enable building of spack issm installation with wrappers #186

justinh2002 · 2025-01-31T01:42:15Z

enable building of Spack issm package installation with wrappers - this allows matlab/python dependencies to be installed; so that Spack can be used to compile issm with pre- and post- processing features, either on a local machine or remote cluster.

harshula · 2025-01-31T01:47:55Z

Hi @justinh2002 , Can you please show what you tested in this PR?

justinh2002 · 2025-01-31T02:59:16Z

ran spack spec issm +with_wrappers, here is the output:

Input spec
--------------------------------
 -   issm+with_wrappers

Concretized
--------------------------------
 -   issm@4.24%gcc@14.1.0+with_wrappers build_system=autotools arch=linux-rocky8-x86_64_v4
[+]      ^autoconf@2.72%gcc@13.2.0 build_system=autotools arch=linux-rocky8-x86_64_v4
[+]          ^gcc-runtime@13.2.0%gcc@13.2.0 build_system=generic arch=linux-rocky8-x86_64_v4
[e]          ^glibc@2.28%gcc@13.2.0 build_system=autotools arch=linux-rocky8-x86_64_v4
[e]          ^perl@5.26.3%gcc@13.2.0+cpanm+opcode+open+shared+threads build_system=generic patches=8cf4302 arch=linux-rocky8-x86_64_v4
[+]      ^automake@1.16.5%gcc@13.2.0 build_system=autotools arch=linux-rocky8-x86_64_v4
 -       ^gcc-runtime@14.1.0%gcc@14.1.0 build_system=generic arch=linux-rocky8-x86_64_v4
[e]      ^glibc@2.28%gcc@14.1.0 build_system=autotools arch=linux-rocky8-x86_64_v4
[+]      ^gmake@4.4.1%gcc@13.2.0~guile build_system=generic arch=linux-rocky8-x86_64_v4
[+]      ^libtool@2.4.7%gcc@13.2.0 build_system=autotools arch=linux-rocky8-x86_64_v4
[+]          ^findutils@4.9.0%gcc@13.2.0 build_system=autotools patches=440b954 arch=linux-rocky8-x86_64_v4
[+]      ^m1qn3@3.3%gcc@13.2.0 build_system=makefile patches=b978437 arch=linux-rocky8-x86_64_v4
[+]      ^m4@1.4.19%gcc@13.2.0+sigsegv build_system=autotools patches=9dc5fbd,bfdffa7 arch=linux-rocky8-x86_64_v4
[+]          ^diffutils@3.10%gcc@13.2.0 build_system=autotools arch=linux-rocky8-x86_64_v4
[+]              ^libiconv@1.17%gcc@13.2.0 build_system=autotools libs=shared,static arch=linux-rocky8-x86_64_v4
[+]          ^libsigsegv@2.14%gcc@13.2.0 build_system=autotools arch=linux-rocky8-x86_64_v4
[e]      ^openmpi@4.1.7%gcc@13.2.0~atomics~cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~internal-libevent~internal-pmix~java~legacylaunchers~lustre~memchecker~openshmem~orterunprefix~romio+rsh~singularity~static+vt+wrapper-rpath build_system=autotools fabrics=none romio-filesystem=none schedulers=none arch=linux-rocky8-x86_64_v4
[+]      ^petsc@3.21.1%gcc@13.2.0~X~batch~cgns~complex~cuda~debug+double~exodusii~fftw+fortran~giflib+hdf5~hpddm~hwloc+hypre~int64~jpeg~knl~kokkos~libpng~libyaml~memkind+metis~mkl-pardiso~mmg~moab~mpfr+mpi+mumps~openmp~p4est~parmmg~ptscotch~random123~rocm~saws+scalapack+shared~strumpack~suite-sparse+superlu-dist~sycl~tetgen~trilinos~valgrind~zoltan build_system=generic clanguage=C memalign=none arch=linux-rocky8-x86_64_v4
[+]          ^hdf5@1.14.3%gcc@13.2.0~cxx~fortran~hl~ipo~java~map+mpi+shared~subfiling~szip~threadsafe+tools api=default build_system=cmake build_type=Release generator=make patches=82088c8 arch=linux-rocky8-x86_64_v4
[e]              ^cmake@3.24.2%gcc@13.2.0~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rocky8-x86_64_v4
[+]              ^pkgconf@2.2.0%gcc@13.2.0 build_system=autotools arch=linux-rocky8-x86_64_v4
[+]          ^hypre@2.31.0%gcc@13.2.0~caliper~complex~cuda~debug+fortran~gptune~gpu-aware-mpi~int64~internal-superlu~magma~mixedint+mpi~openmp~rocm+shared~superlu-dist~sycl~umpire~unified-memory build_system=autotools arch=linux-rocky8-x86_64_v4
[+]          ^metis@5.1.0%gcc@13.2.0~gdb~int64~ipo~real64+shared build_system=cmake build_type=Release generator=make patches=4991da9,93a7903,b1225da arch=linux-rocky8-x86_64_v4
[+]          ^mumps@5.6.2%gcc@13.2.0~blr_mt+complex+double+float~incfort~int64+metis+mpi~openmp+parmetis~ptscotch~scotch+shared build_system=generic patches=373d736 arch=linux-rocky8-x86_64_v4
[+]          ^netlib-scalapack@2.2.0%gcc@13.2.0~ipo~pic+shared build_system=cmake build_type=Release generator=make patches=072b006,1c9ce5f,244a9aa arch=linux-rocky8-x86_64_v4
[+]          ^openblas@0.3.26%gcc@13.2.0~bignuma~consistent_fpcsr+dynamic_dispatch+fortran~ilp64+locking+pic+shared build_system=makefile symbol_suffix=none threads=none arch=linux-rocky8-x86_64_v4
[+]          ^parmetis@4.0.3%gcc@13.2.0~gdb~int64~ipo+shared build_system=cmake build_type=Release generator=make patches=4f89253,50ed208,704b84f arch=linux-rocky8-x86_64_v4
[e]          ^python@3.11.7%gcc@13.2.0+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=13fa8bf,b0615b2,ebdca64,f2fd060 arch=linux-rocky8-x86_64_v4
[+]          ^superlu-dist@8.2.1%gcc@13.2.0~cuda~int64~ipo~openmp+parmetis~rocm+shared build_system=cmake build_type=Release generator=make arch=linux-rocky8-x86_64_v4
[+]          ^zlib-ng@2.1.6%gcc@13.2.0+compat+new_strategies+opt+pic+shared build_system=autotools arch=linux-rocky8-x86_64_v4

