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2017-06-14Adding package namd (#4321)Nicolas Richart3-11/+183
* Initial version of the namd package * Modified charm to consider compile against intel/intel-mpi * Correction of namd to compile with intel-mkl and intel compiler * Adding inclue64 in the prefix * adding property for the build directory * removing useless function build
2017-06-14Updates rose definition (#4411)Josh Asplund4-16/+151
* Adds z3 package * Adds binwalk package * Updates spot package definition * Updates rose package definition * Modifications for code review * Fixes string formatting * Remove python version requirement
2017-06-14Added new package for py-rsa (#4494)Adam J. Stewart1-0/+39
2017-06-14superlu-dist: don't use '_' symbols from BLAS for IBM XL compiler (#4486)serbanmaerean1-1/+3
2017-06-13ipopt 3.12.7 (#4490)Geoffrey Oxberry1-0/+20
* ipopt: update version to 3.12.7 * ipopt: add +coinhsl option * ipopt: add +metis option
2017-06-13coinhsl 2014.01.17: new package (#4482)Geoffrey Oxberry1-0/+47
2017-06-13metis: bugfix: make shared library build portable (#4489)Geoffrey Oxberry1-1/+2
Fixes #4488. When compiling metis as a shared library, the package used the syntax `-rpath=`, followed by a path. This syntax is non-portable, so replace it using Spack's compiler rpath argument property.
2017-06-13visit: Added VisIt version 2.12.2 (#4495)John Roberts1-0/+1
2017-06-13Override partial installs by default - part three (#4331)scheibelp1-0/+43
* During install, remove prior unfinished installs If a user performs an installation which fails, in some cases the install prefix is still present, and the stage path may also be present. With this commit, unless the user specifies '--keep-prefix', installs are guaranteed to begin with a clean slate. The database is used to decide whether an install finished, since a database record is not added until the end of the install process. * test updates * repair_partial uses keep_prefix and keep_stage * use of mock stage object to ensure that stage is destroyed when it should be destroyed (and otherwise not) * add --restage option to 'install' command; when this option is not set, the default is to reuse a stage if it is found.
2017-06-13espresso: fixed compilation for 6.1 (elpa) and added support for hdf5 (#4483)Massimiliano Culpo3-43/+113
* espresso: fixed compilation for 6.1 (elpa) and added support for hdf5 * espresso: addressed items in @davydden review * espresso: fixed behavior for espresso@:5.4.0
2017-06-13Fix/mumps (#4453)serbanmaerean3-3/+84
* Added magma package * Incorporated Serban's change * mumps: Fix compiler error with IBM XL Split the patching between v 5.0.2 and 5.1.1
2017-06-13Fix building shared libraries for gmp (#4464)Michael Kuhn1-0/+7
If specific compiler flags are set, gmp will not build a shared library, causing failures further down the line.
2017-06-13czmq: Fix invocation when building with clang. (#4479)Diana Bite1-3/+10
Also bump to latest stable version.
2017-06-12Add list_url for packages from http://ab-initio.mit.edu/ (#4471)Adam J. Stewart3-34/+25
2017-06-12Add an installcheck phase to MakefilePackage (#4476)Adam J. Stewart1-17/+9
* Add an installcheck phase to MakefilePackage * Minor changes to ESMF
2017-06-12ISAAC Server: Less Strict Deps (#4481)Axel Huebl1-2/+4
The dependencies of the server packages were overly strict and pulled in too many dependencies. This fixes it.
2017-06-11New Package: bml (#4213)Robert Pavel1-0/+49
* New Package: lanl-bml Added LANL's BML library as Spack Package as dependency for future packages * Adjusted lanl-bml versions Specified current master as develop and added v1.1.0 tagged version * Renamed lanlbml package to bml
2017-06-11Convert elk to MakefilePackage (#4477)Adam J. Stewart1-12/+5
2017-06-10gcc: use isl@0.14 for gcc@5 (#4474)Milton Woods1-1/+2
2017-06-09Add default list_url for GitLab, BitBucket, and CRAN (#4439)Adam J. Stewart236-241/+4
* Add default list_url for GitLab, BitBucket, and CRAN * Fix flake and doc tests
2017-06-09scala + spark: added legacy versions (#82) (#4461)Massimiliano Culpo2-3/+7
2017-06-09Fix autotools issues (#4463)Michael Kuhn2-0/+6
Add ACLOCAL_PATH to libtool and pkg-config. Without this, aclocal can not find the .m4 files.
