Commit graph

11382 commits

Author SHA1 Message Date
Daniel Topa
c7725e9ff8 Add Open MPI v3.0.4 (#11221)
tarball posted 2019-04-15
https://www.open-mpi.org/software/ompi/v3.0/

dantopa@cn209:openmpi-3.0.4-5ienfvwpcxky3nz5jt3rygxzxzltkwm4 $ cd lib/

dantopa@cn209:lib $ ls -alh
total 27M
...
lrwxrwxrwx 1 dantopa dantopa   16 Apr 17 10:01 libmpi.so -> libmpi.so.40.0.5

confirmation builds Darwin (LANL):

x86_64
-- linux-centos7-x86_64 / gcc@4.8.5 -----------------------------
5ienfvw    openmpi@3.0.4%gcc
bkkhvej        ^hwloc@1.11.11%gcc
5chyfxo            ^libpciaccess@0.13.5%gcc
bcnjbc3            ^libxml2@2.9.8%gcc
tt2hkol            ^numactl@2.0.12%gcc
64vg6e4        ^zlib@1.2.11%gcc

ARM
-- linux-rhel7-aarch64 / gcc@4.8.5 ------------------------------
cq2y6b3    openmpi@3.0.4%gcc
7gqvelc        ^hwloc@1.11.11%gcc
6a4he35            ^libpciaccess@0.13.5%gcc
6a5uzd6            ^libxml2@2.9.8%gcc
m5neuus            ^numactl@2.0.12%gcc
67s2oqn        ^zlib@1.2.11%gcc

Power9
-- linux-rhel7-ppc64le / gcc@4.8.5 ------------------------------
otirvfn    openmpi@3.0.4%gcc
r6cylpu        ^hwloc@1.11.11%gcc
uzm3xdv            ^libpciaccess@0.13.5%gcc
trik6hj            ^libxml2@2.9.8%gcc
pmgndwh            ^numactl@2.0.12%gcc
4v3ticy        ^zlib@1.2.11%gcc

2019-04-18

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-04-18 12:33:26 -05:00
Zack Galbreath
7febb88c2a improvements to our CDash reporter (#11168)
* Make a separate CDash report for each package installed

Previously, we generated a single CDash report ("build") for the complete results
of running a `spack install` command. Now we create a separate CDash build for
each package that was installed.

This commit also changes some of the tests related to CDash reporting.
Now only one of the tests exercises the code path of uploading to a
(nonexistent) CDash server. The rest of the related tests write their reports
to disk without trying to upload them.

* Don't report errors to CDash for successful packages

Convert errors detected by our log scraper into warnings when the package
being installed reports that it was successful.

* Report a maximum of 50 errors/warnings to CDash

This is in line with what CTest does. The idea is that if you have more than
50 errors/warnings you probably aren't going to read through them all anyway.
This change reduces the amount of data that we need to transfer and store.
2019-04-18 09:39:35 -07:00
Federico Ficarelli
e64ee7e1be Prevent building llvm@8: with an incompatilble gcc (#11220) 2019-04-18 16:58:41 +02:00
Satish Balay
4571a96a43
xsdk: add/update maintainers to xsdk packages (#11146)
pumi
  slepc
  plasma
  magma
  trilinos
  alquimia
  pflotran
  strumpack
  tasmanian
  amrex
  hypre
  omega-h
  superlu-dist
2019-04-18 08:20:22 -05:00
Stephen Herbein
1dc3744d2c new package: kitty terminal (#9621) 2019-04-18 08:53:52 +02:00
Greg Becker
f242f5f8a9 Features: Improve Spec format strings (#10556)
* Update spec format to simpler syntax, maintain backwards compatibility
* Switch to new spec.format method throughout internals
* update package files for new format strings
* documentation and minor code cleanup. removed nonsensical variant sigils
2019-04-17 18:21:40 -07:00
Veselin Dobrev
49334f006d [WIP] CEED 2.0 (#10903)
* Initial commit for v2.0 of the CEED software suite.

* Update Nek packages and gslib

* Help spack concretize the hypre version for ceed-2.0.

* Fix nekcem install error

* Add support for gfortran v8 in nek5000 and nekcem.

* Split Nek5000 into Nek5000 and Nektools

* Get Nektools to build fine in Theta

* Fix travis failure: remove unused 'import numbers' from nek5000.