harshula · 2025-01-31T03:19:21Z

Hi @justinh2002 , Can you please test a spack install issm +with_wrappers and then show if the files you expect are installed by Spack. Use spack find --path to find the location.

packages/issm/package.py

harshula · 2025-02-13T06:32:19Z

Hi @justinh2002 , Can you please add this as the first version() call:

version("main", branch="main", preferred=True)

… config

harshula · 2025-02-19T04:29:01Z

packages/issm/package.py

@@ -12,46 +14,112 @@ class Issm(AutotoolsPackage):
    """Ice-sheet and Sea-Level System Model"""

    homepage = "https://issm.jpl.nasa.gov/"
-    git = "https://github.com/ISSMteam/ISSM.git"
+    git      = "https://github.com/ACCESS-NRI/ISSM.git"


Stick to the style used in the rest of the SPRs.

…o one directory and clears it after compilation

justinh2002 · 2025-03-07T05:22:45Z

==> The following package specs will be reinstalled:

-- linux-rocky8-x86_64 / intel@2021.10.0 ------------------------
lomguu6 issm@access-development%intel +wrappers build_system=autotools
==> Do you want to proceed? [y/N] y
[+] /usr (external glibc-2.28-5elnsoiqgcg5k5zmmwsp33bmnmaa3g5p)
[+] /usr (external glibc-2.28-uuaslxoln7yp3dciqri7e3o6zilg4xyf)
==> python@3.9.2 : has external module in ['python3/3.9.2']
[+] /apps/python3/3.9.2 (external python-3.9.2-vdktqpoh3znzzjyxmdus2erpgewdp7ff)
[+] /usr (external perl-5.26.3-j2iydfbotd473dio57mzyevya77uzttt)
==> openmpi@4.1.5 : has external module in ['openmpi/4.1.5']
[+] /apps/openmpi/4.1.5 (external openmpi-4.1.5-uvea7q2exkjwz2v7azix3x4zfcddnc23)
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/gmake-4.4.1-doeoclgsn63cvh7zfx3trjmyk7rlcqn4
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/gcc-runtime-13.2.0-l7iuzcvlhpwm24dt6ctf6bpqcbft4dzx
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/pkgconf-2.2.0-vrupasu7smpgcbarzpdwap45fcvjbjoa
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/automake-1.16.5-xhxnwib2rx6q76cxv43h6psjascu5dp7
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/zlib-ng-2.1.6-wa2x7rho3km6qpiki56dpjlpsce4c5n6
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/libpthread-stubs-0.5-dotch4gildprcikwlpw2av4vofdz6mft
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/libmd-1.0.4-56stzrbv3sgrr4mt72u5nxsi7y3yq4ei
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/openblas-0.3.26-27sgaqsfiidei6aqxqx3z3rfosurexvx
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/python-venv-1.0-fywvlqtevmbye7yiwlvknvehufebcbrv
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/libsigsegv-2.14-lzpomlzyq3igfj6ui2iiub22daqpvabj
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/findutils-4.9.0-icla2mwkv7v24iqxgtsa2isxzop4nrm7
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/metis-5.1.0-oacrfxlb5in5mckjxqxggioi62nhyb3k
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/m1qn3-3.3-tmevv77pqvgfngh73wlwpqtbqp7xrncw
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/xtrans-1.5.0-2vmqqvclfxsxlo5lgcbdtbtstpkal2ap
