_FLAG([-mavx2], [MAVX2=true], [MAVX2=false])
+
+AC_RUN_IFELSE(
+ [AC_LANG_PROGRAM([#include <stdlib.h>],
+ [__builtin_cpu_init ();])
+ ],
+ [ax_cv_gcc_check_x86_cpu_init=true],
+ [ax_cv_gcc_check_x86_cpu_init=false])
+
+## check CPU supports sse2 and avx2
+if [ "$x86_CPU" == true ] && [ "$ax_cv_gcc_check_x86_cpu_init" == true ]; then
+ AX_GCC_X86_CPU_SUPPORTS(sse2, [SSE2_SUPPORTED=true], [SSE2_SUPPORTED=false])
+ AX_GCC_X86_CPU_SUPPORTS(avx2, [AVX2_SUPPORTED=true], [AVX2_SUPPORTED=false])
+else
+ SSE2_SUPPORTED=false
+ AVX2_SUPPORTED=false
+fi

if [ "$MSSE2" = true ] && [ "$SSE2_SUPPORTED" = true ] ; then
SSE2="-DSHUFFLE_SSE2_ENABLED"
@@ -69,11 +93,6 @@ AC_SUBST(SSE2_BITSHUFFLE_OBJ)
AC_SUBST(SSE2_SHUFFLE_OBJ)
AC_SUBST(SSE2_OBJ_PATH)

-## see if -mavx2 is a supported flag
-AX_CHECK_COMPILE_FLAG([-mavx2], [MAVX2=true], [MAVX2=false])
-## check CPU supports avx2
-AX_GCC_X86_CPU_SUPPORTS(avx2, [AVX2_SUPPORTED=true], [AVX2_SUPPORTED=false])
-
if [ "$MAVX2" = true ] && [ "$AVX2_SUPPORTED" = true ] ; then
AVX2="-DSHUFFLE_AVX2_ENABLED"
MAVX2="-mavx2"

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