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adios2-config cxxflags output missing "-I" or "-isystem"
Describe the bug I built [email protected] via spack on Sunspot using the icpx compiler and found adios2-config does not include the "-I" or "-isystem" prefix to the include path:
ckelly@uan-0002:~/bld/chimbuko_spack_env_9_12_24> /home/ckelly/bld/chimbuko_spack_env_9_12_24/spack/opt/spack/linux-sles15-x86_64/oneapi-2024.04.15.002/adios2-2.10.0-cj255dyxpy3joolxnthsq3rlwqrfavfc/bin/adios2-config --cxx-flags
-DADIOS2_USE_MPI /home/ckelly/bld/chimbuko_spack_env_9_12_24/spack/opt/spack/linux-sles15-x86_64/oneapi-2024.04.15.002/adios2-2.10.0-cj255dyxpy3joolxnthsq3rlwqrfavfc/include
A build with gcc and openmpi in a Docker test environment running on a local machine produces the following
root@fe0859b75c2c:~# /opt/software/linux-ubuntu18.04-broadwell/gcc-7.5.0/adios2-2.10.0-tqtfqjay6ikguvo2bckeoykz7f3i3gfn/bin/adios2-config --cxx-flags
-DADIOS2_USE_MPI -isystem /opt/software/linux-ubuntu18.04-broadwell/gcc-7.5.0/adios2-2.10.0-tqtfqjay6ikguvo2bckeoykz7f3i3gfn/include
which has the "-isystem" prefix.
This missing prefix is preventing libraries using adios2 from being built with spack.
To Reproduce
Here is a complete spack environment:
spack:
specs:
- adios2 % oneapi
concretizer:
unify: true
reuse: false
compilers:
- compiler:
spec: gcc@=12.2.0
paths:
cc: /opt/aurora/24.086.0/spack/gcc/0.7.0/install/linux-sles15-x86_64/gcc-7.5.0/gcc-12.2.0-fxd4zwa64mfswv34rol52zamj7c6r3cz/bin/gcc
cxx: /opt/aurora/24.086.0/spack/gcc/0.7.0/install/linux-sles15-x86_64/gcc-7.5.0/gcc-12.2.0-fxd4zwa64mfswv34rol52zamj7c6r3cz/bin/g++
f77: /opt/aurora/24.086.0/spack/gcc/0.7.0/install/linux-sles15-x86_64/gcc-7.5.0/gcc-12.2.0-fxd4zwa64mfswv34rol52zamj7c6r3cz/bin/gfortran
fc: /opt/aurora/24.086.0/spack/gcc/0.7.0/install/linux-sles15-x86_64/gcc-7.5.0/gcc-12.2.0-fxd4zwa64mfswv34rol52zamj7c6r3cz/bin/gfortran
flags: {}
operating_system: sles15
target: x86_64
modules: []
environment: {}
extra_rpaths: []
- compiler:
spec: "[email protected] ~envmods"
paths:
cc: /opt/aurora/24.086.0/spack/oneapi/0.7.0/oneapi_sym/compiler/2024.04.15.002/bin/icx
cxx: /opt/aurora/24.086.0/spack/oneapi/0.7.0/oneapi_sym/compiler/2024.04.15.002/bin/icpx
f77: /opt/aurora/24.086.0/spack/oneapi/0.7.0/oneapi_sym/compiler/2024.04.15.002/bin/ifx
fc: /opt/aurora/24.086.0/spack/oneapi/0.7.0/oneapi_sym/compiler/2024.04.15.002/bin/ifx
flags:
cflags: -fp-model=precise
cxxflags: -fp-model=precise
fflags: -fp-model=precise
operating_system: sles15
target: x86_64
modules:
- intel_compute_runtime/release/821.36
- oneapi/eng-compiler/2024.04.15.002
- gcc/12.2.0
environment: {}
extra_rpaths: []
repos: []
packages:
all:
compiler: [oneapi]
target: [x86_64]
providers:
mpi: [mpich]
intel-oneapi-compilers:
externals:
- spec: [email protected] ~envmods %[email protected]
prefix: /opt/aurora/24.086.0/spack/oneapi/0.7.0/oneapi_sym
modules:
- oneapi/eng-compiler/2024.04.15.002
- gcc/12.2.0
- spec: [email protected] ~envmods %[email protected]
prefix: /opt/aurora/24.086.0/spack/oneapi/0.7.0/oneapi_sym
modules:
- oneapi/release/2024.1
- gcc/12.2.0
buildable: false
mpich:
require:
- spec: "@:20231026 %oneapi pmi=pmix ~hydra"
when: "%[email protected]"
- spec: "@:20231026 %oneapi pmi=pmix ~hydra"
when: "%[email protected]"
externals:
- spec: "mpich@20231026 %oneapi pmi=pmix ~hydra"
