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hpc / libhio

libhio is a library intended for writing data to hierarchical data store systems.
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libhio-1.4.1.2 fails with openmpi-3.1.0 #42

Closed junghans closed 5 years ago

junghans commented 6 years ago 
Making all in xexec
make[2]: Entering directory '/tmp/junghans/spack-stage/spack-stage-ik_yg78y/libhio-1.4.1.2/test/xexec'
  CC       xexec_x-xexec.o
  CC       xexec_x-xexec_base.o
  CC       xexec_x-xexec_fio.o
  CC       xexec_x-xexec_hio.o
  CC       xexec_x-xexec_mpi.o
  CC       xexec_x-cw_misc.o
  CCLD     xexec.x
xexec_x-xexec_hio.o: In function `hi_run':
/tmp/junghans/spack-stage/spack-stage-ik_yg78y/libhio-1.4.1.2/test/xexec/xexec_hio.c:242: undefined reference to `hio_init_mpi'
../../src/.libs/libhio.so: undefined reference to `hioi_dataset_aggregate_statistics'
../../src/.libs/libhio.so: undefined reference to `hioi_dataset_list_resize'
../../src/.libs/libhio.so: undefined reference to `hioi_dataset_list_alloc'
../../src/.libs/libhio.so: undefined reference to `hioi_dataset_header_cleanup'
../../src/.libs/libhio.so: undefined reference to `hioi_dataset_list_release'
../../src/.libs/libhio.so: undefined reference to `hioi_dataset_list_get'
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:393: xexec.x] Error 1
make[2]: Leaving directory '/tmp/junghans/spack-stage/spack-stage-ik_yg78y/libhio-1.4.1.2/test/xexec'
make[1]: *** [Makefile:533: all-recursive] Error 1
make[1]: Leaving directory '/tmp/junghans/spack-stage/spack-stage-ik_yg78y/libhio-1.4.1.2/test'
make: *** [Makefile:504: all-recursive] Error 1

Full spack-build.txt

giantcone commented 5 years ago

@floquet would you please check the Spack build of libHIO 1.4.1.3 please?

¡Mucho Thanks!

floquet commented 5 years ago

FAIL: Darwin Power 9, Trinitite Login PASS: Darwin Compute, Darwin ARM, Snow Compute, Capulin Compute

Builds using system compilers.

Darwin

Compute node

libhio@1.4.1.2

dantopa@cn123:darwin-general.libhio $ spack install libhio@1.4.1.2 % gcc@4.8.5 ^openmpi@3.1.0
...
==> Installing libhio
...
==> Successfully installed libhio
  Fetch: 0.09s.  Build: 55.97s.  Total: 56.06s.
[+] /scratch/users/dantopa/new-spack/libraries/darwin-general.libhio/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libhio-1.4.1.2-zh4svok5o4m4ysrpu2omkxqazcyonxaz

libhio@1.4.1.3

dantopa@cn123:darwin-general.libhio $ spack install libhio@1.4.1.3 % gcc@4.8.5 ^openmpi@3.1.0
...
==> Installing libhio
...
==> Successfully installed libhio
  Fetch: 0.08s.  Build: 58.01s.  Total: 58.09s.
[+] /scratch/users/dantopa/new-spack/libraries/darwin-general.libhio/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libhio-1.4.1.3-grjmo2dva66qapmw4h4mheagygxvtzxd

ARM node

libhio@1.4.1.2

dantopa@cn818:darwin-arm.libhio $ spack install libhio@1.4.1.2 % gcc@4.8.5 ^openmpi@3.1.0
...
==> Installing libhio
...
==> Successfully installed libhio
  Fetch: 0.08s.  Build: 47.73s.  Total: 47.81s.
[+] /scratch/users/dantopa/new-spack/libraries/darwin-arm.libhio/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/libhio-1.4.1.2-k32ecfrsv35gh3svs7jpop2maiplzovo

libhio@1.4.1.3

dantopa@cn818:darwin-arm.libhio $ spack install libhio@1.4.1.3 % gcc@4.8.5 ^openmpi@3.1.0
...
==> Installing libhio
...
==> Successfully installed libhio
  Fetch: 0.07s.  Build: 47.02s.  Total: 47.09s.
[+] /scratch/users/dantopa/new-spack/libraries/darwin-arm.libhio/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/libhio-1.4.1.3-jnmbafoiosoeb64222adqgnkemlo4qw3

