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Author SHA1 Message Date
Tom Scogland
ba5a251896 package: add asciidoctor gem (#9905) 
* package: add asciidoctor gem

Faster, easier to use, less impossible to install correctly
implementation of asciidoc.

* ritual sacrifice of EOF whitespace to flake8
 2018-11-20 14:32:44 -06:00
Tiziano Müller
84bc1d6654 CP2K related fixes and update (#9308) 
* openblas: enable parallel builds

* cp2k: enable parallel builds

* cp2k: fix building on multilib/Suse distros

use the actual directory path where files where installed to instead of
the default prefix+'/lib'

* cp2k: ensure we have a non-header-only libxsmm

* openblas: disable max num CPU detection on virtualized build

* cp2k: install data and set compiled-in DATA_DIR

* cp2k: make libxc an optional dependency (enabled by default)

* cp2k: link libint statically

* cp2k: declare statically linked library deps as type=build

* cp2k: add support for PGI compiler

* cp2k: rename smm=none to smm=blas for clarification

* cp2k: blacklist unsupported compilers

* cp2k: mark wannier90 a build-time dep since statically linked

* cp2k: make pexsi and elpa optional

* cp2k: add support for v6.1

* libxc: add version 4.2.3

* cp2k: use pkg-config to link properly to libxsmm

* cp2k: fix OpenMP support by making it explicit

Previously, CP2K accepted threaded ELPA or BLAS, leading to #(CPU) processes
being spawned even though no explicit OpenMP was requested. Now the
`popt` variant should truly be thread free while the `psmp` variant uses
threads also internally.

* cp2k: source tarballs moved to GitHub
 2018-11-20 09:23:01 -08:00
dorier
13b95b8ae6 Package: Mercury (#9903) 
* added mercury package

* updating mercury package to satisfy flake8

* improved mercury package
 2018-11-20 11:14:30 -06:00
Jon Rood
128af27c21 Add 2019.1 and 2018.4 version of the Intel performance libraries. (#9899) 
* Add 2019.1 and 2018.4 version of the Intel performance libraries.

* Fixing typo.
 2018-11-20 09:30:53 -06:00
Adam Moody
5127bb590f mpifileutils: add v0.8.1 (#9346) 2018-11-19 20:48:50 -06:00
Michael Kuhn
44d1d928e8 openssl: make 1.1.1 the default version (#9836) 
* openssl: add 1.0.2p, 1.1.0i and 1.1.1

* openssl: make 1.1.1 the default version
 2018-11-19 20:46:38 -06:00
Justin Stanley
7bb9020227 added several new perl modules (#9760) 2018-11-19 20:44:44 -06:00
Justin Stanley
9dfea8ee17 circos: new package starting at 0.69-6 (#9761) 
* circos: new package starting at 0.69-6

* circos: add homepage, simplify paths

* circos: simplified more paths
 2018-11-19 20:44:01 -06:00
Sinan
0a0e5642df gdk-pixbuf: explicitly disable building of gtk-docs (#9882) 2018-11-19 20:42:56 -06:00
Levi Baber
535035b223 r-rrpp: new package (#9887) 2018-11-19 20:42:45 -06:00
Jon Rood
1972376865 Adding openmpi version 4.0.0 (#9888) 2018-11-19 20:42:34 -06:00
Eric
177c5f3c6d breseq: Add version 0.33.1 (#9889) 2018-11-19 20:42:21 -06:00
Sinan
47a641f13b package/harfbuzz: disable building of gtk-docs, add new version (#9891) 2018-11-19 20:42:08 -06:00
Levi Baber
561a561d23 r-crosstalk: remove unnecessary constraint (#9892) 2018-11-19 20:41:41 -06:00
Levi Baber
71943703f2 r-geomorph: new version (#9890) 
* r-geomorph: new version

* r-geomorph: min r version
 2018-11-19 20:41:19 -06:00
Levi Baber
43a26d0850 r-diversitree: new package (#9893) 
* r-diversitree: new package

