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Installation issue: cgns (fPIC issue) #39699
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Description
Steps to reproduce the issue
$ spack spec -lI cgns
Input spec
--------------------------------
- cgns
Concretized
--------------------------------
- m5vc5qo [email protected]%[email protected]+base_scope+fortran+hdf5~int64+ipo+legacy~mem_debug+mpi+scoping+shared+static+testing+tools build_system=cmake build_type=RelWithDebInfo generator=make arch=linux-rhel8-zen2
[+] kzbjptx ^[email protected]%[email protected]~doc+ncurses+ownlibs~qt build_system=generic build_type=Release arch=linux-rhel8-zen2
[+] 2nd5xjs ^[email protected]%[email protected]+symlinks+termlib abi=5 build_system=autotools arch=linux-rhel8-zen2
[+] acpcwrk ^[email protected]%[email protected]~docs+shared build_system=generic certs=system arch=linux-rhel8-zen2
[+] p7qp44w ^[email protected]%[email protected]+guile build_system=autotools patches=599f134 arch=linux-rhel8-zen2
[+] snqs5yc ^[email protected]%[email protected]+readline build_system=autotools threads=posix arch=linux-rhel8-zen2
[+] c26pf64 ^[email protected]%[email protected]+libatomic-ops build_system=autotools threads=posix arch=linux-rhel8-zen2
[+] lhefaa5 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] nwvzdt4 ^[email protected]%[email protected]+bzip2+curses+git+libunistring+libxml2+tar+xz build_system=autotools arch=linux-rhel8-zen2
[+] jmrtao4 ^[email protected]%[email protected] build_system=autotools libs=shared,static arch=linux-rhel8-zen2
[+] 6tl6au3 ^[email protected]%[email protected] build_system=autotools zip=pigz arch=linux-rhel8-zen2
[+] onyctuz ^[email protected]%[email protected] build_system=makefile arch=linux-rhel8-zen2
[+] ogpntgf ^[email protected]%[email protected]+programs build_system=makefile compression=lz4,lzma,zlib libs=shared,static arch=linux-rhel8-zen2
[+] s2yvnqh ^[email protected]%[email protected] build_system=makefile libs=shared,static arch=linux-rhel8-zen2
[+] h5xayww ^[email protected]%[email protected]+pic build_system=autotools libs=shared,static arch=linux-rhel8-zen2
[+] k7tcz64 ^[email protected]%[email protected]+cxx build_system=autotools libs=shared,static patches=69ad2e2 arch=linux-rhel8-zen2
[+] kpsuuut ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] d3bx5oi ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] x3mkx4p ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] ryhrrvu ^[email protected]%[email protected] build_system=autotools patches=682a465,e55be05 arch=linux-rhel8-zen2
[+] rxkfgbd ^[email protected]%[email protected]+internal_glib build_system=autotools arch=linux-rhel8-zen2
[+] stpg6jt ^[email protected]%[email protected]+cxx+fortran+hl+ipo+java+mpi+shared+szip+threadsafe+tools api=default build_system=cmake build_type=RelWithDebInfo generator=make patches=2a1e311 arch=linux-rhel8-zen2
[+] iy5ro4n ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] vqsod6z ^[email protected]_7%[email protected] build_system=generic arch=linux-rhel8-zen2
[+] jpm3doc ^[email protected]%[email protected]+optimize+pic+shared build_system=makefile arch=linux-rhel8-zen2
[+] roegncq ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] at6vdch ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] a2wysy5 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] 3nodp4k ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] 23l2zhm ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] jfsbatp ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] qlyp3o5 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] svszhzp ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] gwfkdc3 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] knlmgzd ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] 2rzdmj2 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] k3erefc ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] t7btf5s ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] qhsvnq2 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] herup77 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] o4aqa47 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] 3c7dro2 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] yo3pway ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] o6mgx5d ^[email protected]%[email protected] build_system=autotools gl=osmesa arch=linux-rhel8-zen2
[+] lvj7wgx ^[email protected]%[email protected]+atomics~cuda+cxx+cxx_exceptions~gpfs~internal-hwloc~java+legacylaunchers~lustre~memchecker+orterunprefix+pmi+romio+rsh~singularity~static~vt+wrapper-rpath build_system=autotools fabrics=ucx schedulers=slurm arch=linux-rhel8-zen2
