Commit graph

13441 commits

Author SHA1 Message Date
Gregory Lee
d60106a3f6 Add newer versions for 51 Python packages (#10738) 2019-02-27 12:45:28 -06:00
Massimiliano Culpo
7eec038690
Update environment-modules package (#10717)
The environment modules package has been updated to include 
versions up to 4.0.0. The url of the package and the homepage
have been updated accordingly.

The `spack bootstrap` command now builds version 3.2.10 of
the environment-modules package, and will do until #10708 
is fixed.
2019-02-27 14:00:46 +01:00
Isaac Whitfield
5efff5d2fc new package: libusb (#10682) 2019-02-26 20:52:47 -06:00
Isaac Whitfield
938939b7e4 new package: libtasn1 (#10681) 2019-02-26 20:52:04 -06:00
Nichols A. Romero
d9b7c1faea QMCPACK package: cuda/hdf5 fixes (#10701)
* Make use of new QE multi-valued HDF5 variant interface
* Remove explicit CUDA dependency (which is handled by inheriting
  from CudaPackage)
* Update cuda_arch unset variant check
2019-02-26 20:50:32 -06:00
Satish Balay
c11f598e0b petsc: add version 3.10.4 (#10724) 2019-02-26 20:41:33 -06:00
Justin Stanley
cbecf9f555 new package: phred (#10700)
Part of the software collection introduced in #10529. Developers must
be contacted via email to receive the source code.
2019-02-26 19:14:58 -06:00
Isaac Whitfield
fbdbed1180 new package: libplist (#10680)
Dependency of Google's Flutter toolchain.
2019-02-26 19:12:41 -06:00
Justin Stanley
df4b77f120 libbeagle package: add cuda support (#10650)
libbeagle compiles against CUDA by default but no there is no mention
of it in the package recipe. This PR adds explicit cuda paths and
variants, and fixes the target architecture as well (for those who
don't have compute_13)
2019-02-26 18:50:08 -06:00
Michael Kuhn
0adf1b5405 vampirtrace: patch for new mpich and openmpi versions (#10665) 2019-02-26 18:48:14 -06:00
Phil Tooley
018ae371d6 new package: routino (#10679) 2019-02-26 18:41:44 -06:00
Janne Blomqvist
312122f169 Don't try to build TARGET=PILEDRIVER on aarch64
Piledriver is a codename for an AMD x86-64 processor, it can't
possibly make sense to compile for that if the architecture is
aarch64.
2019-02-26 18:40:39 -06:00
Neil Flood
2831184e41 kealib package: add version 1.4.11 (#10706) 2019-02-26 18:39:27 -06:00
Daryl W. Grunau
ecd98d1953 eospac package: add version 6.4.0 (#10718) 2019-02-26 18:38:52 -06:00
Justin Stanley
ba2ed96513 beast2 package: add version 2.5.2 (#10723) 2019-02-26 18:38:21 -06:00
Nichols A. Romero
5aa6cbf437 Quantum ESPRESSO package: Serial HDF5 Bug Fix (#10689)
Serial HDF5 in serial QE only works in develop version. This adds
a conflict to the QE package to prevent Spack from trying to build
specs which don't satisfy this constraint.
2019-02-26 18:36:50 -06:00
Massimiliano Culpo
42386dbe94 Use Package.headers for -I options (#10623)
This restores the use of Package.headers when computing -I options
for building a package that was added in #8136 and reverted in
#10604. #8136 used utility logic that located all header files in
an installation prefix, and calculated the -I options as the
immediate roots containing those header files.

In some cases, for a package containing a directory structure like

  prefix/
    include/
	  ex1.h
	  subdir/
	    ex2.h

dependents may expect to include ex2.h relative to 'include', and
adding 'prefix/include/subdir' as a -I was causing errors,
in particular if ex2.h has the same name as a system header.

This updates header utility logic to by default return the base
"include" directory when it exists, rather than subdirectories.
It also makes it possible for package implementers to override
Package.headers to return the subdirectory when it is required
(for example with libxml2).
2019-02-26 12:42:30 -06:00
Justin Stanley
ad25e7f3b0 r-vfs: new package at 1.0.2 (#10697) 2019-02-26 12:21:12 -06:00
Justin Stanley
68318ab076 r-nleqslv: new package at 3.3.2 (#10696) 2019-02-26 12:19:48 -06:00
Daniel Topa
c832479c65 Add libhio v1.4.1.3, 1.4.1.1 (#10699)
- Switch all libhio tarball listings to sha256 checksums
- Correct typo in alert message in /lib/spack/spack/util/module_cmd.py: fucntion -> function

https://github.com/hpc/libhio/releases
Released 2019-02-01

Verification builds on LANL Darwin:

