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oneapi-src / oneDAL

oneAPI Data Analytics Library (oneDAL)
https://software.intel.com/en-us/oneapi/onedal
Apache License 2.0
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Fatal error: stdlib.h: No such file or directory from #include_next <stdlib.h> #2706

Open mattpulver opened 6 months ago

mattpulver commented 6 months ago

Describe the bug Fatal error when building:

In file included from /usr/include/c++/13.2.1/bits/stl_algo.h:71,
                 from /usr/include/c++/13.2.1/algorithm:61,
                 from cpp/oneapi/dal/algo/logistic_regression/parameters/cpu/train_parameters.cpp:17:
/usr/include/c++/13.2.1/cstdlib:79:15: fatal error: stdlib.h: No such file or directory
   79 | #include_next <stdlib.h>
      |               ^~~~~~~~~~
compilation terminated.

To Reproduce Steps to reproduce the behavior:

cd src/oneDAL-2024.1.0
./dev/download_micromkl.sh

LIBRARY_PATH=/usr/lib \
LD_LIBRARY_PATH=/usr/lib \
TBBROOT=/usr \
  make -f makefile daal oneapi_c -j10 COMPILER=gnu PLAT=lnx32e REQCPU="avx2 avx512"

Expected behavior It should build successfully

Diagnosis and Fix The problem first occurs at this step:

g++ -m64 -fwrapv -fno-strict-overflow -fno-delete-null-pointer-checks -Werror -Wreturn-type -Wno-error=dangling-reference  -c -Wformat -Wformat-security -O2 -D_FORTIFY_SOURCE=2 -fstack-protector-strong -fPIC -std=c++17   -DTBB_SUPPRESS_DEPRECATED_MESSAGES -D__TBB_LEGACY_MODE  -pedantic -Wall -Wextra -Wno-unused-parameter -DDAAL_NOTHROW_EXCEPTIONS -DDAAL_HIDE_DEPRECATED -D_ENABLE_ATOMIC_ALIGNMENT_FIX  -D__ONEDAL_ENABLE_DLL_EXPORT__ -D__TBB_NO_IMPLICIT_LINKAGE -DTBB_USE_ASSERT=0 @./__work_gnu/md/lnx32e/oneapi_dynamic/inc_y_folders.txt   -MMD -MT __work_gnu/md/lnx32e/oneapi_dynamic/cpp-oneapi-dal-algo-logistic_regression-parameters-cpu-train_parameters.o -MF __work_gnu/md/lnx32e/oneapi_dynamic/cpp-oneapi-dal-algo-logistic_regression-parameters-cpu-train_parameters.o.d.tmp -o__work_gnu/md/lnx32e/oneapi_dynamic/cpp-oneapi-dal-algo-logistic_regression-parameters-cpu-train_parameters.o cpp/oneapi/dal/algo/logistic_regression/parameters/cpu/train_parameters.cpp &&  sed -n -i -e ':beg' -e '/\\$/N; s/\\\n/ /; tbeg' -e ' s@cpp/oneapi/dal/algo/logistic_regression/parameters/cpu/train_parameters.cpp\( \|$\)@@; s/  */ /g; s/^.*: *$//;' -e 's@ /[^ ][^ ]*@ @g; s/^.*: *$//;' -e '/./{ p; s/^.*://; s/^ *//; /./{ s/ *$/:/; s/  */:\n/g; p; };}' __work_gnu/md/lnx32e/oneapi_dynamic/cpp-oneapi-dal-algo-logistic_regression-parameters-cpu-train_parameters.o.d.tmp && printf '\n%s\n' '__work_gnu/md/lnx32e/oneapi_dynamic/cpp-oneapi-dal-algo-logistic_regression-parameters-cpu-train_parameters.o.mkdeps += makefile dev/make/cmplr.gnu.mkl.mk dev/make/cmplr.dpcpp.mk dev/make/common.mk dev/make/deps.mk dev/make/deps.mkl.mk makefile.ver' '$(__work_gnu/md/lnx32e/oneapi_dynamic/cpp-oneapi-dal-algo-logistic_regression-parameters-cpu-train_parameters.o.mkdeps):' '__work_gnu/md/lnx32e/oneapi_dynamic/cpp-oneapi-dal-algo-logistic_regression-parameters-cpu-train_parameters.o: $(__work_gnu/md/lnx32e/oneapi_dynamic/cpp-oneapi-dal-algo-logistic_regression-parameters-cpu-train_parameters.o.mkdeps)' '__work_gnu/md/lnx32e/oneapi_dynamic/cpp-oneapi-dal-algo-logistic_regression-parameters-cpu-train_parameters.o.trigger = g++ -m64 -fwrapv -fno-strict-overflow -fno-delete-null-pointer-checks -Werror -Wreturn-type -Wno-error=dangling-reference  -c -Wformat -Wformat-security -O2 -D_FORTIFY_SOURCE=2 -fstack-protector-strong -fPIC -std=c++17   -DTBB_SUPPRESS_DEPRECATED_MESSAGES -D__TBB_LEGACY_MODE  -pedantic -Wall -Wextra -Wno-unused-parameter -DDAAL_NOTHROW_EXCEPTIONS -DDAAL_HIDE_DEPRECATED -D_ENABLE_ATOMIC_ALIGNMENT_FIX  -D__ONEDAL_ENABLE_DLL_EXPORT__ -D__TBB_NO_IMPLICIT_LINKAGE -DTBB_USE_ASSERT=0 @./__work_gnu/md/lnx32e/oneapi_dynamic/inc_y_folders.txt   -o__work_gnu/md/lnx32e/oneapi_dynamic/cpp-oneapi-dal-algo-logistic_regression-parameters-cpu-train_parameters.o cpp/oneapi/dal/algo/logistic_regression/parameters/cpu/train_parameters.cpp' >> __work_gnu/md/lnx32e/oneapi_dynamic/cpp-oneapi-dal-algo-logistic_regression-parameters-cpu-train_parameters.o.d.tmp && mv -f __work_gnu/md/lnx32e/oneapi_dynamic/cpp-oneapi-dal-algo-logistic_regression-parameters-cpu-train_parameters.o.d.tmp __work_gnu/md/lnx32e/oneapi_dynamic/cpp-oneapi-dal-algo-logistic_regression-parameters-cpu-train_parameters.o.d