prefix: /opt/aurora/24.086.0/CNDA/mpich/20231026/mpich-ofi-all-icc-default-pmix-gpu-drop20231026
modules:
- mpich/icc-all-pmix-gpu/20231026
buildable: false
oneapi-level-zero:
require:
- spec: "@:821.36"
when: "%[email protected]"
- spec: "@:803.29"
when: "%[email protected]"
externals:
- spec: "[email protected]"
prefix: /opt/aurora/24.086.0/intel-gpu-umd/803.29
modules:
- intel_compute_runtime/release/803.29
- spec: "[email protected]"
prefix: /opt/aurora/24.086.0/intel-gpu-umd/803.45
modules:
- intel_compute_runtime/release/803.45
- spec: "[email protected]"
prefix: /opt/aurora/24.086.0/intel-gpu-umd/821.30
modules:
- intel_compute_runtime/release/821.30
- spec: "[email protected]"
prefix: /opt/aurora/24.086.0/intel-gpu-umd/821.35
modules:
- intel_compute_runtime/release/821.35
- spec: "[email protected]"
prefix: /opt/aurora/24.086.0/intel-gpu-umd/821.36
modules:
- intel_compute_runtime/release/821.36
buildable: false
libfabric:
externals:
- spec: [email protected]
prefix: /opt/cray/libfabric/1.15.2.0
buildable: false
mpi:
buildable: false
perl:
externals:
- spec: [email protected]
prefix: /usr
buildable: false
version: []
python:
version: []
buildable: false
externals:
- modules:
- python/3.10.11
spec: [email protected]
tar:
externals:
- spec: [email protected]
prefix: /usr
buildable: false
version: []
autoconf:
externals:
- spec: [email protected]
prefix: /usr
buildable: false
version: []
automake:
externals:
- spec: [email protected]
prefix: /usr
buildable: false
version: []
openssl:
externals:
- spec: [email protected]
prefix: /usr
buildable: false
version: []
pkg-config:
externals:
- spec: [email protected]
prefix: /usr
buildable: false
version: []
gmake:
externals:
- spec: [email protected]
prefix: /usr
buildable: false
version: []
libtool:
externals:
- spec: [email protected]
prefix: /usr
buildable: false
version: []
m4:
externals:
- spec: [email protected]
prefix: /usr
buildable: false
version: []
boost:
externals:
- spec: [email protected]
prefix: /opt/aurora/24.086.0/spack/oneapi/0.7.0/install/2024.04.15.002/linux-sles15-x86_64/oneapi-2024.04.15.002/boost-1.84.0-kgmlpiv7w2oba3dge2zl7rtotjuorgkr
modules:
- boost/1.84.0
buildable: false
version: []
cmake:
externals:
- spec: [email protected]
prefix: /opt/aurora/24.086.0/spack/gcc/0.7.0/install/linux-sles15-x86_64/gcc-12.2.0/cmake-3.27.7-mbl7dvgbiblpavhu53h5cheyrmpaikdz
modules:
- cmake/3.27.7
buildable: false
version: []
view: true
Please note that the adios2 binaries will fail to link due to the following issue:
>> 1142 /usr/bin/ld: ../../../../lib64/libadios2_core.so.2.10.0: undefined reference to `MPI_Abort'
>> 1143 /usr/bin/ld: ../../../../lib64/libadios2_core.so.2.10.0: undefined reference to `MPI_Bcast'
>> 1144 /usr/bin/ld: ../../../../lib64/libadios2_core.so.2.10.0: undefined reference to `MPI_Barrier'
suggesting one of the dependent libraries on this system includes MPI symbols for some reason. A workaround is to hack the spack package (var/spack/repos/builtin/packages/adios2/package.py) to include the following
args.append("-DCMAKE_EXE_LINKER_FLAGS=-Wl,-rpath=/opt/aurora/24.086.0/CNDA/mpich/20231026/mpich-ofi-all-icc-default-pmix-gpu-drop20231026/lib/ -L/opt/aurora/24.086.0/CNDA/mpich/20231026/mpich-ofi-all-icc-default-pmix-gpu-drop20231026/lib/ -lmpi")
when putting together the cmake args.