* Check for gfortran if it is wrapped

* Tweak the detection of gfortran in nek5000.

* Fix Nek packages to add -std=legacy when FC=gcc

* spack install ceed~petsc works fine on Theta

* Fix flake8 errors

* Fix more flake8 tests

* Fix an import issue

* Tweak the suite-sparse package to avoid interaction with existing system
installations of suite-sparse.

* petsc: update superlu-dist dependency

* Updates in the packages: occa, libceed, and ceed.

* In the libceed package, explicitly tell nvcc which host compiler to use.

* Fix python formatting.

* Simplify the test for gfortran in nek* packages.

* ceed: 2.0 uses petsc@3.11.0

* hpgmg-0.4; use from ceed@2.0.0

* Update the hypre dependency for ceed 2.0.

* Disable the superlu-dist dependency (through hypre) when using a
+quickbuild of ceed 2.0.

* petsc-3.11.0: add xlf fix

* nekcem: has a build dependency on Python 2.7+

* hpgmg: better setting of compiler options and use python for configure

* libceed: use v0.4 tag

* libceed: fix 0.4 release oops (pkgconfig version)

* Add a patch for magma-2.5.0 that brings it up the current 'master'.

* In the mfem package, install the examples, miniapps, and data under
$prefix/share/mfem.

* In the magma package, apply a patch to v2.5.0 that disables
magma_sparse - for testing purposes.

* In the magma package, link the 'magma' library with the
'nvToolsExt' library.

* In the magma package, update the 'magma-2.5.0.patch' with the latest
commits from the magma source repository. Also, remove the library
'nvToolsExt' from the 'magma-2.5.0-cmake.patch' - now it is not
needed.

* In the magma package, disable OpenMP when using v2.5.0 with the
IBM XL compiler.

 Please enter the commit message for your changes. Lines starting

* In the mfem package, add version for the 'laghos-v2.0' tag; also,
prefix the versions `laghos-v*` with their respective development
version numbers -- this way they are properly ordered within spack
relative to the official numbered versions.

* petsc: add version 3.11.1 (#11179)


(cherry picked from commit 1eab6e3c86)

* ceed-2.0: use petsc-3.11.1

* this-is-so-dumb.f -> empty.f
2019-04-17 17:37:41 -07:00
Elsa Gonsiorowski, PhD
a26aec520b mpifileutils v0.9.1 (#11216)
* mpifileutils v0.9.1

* mpifileutils v0.9.1 for realz
2019-04-17 18:11:14 -05:00
Michael Kuhn
b61dd57fdc sublime-text: Miscellaneous improvements (#11154)
- Add 3.2.1
- Reformat versions to include proper upstream version tags
- Add gtk dependency
- Add prefix to PATH so sublime_text can be found
2019-04-17 13:44:34 -07:00
Satish Balay
7280f21397 Add ftn to lib/spack/env (#11180)
Fixes #11070 #11010

Spack attempts to intercede on behalf of all compiler invocations for
a build. This involves adding its wrappers to PATH. Cray systems
include a "ftn" executable and Spack was only redirecting this call
when the Spec was built with cce. This updates the compiler wrappers
to add "ftn" in all cases.
2019-04-17 13:12:25 -07:00
Oliver Breitwieser
f276b3ffa0 ruby: Install certificate for +openssl only (#11184)
If specifying ~openssl, the post-install step will still try to install
the non-existent certificate, leading to an IOError.
2019-04-17 13:03:58 -05:00
Christoph Junghans
c628ca99cf gromacs: added 2019 patch releases (#11211) 2019-04-17 12:48:06 -05:00
Satish Balay
4731041f88
strumpack@3.1.1: add patch for Intel-19 build failure on cori (#11204)
Ref: https://github.com/spack/spack/issues/11202
2019-04-17 12:10:05 -05:00
Justin S
01ada1a3de astral: add 5.6.1 (#11195) 2019-04-17 09:32:50 -05:00
sknigh
e372464611 Add llvm 8.0.0 (#11197) 2019-04-17 09:31:42 -05:00
Michael Kuhn
ea2a85dbd3 lz4: Add 1.9.0 (#11207) 2019-04-17 09:30:23 -05:00
Michael Kuhn
3028f5674c zstd: Add 1.4.0 (#11208) 2019-04-17 09:29:52 -05:00
Peter Scheibel
ef8b5c73ce
don't record 'view: True' in environment config (#11182)
The default (implied) behavior for all environments, as of ea1de6b,
is that an environment will maintain a view in a location of its
choosing. ea1de6b explicitly recorded all three possible states of
maintaining a view:

 1. Maintain a view, and let the environment decide where to put it
    (default)
 2. Maintain a view, and let the user decide
 3. Don't maintain a view

This commit updates the config writer so that for case [1], nothing
will be written to the config.yaml. This will not change any existing
behavior, it just serves to keep the config more compact.
2019-04-16 19:08:10 -07:00
sknigh
308805cd54 Added rust 1.34.0 (#11200) 2019-04-16 18:32:11 -05:00
sknigh
a287ad6edd Added openmpi 3.1.4 (#11201)
* Added openmpi 3.1.4

* fix suffix comment
2019-04-16 18:31:54 -05:00
Matthias Mayr
e07cf4d661 New package: CLN library (#11167) 2019-04-16 16:03:51 -07:00
Frédéric Simonis
2ef7287a3b precice package: add versions and dependencies (#11176)
* Add versions 1.4.0, 1.3.0, and 1.2.0
* Add dependencies and update constraints (e.g. version 1.4.0 of
  precice requires a later version of boost)
* Add maintainers
2019-04-16 12:38:08 -07:00
paulanda
88cc895a70 setup-env.sh: fix zsh compatibility error (#11153)
Still look for BASH_SOURCE[0] first, but if it's not set,
_sp_source_file is initialized to an empty value addressing the
unset parameter error (line 217).
2019-04-16 12:33:02 -07:00
Nichols A. Romero
9a79a2345d QMCPACK package: Remove Spack MKL hack for older version (#11127)
A Spack hack for MKL usage was needed in QMCPACK prior to version 3.5
when non-Intel compilers were used. This Spack hack could have
undesirable side-effects and led to ugly code that was extra work to
maintain. For older versions of QMCPACK, we throw a conflict if you
want to use Intel MKL with the other compilers commonly found on x86.

Note that there is no impact to version of QMCPACK since 3.5.
2019-04-16 12:04:40 -07:00
Satish Balay
c25d162b3c
superlu-dist: fix issue with adding system blas/lapack - when MKL is explicitly specified (#11187)
Version 6 added dependency on LAPACK - so additional -DTPL_LAPACK_LIBRARIES option is required

Ref: https://github.com/xiaoyeli/superlu_dist/issues/36
Ref: https://github.com/spack/spack/issues/10173
2019-04-16 08:52:48 -05:00
Adam J. Stewart
dbfa928cdb Add unit tests for Cray compiler detection (#11191) 2019-04-16 10:01:42 +02:00
Greg Becker
5f74f22dc6 Bugfix: Install missing compilers for dependency packages (#11175)
Compilers are treated separately from other dependencies in Spack.
#10761 added the option to automatically install compilers when a
package specifies using a compiler that is not available in Spack.
However, this did not work correctly for dependency packages (it
would only build a compiler for the root of an install DAG). This
commit enables the building of compilers for dependency packages.
2019-04-15 17:41:15 -07:00
Jordan Ogas
a49de9eb09 add charliecloud 0.9.9 (#11190) 2019-04-15 17:59:10 -05:00
Matthias Diener
dd97cf9315 cmake: add version 3.14.2 (#11192) 2019-04-15 17:17:24 -05:00
Denis Davydov
06a17ef052 pixman: fix patch (#11173) 2019-04-15 14:49:02 +02:00
Denis Davydov
0341e19540 boost: add 1.70.0 (#11183) 2019-04-15 09:59:04 +02:00
Oliver Breitwieser
dadbd723a3 verilator: Fix FlexLexer.h not found (#11185)
Similar to #10956 flex needs to be a link-dependency for verilator in
order for FlexLexer.h to be found during install.
2019-04-15 09:56:07 +02:00
Satish Balay
5b5e00aaa9 petsc4py: add verson 3.11.0 (#11186)
Also added maintainers
2019-04-15 09:54:40 +02:00
Mark C. Miller
1ae7477d20 Update FASTMath metapackage (#11171)
* Limit to FASTMath-only packages
* Replace boxlib with amrex

