Fix JasPer for Icontools #1041

efmkoene · 2025-01-17T16:36:56Z

This change adds the JasPer library into the spack-c2sm project, merely to add a variant for building on aarch64 which, at least for me, didn't work out of the box.

As you can see below, for reasons unclear to me, we need a double pass of spack install icontools because otherwise openmpi fails to build. But that's not the topic of this PR.

I've made the aarch64 variant the default version, which should suffice on Alps for now.

Please verify that you can reproduce the issue that this PR solves, too.

(base) ekoene@santis-ln001:/capstor/scratch/cscs/ekoene/tmp> CLUSTER_NAME=todi uenv start icon-wcp
(base) ekoene@santis-ln001:/capstor/scratch/cscs/ekoene/tmp> . spack-c2sm/setup-env.sh /user-environment/
Spack configured with upstream /user-environment/.
(base) ekoene@santis-ln001:/capstor/scratch/cscs/ekoene/tmp> spack install icontools@c2sm-master%gcc
[+] /usr (external autoconf-2.69-oxar3yab7bb47sxf52qqbq555muwwga7)
[+] /usr (external perl-5.26.1-jxi7g4iwyosifl53aft7g7sgpuo2qf33)
[+] /usr (external curl-8.0.1-ugo4qtzxc2dki7ir3l54w2ksrh63ayzh)
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/ncurses-6.4-iv6mwhw6gkc7cz7criwqhp7tazsukuwx
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/zlib-ng-2.1.4-43zfkjowmqng5ttdtqtknbzj4o3fv6jr
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/gmake-4.4.1-vzomhfqre2ukrurdztruakojdxf4z5uu
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/gnuconfig-2022-09-17-xpuu2muvlqpq6aacbmywusj2mmzpiw6g
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libjpeg-turbo-3.0.0-iwktrx65evwkatxoxqjonfswvuob6yzc
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/bzip2-1.0.8-qa5diypihzopxxc3che7gkfwzepzqvyz
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/lz4-1.9.4-obnimcss2ifr3gb5lxkktkc7k3v45ill
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/snappy-1.1.10-zcf6cbbgzr5vfuk27nzrbxqq4z7cdxyw
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/zstd-1.5.5-kcvdyk3zk4nc7eylk4xed2ytqvtpmfbb
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libaec-1.0.6-mkmj4wih4kdfi3yl3he43ic2ooefysb2
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/cmake-3.27.7-j2m2jyxcinpshbyulfxfthsa2t2kx4rn
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/pigz-2.7-2d4r6mxlafbh76lyusir4j4mwy4wjjzd
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/openssl-3.1.3-klgt2v2wwmdeh6lzffaplhletsbhhdck
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/automake-1.16.5-3h5a5xe5j2v5fvhz3yh4r27fnmthq673
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libtool-2.4.7-jxlpxrk2ss6gs36waiwjshix6sl3wxiy
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/pkgconf-1.9.5-6wajaqmcehgljwoo7zfhxtmqxhridfca
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/xz-5.4.1-zzcvonp6lohwukm2262x55wgmxwe7lnt
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libsigsegv-2.14-3xhstimclute2hkqzov7rlt4rp6vqbry
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libxcrypt-4.4.35-htffpvr5wewidzm4tgobnpartr257bdd
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/findutils-4.9.0-oyuwhk2fj3tuiu5smxpx2qysvnvqoedp
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libiconv-1.17-zr7yi6s3n33bonlj2xqg5v5scaiwat36
==> Installing jasper-1.900.1-nu7itisyyd6tdgrwtckybljdf6vqredw [25/48]