Power9 node FAIL

libhio@1.4.1.2

dantopa@cn2034:darwin-power9.libhio $ spack install libhio@1.4.1.2 % gcc@4.8.5 ^openmpi@3.1.0
...
==> Installing libhio
...
==> Error: ProcessError: Command exited with status 1:
    '/scratch/users/dantopa/new-spack/libraries/darwin-power9.libhio/var/spack/stage/libhio-1.4.1.2-idoisps6aiy5mfb6zspwefvjhslnk4ky/libhio-1.4.1.2/configure' '--prefix=/scratch/users/dantopa/new-spack/libraries/darwin-power9.libhio/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/libhio-1.4.1.2-idoisps6aiy5mfb6zspwefvjhslnk4ky' '--with-external_bz2=/usr' '--with-hdf5=/scratch/users/dantopa/new-spack/libraries/darwin-power9.libhio/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/hdf5-1.8.17-aqseihmpjt6ecj3klaiuyud7wgnjbe2e'

1 error found in build log:
     133    checking for sys/mount.h... yes
     134    checking for sys/vfs.h... yes
     135    checking for bzlib.h... no
     136    checking for AvailabilityMacros.h... no
     137    checking for library containing dlopen... no
     138    checking for library containing floor... no
  >> 139    configure: error: Could not find math libraries

libhio@1.4.1.3

dantopa@cn2034:darwin-power9.libhio $ spack install libhio@1.4.1.3 % gcc@4.8.5 ^openmpi@3.1.0
...
==> Installing libhio
...
==> Executing phase: 'configure'
==> Error: ProcessError: Command exited with status 1:
    '/scratch/users/dantopa/new-spack/libraries/darwin-power9.libhio/var/spack/stage/libhio-1.4.1.3-x7respk45vgtn6cgxb7dnzb46hglkvi5/libhio-1.4.1.3/configure' '--prefix=/scratch/users/dantopa/new-spack/libraries/darwin-power9.libhio/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/libhio-1.4.1.3-x7respk45vgtn6cgxb7dnzb46hglkvi5' '--with-external_bz2=/usr' '--with-hdf5=/scratch/users/dantopa/new-spack/libraries/darwin-power9.libhio/opt/spack/linux-rhel7-ppc64le/gcc-4.8.5/hdf5-1.8.17-aqseihmpjt6ecj3klaiuyud7wgnjbe2e'

1 error found in build log:
     133    checking for sys/mount.h... yes
     134    checking for sys/vfs.h... yes
     135    checking for bzlib.h... no
     136    checking for AvailabilityMacros.h... no
     137    checking for library containing dlopen... no
     138    checking for library containing floor... no
  >> 139    configure: error: Could not find math libraries

Capulin

Compute node

libhio@1.4.1.2

dantopa@nid00185:capulin-arm.libhio $ spack install libhio@1.4.1.2 % gcc@7.3.0 ^openmpi@3.1.0
...
==> Installing libhio
...
==> Successfully installed libhio
  Fetch: 0.06s.  Build: 1m 3.80s.  Total: 1m 3.87s.
[+] /pfs/cpscratch1/yellow/dantopa/repos/github/libraries/capulin-arm.libhio/opt/spack/cray-cnl6-arm_thunderx2/gcc-7.3.0/libhio-1.4.1.2-id5ays2h34ovmhrxoeiynsn5pfgsmse3
d

libhio@1.4.1.3

dantopa@nid00185:capulin-arm.libhio $ spack install libhio@1.4.1.3 % gcc@7.3.0 ^openmpi@3.1.0
...
==> Installing libhio
...
==> Successfully installed libhio
  Fetch: 0.07s.  Build: 1m 3.91s.  Total: 1m 3.98s.
[+] /pfs/cpscratch1/yellow/dantopa/repos/github/libraries/capulin-arm.libhio/opt/spack/cray-cnl6-arm_thunderx2/gcc-7.3.0/libhio-1.4.1.3-arjpwak66rplw75aew7rcfswfqi2lehx

Snow

Compute node

libhio@1.4.1.2

dantopa@sn065.localdomain:snow-standard.libhio $ spack install libhio@1.4.1.2 % gcc@4.8.5 ^openmpi@3.1.0
...
==> Installing libhio
...
==> Successfully installed libhio
  Fetch: 0.05s.  Build: 54.17s.  Total: 54.22s.
[+] /net/scratch4/.mdt2/dantopa/spack/libraries/snow-standard.libhio/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/libhio-1.4.1.2-zxfnijiriocwahgjh7hpvmbvhdnkyssz

libhio@1.4.1.3

dantopa@sn065.localdomain:snow-standard.libhio $ spack install libhio@1.4.1.3 % gcc@4.8.5 ^openmpi@3.1.0
...
==> Installing libhio
...
==> Successfully installed libhio
  Fetch: 0.05s.  Build: 49.07s.  Total: 49.12s.
[+] /net/scratch4/.mdt2/dantopa/spack/libraries/snow-standard.libhio/opt/spack/linux-rhel7-x86_64/gcc-4.8.5/libhio-1.4.1.3-lucv6lhcuabglrdpsbaqery66ncwvp3a

