Commit graph

12820 commits

Author SHA1 Message Date
Greg Sjaardema
d580d2a033 seacas: Update NetCDF version requirement (#10787)
Modified NetCDF requirement to allow NetCDF-4.6.2 and subsequent versions.
2019-03-05 14:05:52 +01:00
Justin Stanley
f19a214a19 libbeagle: add 3.1.2 (#10789) 2019-03-05 14:02:52 +01:00
Peter Scheibel
af4a36c4d9
Header subdirectories for Python and Eigen (#10773)
Fixes #10769 

This updates the .headers property to include header subdirectories
for Python and Eigen (as is recommended by these packages).

#10623 updated the default behavior of .headers.directories to
exclude subdirectories (since this can cause clashes with system
headers). This broke some packages which depended on the old behavior
of .headers.directories: for example if you had
<package-prefix>/include/subdir/ex1.h, .headers.directories would
include <package-prefix>/include/subdir.
2019-03-04 12:36:51 -06:00
Brian Van Essen
0ce1500376 Package Updates for ECP CANDLE Supervisor (#10760)
* Add EQ-R package
* Add Fansi, Pillar, UTF8 (R) packages
* Add new versions for py-mdanalysis, r-cli, r-dplyr, r-pkgconfig,
  r-rlang, r-tibble, stc, and turbine packages
* Add hdf5 support for turbine
* Specify configure directory for stc package
2019-03-01 14:46:13 -06:00
Justin Stanley
c8557ba7d8 blast2go: new package at 5.2.5 (#10725)
* blast2go: new package at 5.2.5

* blast2go: remove redundant url
2019-03-01 12:36:00 -06:00
Matthias Diener
ee5e5ce3c6 new package: intel-pin (#10546) 2019-03-01 12:29:01 -06:00
Justin Stanley
1a8161a982 r-bfastspatial: new package at 0.6.2 (#10734) 2019-03-01 10:18:14 -06:00
Justin Stanley
cbc6a2070a r-bfast: new package at 1.5.7 (#10733) 2019-03-01 10:17:37 -06:00
Justin Stanley
94357a274c bedops: avoid static linking with glibc (#10456) 2019-03-01 10:17:01 -06:00
Justin Stanley
165d8da0c2 blast-legacy: new package at 2.2.26 (#10610)
* blast-legacy: new package at 2.2.26

* blast-legacy: compile from source

* blast-legacy: add missing os.symlink import

* blast-legacy: fix build script interpreter
2019-03-01 10:14:37 -06:00
Justin Stanley
f9947333ca bridger: new package at 2014-12-01 (#10611) 2019-03-01 10:09:23 -06:00
Justin Stanley
c4aba6a204 r-spatial: new package at 7.3-11 (#10728) 2019-03-01 09:57:59 -06:00
Justin Stanley
16af5f31d9 r-nortest: new package at 1.0-4 (#10729) 2019-03-01 09:55:30 -06:00
Justin Stanley
4f1044a072 r-xts: add 0.11-2 (#10730) 2019-03-01 09:54:26 -06:00
Justin Stanley
104a8a1422 r-gdalutils: new package at 2.0.1.14 (#10731) 2019-03-01 09:53:30 -06:00
Justin Stanley
0766e7fbbb r-rgdal: add 1.3-9 (#10732) 2019-03-01 09:52:07 -06:00
Justin Stanley
89f59f7ab0 hyphy: new package at 2.3.14 (#10759) 2019-03-01 09:31:46 -06:00
Patrick Gartung
1d4289afdd
This fixes a problem where the placeholder path was not in the first rpath entry.
* Rework of buildcache creation and install prefix checking using the functions introduced in
https://github.com/spack/spack/pull/9199

Instead of replacing rpaths with placeholder and then checking strings, make use of the functions
relocate.is_recocatable and relocate.is_file_relocatable to decide if a package needs the allow-root option.

This fixes a problem where the placeholder path was not in the first rpath entry. This was seen in c++ libraries and binaries because the compiler was outside the spack install base path and always appears first in the rpath.

Instead of checking the first rpath entry, all rpaths have the placeholder path and the old install path (if it exists) replaced with the new install path.

* flake8
2019-03-01 07:47:26 -06:00
Jiawei Zhuang
433cc4a972 Fix sha256 sum for IOR (#10765) 2019-03-01 09:59:36 +01:00
Massimiliano Culpo
e3af8ed454 Added a sub-command to show if packages are relocatable (#9199)
* Added the `spack buildcache preview` sub-command

This is similar to `spack spec -I` but highlights which nodes in a DAG
are relocatable and which are not.

spec.tree has been generalized a little to accept a status function,
instead of always showing the install status

The current implementation works only for ELF, and needs to be
generalized to other platforms.

* Added a test to check if an executable is relocatable or not

This test requires a few commands to be present in the environment.
Currently it will run only under python 3.7 (which uses Xenial instead
of Trusty).

* Added tests for the 'buildcache preview' command.

* Fixed codebase after rebase

* Fixed the list of apt addons for Python 3.7 in travis.yaml

* Only check ELF executables and shared libraries. Skip checking virtual or external packages. (#229)

* Fixed flake8 issues

* Add handling for macOS mach binaries (#231)
2019-02-28 15:36:47 -06:00
Sajid Ali
6d20e938da petsc: add +knl variant 2019-02-28 11:07:04 -06:00
Satish Balay
f8da8dbd0e
Trilinos: add release 12.14.1 (#10740)
xsdk: switch from 12.14.0-rc1 to 12.14.1
2019-02-28 11:05:05 -06:00
Michael Kuhn
617c1a3706 Fix shell integration with environment-modules@4 (#10736) 2019-02-28 13:22:44 +01:00
Eric Martin
4e80977506 py-tetoolkit: Add version 2.0.3 (#10749) 2019-02-28 12:59:30 +01:00
Owen Solberg
fac2dbda07 git-lfs: patch Makefile for v2.7.0 (#10720)
Fixes #10702

Same fix merged upstream in git-lfs/git-lfs#3545 -- it may appear
in future release v2.7.2 according to package maintainer.
2019-02-27 16:02:25 -06:00
Adam J. Stewart
a25edb51a9 Fix 'make test' detection when LANG is not in English (#10499) 2019-02-27 14:01:50 -06:00
Justin Stanley
2f4f828b45 wtdbg2: new package (#10639)
* wtdbg2: new package at 2.3

* wtdbg2: flake8 fix
2019-02-27 13:27:45 -06:00
Michael Kuhn
b1a04b7699 mpich: Improve package (#10643)
- Add missing pkg-config, libpciaccess and libxml2 dependencies
- Add slurm variant for nodelist parsing
- Add missing configure flag for libfabric
- Unset F90 and F90FLAGS
- Allow selecting different PMI interfaces
2019-02-27 13:13:44 -06:00
Paschalis Korosoglou
ab499a958d otf2 package: fix download URL (#10735) 2019-02-27 12:47:56 -06:00
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