* r-diversitree: system reqs
 2018-11-19 20:41:01 -06:00
Levi Baber
7e1f96c0aa r-paleotree: new package (#9895) 2018-11-19 20:39:42 -06:00
Sinan
000bb8ca39 package/pango: disable gtk-docs (#9896) 2018-11-19 20:38:52 -06:00
Sinan
71464a8b0a package/gtkplus: disable gtk-docs (#9897) 2018-11-19 20:38:34 -06:00
Mark C. Miller
a6efd22e60 Explicitly set FC= empty for non-fortran builds (#9898) 2018-11-19 20:38:06 -06:00
Eric
0c1988ffdf Trimmomatic: Add version 0.38 (#9883) 2018-11-19 15:56:49 -06:00
Jon Rood
c8a1a81a87 Adding intel-parallel-studio cluster 2019.1 version (#9884) 2018-11-19 15:56:31 -06:00
Daniel Topa
7402112b1f Add UCX v1.4.0 (#9881) 
Verification build
dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ spack install ucx % gcc @ 4.8.5
==> Installing libsigsegv
==> Installing m4
==> Installing pkgconf
==> Installing ncurses
==> Installing readline
==> Installing gdbm
==> Installing perl
==> Installing autoconf
==> Installing automake
==> Installing libtool
==> Installing numactl
==> Installing zlib
==> Installing openssl
==> Installing diffutils
==> Installing bzip2
==> Installing xz
==> Installing libxml2
==> Installing tar
==> Installing gettext
==> Installing help2man
==> Installing bison
==> Installing flex
==> Installing libnl
==> Installing rdma-core
==> Installing ucx
==> Successfully installed ucx
  Fetch: 1.17s.  Build: 40.59s.  Total: 41.76s.
[+] /scratch/users/dantopa/new-spack/pr.ucx.spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/ucx-1.4.0-ilfonxj2f5my4ur65li3sr7kuvfg3kim

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ spack spec ucx
Input spec
--------------------------------
ucx

Concretized
--------------------------------
ucx@1.4.0%gcc@4.8.5 arch=linux-centos7-x86_64
    ^numactl@2.0.11%gcc@4.8.5 patches=592f30f7f5f757dfc239ad0ffd39a9a048487ad803c26b419e0f96b8cda08c1a arch=linux-centos7-x86_64
        ^autoconf@2.69%gcc@4.8.5 arch=linux-centos7-x86_64
            ^m4@1.4.18%gcc@4.8.5 patches=3877ab548f88597ab2327a2230ee048d2d07ace1062efe81fc92e91b7f39cd00,c0a408fbffb7255fcc75e26bd8edab116fc81d216bfd18b473668b7739a4158e,fc9b61654a3ba1a8d6cd78ce087e7c96366c290bc8d2c299f09828d793b853c8 +sigsegv arch=linux-centos7-x86_64
                ^libsigsegv@2.11%gcc@4.8.5 arch=linux-centos7-x86_64
            ^perl@5.26.2%gcc@4.8.5+cpanm patches=0eac10ed90aeb0459ad8851f88081d439a4e41978e586ec743069e8b059370ac +shared+threads arch=linux-centos7-x86_64
                ^gdbm@1.18.1%gcc@4.8.5 arch=linux-centos7-x86_64
                    ^readline@7.0%gcc@4.8.5 arch=linux-centos7-x86_64
                        ^ncurses@6.1%gcc@4.8.5~symlinks~termlib arch=linux-centos7-x86_64
                            ^pkgconf@1.5.4%gcc@4.8.5 arch=linux-centos7-x86_64
        ^automake@1.16.1%gcc@4.8.5 arch=linux-centos7-x86_64
        ^libtool@2.4.6%gcc@4.8.5 arch=linux-centos7-x86_64
    ^rdma-core@20%gcc@4.8.5 build_type=RelWithDebInfo arch=linux-centos7-x86_64
        ^cmake@3.12.4%gcc@4.8.5~doc+ncurses+openssl+ownlibs patches=dd3a40d4d92f6b2158b87d6fb354c277947c776424aa03f6dc8096cf3135f5d0 ~qt arch=linux-centos7-x86_64
            ^openssl@1.0.2o%gcc@4.8.5+systemcerts arch=linux-centos7-x86_64
                ^zlib@1.2.11%gcc@4.8.5+optimize+pic+shared arch=linux-centos7-x86_64
        ^libnl@3.3.0%gcc@4.8.5 arch=linux-centos7-x86_64
            ^bison@3.0.5%gcc@4.8.5 arch=linux-centos7-x86_64
                ^diffutils@3.6%gcc@4.8.5 arch=linux-centos7-x86_64
                ^help2man@1.47.4%gcc@4.8.5 arch=linux-centos7-x86_64
                    ^gettext@0.19.8.1%gcc@4.8.5+bzip2+curses+git~libunistring+libxml2 patches=9acdb4e73f67c241b5ef32505c9ddf7cf6884ca8ea661692f21dca28483b04b8 +tar+xz arch=linux-centos7-x86_64
                        ^bzip2@1.0.6%gcc@4.8.5+shared arch=linux-centos7-x86_64
                        ^libxml2@2.9.8%gcc@4.8.5~python arch=linux-centos7-x86_64
                            ^xz@5.2.4%gcc@4.8.5 arch=linux-centos7-x86_64
                        ^tar@1.30%gcc@4.8.5 arch=linux-centos7-x86_64
            ^flex@2.6.3%gcc@4.8.5+lex arch=linux-centos7-x86_64