==> No binary for jasper-1.900.1-nu7itisyyd6tdgrwtckybljdf6vqredw found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/c2/c2b03f28166f9dc8ae434918839ae9aa9962b880fcfd24eebddd0a2daeb9192c.tar.gz
==> Applied patch /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/repos/c2sm/packages/jasper/fix_alpha_channel_assert_fail.patch
==> jasper: Executing phase: 'install'
==> jasper: Successfully installed jasper-1.900.1-nu7itisyyd6tdgrwtckybljdf6vqredw
  Stage: 0.64s.  Install: 20.86s.  Post-install: 0.16s.  Total: 21.95s
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/jasper-1.900.1-nu7itisyyd6tdgrwtckybljdf6vqredw
==> Installing openjpeg-2.3.1-dfzvv5pw3rhqg2x6bzey57wmym32eyqg [26/48]
==> No binary for openjpeg-2.3.1-dfzvv5pw3rhqg2x6bzey57wmym32eyqg found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/63/63f5a4713ecafc86de51bfad89cc07bb788e9bba24ebbf0c4ca637621aadb6a9.tar.gz
==> No patches needed for openjpeg
==> openjpeg: Executing phase: 'cmake'
==> openjpeg: Executing phase: 'build'
==> openjpeg: Executing phase: 'install'
==> openjpeg: Successfully installed openjpeg-2.3.1-dfzvv5pw3rhqg2x6bzey57wmym32eyqg
  Stage: 2.88s.  Cmake: 4.23s.  Build: 2.92s.  Install: 0.24s.  Post-install: 0.12s.  Total: 10.63s
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/openjpeg-2.3.1-dfzvv5pw3rhqg2x6bzey57wmym32eyqg
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/c-blosc-1.21.5-qq5mdx7yid2hxxdke5yefbaj2nu5mqh5
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/numactl-2.0.14-di4gffn44hyhqjs3psi2xtkpxnm6oz3e
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libpciaccess-0.17-jjii4uwlk3fcvv5jspxvk3aikzqgtqqr
==> Installing libevent-2.1.12-4tg3nalvruhrkva7q7t3xee4t5hks4bm [30/48]
==> No binary for libevent-2.1.12-4tg3nalvruhrkva7q7t3xee4t5hks4bm found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/92/92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb.tar.gz
==> Ran patch() for libevent
==> libevent: Executing phase: 'autoreconf'
==> libevent: Executing phase: 'configure'
==> libevent: Executing phase: 'build'
==> libevent: Executing phase: 'install'
==> libevent: Successfully installed libevent-2.1.12-4tg3nalvruhrkva7q7t3xee4t5hks4bm
  Stage: 0.84s.  Autoreconf: 3.87s.  Configure: 12.23s.  Build: 3.01s.  Install: 0.60s.  Post-install: 0.24s.  Total: 21.18s
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/libevent-2.1.12-4tg3nalvruhrkva7q7t3xee4t5hks4bm
==> Installing hdf5-1.14.3-c65v3gtbiyoyspp745ux7ukj2aa2oc7c [31/48]
==> No binary for hdf5-1.14.3-c65v3gtbiyoyspp745ux7ukj2aa2oc7c found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/09/09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7.tar.gz
==> Ran patch() for hdf5
==> hdf5: Executing phase: 'cmake'
==> hdf5: Executing phase: 'build'
==> hdf5: Executing phase: 'install'
==> hdf5: Successfully installed hdf5-1.14.3-c65v3gtbiyoyspp745ux7ukj2aa2oc7c
  Stage: 12.69s.  Cmake: 20.72s.  Build: 21.05s.  Install: 2.26s.  Post-install: 0.53s.  Total: 57.57s
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/hdf5-1.14.3-c65v3gtbiyoyspp745ux7ukj2aa2oc7c
==> Installing libedit-3.1-20210216-w6lwp5to2uhqo7m5jo5cjqpjch7uypht [32/48]
==> No binary for libedit-3.1-20210216-w6lwp5to2uhqo7m5jo5cjqpjch7uypht found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/22/2283f741d2aab935c8c52c04b57bf952d02c2c02e651172f8ac811f77b1fc77a.tar.gz