Expected behavior The output of "adios2-config --cxx-flags" should include "-I" or "-isystem" before the include path
Desktop:
- OS/Platform: Sunspot
- Build: compiler
[email protected] cmake [email protected]built via spack with spec[email protected]%[email protected] cflags='-fp-model=precise' cxxflags='-fp-model=precise' fflags='-fp-model=precise' ~aws+blosc2+bzip2~campaign~cuda~dataspaces+fortran~hdf5~ipo~kokkos+libcatalyst~libpressio+mgard+mpi~pic+png~python~rocm+sst~sycl+sz+zfp build_system=cmake build_type=Release generator=make arch=linux-sles15-x86_64
Update:
I tried compiling the spec [email protected] % oneapi on Sunspot instead, using the otherwise same environment as above, and found that it compiled successfully without the MPI link errors and also produces an adios2-config that gives the expected output
ckelly@uan-0002:~/bld/chimbuko_spack_env_9_12_24/adios2_env_vers_test> /home/ckelly/bld/chimbuko_spack_env_9_12_24/spack/opt/spack/linux-sles15-x86_64/oneapi-2024.04.15.002/adios2-2.9.2-kiiwf3oo2qouajt4lpfrqevwuxb2xxsx/bin/adios2-config --cxx-flags
-DADIOS2_USE_MPI -isystem /home/ckelly/bld/chimbuko_spack_env_9_12_24/spack/opt/spack/linux-sles15-x86_64/oneapi-2024.04.15.002/adios2-2.9.2-kiiwf3oo2qouajt4lpfrqevwuxb2xxsx/include
This suggests that both issues (possibly related, although I can't see how they would be) stem from changes between 2.9.2 and 2.10.0.
For more information regarding the MPI link issue, the build of 2.10.0 fails with
1139 [ 75%] Linking CXX executable ../../../../bin/adios2_remote_server
1140 cd /tmp/ckelly/spack-stage/spack-stage-adios2-2.10.0-rkkwyaqfyxywyk55hmmr7ow625kcbfje/spack-build-rkkwyaq/source/adios2/toolkit/remote && /home/ckelly/bld/chimbuko_spack_env_9_12_24/spack/opt/spack
/linux-sles15-x86_64/oneapi-2024.04.15.002/cmake-3.27.9-34sy6yon6urhi5e6szgdlk7kcvjlakgr/bin/cmake -E cmake_link_script CMakeFiles/adios2_remote_server.dir/link.txt --verbose=1
1141 /home/ckelly/bld/chimbuko_spack_env_9_12_24/spack/lib/spack/env/oneapi/icpx -O3 -DNDEBUG CMakeFiles/adios2_remote_server.dir/remote_server.cpp.o CMakeFiles/adios2_remote_server.dir/remote_common.cp
p.o -o ../../../../bin/adios2_remote_server -Wl,-rpath,/tmp/ckelly/spack-stage/spack-stage-adios2-2.10.0-rkkwyaqfyxywyk55hmmr7ow625kcbfje/spack-build-rkkwyaq/lib64:/home/ckelly/bld/chimbuko_spack_
env_9_12_24/spack/opt/spack/linux-sles15-x86_64/gcc-12.2.0/c-blosc2-2.11.1-r4lknhue5cmioynluyak4dupnoqjpfxn/lib64:/home/ckelly/bld/chimbuko_spack_env_9_12_24/spack/opt/spack/linux-sles15-x86_64/one
api-2024.04.15.002/zstd-1.5.6-rjqalogquhy65go25uuaolps5e4npyaj/lib:/home/ckelly/bld/chimbuko_spack_env_9_12_24/spack/opt/spack/linux-sles15-x86_64/gcc-12.2.0/lz4-1.9.4-jeh3svnxgjqkufwqc6zosl7mo5trs