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/inputproto-2.3.2-n37n5kwllyix64r2p662iiyfnvuc522i
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/kbproto-1.0.7-4m3zppkd4kbq3vka2xoakubseahbgmrv
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/xextproto-7.3.0-bzesygn3tvtsobeokxiljclf7nadjnv3
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/xproto-7.0.31-wgxisqcpkrpqz7wx2njgh2xtlwfbqpao
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/hdf5-1.14.3-aumsrgzvbh6grtyyegzuufilnqa7ftm7
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/libbsd-0.12.1-nxranwhajvnzvkcobyxelnbqlmup7jm6
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/hypre-2.31.0-uazvgfbppefyyio34ats4ep5mvxaolqf
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/netlib-scalapack-2.2.0-sc6ignl4jpbkglfsnwkpjj64oaj5qtks
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/xcb-proto-1.16.0-bfoxclrxh323cmzrafkhipfwphuzqxw7
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/m4-1.4.19-srkd3efxh7a2cx6tejshjslbivocktck
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/parmetis-4.0.3-cw4qhzoh4owtlqxui6vilmn4fyrlla4b
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/libxau-1.0.11-7b5vcmg7gcc4u2w7bq4fvudeygac23fk
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/gcc-13.2.0/libxdmcp-1.1.4-o4llmszcdtnlrluttkwczehfva6dsukf
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/autoconf-2.72-zkg7fpzb224l6ay3c2kggaz62uazgvbw
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/libtool-2.4.7-j2xeapd6mxt4owgj7p2elc32ucuqzqpz
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/mumps-5.6.2-veuf6uu3glim2usq6zhbqtbjcuvujpty
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/superlu-dist-8.2.1-4uxhwa72ox6tspbczzzxzkqs4zmxwdbq
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/libxcb-1.16-bwjihgdrx5532czilec7yp6xvle564xk
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/petsc-3.21.1-b7jnomxtbspa3s3dlnelibnzr2yhuvlh
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/libx11-1.8.7-mwsoaixsexit5gqtqsqwz4m3q75gk5qz
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/access-triangle-main-qlzfpeyb635vhvl4eetr3gs4hm57vvc5
==> Installing issm-access-development-lomguu6j4lrcsjtusz6442qlrdyevp5u [41/41]
==> No binary for issm-access-development-lomguu6j4lrcsjtusz6442qlrdyevp5u found: installing from source
==> No patches needed for issm
==> issm: Executing phase: 'autoreconf'
==> issm: Executing phase: 'configure'
==> issm: Executing phase: 'build'
==> issm: Executing phase: 'install'
==> Warning: Module file /g/data/au88/jh7060/spack/0.22/release/modules/linux-rocky8-x86_64/issm/access-development-lomguu6 exists and will not be overwritten
==> issm: Successfully installed issm-access-development-lomguu6j4lrcsjtusz6442qlrdyevp5u
  Stage: 10.31s.  Autoreconf: 13.85s.  Configure: 1m 16.40s.  Build: 47m 44.20s.  Install: 6m 20.50s.  Post-install: 1m 34.37s.  Total: 57m 36.09s
[+] /g/data/au88/jh7060/spack/0.22/release/linux-rocky8-x86_64/intel-2021.10.0/issm-access-development-lomguu6j4lrcsjtusz6442qlrdyevp5u```