[+] ctfnt3p ^[email protected]%[email protected]~cairo~cuda~gl+libudev+libxml2~netloc~nvml~oneapi-level-zero~opencl+pci~rocm build_system=autotools libs=shared,static arch=linux-rhel8-zen2
[+] oktvvq3 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] zteihso ^[email protected]%[email protected]~python build_system=autotools patches=3e06d42 arch=linux-rhel8-zen2
[+] 6p53zmi ^[email protected]%[email protected] build_system=autotools patches=4e1d78c,62fc8a8,ff37630 arch=linux-rhel8-zen2
[+] e5cktjy ^[email protected]%[email protected] build_system=autotools patches=35c4492,7793209,a49dd5b arch=linux-rhel8-zen2
[+] 6mgpv7j ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] cjebbaj ^[email protected]%[email protected]+sigsegv build_system=autotools patches=9dc5fbd,bfdffa7 arch=linux-rhel8-zen2
[+] uvi2god ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] soukbeu ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] qtcped7 ^[email protected]%[email protected]+gssapi build_system=autotools arch=linux-rhel8-zen2
[+] ko25i4e ^[email protected]%[email protected]+shared build_system=autotools arch=linux-rhel8-zen2
[+] 43xbx5l ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] 2tqklmb ^[email protected]%[email protected]~obsolete_api build_system=autotools arch=linux-rhel8-zen2
[+] 4grunmz ^[email protected]%[email protected]+cpanm+open+shared+threads build_system=generic arch=linux-rhel8-zen2
[+] nkkrcue ^[email protected]%[email protected]+cxx+docs+stl build_system=autotools patches=26090f4 arch=linux-rhel8-zen2
[+] hjzedoe ^[email protected]%[email protected]~debug+pic+shared build_system=generic arch=linux-rhel8-zen2
[+] tsdsqho ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] xbiwwfl ^[email protected]%[email protected]~docs+pmi_backwards_compatibility build_system=autotools arch=linux-rhel8-zen2
[+] ug5dirg ^slurm@system%[email protected]~gtk~hdf5~hwloc~mariadb~pmix+readline~restd build_system=autotools sysconfdir=/etc/slurm arch=linux-rhel8-zen2
[+] oq3hlnb ^[email protected]%[email protected]~assertions~backtrace_detail+cma~cuda~dc~debug~dm+examples~gdrcopy~gtest~ib_hw_tm~java+knem~logging~mlx5_dv+openmp+optimizations~parameter_checking+pic~rc+rdmacm~rocm+thread_multiple~ucg~ud~verbs~vfs+xpmem build_system=autotools libs=shared opt=3 simd=auto arch=linux-rhel8-zen2
[+] 5gqoewn ^[email protected]%[email protected] build_system=bundle arch=linux-rhel8-zen2
[+] ronsr6s ^[email protected]%[email protected]+glx~llvm+opengl+opengles+osmesa~strip build_system=meson buildtype=debugoptimized default_library=shared,static patches=ee737d1 arch=linux-rhel8-zen2
[+] fxc4ppz ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] lazftoc ^[email protected]%[email protected]+libbsd build_system=autotools arch=linux-rhel8-zen2
[+] rs2ddq5 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] hkztvet ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] foha5hv ^[email protected]%[email protected]+lex+nls build_system=autotools patches=f8b85a0 arch=linux-rhel8-zen2
[+] lr5iwpq ^[email protected]%[email protected] build_system=autotools patches=440b954 arch=linux-rhel8-zen2
[+] lutg2mh ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] 2yshqcu ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] 65dpibi ^[email protected]%[email protected]~block_signals~conservative_checks~cxx_exceptions~debug~debug_frame+docs+pic+tests+weak_backtrace+xz+zlib build_system=autotools components=coredump,ptrace,setjump libs=shared,static arch=linux-rhel8-zen2
[+] oozqy34 ^[email protected]%[email protected] build_system=python_pip patches=0f0b1bd arch=linux-rhel8-zen2
[+] dcjyras ^[email protected]%[email protected] build_system=generic arch=linux-rhel8-zen2
[+] 3f4dteo ^[email protected]%[email protected] build_system=generic arch=linux-rhel8-zen2
[+] zu7kuev ^[email protected]%[email protected] build_system=generic arch=linux-rhel8-zen2
[+] gsrt7hl ^[email protected]%[email protected]+re2c build_system=generic arch=linux-rhel8-zen2
[+] npv6wpd ^[email protected]%[email protected] build_system=generic arch=linux-rhel8-zen2
[+] 5meqv3b ^[email protected]%[email protected] build_system=python_pip arch=linux-rhel8-zen2
[+] 26xogaz ^[email protected]%[email protected] build_system=python_pip arch=linux-rhel8-zen2
[+] t45xqwm ^[email protected]%[email protected]+bz2+crypt+ctypes+dbm~debug+libxml2+lzma+nis+optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=0d98e93,4c24573,f2fd060 arch=linux-rhel8-zen2