==> No patches needed for libedit
==> libedit: Executing phase: 'autoreconf'
==> libedit: Executing phase: 'configure'
==> libedit: Executing phase: 'build'
==> libedit: Executing phase: 'install'
==> libedit: Successfully installed libedit-3.1-20210216-w6lwp5to2uhqo7m5jo5cjqpjch7uypht
  Stage: 0.34s.  Autoreconf: 0.04s.  Configure: 6.27s.  Build: 1.75s.  Install: 0.23s.  Post-install: 0.11s.  Total: 8.94s
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/libedit-3.1-20210216-w6lwp5to2uhqo7m5jo5cjqpjch7uypht
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/m4-1.4.19-gee3altseiqdh4rgdf3xl5qcla33ii7y
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/tar-1.34-n4q3usgrphw5tgb2n7i52rmwjvvshrh4
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/diffutils-3.9-gpq5i7dfly6i433neqnlgdaiancl7gcd
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libxml2-2.10.3-ig7ype3strik4wff3tstj3cclajudalt
==> Installing eccodes-2.25.0-pgjm4zjel7gmypnft3oyza6te364euxg [37/48]
==> No binary for eccodes-2.25.0-pgjm4zjel7gmypnft3oyza6te364euxg found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/89/8975131aac54d406e5457706fd4e6ba46a8cc9c7dd817a41f2aa64ce1193c04e.tar.gz
==> No patches needed for eccodes
==> eccodes: Executing phase: 'cmake'
==> eccodes: Executing phase: 'build'
==> eccodes: Executing phase: 'install'
==> eccodes: Successfully installed eccodes-2.25.0-pgjm4zjel7gmypnft3oyza6te364euxg
  Stage: 36.99s.  Cmake: 12.09s.  Build: 30.32s.  Install: 2m 31.36s.  Post-install: 40.48s.  Total: 4m 31.51s
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/eccodes-2.25.0-pgjm4zjel7gmypnft3oyza6te364euxg
==> Installing netcdf-c-4.9.2-yvo27bpftwpcq2ymo2jl2v2ibpmk4kzy [38/48]
==> No binary for netcdf-c-4.9.2-yvo27bpftwpcq2ymo2jl2v2ibpmk4kzy found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/bc/bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7.tar.gz
==> Fetching https://mirror.spack.io/_source-cache/archive/01/0161eb870fdfaf61be9d70132c9447a537320342366362e76b8460c823bf95ca
==> Applied patch https://github.com/Unidata/netcdf-c/commit/f8904d5a1d89420dde0f9d2c0e051ba08d08e086.patch?full_index=1
==> netcdf-c: Executing phase: 'autoreconf'
==> netcdf-c: Executing phase: 'configure'
==> netcdf-c: Executing phase: 'build'
==> netcdf-c: Executing phase: 'install'
==> netcdf-c: Successfully installed netcdf-c-4.9.2-yvo27bpftwpcq2ymo2jl2v2ibpmk4kzy
  Stage: 5.00s.  Autoreconf: 0.00s.  Configure: 16.74s.  Build: 11.98s.  Install: 1.29s.  Post-install: 0.24s.  Total: 35.73s
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/netcdf-c-4.9.2-yvo27bpftwpcq2ymo2jl2v2ibpmk4kzy
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/gettext-0.22.3-c4emy5kuud3dtsdpk3lbqvm454meurpd
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/cuda-12.3.0-dpv4zkhn6js7p5kvjqtf74x5suknx3t4
==> Installing netcdf-fortran-4.6.1-wt3rfcwmuudi2x2r5ldxyna2qhtkbrzb [41/48]
==> No binary for netcdf-fortran-4.6.1-wt3rfcwmuudi2x2r5ldxyna2qhtkbrzb found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/b5/b50b0c72b8b16b140201a020936aa8aeda5c79cf265c55160986cd637807a37a.tar.gz
==> No patches needed for netcdf-fortran
==> netcdf-fortran: Executing phase: 'autoreconf'
==> netcdf-fortran: Executing phase: 'configure'
==> netcdf-fortran: Executing phase: 'build'