which results in the above fatal error. We can see the reason for this by adding -v to the g++ command. It reports:

#include "..." search starts here:
#include <...> search starts here:
./cpp
./__release_lnx_gnu/daal/latest/include
./cpp/daal
./__work_gnu/md/lnx32e
./__deps/mklfpk/include
./__deps/mklfpk/lnx/include
 ./__deps/mklgpufpk/lnx/include
 /usr/include/tbb
 /usr/include
 /usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1/../../../../include/c++/13.2.1
 /usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1/../../../../include/c++/13.2.1/x86_64-pc-linux-gnu
 /usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1/../../../../include/c++/13.2.1/backward
 /usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1/include
 /usr/local/include
 /usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1/include-fixed
End of search list.

From the error message:

/usr/include/c++/13.2.1/cstdlib:79:15: fatal error: stdlib.h: No such file or directory
   79 | #include_next <stdlib.h>
      |               ^~~~~~~~~~

In context, that line in /usr/include/c++/13.2.1/cstdlib is:

// Need to ensure this finds the C library's <stdlib.h> not a libstdc++
// wrapper that might already be installed later in the include search path.
#define _GLIBCXX_INCLUDE_NEXT_C_HEADERS
#include_next <stdlib.h>
#undef _GLIBCXX_INCLUDE_NEXT_C_HEADERS

What should happen is that stdlib.h is included from /usr/include. However since /usr/include precedes /usr/lib/gcc/x86_64-pc-linux-gnu/13.2.1/../../../../include/c++/13.2.1 in the above #include <...> search paths, it doesn't find it, resulting in the error.

The source of how these #include <...> search paths got mixed up is from @./__work_gnu/md/lnx32e/oneapi_dynamic/inc_y_folders.txt which is in the above g++ command:

cat __work_gnu/md/lnx32e/oneapi_dynamic/inc_y_folders.txt
-I./cpp -isystem./__release_lnx_gnu/daal/latest/include -isystem./cpp/daal -isystem./__work_gnu/md/lnx32e -isystem./__deps/mklfpk/include -isystem./__deps/mklfpk/lnx/include -isystem./__deps/mklgpufpk/lnx/include -isystem/usr/include/tbb -isystem/usr/include

Note the last parameter -isystem/usr/include. By simply excluding this from the inc_a_folders.txt and inc_y_folders.txt generated files fixes the problem. Making this change results in /usr/include coming correctly after /usr/include/c++/13.2.1 in the #include <...> search paths.

Environment:

syakov-intel commented 5 months ago

Hello @mattpulver ,

We've tried to reproduce the issue with all the software versions as reported except Arch Linux though with no luck. Did you have any progress on your side meanwhile?

mattpulver commented 5 months ago

Yes I'm able to get through this by adding

  awk '{print} /\(ONEAPI\.include_options\)/{print "\tsed -i \x27s# -isystem/usr/include$$##\x27 $@"}' \
      makefile > makefile.tmp && mv makefile.tmp makefile

to the prepare() step in the PKGBUILD file.

I haven't tracked down where the /usr/include entry is coming from that appears in the intermediate inc_[ay]_folders.txt files but I think this would be fixed if they were omitted. I'm not sure why they need to be included, as they seem to mess up

#include_next <stdlib.h>

in cstdlib: https://github.com/gcc-mirror/gcc/blob/cacc55a4c0be8d0bc7417b6a28924eadbbe428e3/libstdc%2B%2B-v3/include/c_global/cstdlib#L79