Provides a patch for the fix in
https://github.com/ornladios/ADIOS/pull/182
Installed ADIOS MPI-enabled libraries are with that able to also
perform serial I/O without the need to start the whole app via
`mpiexec`.
* trilinos: add more package conflicts
This was done by putting in required lib dependencies from each
package's `cmake/Dependencies.cmake`.
* trilinos: added few more trilinos packages
* trilinos: hiccup fix
* add 1.4.13.4 for SZ
* undo spack link (change llnl/spack to spack/spack) and change .zip to .tar.gz
* revise package.py for SZ 1.4.13.4 based on Adam's comments.
* adding partially completed recipe for phast. will need clapack as dependency
* try to install phast
* seems to still need CLAPCK
* using CLAPACK instead
* phast: updated
* fixed flake8 error
* phast cannot build with clapack built with external blas?
* phast: depend on clapack built without external blas
* fixed flake8 errors
* phast: updated build_directory
* pybind11: test support
Add a test functionality to pybind11.
* CMake: test also on "make check"
Some projects use non-CTest manual targets for tests.
* Fix digest for abyss@1.5.2
The digest value for v1.5.2 appears to have changed. This value works
for me, today.
The existing value v2.0.2 works as is.
* Use "download" URL for ABYSS
Following the suggestion of the project team, switch to using the
release tarballs from the "download" URL instead of the automagically
generated ones at the "archive" URL.
Converstation here: https://github.com/bcgsc/abyss/issues/232
The URL that we were using for pigz only provides the current
version. When the author released v2.4 the package became
uninstallable (unless you have the tarball cached).
It turns out that their are tarballs of the tagged source tree
available on GitHub and they're sufficient to build things (no
additional bits needed).
This commit switches the URL to the GitHub archive URL.
Sadly, this changes the v2.3.4 digest, but that version was no longer
available/install-able anyway, so "net-net we're still in positive
territory".
Installing the current version of Picard fails with:
```
==> Error: Unable to parse extension from https://github.com/broadinstitute/picard/releases/download/2.18.3/picard.jar.
If this URL is for a tarball but does not include the file extension
in the name, you can explicitly declare it with the following syntax:
version('1.2.3', 'hash', extension='tar.gz')
If this URL is for a download like a .jar or .whl that does not need
to be expanded, or an uncompressed installation script, you can tell
Spack not to expand it with the following syntax:
version('1.2.3', 'hash', expand=False)
```
Fix it, but adding `expand=False`, like the other versions.
* fix missing -lrt for Centos6, issue: #7552
* fix missing -lrt for Centos6, issue: #7552
* fix using make() as opposed to patching
* remove patch, as the fix is provided withing package.py instead
* make flake8 happy
* Update package: add info for emacs@26.1
In addition to the digest, it needs gnutls (perhaps there's a way to
turn it off, but it seems like a Good Thing to encourage, so...).
* Clean up tls variant handling
- Don't to specify the dependency for @26.1:, just need to fix what's
already there.
- Don't assume that configure will DTRT w.r.t. gnutls when it's
discovered in the environmnet, use explicit configure switches.
- Clean up some unnecessary dependencies when +tls. Why would you
need libxpm when building +tls? Will ask the original author about
this.
* Use append when adding configure switches
* Add dependency on pcre
When one builds +X, Spack's pcre is pulled into the build via
the X dependencies. When one builds without it, the build discovers
and links against the system library.
We might as well just depend on it and have a consistent outcome.
The recipe previously did not include -DWITH_JASPER
Other edits:
* BUILD_IPP_IW is BUILD instead of WITH; it was in a different section of the CMakeLists.txt. Move it to the top
* Several options were missing :BOOL, add them
* -DWITH_ZLIB doesn't actually exist as an option, at least in the latest version.
* Added new package Camellia.
* Fixed an issue with a missing blank line.
Added a couple more Trilinos packages (things I expect to depend on eventually).
* Fixed a couple issues raised by @adamjstewart.
* Specified 4.9.2 as the supported MOAB version.
5.0.0 causes build issues on Macs during the link of Camellia's drivers. The issue is that we end up with -framework -lAccelerate in the link line, where it should read -framework Accelerate, I believe. I'm not sure where this comes from, but 4.9.2 does not have this issue.
* Trimmed slightly the Trilinos requirements.
Also deleted a blank line that had spaces in it because the Travis-CI thing didn't like that.
* Reduced length of MOAB description (Travis-CI complained).
* Reduced the MOAB line further; didn't quite get there last time!
This is to satisfy Travis-CI's requirement that the description be less than 80 characters long (E501).
* Put in my GitHub handle, in place of an allusion to my email address.
Also added a new argument for Camellia build, and made the MOAB description longer (thanks to @adamjstewart's note that long lines are allowed so long as they are not split).
* Added MPI dependency.
Added explicit OFF for MOAB enablement when ~moab.
Swapped order of variant and version.
* Add Tophat v2.1.2, fixes automake issues
The Tophat team merged the patch from
https://github.com/spack/spack/pull/8244 and release v2.1.2
This change requires the old automake if you're building the older
release and is relaxed about the automake it requires if you're
building the v2.1.2 release.
Building v2.1.1 and v2.1.2 works on a CentOS 7 system, I don't have
the necessary bit to actually test the resulting binaries.
Here's the commit note from the change that was ultimately merged
upstream.
Fixes#8025
> Tophat was failing to build with automake@1.16.1, it worked with the
> older automake@1.15.1. This commit adds a patch to Tophat's
> src/Makefile.am which cleans up a few things. The result builds
> successfully with both automake@1.15.1 and automake@1.16.1. I have no
> way to check that the resulting builds Do The Right Thing.
>
> It changes two things:
>
> the original Makefile.am had a rule for $(SAMPROG) with no
> actions, and since there was a directory there with a tempting name
> the newer automake was trying to do something with it, but lacked
> the appropriate clues. Since that target is actually made as a side
> effect of making the library (sigh...), it seems to work to just
> give that rule something harmless to do (the Peter Principle
> triumphs again...).
>
> a bunch of the targets need a libtophat.a and libgc.a; the older
> automake was probably able to guess what to do given the list of
> sources but the newer automake apparently won't make the necessary
> assumptions. This patch wires up a simple rule and cleans up the
> appropriate dependencies so that things work.
>
> While it may appear that I'm someone who understands automake, keep in
> mind that I only play such a person on a TV reality show. YMMV.
* Remove extraneous when constraint
* kokkos: update kokkos spackage to add current host/gpu architectures.
* kokkos: simplify host/gpu architecture selection and make intent of arg population logic more clear.
* kokkos: mollify flake8.
* Make strings and logic more pythonic. Add error for GPU arch without CUDA.
* kokkos: simplify conflicts behaviour. make args population more pythonic.
* kokkos: move gpu values to list for use in variant and conflicts checking.
* kokkos: How fortunate the man with None.
* kokkos: fix gpu_arch conflict loop error. add conflict to guard against +cuda and 2.5.00:develop versions, until kokkos issue #1296 is resolved.
* kokkos: mollify flake8.
* kokkos: add descriptive message to version conflict with +cuda.
* update globalarrays package to current releases
* rename class to Globalarrays to match package folder
* rename bytes to int64, minor cleanup of descriptions
* int64 False by default
* remove reference to external as we aren't supplying paths, and use args.append()
* correcting args.append syntax
* add conflicts
* Fix bug; don't know why this ever worked in the first place.
* Add fix to netcdf-fortran too; flake8
* Simplify configure_args()
* netcdf-fortran: simplify that too