Trinitite FAIL

login node

Compute nodes unavailable due to DST

libhio@1.4.1.2

dantopa@tt-fey1:trinitite-standard.libhio $ spack install libhio@1.4.1.2 % gcc@7.3.0 ^openmpi@3.1.0
...
==> Installing libhio
...
==> Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
    'make' '-j40'

4 errors found in build log:
     317    /usr/bin/ld: .libs/libhio_la-builtin-datawarp.o: relocation R_X86_64_32 against `.rodata.str1.8' can not be used when making a shared obje
            ct; recompile with -fPIC
     318    /usr/bin/ld: ../extra/json/build/.libs/libjson-c.a(json_object.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when ma
            king a shared object; recompile with -fPIC
     319    /usr/bin/ld: ../extra/json/build/.libs/libjson-c.a(json_tokener.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when m
            aking a shared object; recompile with -fPIC
     320    /usr/bin/ld: ../extra/json/build/.libs/libjson-c.a(json_util.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when maki
            ng a shared object; recompile with -fPIC
     321    /usr/bin/ld: ../extra/json/build/.libs/libjson-c.a(linkhash.o): relocation R_X86_64_32S against `.rodata' can not be used when making a sh
            ared object; recompile with -fPIC
     322    /usr/bin/ld: ../extra/json/build/.libs/libjson-c.a(random_seed.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when ma
            king a shared object; recompile with -fPIC
  >> 323    /usr/bin/ld: final link failed: nonrepresentable section on output
  >> 324    collect2: error: ld returned 1 exit status
     325    Makefile:543: recipe for target 'libhio.la' failed
  >> 326    make[1]: *** [libhio.la] Error 1
     327    make[1]: Leaving directory '/tmp/dantopa/spack-stage/spack-stage-V4qQ14/libhio-1.4.1.2/src'
     328    Makefile:495: recipe for target 'all-recursive' failed
  >> 329    make: *** [all-recursive] Error 1

libhio@1.4.1.3

dantopa@tt-fey1:trinitite-standard.libhio $ spack install libhio@1.4.1.3 % gcc@7.3.0 ^openmpi@3.1.0
...
==> Installing libhio
...
==> Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
    'make' '-j40'

4 errors found in build log:
     317    /usr/bin/ld: .libs/libhio_la-builtin-datawarp.o: relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a shared obje
            ct; recompile with -fPIC
     318    /usr/bin/ld: ../extra/json/build/.libs/libjson-c.a(json_object.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when ma
            king a shared object; recompile with -fPIC
     319    /usr/bin/ld: ../extra/json/build/.libs/libjson-c.a(json_tokener.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when m
            aking a shared object; recompile with -fPIC
     320    /usr/bin/ld: ../extra/json/build/.libs/libjson-c.a(json_util.o): relocation R_X86_64_32 against `.rodata.str1.8' can not be used when maki
            ng a shared object; recompile with -fPIC
     321    /usr/bin/ld: ../extra/json/build/.libs/libjson-c.a(linkhash.o): relocation R_X86_64_32S against `.rodata' can not be used when making a sh
            ared object; recompile with -fPIC
     322    /usr/bin/ld: ../extra/json/build/.libs/libjson-c.a(random_seed.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when ma
            king a shared object; recompile with -fPIC
  >> 323    /usr/bin/ld: final link failed: nonrepresentable section on output
  >> 324    collect2: error: ld returned 1 exit status
     325    Makefile:543: recipe for target 'libhio.la' failed
  >> 326    make[1]: *** [libhio.la] Error 1
     327    make[1]: Leaving directory '/tmp/dantopa/spack-stage/spack-stage-J5VqNO/libhio-1.4.1.3/src'
     328    Makefile:495: recipe for target 'all-recursive' failed
  >> 329    make: *** [all-recursive] Error 1
junghans commented 5 years ago

libhio@1.4.1.3 works for me as well.

hjelmn commented 5 years ago

Yup. Was a bug in the configure script. Thanks for testing.