==> netcdf-fortran: Executing phase: 'install'
==> netcdf-fortran: Successfully installed netcdf-fortran-4.6.1-wt3rfcwmuudi2x2r5ldxyna2qhtkbrzb
  Stage: 0.64s.  Autoreconf: 0.05s.  Configure: 9.26s.  Build: 28.74s.  Install: 0.36s.  Post-install: 0.21s.  Total: 39.72s
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/netcdf-fortran-4.6.1-wt3rfcwmuudi2x2r5ldxyna2qhtkbrzb
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/bison-3.8.2-yy43npv27g6ldqo6daakgzlzetn6nnur
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/hwloc-2.9.1-tcfta4qzkfircj2qqk6ehcpo5vfqjqc3
==> Installing krb5-1.20.1-xtmzjdarygew36diqr7yr67kroot55kk [44/48]
==> No binary for krb5-1.20.1-xtmzjdarygew36diqr7yr67kroot55kk found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/70/704aed49b19eb5a7178b34b2873620ec299db08752d6a8574f95d41879ab8851.tar.gz
==> Ran patch() for krb5
==> krb5: Executing phase: 'autoreconf'
==> krb5: Executing phase: 'configure'
==> krb5: Executing phase: 'build'
==> krb5: Executing phase: 'install'
==> krb5: Successfully installed krb5-1.20.1-xtmzjdarygew36diqr7yr67kroot55kk
  Stage: 7.42s.  Autoreconf: 0.30s.  Configure: 16.93s.  Build: 17.05s.  Install: 1.98s.  Post-install: 0.61s.  Total: 44.84s
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/krb5-1.20.1-xtmzjdarygew36diqr7yr67kroot55kk
==> Installing pmix-5.0.1-poc2g4y6muab7an3fab7wdhxadqh7noy [45/48]
==> No binary for pmix-5.0.1-poc2g4y6muab7an3fab7wdhxadqh7noy found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/d4/d4371792d4ba4c791e1010100b4bf9a65500ababaf5ff25d681f938527a67d4a.tar.bz2
==> No patches needed for pmix
==> pmix: Executing phase: 'autoreconf'
==> pmix: Executing phase: 'configure'
==> pmix: Executing phase: 'build'
==> pmix: Executing phase: 'install'
==> pmix: Successfully installed pmix-5.0.1-poc2g4y6muab7an3fab7wdhxadqh7noy
  Stage: 3.02s.  Autoreconf: 0.24s.  Configure: 23.81s.  Build: 51.10s.  Install: 4.37s.  Post-install: 0.99s.  Total: 1m 24.00s
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/pmix-5.0.1-poc2g4y6muab7an3fab7wdhxadqh7noy
==> Installing openssh-9.5p1-x7v3bpdowzkug2xgvul4zqzuecdese6l [46/48]
==> No binary for openssh-9.5p1-x7v3bpdowzkug2xgvul4zqzuecdese6l found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/f0/f026e7b79ba7fb540f75182af96dc8a8f1db395f922bbc9f6ca603672686086b.tar.gz
==> Ran patch() for openssh
==> openssh: Executing phase: 'autoreconf'
==> openssh: Executing phase: 'configure'
==> openssh: Executing phase: 'build'
==> openssh: Executing phase: 'install'
==> openssh: Successfully installed openssh-9.5p1-x7v3bpdowzkug2xgvul4zqzuecdese6l
  Stage: 1.87s.  Autoreconf: 0.08s.  Configure: 32.51s.  Build: 3.71s.  Install: 0.73s.  Post-install: 0.31s.  Total: 39.87s
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/openssh-9.5p1-x7v3bpdowzkug2xgvul4zqzuecdese6l
==> Installing openmpi-4.1.6-hu3xn3vsxchfszndpdo2iytbf4u6ry6h [47/48]
==> No binary for openmpi-4.1.6-hu3xn3vsxchfszndpdo2iytbf4u6ry6h found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/f7/f740994485516deb63b5311af122c265179f5328a0d857a567b85db00b11e415.tar.bz2
==> No patches needed for openmpi
==> openmpi: Executing phase: 'autoreconf'
==> openmpi: Executing phase: 'configure'
==> openmpi: Executing phase: 'build'
==> Error: ProcessError: Command exited with status 2:
    'make' '-j16' 'V=1'