Environment:
dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ echo $HOSTNAME
darwin-fe2.lanl.gov

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ grep -i 'model name' /proc/cpuinfo | sort | uniq
model name      : Intel(R) Xeon(R) CPU E5-2695 v3 @ 2.30GHz

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ lsb_release -d
-bash: lsb_release: command not found

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ uname -a
Linux darwin-fe2.lanl.gov 4.18.8-1.el7.elrepo.x86_64 #1 SMP Sat Sep 15 10:10:09 EDT 2018 x86_64 x86_64 x86_64 GNU/Linux

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ date
Mon Nov 19 10:47:47 MST 2018

dantopa@darwin-fe2.lanl.gov:pr.ucx.spack $ pwd
/scratch/users/dantopa/new-spack/pr.ucx.spack

Signed-off-by: Daniel Topa <dantopa@lanl.gov>
 2018-11-19 13:20:22 -06:00
Andrea Negri
494d48f012 new package: mongo-cxx-driver (#9880) 
* new package: mongo-cxx-driver

* fixed url
 2018-11-19 13:19:19 -06:00
Eric
36b4758a97 samtools: make zlib/bzip2 dependencies unconditional (#9866) 2018-11-19 10:36:48 -08:00
Andrea Negri
9aa9359604 libmongoc: updated versions (#9877) 2018-11-18 20:35:24 -06:00
Alberto Chiusole
c61250e2ef New package: ecFlow, a work flow manager. (#9867) 
* New package: ecFlow, a work flow manager.

* Fix pep8 style issues.
 2018-11-18 10:13:31 -06:00
Sajid Ali
c45080398c Add +x variant to petsc. (#9830) 
* 	modified:   var/spack/repos/builtin/packages/petsc/package.py

* Update package.py

* Update package.py

* Update package.py

* Update package.py
 2018-11-17 21:35:37 -06:00
simo-tuomisto
93879e575d mixcr: Added a new package for MiXCR. (#9864) 
* mixcr: Added a new package for MiXCR.