As requested by @asalmgren
2019-04-12 16:54:19 -05:00
Satish Balay
832a1ddbaa
petsc: add fftw variant (#11178) 2019-04-12 09:46:23 -05:00
Satish Balay
1eab6e3c86
petsc: add version 3.11.1 (#11179) 2019-04-12 09:45:43 -05:00
Owen Solberg
227f9c9026 py-deeptools: adding release 3.2.1 sha256 sum (#11174) 2019-04-12 09:45:04 +02:00
Massimiliano Culpo
263d8a818a Updated Sphinx configuration (#11165) 2019-04-11 14:38:52 -07:00
Denis Davydov
177b7f111a intel: optionally take gcc executable from cflags (#11136) 2019-04-11 12:33:59 -07:00
Satish Balay
6b09781936
xsdk@develop: enable amrex@develop+sundials (#11169) 2019-04-11 12:16:23 -05:00
Cody Balos
0d0358733d amrex: add sundials variant (#11147) 2019-04-11 10:43:11 -05:00
brietzke
d0e281e201 libxsmm package: add variant to build generator executables (#11114) 2019-04-10 16:34:38 -07:00
clellsolomon
7ec12c59ab fzf package: change mirror and add vim plugin (#10920)
This commit edits the Makefile to use github.com mirrors rather than the
default mirrors of the dependency packages installed by GO.
2019-04-10 16:23:37 -07:00
Chuck Atkins
f1bdaa11d4 New Packages: ecp-io-sdk and ecp-viz-sdk (#11073) 2019-04-10 16:18:05 -07:00
Peter Scheibel
ea1de6b941 Maintain a view for an environment (#10017)
Environments are nowm by default, created with views.  When activated, if an environment includes a view, this view will be added to `PATH`, `CPATH`, and other shell variables to expose the Spack environment in the user's shell.

Example:

```
spack env create e1 #by default this will maintain a view in the directory Spack maintains for the env
spack env create e1 --with-view=/abs/path/to/anywhere
spack env create e1 --without-view
```

The `spack.yaml` manifest file now looks like this:

```
spack:
  specs:
  - python
  view: true #or false, or a string
```

These commands can be used to control the view configuration for the active environment, without hand-editing the `spack.yaml` file:

```
spack env view enable
spack env view envable /abs/path/to/anywhere
spack env view disable
```

Views are automatically updated when specs are installed to an environment. A view only maintains one copy of any package. An environment may refer to a package multiple times, in particular if it appears as a dependency. This PR establishes a prioritization for which environment specs are added to views: a spec has higher priority if it was concretized first. This does not necessarily exactly match the order in which specs were added, for example, given `X->Z` and `Y->Z'`:

```
spack env activate e1
spack add X
spack install Y # immediately concretizes and installs Y and Z'
spack install # concretizes X and Z
```

In this case `Z'` will be favored over `Z`. 

Specs in the environment must be concrete and installed to be added to the view, so there is another minor ordering effect: by default the view maintained for the environment ignores file conflicts between packages. If packages are not installed in order, and there are file conflicts, then the version chosen depends on the order.

Both ordering issues are avoided if `spack install`/`spack add` and `spack install <spec>` are not mixed.
2019-04-10 16:00:12 -07:00
Eric Martin
8f1ebfc73c py-requests: Add missing dependencies for versions 2.16.0 and up (#10996) 2019-04-10 15:38:28 -07:00
Mario Melara
a1db22ba1a Unload altd and darshan (#11162) 2019-04-10 13:19:41 -07:00
Peter Scheibel
c1f8fdd5df
Add documentation for chaining Spack instances (#11152)
Add documentation for the Spack chain feature added in #8772
2019-04-10 11:54:13 -07:00
Patrick Gartung
a5315f3878
Fix bug when system perl is used. (#11034)
* Fix bug when system perl is used.

If system perl is being used through packages.yaml there cannot be dependent modules.
The  setup_dependent_packages function should not do anything in that case.
2019-04-10 08:44:27 -05:00
Denis Davydov
1e9748a3c8 dealii: fix build with tbb from intel parallel studio (#11138) 2019-04-10 14:51:38 +02:00