19 errors found in build log:
     5593    libtool: link: ranlib .libs/libmca_btl_tcp.a
     5594    libtool: link: ( cd ".libs" && rm -f "libmca_btl_tcp.la" && ln -s "../libmca_btl_tcp.la" "libmca_btl_tcp.la" )
     5595    make[2]: Leaving directory '/capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack-build_stage/spack-stage-openmpi-4.1.6-hu3xn3vsxchfszndpdo2iytbf4u6ry6h/spack-src/opal/mca/btl/tcp'
     5596    Making all in mca/btl/vader
     5597    make[2]: Entering directory '/capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack-build_stage/spack-stage-openmpi-4.1.6-hu3xn3vsxchfszndpdo2iytbf4u6ry6h/spack-src/opal/mca/btl/vader'
     5598     cd ../../../.. && /bin/sh /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack-build_stage/spack-stage-openmpi-4.1.6-hu3xn3vsxchfszndpdo2iytbf4u6ry6h/spack-src/config/missing automake-1.15 --foreign o
             pal/mca/btl/vader/Makefile
  >> 5599    sh: config/opal_get_version.sh: No such file or directory
  >> 5600    sh: config/opal_get_version.sh: No such file or directory
  >> 5601    sh: config/opal_get_version.sh: No such file or directory
  >> 5602    sh: config/opal_get_version.sh: No such file or directory
  >> 5603    sh: config/opal_get_version.sh: No such file or directory
  >> 5604    sh: config/opal_get_version.sh: No such file or directory
  >> 5605    sh: config/opal_get_version.sh: No such file or directory
  >> 5606    sh: config/opal_get_version.sh: No such file or directory
  >> 5607    sh: config/opal_get_version.sh: No such file or directory
  >> 5608    sh: config/opal_get_version.sh: No such file or directory
  >> 5609    sh: config/opal_get_version.sh: No such file or directory
  >> 5610    sh: config/opal_get_version.sh: No such file or directory
  >> 5611    configure.ac:103: error: version mismatch.  This is Automake 1.15.1,
  >> 5612    configure.ac:103: but the definition used by this AM_INIT_AUTOMAKE
  >> 5613    configure.ac:103: comes from Automake 1.15.  You should recreate
  >> 5614    configure.ac:103: aclocal.m4 with aclocal and run automake again.
     5615    WARNING: 'automake-1.15' is probably too old.
     5616             You should only need it if you modified 'Makefile.am' or
     5617             'configure.ac' or m4 files included by 'configure.ac'.
     5618             The 'automake' program is part of the GNU Automake package:
     5619             <http://www.gnu.org/software/automake>
     5620             It also requires GNU Autoconf, GNU m4 and Perl in order to run:
     5621             <http://www.gnu.org/software/autoconf>
     5622             <http://www.gnu.org/software/m4/>
     5623             <http://www.perl.org/>
  >> 5624    make[2]: *** [Makefile:1805: Makefile.in] Error 63
     5625    make[2]: Leaving directory '/capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack-build_stage/spack-stage-openmpi-4.1.6-hu3xn3vsxchfszndpdo2iytbf4u6ry6h/spack-src/opal/mca/btl/vader'
  >> 5626    make[1]: *** [Makefile:2387: all-recursive] Error 1
     5627    make[1]: Leaving directory '/capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack-build_stage/spack-stage-openmpi-4.1.6-hu3xn3vsxchfszndpdo2iytbf4u6ry6h/spack-src/opal'
  >> 5628    make: *** [Makefile:1905: all-recursive] Error 1