* mixcr: Fixed spack license string.
 2018-11-17 21:19:04 -06:00
Christoph Junghans
26e51ff170 lammps package: added new versions (#9868) 2018-11-16 14:52:26 -08:00
Sinan
22cd6494be py-cython: add new versions (#9846) 2018-11-16 13:20:34 -08:00
Justin Stanley
9dff444570 new package: r-gensa (starting at 1.1.7) (#9858) 2018-11-16 13:13:48 -08:00
Eric
dc2911208f py-ply: fix download url (#9862) 2018-11-16 13:12:05 -08:00
Eric
61adf39fe1 vt package: add zlib dependency (#9870) 2018-11-16 12:52:15 -08:00
Denis Davydov
abd7b185f7 intel-mkl: fix usage of openmp_libs and tbb_libs (#9863) 
* intel-mkl: fix usage of openmp_libs and tbb_libs
* intel-mkl: remove trailing whitespace from openmp lib
 2018-11-16 10:25:15 -08:00
Levi Baber
0a57f90d75 r-rgl: update url, add new version (#9796) 2018-11-16 15:26:09 +01:00
Michael Kuhn
c645c8e2a6 py-cffi: add missing pkgconfig dependency (#9784) 2018-11-15 19:38:52 +01:00
Michael Kuhn
d4f8bd5b8d py-cryptography: add 2.3.1 (#9785) 
Required for openssl@1.1 compatibility.
 2018-11-15 18:27:29 +01:00
Michael Kuhn
480951c231 krb5: add missing bison dependency for yacc (#9778) 2018-11-15 17:54:51 +01:00
Michael Kuhn
4d426e63f0 globus-toolkit: add missing pkgconfig dependency (#9775) 2018-11-15 17:54:22 +01:00
Justin Stanley
5be2169c9b hybpiper: add 1.3.1 (#9762) 2018-11-15 17:41:56 +01:00
Hadrien G
d7983e2aa4 Fix and update verrou (#9847) 
* Fix verrou-python integration

* Add verrou 2.1.0

* Patch level changed in v2.1.0
 2018-11-15 10:22:13 -06:00
Denis Davydov
32884dbc03 dbcsr: minor fixes due to upstream changes (#9799) 2018-11-15 17:10:50 +01:00
Leonhard Reichenbach
2b64047e07 Updated protobuf and py-protobuf to version 3.6.1 (#9536) 
* Updated protobuf and py-protobuf to version 3.6.1

also updated the download link as the repository has moved

* protobuf: modified conflict
 2018-11-15 16:59:04 +01:00
Adam J. Stewart
2723db9f73
Add GMT, CitcomS, and fstrack packages (#9768) 
* Add initial packages for citcoms and dependencies

* Ignore Pythia imports

* Add py-merlin package

* Add GMT package

* Fixes to get GMT working

* Get hc package building

* Get CitcomS 3.2.0 working

* Add fstrack package

* Fix hash
 2018-11-14 23:30:44 -06:00
Levi Baber
b9c50249cf r-cairo: new package (#9794) 
* r-cairo: new package

* Update var/spack/repos/builtin/packages/r-cairo/package.py

Co-Authored-By: baberlevi <baberlevi@gmail.com>
 2018-11-14 21:44:55 -06:00
dorier
8a41cbf813 Argobots: added @develop version and +valgrind variant (#9664) 
* added develop version in argobots package and added valgrind variant

* made autotools required only for develop version

* corrected style

* Added --disable-valgrind

Added --disable-valgrind to explicitly disable it when +valgrind isn't provided.
 2018-11-14 21:39:35 -06:00
Justin Stanley
12177e41f0 r-phytools: new package at 0.6-60 (#9766) 
* r-phytools: new package at 0.6-60

* r-phytools: add list_url

* r-phytools: add deps, dep versions
 2018-11-14 21:39:05 -06:00
Geoffrey Oxberry
605dc8bf85 openblas: add headers property (#9831) 
This commit adds only the public headers from the full list of headers
installed by OpenBLAS; this list of headers is the same as in
netlib-lapack.
 2018-11-14 21:35:42 -06:00
Mark W. Krentel
b53eb2026a elfutils: add version 0.174. (#9812) 
Pass cflags to configure so that configure gets the values from the
spack install line.

Disable -Werror so that we don't fail the build over a stray warning.
 2018-11-14 19:05:08 -06:00