[+] qna53es ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] icy23ix ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] jbj5l5f ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] hhwsw3i ^[email protected]%[email protected]+column_metadata+dynamic_extensions+fts+functions+rtree build_system=autotools arch=linux-rhel8-zen2
[+] rckoxz7 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] 4zbzlco ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] 6fgglfp ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] 4tvhibv ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] uv323sa ^[email protected]%[email protected]+xft+xss build_system=autotools arch=linux-rhel8-zen2
[+] 3oevaar ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] ebtsjlq ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] ruxdkjg ^[email protected]%[email protected] build_system=autotools fonts=encodings,font-adobe-100dpi,font-adobe-75dpi,font-adobe-utopia-100dpi,font-adobe-utopia-75dpi,font-adobe-utopia-type1,font-alias,font-arabic-misc,font-bh-100dpi,font-bh-75dpi,font-bh-lucidatypewriter-100dpi,font-bh-lucidatypewriter-75dpi,font-bh-type1,font-bitstream-100dpi,font-bitstream-75dpi,font-bitstream-speedo,font-bitstream-type1,font-cronyx-cyrillic,font-cursor-misc,font-daewoo-misc,font-dec-misc,font-ibm-type1,font-isas-misc,font-jis-misc,font-micro-misc,font-misc-cyrillic,font-misc-ethiopic,font-misc-meltho,font-misc-misc,font-mutt-misc,font-schumacher-misc,font-screen-cyrillic,font-sun-misc,font-winitzki-cyrillic,font-xfree86-type1 arch=linux-rhel8-zen2
[+] v4lwqfy ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] kztf3jt ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] q7rswc7 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] el4zigk ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] cjqnhw3 ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] r4tsdwi ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] pcfi3uy ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] 6cupoxl ^[email protected]%[email protected]+pic+shared build_system=autotools arch=linux-rhel8-zen2
[+] yj4wdtz ^[email protected]%[email protected]+ipo build_system=cmake build_type=RelWithDebInfo generator=make libs=shared,static arch=linux-rhel8-zen2
[+] swbnj5g ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] s4fgvuq ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] kdzyy7n ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
[+] g7lhvjh ^[email protected]%[email protected] build_system=autotools arch=linux-rhel8-zen2
...Error message
Error message
... /cvmfs/hpcsw.umd.edu/spack-software/2023.05.30/linux-rhel8-zen2/gcc-9.4.0/openmpi-4.1.1-lvj7wgxqp223cb6msiwgof2ms3qcij4o/bin/mpif90 -fPIC -DNO_CONCATENATION -O2 -g -DNDEBUG -shared -Wl,-soname,libcgns.so.4.2 -o libcgns.so.4.2 CMakeFiles/cgns_shared.dir/cgns_error.c.o CMakeFiles/cgns_shared.dir/cgns_internals.c.o CMakeFiles/cgns_shared.dir/cgns_io.c.o CMakeFiles/cgns_shared.dir/cgnslib.c.o CMakeFiles/cgns_shared.dir/cg_hashmap.c.o CMakeFiles/cgns_shared.dir/adf/ADF_interface.c.o CMakeFiles/cgns_shared.dir/adf/ADF_internals.c.o CMakeFiles/cgns_shared.dir/adfh/ADFH.c.o CMakeFiles/cgns_shared.dir/pcgnslib.c.o CMakeFiles/cgns_shared.dir/cg_ftoc.c.o CMakeFiles/cgns_shared.dir/cgio_ftoc.c.o CMakeFiles/cgns_f2c.dir/cgns_f.F90.o -Wl,-rpath,/cvmfs/hpcsw.umd.edu/spack-software/2023.05.30/linux-rhel8-zen2/gcc-9.4.0/hdf5-1.10.7-stpg6jtn3e2ollbzguvwdhse65o57hjk/lib:/cvmfs/hpcsw.umd.edu/spack-software/2023.05.30/linux-rhel8-zen2/gcc-9.4.0/zlib-1.2.13-jpm3doc2g37hjstjg5rhj7vrtrusrtxi/lib:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: /cvmfs/hpcsw.umd.edu/spack-software/2023.05.30/linux-rhel8-zen2/gcc-9.4.0/hdf5-1.10.7-stpg6jtn3e2ollbzguvwdhse65o57hjk/lib/libhdf5.so.103.3.0 -ldl /cvmfs/hpcsw.umd.edu/spack-software/2023.05.30/linux-rhel8-zen2/gcc-9.4.0/zlib-1.2.13-jpm3doc2g37hjstjg5rhj7vrtrusrtxi/lib/libz.so /bin/ld: CMakeFiles/cgns_f2c.dir/cgns_f.F90.o: relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC /bin/ld: final link failed: Nonrepresentable section on output collect2: error: ld returned 1 exit status ...
Information on your system
$ spack debug report
* **Spack:** 0.21.0.dev0 (84faf5a6cf342efddb976b7432e44aff12f1c985)
* **Python:** 3.6.8
* **Platform:** linux-rhel8-zen2
* **Concretizer:** clingoAdditional information
spack-build-env.txt
spack-build-out.txt
Maintainers: @gsjaardema
Basically, it looks like we need to add -fPIC to the compilation flags
General information
- I have run
spack debug reportand reported the version of Spack/Python/Platform - I have run
spack maintainers <name-of-the-package>and @mentioned any maintainers - I have uploaded the build log and environment files
- I have searched the issues of this repo and believe this is not a duplicate
Reactions are currently unavailable