justinh2002 · 2025-03-07T05:25:09Z

Does this need to be rebased to main before we put it in vk83? I would like to finish configuring spack.yaml in the deployment repo as we have a user who would like to start fiddling around with the code.

harshula · 2025-03-07T07:45:17Z

Hi @justinh2002 , This needs to be tested, verified against Gadi non-spack build with wrappers, reviewed and merged before it appears on vk83.

harshula · 2025-03-07T07:48:13Z

packages/issm/package.py

+        # Copy the entire source tree into an additional directory
+        install_tree(self.stage.source_path, prefix.src)


Are you sure that the ISSM Spack package should install all the source? That's very unusual.

harshula · 2025-03-07T08:48:53Z

Hi @justinh2002 , Make a new Pull Request for the access-triangle SPR only. Let's get that reviewed and merged ASAP. Then come back to ISSM.

enable building of spack issm installation with wrappers

73d42ee

justinh2002 mentioned this pull request Jan 31, 2025

allow spack installation of issm to include wrappers #184

Open

justinh2002 requested review from harshula and aidanheerdegen January 31, 2025 01:44

harshula assigned justinh2002 Jan 31, 2025

harshula reviewed Feb 13, 2025

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packages/issm/package.py Outdated Show resolved Hide resolved

now using ACCESS-NRI fork of ISSM instead of upstream repo

1165414

justinh2002 force-pushed the 184-spack-issm_wrappers branch from 771db2e to 1165414 Compare February 13, 2025 04:39

added access-nri triangle dependency with others required for wrapper…

f913959

… config

harshula reviewed Feb 19, 2025

View reviewed changes

justinh2002 marked this pull request as draft February 20, 2025 04:11

justinh2002 added 5 commits February 24, 2025 11:58

spack packaging of triangle follows issm compilation method

7016b14

include all build config for triangle required by issm

d8b5f95

created new access triangle spack directory, SPR brings all files int…

579d144

…o one directory and clears it after compilation

cleanup docstrings and comments

9d7196c

added packaging features for +wrappers installation

88ee4a8

harshula reviewed Mar 7, 2025

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enable building of spack issm installation with wrappers #186

enable building of spack issm installation with wrappers #186

justinh2002 commented Jan 31, 2025

harshula commented Jan 31, 2025

justinh2002 commented Jan 31, 2025 •

edited

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justinh2002 commented Mar 7, 2025

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harshula commented Mar 7, 2025

harshula Mar 7, 2025

harshula commented Mar 7, 2025

		# Copy the entire source tree into an additional directory
		install_tree(self.stage.source_path, prefix.src)

enable building of spack issm installation with wrappers #186

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enable building of spack issm installation with wrappers #186

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