{"action":"created","issue":{"url":"https://api.github.com/repos/LLNL/spack/issues/2161","repository_url":"https://api.github.com/repos/LLNL/spack","labels_url":"https://api.github.com/repos/LLNL/spack/issues/2161/labels{/name}","comments_url":"https://api.github.com/repos/LLNL/spack/issues/2161/comments","events_url":"https://api.github.com/repos/LLNL/spack/issues/2161/events","html_url":"https://github.com/LLNL/spack/issues/2161","id":185934995,"number":2161,"title":"Undefined reference to 'scotchyylex' during installation of scotch","user":{"login":"Philou31","id":8888549,"avatar_url":"https://avatars.githubusercontent.com/u/8888549?v=3","gravatar_id":"","url":"https://api.github.com/users/Philou31","html_url":"https://github.com/Philou31","followers_url":"https://api.github.com/users/Philou31/followers","following_url":"https://api.github.com/users/Philou31/following{/other_user}","gists_url":"https://api.github.com/users/Philou31/gists{/gist_id}","starred_url":"https://api.github.com/users/Philou31/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Philou31/subscriptions","organizations_url":"https://api.github.com/users/Philou31/orgs","repos_url":"https://api.github.com/users/Philou31/repos","events_url":"https://api.github.com/users/Philou31/events{/privacy}","received_events_url":"https://api.github.com/users/Philou31/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-10-28T14:18:21Z","updated_at":"2017-01-09T17:18:37Z","closed_at":"2017-01-09T17:18:37Z","body":"I am currently trying to install qr_mumps with spack fork fpruvost on a cluster under CentOS release 6.6. \nOne of the required dependencies is scotch@6.0.4%gcc@5.4.0~compression+esmumps~grf~idx64~mpi+pthread+shared arch=linux-x86_64. Sadly, upon installation, an error is returned:\n\n``` bash\n$ spack install qr_mumps \n==> Installing qr_mumps\n==> hwloc is already installed in /scratch/algo/leleux/spack/opt/spack/linux-x86_64/gcc-5.4.0/hwloc-1.11.4-ek6anw4f44p6jti4pnc34y46fxkt5x3z\n==> starpu is already installed in /scratch/algo/leleux/spack/opt/spack/linux-x86_64/gcc-5.4.0/starpu-1.2.0-wwvw32o4qqqoz7rq3ys2acmaypoijf2o\n==> metis is already installed in /scratch/algo/leleux/spack/opt/spack/linux-x86_64/gcc-5.4.0/metis-5.1.0-rvrnhec7jslgnhl3cik5bdzqbmd53d72\n==> colamd is already installed in /scratch/algo/leleux/spack/opt/spack/linux-x86_64/gcc-5.4.0/colamd-4.4.6-ok27qzictplufjjhzkcmlrr5sszbxmrh\n==> Installing scotch\n==> Already downloaded /scratch/algo/leleux/spack/var/spack/stage/scotch-6.0.4-wszgyliyepnqz36xo7optynyzwleazmm/scotch_6.0.4.tar.gz\n==> Already staged scotch-6.0.4-wszgyliyepnqz36xo7optynyzwleazmm in /scratch/algo/leleux/spack/var/spack/stage/scotch-6.0.4-wszgyliyepnqz36xo7optynyzwleazmm\n==> No patches needed for scotch\n==> Building scotch\n==> Error: Command exited with status 2:\n'make' 'scotch'\n\nSee build log for details:\n  /tmp/leleux/spack-stage/spack-stage-UBqDX5/scotch_6.0.4/spack-build.out\n\n/scratch/algo/leleux/spack/var/spack/repos/builtin/packages/scotch/package.py:183, in install:\n     169      def install(self, spec, prefix):\n     170          self.setup()\n     171  \n     172          targets = ['scotch']\n     173          if spec.satisfies('+mpi'):\n     174              targets.append('ptscotch')\n     175  \n     176          if spec.satisfies('+esmumps'):\n     177              targets.append('esmumps')\n     178              if spec.satisfies('+mpi'):\n     179                  targets.append('ptesmumps')\n     180  \n     181          with working_dir('src'):\n     182              for app in targets:\n  >> 183                  make(app, parallel=0)\n     184              make('prefix=%s' % prefix, 'install')\n     185              # esmumps libs are not installed by default (is it a mistake?)\n     186              if spec.satisfies('+shared'):\n     187                  if platform.system() == 'Darwin':\n     188                      libext = \".dylib\"\n     189                  else:\n     190                      libext = \".so\"\n     191              else:\n     192                  libext = \".a\"\n     193              if spec.satisfies('+esmumps'):\n     194                  install('../include/esmumps.h',   prefix.include)\n     195                  install('../lib/libesmumps%s' % libext,   prefix.lib)\n     196                  if spec.satisfies('+mpi'):\n     197                      install('../lib/libptesmumps%s' % libext, prefix.lib)\n     198  \n     199          if spec.satisfies('+grf'):\n     200              with working_dir('grf'):\n     201                  for f in os.listdir('.'):\n     202                      gunzip(f)\n     203              install_tree('grf', prefix + '/grf')\n==> Error: Installation process had nonzero exit code.