See build log for details:
  /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack-build_stage/spack-stage-openmpi-4.1.6-hu3xn3vsxchfszndpdo2iytbf4u6ry6h/spack-build-out.txt

==> Warning: Skipping build of icontools-c2sm-master-5zc7ndoeeozjqipstyyvnckodpdaellz since openmpi-4.1.6-hu3xn3vsxchfszndpdo2iytbf4u6ry6h failed
==> Error: icontools-c2sm-master-5zc7ndoeeozjqipstyyvnckodpdaellz: Package was not installed
==> Error: Installation request failed.  Refer to reported errors for failing package(s).
(base) ekoene@santis-ln001:/capstor/scratch/cscs/ekoene/tmp> spack install icontools
[+] /usr (external autoconf-2.69-oxar3yab7bb47sxf52qqbq555muwwga7)
[+] /usr (external perl-5.26.1-jxi7g4iwyosifl53aft7g7sgpuo2qf33)
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/openjpeg-2.3.1-dfzvv5pw3rhqg2x6bzey57wmym32eyqg
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/gmake-4.4.1-vzomhfqre2ukrurdztruakojdxf4z5uu
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/gnuconfig-2022-09-17-xpuu2muvlqpq6aacbmywusj2mmzpiw6g
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libjpeg-turbo-3.0.0-iwktrx65evwkatxoxqjonfswvuob6yzc
[+] /usr (external m4-1.4.18-qep7waivk25sb5h3uwljvlulp3h6zel5)
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/bzip2-1.0.8-qa5diypihzopxxc3che7gkfwzepzqvyz
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/lz4-1.9.4-obnimcss2ifr3gb5lxkktkc7k3v45ill
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/snappy-1.1.10-zcf6cbbgzr5vfuk27nzrbxqq4z7cdxyw
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/zstd-1.5.5-kcvdyk3zk4nc7eylk4xed2ytqvtpmfbb
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libaec-1.0.6-mkmj4wih4kdfi3yl3he43ic2ooefysb2
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/eccodes-2.25.0-pgjm4zjel7gmypnft3oyza6te364euxg
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libxcrypt-4.4.35-htffpvr5wewidzm4tgobnpartr257bdd
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libiconv-1.17-zr7yi6s3n33bonlj2xqg5v5scaiwat36
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/xz-5.4.1-zzcvonp6lohwukm2262x55wgmxwe7lnt
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libtool-2.4.7-jxlpxrk2ss6gs36waiwjshix6sl3wxiy
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/zlib-ng-2.1.4-43zfkjowmqng5ttdtqtknbzj4o3fv6jr
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/ncurses-6.4-iv6mwhw6gkc7cz7criwqhp7tazsukuwx
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/automake-1.16.5-3h5a5xe5j2v5fvhz3yh4r27fnmthq673
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/pkgconf-1.9.5-6wajaqmcehgljwoo7zfhxtmqxhridfca
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/jasper-1.900.1-nu7itisyyd6tdgrwtckybljdf6vqredw
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libpciaccess-0.17-jjii4uwlk3fcvv5jspxvk3aikzqgtqqr
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/libxml2-2.10.3-ig7ype3strik4wff3tstj3cclajudalt
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/c-blosc-1.21.5-qq5mdx7yid2hxxdke5yefbaj2nu5mqh5
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/openssl-3.1.3-klgt2v2wwmdeh6lzffaplhletsbhhdck
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/pigz-2.7-2d4r6mxlafbh76lyusir4j4mwy4wjjzd
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/numactl-2.0.14-di4gffn44hyhqjs3psi2xtkpxnm6oz3e
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/libedit-3.1-20210216-w6lwp5to2uhqo7m5jo5cjqpjch7uypht
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/hdf5-1.14.3-c65v3gtbiyoyspp745ux7ukj2aa2oc7c
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/cuda-12.3.0-dpv4zkhn6js7p5kvjqtf74x5suknx3t4
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/libevent-2.1.12-4tg3nalvruhrkva7q7t3xee4t5hks4bm
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/tar-1.34-n4q3usgrphw5tgb2n7i52rmwjvvshrh4
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/netcdf-c-4.9.2-yvo27bpftwpcq2ymo2jl2v2ibpmk4kzy
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/hwloc-2.9.1-tcfta4qzkfircj2qqk6ehcpo5vfqjqc3
[+] /user-environment/linux-sles15-neoverse_v2/gcc-12.3.0/gettext-0.22.3-c4emy5kuud3dtsdpk3lbqvm454meurpd
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/netcdf-fortran-4.6.1-wt3rfcwmuudi2x2r5ldxyna2qhtkbrzb
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/pmix-5.0.1-poc2g4y6muab7an3fab7wdhxadqh7noy
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/krb5-1.20.1-xtmzjdarygew36diqr7yr67kroot55kk
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/openssh-9.5p1-x7v3bpdowzkug2xgvul4zqzuecdese6l
==> Installing openmpi-4.1.6-hu3xn3vsxchfszndpdo2iytbf4u6ry6h [41/42]
==> No binary for openmpi-4.1.6-hu3xn3vsxchfszndpdo2iytbf4u6ry6h found: installing from source
==> Using cached archive: /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/var/spack/cache/_source-cache/archive/f7/f740994485516deb63b5311af122c265179f5328a0d857a567b85db00b11e415.tar.bz2
==> No patches needed for openmpi
==> openmpi: Executing phase: 'autoreconf'
==> openmpi: Executing phase: 'configure'
==> openmpi: Executing phase: 'build'
==> openmpi: Executing phase: 'install'
==> openmpi: Successfully installed openmpi-4.1.6-hu3xn3vsxchfszndpdo2iytbf4u6ry6h
  Stage: 10.83s.  Autoreconf: 0.74s.  Configure: 2m 0.64s.  Build: 2m 58.60s.  Install: 22.55s.  Post-install: 1.54s.  Total: 5m 39.82s
[+] /capstor/scratch/cscs/ekoene/tmp/spack-c2sm/spack/opt/spack/linux-sles15-neoverse_v2/gcc-12.3.0/openmpi-4.1.6-hu3xn3vsxchfszndpdo2iytbf4u6ry6h
==> Installing icontools-2.5.2-j2qaqyr4f2x5g4xsunhllvf3nzq6txeo [42/42]
==> No binary for icontools-2.5.2-j2qaqyr4f2x5g4xsunhllvf3nzq6txeo found: installing from source

