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2019-03-01r-spatial: new package at 7.3-11 (#10728)Justin Stanley1-0/+19
2019-03-01r-nortest: new package at 1.0-4 (#10729)Justin Stanley1-0/+18
2019-03-01r-xts: add 0.11-2 (#10730)Justin Stanley1-1/+2
2019-03-01r-gdalutils: new package at 2.0.1.14 (#10731)Justin Stanley1-0/+23
2019-03-01r-rgdal: add 1.3-9 (#10732)Justin Stanley1-1/+2
2019-03-01hyphy: new package at 2.3.14 (#10759)Justin Stanley1-0/+20
2019-03-01This fixes a problem where the placeholder path was not in the first rpath ↵Patrick Gartung3-105/+76
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
2019-03-01Fix sha256 sum for IOR (#10765)Jiawei Zhuang1-1/+1
2019-02-28Added a sub-command to show if packages are relocatable (#9199)Massimiliano Culpo11-25/+327
* 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)
2019-02-28petsc: add +knl variantSajid Ali1-1/+5
2019-02-28Trilinos: add release 12.14.1 (#10740)Satish Balay2-3/+3
xsdk: switch from 12.14.0-rc1 to 12.14.1
2019-02-28Fix shell integration with environment-modules@4 (#10736)Michael Kuhn2-5/+11
2019-02-28py-tetoolkit: Add version 2.0.3 (#10749)Eric Martin1-1/+3
2019-02-27git-lfs: patch Makefile for v2.7.0 (#10720)Owen Solberg2-0/+14
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.
2019-02-27Fix 'make test' detection when LANG is not in English (#10499)Adam J. Stewart1-1/+5
2019-02-27wtdbg2: new package (#10639)Justin Stanley1-0/+20
* wtdbg2: new package at 2.3 * wtdbg2: flake8 fix
2019-02-27mpich: Improve package (#10643)Michael Kuhn1-2/+39
- 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
2019-02-27otf2 package: fix download URL (#10735)Paschalis Korosoglou1-1/+1
2019-02-27Add newer versions for 51 Python packages (#10738)Gregory Lee51-4/+53
2019-02-27Update environment-modules package (#10717)Massimiliano Culpo2-32/+60
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.
2019-02-26new package: libusb (#10682)Isaac Whitfield1-0/+35
2019-02-26new package: libtasn1 (#10681)Isaac Whitfield1-0/+33
2019-02-26QMCPACK package: cuda/hdf5 fixes (#10701)Nichols A. Romero1-4/+8
* 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
2019-02-26petsc: add version 3.10.4 (#10724)Satish Balay1-0/+1
2019-02-26new package: phred (#10700)Justin Stanley1-0/+21
Part of the software collection introduced in #10529. Developers must be contacted via email to receive the source code.
2019-02-26new package: libplist (#10680)Isaac Whitfield1-0/+44
Dependency of Google's Flutter toolchain.
2019-02-26libbeagle package: add cuda support (#10650)Justin Stanley1-1/+28
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)
2019-02-26vampirtrace: patch for new mpich and openmpi versions (#10665)Michael Kuhn2-0/+32
2019-02-26new package: routino (#10679)Phil Tooley1-0/+24
2019-02-26Don't try to build TARGET=PILEDRIVER on aarch64Janne Blomqvist1-1/+0
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.
2019-02-26kealib package: add version 1.4.11 (#10706)Neil Flood1-0/+1
2019-02-26eospac package: add version 6.4.0 (#10718)Daryl W. Grunau1-0/+2
2019-02-26beast2 package: add version 2.5.2 (#10723)Justin Stanley1-0/+1
2019-02-26Quantum ESPRESSO package: Serial HDF5 Bug Fix (#10689)Nichols A. Romero1-3/+9
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.
2019-02-26Use Package.headers for -I options (#10623)Massimiliano Culpo7-29/+174
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).
2019-02-26r-vfs: new package at 1.0.2 (#10697)Justin Stanley1-0/+23
2019-02-26r-nleqslv: new package at 3.3.2 (#10696)Justin Stanley1-0/+16
2019-02-26Add libhio v1.4.1.3, 1.4.1.1 (#10699)Daniel Topa2-3/+5
- 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>
2019-02-25Add /hash to spack help --spec (#10691)Adam J. Stewart1-1/+5
* Add /hash to spack help --spec * Make /hash gray, add ^/hash
2019-02-25libEnsemble package: add v0.4.1 (#10688)Stephen Hudson1-2/+4
Also add v0.4.0 and remove version lower bound on petsc4py
2019-02-25slurm: Add PMI support (#10683)Michael Kuhn1-0/+11
- Add support for pmix (optional) - Install pmi2 header and library
2019-02-25mpiFileUtils v0.9 (#10676)Elsa Gonsiorowski, PhD1-5/+65
* working on updating to cmake * generic package, any ver of cmake * install for autotools or cmake
2019-02-25ACTS: new package (#10600)Hadrien G1-0/+81
2019-02-25py-unicycler: new package (#7727)Sinan1-0/+35
2019-02-24dealii: fix default of cuda_arch (#10690)Denis Davydov1-1/+1
2019-02-23Python: optional dependencies and post-installation tests (#10335)Adam J. Stewart15-88/+336
* 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
2019-02-22beast-tracer: new package at 1.7.1 (#10652)Justin Stanley2-0/+32
2019-02-22stacks package: add version 2.3b (#10653)Levi Baber1-0/+3
2019-02-22cdo package: add version 1.9.6 (#10654)Brian Spilner1-0/+1
2019-02-22automake package: add version 1.13.4 (#10662)Geoffrey Oxberry1-5/+6
Also replace MD5 hashes with SHA256 hashes for older versions