**Intel Xeon**
Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                40
On-line CPU(s) list:   0-39
Thread(s) per core:    2
Core(s) per socket:    10
Socket(s):             2
NUMA node(s):          2
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 63
Model name:            Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz
Stepping:              2
CPU MHz:               1198.779
CPU max MHz:           3300.0000
CPU min MHz:           1200.0000
BogoMIPS:              5193.70
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              25600K
NUMA node0 CPU(s):     0-9,20-29
NUMA node1 CPU(s):     10-19,30-39
Flags:                 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt aes xsave avx f16c rdrand lahf_lm abm cpuid_fault epb invpcid_single pti intel_ppin tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc dtherm ida arat pln pts
`
[+] /scratch/users/dantopa/new-spack/strawman.pr.libhio/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libhio-1.4.1.3-s4fnmesfp65trhks5qi3it5p73ssfpsp
[+] /scratch/users/dantopa/new-spack/strawman.pr.libhio/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libhio-1.4.1.2-fkgh5vqpijvwqywffmokgmsglqxwfrtl
`

**Arm**
Architecture:          aarch64
Byte Order:            Little Endian
CPU(s):                256
On-line CPU(s) list:   0-255
Thread(s) per core:    4
Core(s) per socket:    32
Socket(s):             2
NUMA node(s):          2
Model:                 0
BogoMIPS:              400.00
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              32768K
NUMA node0 CPU(s):     0-127
NUMA node1 CPU(s):     128-255
Flags:                 fp asimd evtstrm aes pmull sha1 sha2 crc32 atomics cpuid asimdrdm
`
[+] /scratch/users/dantopa/new-spack/strawman.pr.libhio/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/libhio-1.4.1.3-q6nnwiy6bi7ktnghdsngwamom23zpmgy
[+] /scratch/users/dantopa/new-spack/strawman.pr.libhio/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/libhio-1.4.1.2-y6nwovff3qbdy242zc4x2toloz6xpcvm
`

2019-02-25

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
2019-02-26 09:56:20 +01:00
Adam J. Stewart
a75a6ee1b7 Add /hash to spack help --spec (#10691)
* Add /hash to spack help --spec
* Make /hash gray, add ^/hash
2019-02-25 16:20:28 -08:00
Stephen Hudson
7c38dc06dc libEnsemble package: add v0.4.1 (#10688)
Also add v0.4.0 and remove version lower bound on petsc4py
2019-02-25 14:37:51 -06:00
Michael Kuhn
385d108b5d slurm: Add PMI support (#10683)
- Add support for pmix (optional)
- Install pmi2 header and library
2019-02-25 13:05:31 -06:00
Elsa Gonsiorowski, PhD
d85a0bae8f mpiFileUtils v0.9 (#10676)
* working on updating to cmake

* generic package, any ver of cmake

* install for autotools or cmake
2019-02-25 09:24:52 -08:00
Hadrien G
236180c109 ACTS: new package (#10600) 2019-02-25 11:11:01 +01:00
Sinan
691a2f4b71 py-unicycler: new package (#7727) 2019-02-25 09:44:05 +01:00
Denis Davydov
2851b3f57c dealii: fix default of cuda_arch (#10690) 2019-02-24 08:53:13 +01:00
Adam J. Stewart
b43e8fcaa7
Python: optional dependencies and post-installation tests (#10335)
* Add post-installation tests to Python package

* libbsd does not build on macOS

* Make Python dependencies optional

* Add readline dep, remove ncurses patch, fix autoreconf
2019-02-23 12:36:26 -06:00
Justin Stanley
68af6148d1 beast-tracer: new package at 1.7.1 (#10652) 2019-02-22 19:22:30 -06:00
Levi Baber
0e7b19adf4 stacks package: add version 2.3b (#10653) 2019-02-22 19:16:44 -06:00
Brian Spilner
ba70d6e706 cdo package: add version 1.9.6 (#10654) 2019-02-22 18:38:35 -06:00
Geoffrey Oxberry
219c17a340 automake package: add version 1.13.4 (#10662)
Also replace MD5 hashes with SHA256 hashes for older versions
2019-02-22 18:38:00 -06:00
Eric Martin
49f56cb49c gmap-gsnap package: Add version 2019-02-15 (#10677) 2019-02-22 18:36:40 -06:00
Axel Huebl
7bd960ba86 ADIOS package: add version 2.3.1 (#10666)
Update older md5 checksums to sha256. Require CMake >= 3.6.0 (updated
from 3.5.0). Remove some third-party depends_on statements (which
were commented out before).
2019-02-22 18:36:04 -06:00
Hadrien G
510a28d156 Gaudi package: new version + xenv bugfix (#10668)
Extract implicit xenv dependency into a new package and add it as an
explicit dependency. Update Gaudi to explicitly depend on older
versions of xenv rather than the latest develop because that
conflicts with Spack's compiler wrappers.
2019-02-21 19:04:03 -06:00
cedricchevalier19
3b10e450d2 mono package: add new versions (#10670) 2019-02-21 18:52:30 -06:00
Daniel Topa
e230b0a00f UCX package: add version 1.5.0 (#10678) 2019-02-21 18:22:32 -06:00
Peter Scheibel
98f1c9a291
CPATH warning: downgrade to debug message (#10675)
Spack warns users when a dependency package updates CPATH. This
warning message is generating bug reports and alarm in cases where
there is no problem. For now this downgrades the warning message to
the debug level, so it only shows up if something goes wrong for the
user and they ask for more information from Spack.
2019-02-21 17:26:38 -06:00
Daryl W. Grunau
4f5be841d4 gcc package: skip nvptx_install for gcc~nvptx (#10672)
The nvptx installation support phase (added in 040b658) was always
running for gcc regardless of whether +nvptx was enabled. This
removes the "@when" syntax (which apparently is not working) and
adds a check inside of the "nvptx_install" function to bail out if
+nvptx is not enabled.
2019-02-21 15:43:29 -06:00
Scott Wittenburg
5600c9f0d9 release workflow: Add build scripts for jobs and means to upload pkgs 2019-02-21 15:37:35 -06:00
Scott Wittenburg
a6e8e889b2 release workflow: Add spack command for generating the .gitlab-ci.yml
This spack command adds a new schema for a file which describes the
builder containers available, along with the compilers availabe on
each builder.  The release-jobs command then generates the .gitlab-ci.yml
file by first expanding the release spec set, concretizing each spec
(in an appropriate docker container if --this-machine-only argument is
not provided on command line), and then combining and staging all the
concrete specs as jobs to be run by gitlab.
2019-02-21 15:37:35 -06:00
Scott Wittenburg
05cdb5a0bb docker: Add Dockerfiles for images needed by AWS gitlab-runners
The built images are set up with fairly recent versions of gcc and
clang:

  - centos_7:     [ gcc@5.5.0 (built from src), clang@6.0.0 (spack-built from src) ]
  - ubuntu_18.04: [ gcc@5.5.0 (system), clang@6.0.0-1ubuntu2 (system) ]
2019-02-21 15:37:35 -06:00
Scott Wittenburg
fce1c4133f buildcache: Add sub-commands needed by release workflow
Adds four new sub-commands to the buildcache command:

1. save-yaml: Takes a root spec and a list of dependent spec names,
along with a directory in which to save yaml files, and writes out
the full spec.yaml for each of the dependent specs.  This only needs
to concretize the root spec once, then indexes it with the names of
the dependent specs.

2. check: Checks a spec (via either an abstract spec or via a full
spec.yaml) against remote mirror to see if it needs to be rebuilt.
Comparies full_hash stored on remote mirror with full_hash computed
locally to determine whether spec needs to be rebuilt.  Can also
generate list of specs to check against remote mirror by expanding
the set of release specs expressed in etc/spack/defaults/release.yaml.

3. get-buildcache-name: Makes it possible to attempt to read directly
the spec.yaml file on a remote or local mirror by providing the path
where the file should live based on concretizing the spec.

4. download: Downloads all buildcache files associated with a spec
on a remote mirror, including any .spack, .spec, and .cdashid files
that might exist.  Puts the files into the local path provided on
the command line, and organizes them in the same hierarchy found on
the remote mirror

This commit also refactors lib/spack/spack/util/web.py to expose
functionality allowing other modules to read data from a url.
2019-02-21 15:37:35 -06:00
Todd Gamblin
be4b95ee30 add CombinatorialSpecSet class for taking cross-products of Specs.
- add CombinatorialSpecSet in spack.util.spec_set module.
  - class is iterable and encaspulated YAML parsing and validation.

- Adjust YAML format to be more generic
  - YAML spec-set format now has a `matrix` section, which can contain
    multiple lists of specs, generated different ways. Including:
    - specs: a raw list of specs.
    - packages: a list of package names and versions
    - compilers: a list of compiler names and versions

  - All of the elements of `matrix` are dimensions for the build matrix;
    we take the cartesian product of these lists of specs to generate a
    build matrix.  This means we can add things like [^mpich, ^openmpi]
    to get builds with different MPI versions.  It also means we can
    multiply the build matrix out with lots of different parameters.

- Add a schema format for spec-sets
2019-02-21 15:37:35 -06:00
Jordan Ogas
ad8036e5a2 add charliecloud 0.9.7 (#10661) 2019-02-21 09:58:37 +01:00
Levi Baber
040b65876b gcc: add nvptx offload capability (#9406)
Add optional support for Nvidia PTX
2019-02-20 20:52:15 -06:00
Adam J. Stewart
af8d84197d
Download GNU packages from mirrors (Part 2) (#10555) 2019-02-20 09:08:42 -06:00
Massimiliano Culpo
0a252eccc4
uvw: new package (#10645) 2019-02-20 13:53:07 +01:00
Ben Morgan
fb6a2b5cab xxhash: edit prefix in Makefile for macOS (#10606)
On macOS, the build of libxxhash is performed by a bare `make`
launched by `MakePackage`s default `build` phase. As `prefix`
is not set at this point, the library gets compiled with a hard-coded
install name of `/usr/local/libxxhash.dylib`. Downstream clients,
in the tested case Root, will then fail to build as the install name
is incorrect.

Move setting of `prefix` from `install` to `edit` so that it
propagates to subsequent `build` and `install` phases.
2019-02-20 10:55:09 +01:00
Isaac Whitfield
286da7f47b new package: libyaml (#10634) 2019-02-19 12:45:31 -06:00