jonasjucker · 2025-01-27T13:39:51Z

launch jenkins

jonasjucker · 2025-01-27T16:39:10Z

thanks for your contribution, I'll have a look as soon as we are done with the major upgrade to spack v0.22.

jonasjucker · 2025-02-06T08:13:02Z

@efmkoene The uenv currently available on Santis provides jasper, and it only uses at max spack v0.22.
So this makes we wonder why you had to apply the patch here in the first place.

efmkoene · 2025-02-07T09:38:56Z

OK, that's very confusing. My user environment has JasPer jasper-2.0.32-hwd4yk6ainbiwntd3mlhx6xa4xmlaw4s/, but icontools (as given in this spack instance) specifies an older version:.

spack-c2sm/repos/c2sm/packages/icontools/package.py

Line 52 in bbc220d

depends_on('jasper@1.900.1')

Is that not the case for you?

jonasjucker · 2025-02-12T10:31:19Z

@efmkoene Could you try to compile icontools using this branch?
#902

I completely revised the recipe, it is in a much cleaner state right now.

efmkoene · 2025-02-12T16:35:27Z

When installing with the icontools branch (either spack install icontools or spack install icontools@c2sm-master%gcc), it doesn't seem to use any of the /user-environment/ packages from the icon-wcp (v4). Is that normal? It's in the slow process of installing every single package from source now.

jonasjucker · 2025-02-12T16:49:13Z

Hm that should not be, I'll have a look tomorrow

efmkoene · 2025-02-12T17:23:32Z

On the plus side, after more than an hour, it did compile everything correctly (without needing to do anything twice, or fix the JasPer compilation)!

jonasjucker · 2025-02-13T08:36:21Z

So finally I have something for you:

uenv image pull build::icon/25.2:1656679281
uenv start icon/25.2:1656679281
. setup_env.sh /user-environment
spack install icontools%gcc ~mpi ^netcdf-fortran%gcc

All with branch icontools.

jonasjucker · 2025-02-13T08:38:55Z

Some context for you:

This is the new uenv based on spackl v0.22 that we will soon use for ICON on Santis.
There is no mpi for gcc, therefore we compile it without. BUt this should be fine.
The concretizer pick netcdf-fortran%nvhpc, but this does not work, so we force it to use %nvhpc.

Please let me know if this reduces builds times on your side AND if icontools runs for your usecase.

efmkoene · 2025-02-14T10:20:05Z

I did

rm -rf $SCRATCH/.uenv-images # My previous images were from CLUSTER_NAME=todi
uenv repo create
uenv image pull build::icon/25.2:1656679281
uenv start icon
cd $SCRATCH && git clone --depth 1 --recurse-submodules --shallow-submodules https://github.com/C2SM/spack-c2sm.git # As it now lives in the main branch
eval $(ssh-agent) # I seem to need this for git retrievals sometimes
spack install icontools%gcc ~mpi ^netcdf-fortran%gcc
spack load icontools

It compiles quickly (only builds netcdf-fortran and icontools, the rest is pulled from the /user-environment/). Not more than 30 seconds really!