\n```\n\nHere is the content of the log file \"spack-build.out\":\n\n``` bash\n==> 'make' 'scotch'\n(cd libscotch ;      make VERSION=6 RELEASE=0 PATCHLEVEL=4 scotch && make install)\nmake[1]: Entering directory `/tmp/leleux/spack-stage/spack-stage-1t0gKq/scotch_6.0.4/src/libscotch'\nmake CC=\"cc\" CCD=\"cc\"   \\\n                    scotch.h                \\\n                    scotchf.h               \\\n                    libscotch.so                \\\n                    libscotcherr.so         \\\n                    libscotcherrexit.so\nmake[2]: Entering directory `/tmp/leleux/spack-stage/spack-stage-1t0gKq/scotch_6.0.4/src/libscotch'\nmake[2]: `scotch.h' is up to date.\nmake[2]: `scotchf.h' is up to date.\nmake[2]: `libscotch.so' is up to date.\nmake[2]: `libscotcherr.so' is up to date.\nmake[2]: `libscotcherrexit.so' is up to date.\nmake[2]: Leaving directory `/tmp/leleux/spack-stage/spack-stage-1t0gKq/scotch_6.0.4/src/libscotch'\nmake[1]: Leaving directory `/tmp/leleux/spack-stage/spack-stage-1t0gKq/scotch_6.0.4/src/libscotch'\nmake[1]: Entering directory `/tmp/leleux/spack-stage/spack-stage-1t0gKq/scotch_6.0.4/src/libscotch'\nmake[1]: Nothing to be done for `install'.\nmake[1]: Leaving directory `/tmp/leleux/spack-stage/spack-stage-1t0gKq/scotch_6.0.4/src/libscotch'\n(cd scotch ;         make VERSION=6 RELEASE=0 PATCHLEVEL=4 scotch && make install)\nmake[1]: Entering directory `/tmp/leleux/spack-stage/spack-stage-1t0gKq/scotch_6.0.4/src/scotch'\nmake CC=\"cc\" SCOTCHLIB=scotch   \\\n                    acpl                \\\n                    amk_ccc             \\\n                    amk_fft2                \\\n                    amk_grf             \\\n                    amk_hy              \\\n                    amk_m2              \\\n                    amk_p2              \\\n                    atst                \\\n                    gbase               \\\n                    gcv             \\\n                    gmap                \\\n                    gmk_hy              \\\n                    gmk_m2              \\\n                    gmk_m3              \\\n                    gmk_msh             \\\n                    gmk_ub2             \\\n                    gmtst               \\\n                    gord                \\\n                    gotst               \\\n                    gout                \\\n                    gpart               \\\n                    gscat               \\\n                    gtst                \\\n                    mcv             \\\n                    mmk_m2              \\\n                    mmk_m3              \\\n                    mord                \\\n                    mtst\nmake[2]: Entering directory `/tmp/leleux/spack-stage/spack-stage-1t0gKq/scotch_6.0.4/src/scotch'\ncc -O3 -DCOMMON_TIMING_OLD -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_DETERMINISTIC -DSCOTCH_RENAME -Drestrict=__restrict -DCOMMON_PTHREAD -DCOMMON_PTHREAD_BARRIER -I../../include -I../libscotch acpl.c -o acpl -L../../lib -lscotch -lscotch -lscotcherrexit -lm -lrt -pthread\n../../lib/libscotch.so: undefined reference to `scotchyylex'\ncollect2: error: ld returned 1 exit status\nmake[2]: *** [acpl] Error 1\nmake[2]: Leaving directory `/tmp/leleux/spack-stage/spack-stage-1t0gKq/scotch_6.0.4/src/scotch'\nmake[1]: *** [scotch] Error 2\nmake[1]: Leaving directory `/tmp/leleux/spack-stage/spack-stage-1t0gKq/scotch_6.0.4/src/scotch'\nmake: *** [scotch] Error 2\n```\n\nIt seems to be a problem of linking with the scotch library but I cannot figure out how to make it compile. Do you think of any way I could solve this ?\n"},"comment":{"url":"https://api.github.com/repos/LLNL/spack/issues/comments/271345836","html_url":"https://github.com/LLNL/spack/issues/2161#issuecomment-271345836","issue_url":"https://api.github.com/repos/LLNL/spack/issues/2161","id":271345836,"user":{"login":"Philou31","id":8888549,"avatar_url":"https://avatars.githubusercontent.com/u/8888549?v=3","gravatar_id":"","url":"https://api.github.com/users/Philou31","html_url":"https://github.com/Philou31","followers_url":"https://api.github.com/users/Philou31/followers","following_url":"https://api.github.com/users/Philou31/following{/other_user}","gists_url":"https://api.github.com/users/Philou31/gists{/gist_id}","starred_url":"https://api.github.com/users/Philou31/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Philou31/subscriptions","organizations_url":"https://api.github.com/users/Philou31/orgs","repos_url":"https://api.github.com/users/Philou31/repos","events_url":"https://api.github.com/users/Philou31/events{/privacy}","received_events_url":"https://api.github.com/users/Philou31/received_events","type":"User","site_admin":false},"created_at":"2017-01-09T17:18:37Z","updated_at":"2017-01-09T17:18:37Z","body":"It seems this issue is related to the issue [https://github.com/LLNL/spack/issues/2521](https://github.com/LLNL/spack/issues/2521)\r\n\r\nIt can thus be solved by switching flex back to version 2.6.1 or previous."}}
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