5yb/lib:/home/ckelly/bld/chimbuko_spack_env_9_12_24/spack/opt/spack/linux-sles15-x86_64/oneapi-2024.04.15.002/zlib-ng-2.1.6-2sjoqerebjgnkrjzjleemexeuha6mswe/lib:/home/ckelly/bld/chimbuko_spack_env_
9_12_24/spack/opt/spack/linux-sles15-x86_64/oneapi-2024.04.15.002/zfp-0.5.5-5n2irrjgchglgzqjaoidvapjftko4fhz/lib64:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
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:::::::::::::::::::::::::::::::::::::::::::::::::::: ../../../../lib64/libadios2_evpath.so.2.10.0 ../../../../lib64/libadios2_core.so.2.10.0 ../../../../lib64/libadios2_ffs.so.2.10.0 ../../../../li
b64/libadios2_atl.so.2.10.0 -pthread -ldl -Wl,-rpath-link,/tmp/ckelly/spack-stage/spack-stage-adios2-2.10.0-rkkwyaqfyxywyk55hmmr7ow625kcbfje/spack-build-rkkwyaq/lib64:/home/ckelly/bld/chimbuko_spac
k_env_9_12_24/spack/opt/spack/linux-sles15-x86_64/gcc-12.2.0/c-blosc2-2.11.1-r4lknhue5cmioynluyak4dupnoqjpfxn/lib64:/home/ckelly/bld/chimbuko_spack_env_9_12_24/spack/opt/spack/linux-sles15-x86_64/o
neapi-2024.04.15.002/zstd-1.5.6-rjqalogquhy65go25uuaolps5e4npyaj/lib:/home/ckelly/bld/chimbuko_spack_env_9_12_24/spack/opt/spack/linux-sles15-x86_64/gcc-12.2.0/lz4-1.9.4-jeh3svnxgjqkufwqc6zosl7mo5t
rs5yb/lib:/home/ckelly/bld/chimbuko_spack_env_9_12_24/spack/opt/spack/linux-sles15-x86_64/oneapi-2024.04.15.002/zlib-ng-2.1.6-2sjoqerebjgnkrjzjleemexeuha6mswe/lib:/home/ckelly/bld/chimbuko_spack_en
v_9_12_24/spack/opt/spack/linux-sles15-x86_64/oneapi-2024.04.15.002/zfp-0.5.5-5n2irrjgchglgzqjaoidvapjftko4fhz/lib64
>> 1142 /usr/bin/ld: ../../../../lib64/libadios2_core.so.2.10.0: undefined reference to `MPI_Abort'
>> 1143 /usr/bin/ld: ../../../../lib64/libadios2_core.so.2.10.0: undefined reference to `MPI_Bcast'
>> 1144 /usr/bin/ld: ../../../../lib64/libadios2_core.so.2.10.0: undefined reference to `MPI_Barrier'
>> 1145 icpx: error: linker command failed with exit code 1 (use -v to see invocation)
>> 1146 make[2]: *** [source/adios2/toolkit/remote/CMakeFiles/adios2_remote_server.dir/build.make:120: bin/adios2_remote_server] Error 1
1147 make[2]: Leaving directory '/tmp/ckelly/spack-stage/spack-stage-adios2-2.10.0-rkkwyaqfyxywyk55hmmr7ow625kcbfje/spack-build-rkkwyaq'
>> 1148 make[1]: *** [CMakeFiles/Makefile2:1257: source/adios2/toolkit/remote/CMakeFiles/adios2_remote_server.dir/all] Error 2
1149 make[1]: Leaving directory '/tmp/ckelly/spack-stage/spack-stage-adios2-2.10.0-rkkwyaqfyxywyk55hmmr7ow625kcbfje/spack-build-rkkwyaq'
>> 1150 make: *** [Makefile:139: all] Error 2
My first thought was that this issue would affect every binary but it may also be just adios2_remote_server as I notice that this application did not exist in 2.9.2.
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