However, unfortunately it returns a segmentation fault on this simple input file,

&iconsub_nml
    grid_filename = '/capstor/scratch/cscs/ekoene/processing-chain/work/icon-art-CTDAS/2018010100_2018011100/icon/input/icon_europe_DOM01.nc',
    output_type = 4,
    lwrite_grid = .TRUE.,
/
&subarea_nml
    ORDER = "outgrid",
    grf_info_file = '/capstor/scratch/cscs/ekoene/processing-chain/work/icon-art-CTDAS/2018010100_2018011100/icon/input/icon_europe_DOM01.nc',
    min_refin_c_ctrl = 1,
    max_refin_c_ctrl = 120
/

which is run using the command iconsub --nml=<the_above_file> after doing spack load icontools

The icontools that worked (i.e., this pull request branch) returns

(base) ekoene@santis-ln002:/capstor/scratch/cscs/ekoene> iconsub --nml=processing-chain/NAMELIST_ICONSUB 
 # Repository : git@github.com:C2SM/icontools.git
 # Branch     : master
 # Revision   : b3bff9b6f726bb645c41f35dadbd4211deedd617


 
 # ICONSUB: ICOsahedral Nonhydrostatic model SUBgrid extraction
 
 # subarea 1: outgrid
 # grid refinement info file = '/capstor/scratch/cscs/ekoene/processing-chain/work/icon-art-CTDAS/2018010100_2018011100/icon/input/icon_europe_DOM01.nc'
 #   min_refin_c_ctrl        =            1
 #   max_refin_c_ctrl        =          120
 
 # generate UUID for subarea.
 # write grid topology file for 'outgrid'
 # ICONSUB: done.
 # performance measurements:
 #    load grid      :      -0.74
 #    setup subgrids :       0.00
 #    write grids    :       0.00

Whereas the icontools/main branch returns

(base) ekoene@santis-ln002:/capstor/scratch/cscs/ekoene> iconsub --nml=processing-chain/NAMELIST_ICONSUB 
 # Repository : git@gitlab.dkrz.de:dwd-sw/dwd_icon_tools.git
 # Branch     : (no branch)
 # Revision   : 4bcc2b282bac0292fea1a4dbb4241ef05e30a982
 # Git tag    : icontools-2.5.2


Segmentation fault (core dumped)

Any suggestion? Thanks for going through this with me...

jonasjucker · 2025-02-14T10:31:04Z

From the log I see that you dont specify the version in the spec.
icontools@c2sm-master is the correct one. This is also the version used I see in the logfile of working icontools.
Not specifying a version lead to the build of @2.xx an older version

jonasjucker · 2025-02-14T10:32:37Z

You can run spack info icontools, this shows all available versions of the package

efmkoene · 2025-02-14T10:39:12Z

Unfortunately, it performs no better. Can you confirm that on your end, too?

(base) ekoene@santis-ln002:/capstor/scratch/cscs/ekoene> uenv start icon
(base) ekoene@santis-ln002:/capstor/scratch/cscs/ekoene> source spack-c2sm/setup-env.sh /user-environment
Spack configured with upstream /user-environment.
(base) ekoene@santis-ln002:/capstor/scratch/cscs/ekoene> spack install icontools@c2sm-master%gcc ~mpi ^netcdf-fortran%gcc
...
(base) ekoene@santis-ln002:/capstor/scratch/cscs/ekoene> spack load icontools@c2sm-master
(base) ekoene@santis-ln002:/capstor/scratch/cscs/ekoene> iconsub --nml=processing-chain/NAMELIST
_ICONSUB 
 # Repository : git@github.com:C2SM/icontools.git
 # Branch     : master
 # Revision   : b3bff9b6f726bb645c41f35dadbd4211deedd617


Segmentation fault (core dumped)

jonasjucker · 2025-02-14T11:09:20Z

I am off today, will be back on. Tuesday.
But since this is a potential issue on our sw-stack it would be good to move forward and fix the problem before it has been deployed
@mjaehn @AnnikaLau can you have a look at it and coordinate with @leclairm .

This might be an issue for Ben to fix

efmkoene and others added 2 commits January 17, 2025 16:49

Add aarch64 build guide to Jasper for use on Santis

58d7f85

Added alpha channel patch

d89b8ee

jonasjucker self-assigned this Jan 27, 2025

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Fix JasPer for Icontools #1041

Fix JasPer for Icontools #1041

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Fix JasPer for Icontools #1041

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Fix JasPer for Icontools #1041

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