Compiling OpenBLAS from source produces strange error message
Trying to compile OpenBLAS from the included tarball (0.2.19.a) produces a strange error message (gcc 9.3.1):
gcc -g -std=gnu99 -O2 -fopenmp -Wall -O2 -DMAX_STACK_ALLOC=2048 -Wall -m64 -DF_INTERFACE_GFORT -fPIC -DSMP_SERVER -DNO_WARMUP -DMAX_CPU_NUMBER=24 -DASMNAME= -DASMFNAME=_ -DNAME=_ -DCNAME= -DCHAR_NAME=\"_\" -DCHAR_CNAME=\"\" -DNO_AFFINITY -I.. -rdynamic -w -o linktest linktest.c ../libopenblas_nehalemp-r0.2.19.so -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. -lgfortran -lm -lquadmath -lm -lc NAME=/data/rhaas/postdoc/gr/cactus/CactusAMReX/configs/amrex/lib/libthorn_OpenBLAS.a && echo OK.
gcc: error: NAME=/data/rhaas/postdoc/gr/cactus/CactusAMReX/configs/amrex/lib/libthorn_OpenBLAS.a: No such file or directory
make[5]: *** [Makefile:134: ../libopenblas_nehalemp-r0.2.19.so] Error 1
As far as I can tell the incorrect string may (though I have no idea really) produced by c_check
and in particular the line:
$link = `$compiler_name -c ctest2.c -o ctest2.o 2>&1 && $compiler_name $openmp -v ctest2.o -o ctest2 2>&1 && rm -f ctest2.o ctest2 ctest2.exe`;
which sets $link
to the output of gcc -v
for a compiler call.
Possibly this goes away when updating the tarball.
Comments (7)
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The
NAME=...
nonsense comes fromgcc -v
apparently outputtingMAKEFLAGS=…
which hasNAME=
in it.$linker
is:Using built-in specs. COLLECT_GCC=gcc COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none:hsa OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-linux-gnu Configured with: ../src/configure -v --with-pkgversion='Debian 9.3.0-13' --with-bugurl=file:///usr/share/doc/gcc-9/README.Bugs --enable-languages=c,ada,c++,go,brig,d,fortran,objc,obj-c++,gm2 --prefix=/usr --with-gcc-major-version-only --program-suffix=-9 --program-prefix=x86_64-linux-gnu- --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --libdir=/usr/lib --enable-nls --enable-bootstrap --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --with-default-libstdcxx-abi=new --enable-gnu-unique-object --disable-vtable-verify --enable-plugin --enable-default-pie --with-system-zlib --with-target-system-zlib=auto --enable-objc-gc=auto --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --enable-multilib --with-tune=generic --enable-offload-targets=nvptx-none=/build/gcc-9-F9gimE/gcc-9-9.3.0/debian/tmp-nvptx/usr,hsa --without-cuda-driver --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnu --with-build-config=bootstrap-lto-lean --enable-link-mutex Thread model: posix gcc version 9.3.0 (Debian 9.3.0-13) MAKEFLAGS=s -j12 -- TARGET= ONLY_CBLAS=0 TARGET_CORE= USE_OPENMP= BINARY= CFLAGS=-g\ -std=gnu99\ -O2\ -fopenmp\ -Wall HOST_CFLAGS=-march=native\ -DGEMM_MULTITHREAD_THRESHOLD=4\ -DNO_PARALLEL_MAKE=0 HOSTCC=gcc FC=gfortran CC=gcc USESTHORNS= THORN=OpenBLAS NAME=/data/rhaas/postdoc/gr/cactus/CactusAMReX/configs/amrex/lib/libthorn_OpenBLAS.a CONFIG=/data/rhaas/postdoc/gr/cactus/CactusAMReX/configs/amrex/config-data SRCDIR=/data/rhaas/postdoc/gr/cactus/CactusAMReX/arrangements/ExternalLibraries/OpenBLAS/src TOP=/data/rhaas/postdoc/gr/cactus/CactusAMReX/configs/amrex CCTK_HOME=/data/rhaas/postdoc/gr/cactus/CactusAMReX CCTK_TARGET=make.checked COMPILER_PATH=/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/ LIBRARY_PATH=/usr/lib/gcc/x86_64-linux-gnu/9/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib/:/lib/x86_64-linux-gnu/:/lib/../lib/:/usr/lib/x86_64-linux-gnu/:/usr/lib/../lib/:/usr/lib/gcc/x86_64-linux-gnu/9/../../../:/lib/:/usr/lib/ Reading specs from /usr/lib/gcc/x86_64-linux-gnu/9/libgomp.spec COLLECT_GCC_OPTIONS='-g' '-std=gnu99' '-O2' '-fopenmp' '-Wall' '-v' '-o' 'ctest2' '-mtune=generic' '-march=x86-64' '-pthread' /usr/lib/gcc/x86_64-linux-gnu/9/collect2 -plugin /usr/lib/gcc/x86_64-linux-gnu/9/liblto_plugin.so -plugin-opt=/usr/lib/gcc/x86_64-linux-gnu/9/lto-wrapper -plugin-opt=-fresolution=/tmp/cc2KnInP.res -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s -plugin-opt=-pass-through=-lpthread -plugin-opt=-pass-through=-lc -plugin-opt=-pass-through=-lgcc -plugin-opt=-pass-through=-lgcc_s --build-id --eh-frame-hdr -m elf_x86_64 --hash-style=gnu --as-needed -dynamic-linker /lib64/ld-linux-x86-64.so.2 -pie -o ctest2 /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/Scrt1.o /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crti.o /usr/lib/gcc/x86_64-linux-gnu/9/crtbeginS.o /usr/lib/gcc/x86_64-linux-gnu/9/crtoffloadbegin.o -L/usr/lib/gcc/x86_64-linux-gnu/9 -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu -L/usr/lib/gcc/x86_64-linux-gnu/9/../../../../lib -L/lib/x86_64-linux-gnu -L/lib/../lib -L/usr/lib/x86_64-linux-gnu -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-linux-gnu/9/../../.. ctest2.o -lgomp -lgcc --push-state --as-needed -lgcc_s --pop-state -lpthread -lc -lgcc --push-state --as-needed -lgcc_s --pop-state /usr/lib/gcc/x86_64-linux-gnu/9/crtendS.o /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/crtn.o /usr/lib/gcc/x86_64-linux-gnu/9/crtoffloadend.o COLLECT_GCC_OPTIONS='-g' '-std=gnu99' '-O2' '-fopenmp' '-Wall' '-v' '-o' 'ctest2' '-mtune=generic' '-march=x86-64' '-pthread'
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This fragment fixes the issue:
Index: build.sh =================================================================== --- build.sh (revision 235) +++ build.sh (working copy) @@ -14,8 +14,8 @@ # Set locations THORN=OpenBLAS -NAME=OpenBLAS-0.2.19 -TARNAME=v0.2.19 +NAME=OpenBLAS-0.3.9 +TARNAME=v0.3.9 SRCDIR="$(dirname $0)" BUILD_DIR=${SCRATCH_BUILD}/build/${THORN} if [ -z "${OPENBLAS_INSTALL_DIR}" ]; then @@ -33,6 +33,9 @@ if echo '' ${ARFLAGS} | grep 64 > /dev/null 2>&1; then export OBJECT_MODE=64 fi +# Keep only -j option in Makeflags but not Cactus' make variables (some confuse +# OpenBLAS's c_check script) +MAKEFLAGS=${MAKEFLAGS%% -- *} echo "OpenBLAS: Preparing directory structure..." cd ${SCRATCH_BUILD}
by removing all Cactus build system make variables from
MAKEFLAGS
(but keeping eg-j
for parallelism).Using
gcc -v
to learn about libraries that need to be linked against seems very wrong to me and modifying MAKEFLAGS is a poor way of working around this issue.To be applied after the release and code deep freeze (on May 28th) and backported, along with an update of the tarball to 0.3.9.
-
- changed status to open
Please review.
-
To be backported after ET_2020_05.
-
Unless objected I will apply this after 2020-07-26
-
- changed status to resolved
Applied as git hash 73f3ba9 "OpenBLAS: work around OpenBLAS's strange way of determining linked libs" of ExternalLibraries-OpenBLAS
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Updating the tarball to 0.3.9 (stable version of March 2020) does not help.