[petsc-users] VecView to hdf5 broken for large (complex) vectors

[Balay, Satish]

On Wed, 17 Apr 2019, Satish Balay wrote:

> Its not ideal - but having local changes in our spack clones (change
> git url, add appropriate version lines to branches that one is
> working on) is possible [for a group working in this mode].

[balay at pj03 petsc]$ pwd
/home/balay/petsc
[balay at pj03 petsc]$ git branch
* barry/fix-vecview-mpi-hdf5/maint
  maint
  master

[balay at pj03 spack]$ git diff
diff --git a/var/spack/repos/builtin/packages/petsc/package.py b/var/spack/repos/builtin/packages/petsc/package.py
index 3d9686eb2..57932f93c 100644
--- a/var/spack/repos/builtin/packages/petsc/package.py
+++ b/var/spack/repos/builtin/packages/petsc/package.py
@@ -17,13 +17,16 @@ class Petsc(Package):
 
     homepage = "http://www.mcs.anl.gov/petsc/index.html"
     url      = "http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-3.5.3.tar.gz"
-    git      = "https://bitbucket.org/petsc/petsc.git"
+    git      = "/home/balay/petsc"
 
     maintainers = ['balay', 'barrysmith', 'jedbrown']
 
     version('develop', branch='master')
     version('xsdk-0.2.0', tag='xsdk-0.2.0')
 
+    version('3.11.99-maint', branch='maint')
+    version('3.11.98-fix-vecview-mpi-hdf5', branch='barry/fix-vecview-mpi-hdf5/maint')
+
     version('3.11.1', 'cb627f99f7ce1540ebbbf338189f89a5f1ecf3ab3b5b0e357f9e46c209f1fb23')
     version('3.11.0', 'b3bed2a9263193c84138052a1b92d47299c3490dd24d1d0bf79fb884e71e678a')
     version('3.10.5', '3a81c8406410e0ffa8a3e9f8efcdf2e683cc40613c9bb5cb378a6498f595803e')
[balay at pj03 spack]$ spack install petsc at develop~hdf5~hypre~superlu-dist~metis
==> mpich at 3.3b1 : externally installed in /home/petsc/soft/mpich-3.3b1
==> mpich at 3.3b1 : already registered in DB
==> openblas is already installed in /home/balay/spack/opt/spack/linux-fedora29-x86_64/gcc-8.3.1/openblas-0.3.5-xokonl5jhgandxuwswkaabijra337l2d
==> python at 3.7.2 : externally installed in /usr
==> python at 3.7.2 : already registered in DB
==> sowing is already installed in /home/balay/spack/opt/spack/linux-fedora29-x86_64/gcc-8.3.1/sowing-1.1.25-p1-6wiuwedg5ufoabro3ip4j7ssd43a66je
==> Installing petsc
==> Searching for binary cache of petsc
==> Warning: No Spack mirrors are currently configured
==> No binary for petsc found: installing from source
==> Cloning git repository: /home/balay/petsc on branch master
warning: --depth is ignored in local clones; use file:// instead.
==> No checksum needed when fetching with git
==> Already staged petsc-develop-qcfn35x2lvixtk4u5reczf5y3pjq6a3r in /home/balay/spack/var/spack/stage/petsc-develop-qcfn35x2lvixtk4u5reczf5y3pjq6a3r
==> No patches needed for petsc
==> Building petsc [Package]
==> Executing phase: 'install'
==> [2019-04-17-01:18:20.792426] 'make' '-j16' 'install'
==> Successfully installed petsc
  Fetch: 0.82s.  Build: 2m 22.90s.  Total: 2m 23.71s.
[+] /home/balay/spack/opt/spack/linux-fedora29-x86_64/gcc-8.3.1/petsc-develop-qcfn35x2lvixtk4u5reczf5y3pjq6a3r
[balay at pj03 spack]$ spack install petsc at 3.11.98-fix-vecview-mpi-hdf5~hdf5~hypre~superlu-dist~metis
==> mpich at 3.3b1 : externally installed in /home/petsc/soft/mpich-3.3b1
==> mpich at 3.3b1 : already registered in DB
==> openblas is already installed in /home/balay/spack/opt/spack/linux-fedora29-x86_64/gcc-8.3.1/openblas-0.3.5-xokonl5jhgandxuwswkaabijra337l2d
==> python at 3.7.2 : externally installed in /usr
==> python at 3.7.2 : already registered in DB
==> Installing petsc
==> Searching for binary cache of petsc
==> Warning: No Spack mirrors are currently configured
==> No binary for petsc found: installing from source
==> Cloning git repository: /home/balay/petsc on branch barry/fix-vecview-mpi-hdf5/maint
warning: --depth is ignored in local clones; use file:// instead.
==> No checksum needed when fetching with git
==> Already staged petsc-3.11.98-fix-vecview-mpi-hdf5-2i6pmomvyacyefcq7hxqe22gogepf6os in /home/balay/spack/var/spack/stage/petsc-3.11.98-fix-vecview-mpi-hdf5-2i6pmomvyacyefcq7hxqe22gogepf6os
==> No patches needed for petsc
==> Building petsc [Package]
==> Executing phase: 'install'
==> Successfully installed petsc
  Fetch: 0.79s.  Build: 2m 31.08s.  Total: 2m 31.88s.
[+] /home/balay/spack/opt/spack/linux-fedora29-x86_64/gcc-8.3.1/petsc-3.11.98-fix-vecview-mpi-hdf5-2i6pmomvyacyefcq7hxqe22gogepf6os
[balay at pj03 spack]$ spack install petsc at 3.11.99-maint~hdf5~hypre~superlu-dist~metis
==> mpich at 3.3b1 : externally installed in /home/petsc/soft/mpich-3.3b1
==> mpich at 3.3b1 : already registered in DB
==> openblas is already installed in /home/balay/spack/opt/spack/linux-fedora29-x86_64/gcc-8.3.1/openblas-0.3.5-xokonl5jhgandxuwswkaabijra337l2d
==> python at 3.7.2 : externally installed in /usr
==> python at 3.7.2 : already registered in DB
==> Installing petsc
==> Searching for binary cache of petsc
==> Warning: No Spack mirrors are currently configured
==> No binary for petsc found: installing from source
==> Cloning git repository: /home/balay/petsc on branch maint
warning: --depth is ignored in local clones; use file:// instead.
==> No checksum needed when fetching with git
==> Already staged petsc-3.11.99-maint-ivdk3dhyirqwjv7fplbkvha6d27hhzmk in /home/balay/spack/var/spack/stage/petsc-3.11.99-maint-ivdk3dhyirqwjv7fplbkvha6d27hhzmk
==> No patches needed for petsc
==> Building petsc [Package]
==> Executing phase: 'install'
==> Successfully installed petsc
  Fetch: 0.82s.  Build: 2m 30.67s.  Total: 2m 31.49s.
[+] /home/balay/spack/opt/spack/linux-fedora29-x86_64/gcc-8.3.1/petsc-3.11.99-maint-ivdk3dhyirqwjv7fplbkvha6d27hhzmk
[balay at pj03 spack]$ spack find
==> 7 installed packages
-- linux-fedora29-x86_64 / gcc at 8.3.1 ----------------------------
mpich at 3.3b1  openblas at 0.3.5  petsc at 3.11.98-fix-vecview-mpi-hdf5  petsc at 3.11.99-maint  petsc at develop  python at 3.7.2  sowing at 1.1.25-p1
[balay at pj03 spack]$ 

Satish