2017-06-09add teuchos to Trilinos, update dealii to explicitly require certain ↵Denis Davydov2-8/+11
packages (#4460)
2017-06-08Package for mono (#4435)George Hartzell1-0/+65
* First draft package for mono Mono's vendor'ed boringssl interacts badly with openssl, so you need to use `cmake~openssl`. Left to its own devices, it wants to refer to things in `/usr/share/.mono`. This doesn't work for installs that don't run as root, etc... This package includes a variant to redirect those paths to `prefix.share`. * Whitespace/Flake8
2017-06-08Adding Nalu package. (#4428)Jon Rood4-109/+315
* Adding Nalu package. * Fixing flake8 stuff. * Fixing flake8 stuff. * Reorganizing trilinos package file a little to make it less verbose. * Reorganizing trilinos package file for more general use as well as use as a dependency of the Nalu package. Setting fpic as default for yaml-cpp and superlu. * Explicitly stating fpic variants in dependent packages. * Updating nalu and trilinos package files with suggested changes. * Fixing formatting issues. Making suggested changes. * Fixing formatting. * Reducing amount of explicit variants in Nalu. Adding suggested changes to Trilinos package file. * Making suggested changes to Nalu package. * Turning off superlu-dist variant. * Cleaning up yaml-cpp file. * Fixing pnetcdf requirements in trilinos.
2017-06-08fix mfem build for ppc with gcc (#4452)Gregory Lee2-0/+12
2017-06-07Open MPI: add 2.0.3 (#4450)Howard Pritchard1-0/+1
Add Open MPI bug fix release 2.0.3 Signed-off-by: Howard Pritchard <howardp@lanl.gov>
2017-06-07folly: added new package. Also modified double-conversion to use 'pic'. (#4449)Massimiliano Culpo2-0/+63
2017-06-07Bug/cctools syscall (#4440)George Hartzell1-0/+12
* Handle missing defn of __NR_memfd_create Generally SYS_foo is defined to __NR_foo (in sys/syscall.h) which is then defined to a syscall number (in asm/unistd_64.h). Certain CentOS systems have SYS_memfd_create defined to __NR_memfd_create but are missing the second definition. This is a belt and suspenders solution to the problem. See [this post][syscall] for a nice general description of how these parts fit together. [syscall]: https://www.uninformativ.de/blog/postings/2017-02-11/0/POSTING-en.html * Avoid flake8 warning
2017-06-07Added latest version of image-magick 7.0.5-9 (#4447)Stas Sergienko1-0/+1
2017-06-07postgresql: Fix build with threadsafe and add variant. (#4403)Diana Bite1-6/+11
* postgresql: Fix build with threadsafe and add variant. * postgresql: Convert Package to AutotoolsPackage. Also add explicit enable flag for +threadsafe variant.
2017-06-06Fix intel-mpi installation (#4438)Michael Kuhn1-0/+2
2017-06-06Add add'l output formats for graphviz (#4431)George Hartzell2-0/+23
* Add add'l output formats for graphviz Add support for additional output formats to graphviz, including gif, jpg, pdf, and png. Graphviz calls its pango+cairo option *pangocairo* so I followed suit. Libgd was missing jpeg/jpg support. None of the other supported formats are conditionalized and there is no --with/--without support, so I followed suit. * Fix ghostscript plugin When I installed thusly: spack install graphviz+pangocairo+libgd^cairo+X^pango+X the ghostscript plugin tripped over some variable names that had changes in `gs@9.18:`. This fixes them. * Remove wayward import of tty
2017-06-06ncl: cairo and math libraries (#4434)Milton Woods1-2/+2
* ncl: depends on cairo+X (cairo~X is built by default) * ncl: '-lm' is needed when linking fortran with gcc
2017-06-06Update bazel to 0.4.5 (#4436)Michael Kuhn1-3/+11
2017-06-05Need to help Makefile.PL find the expat bits (#4422)George Hartzell1-0/+10
* Need to help Makefile.PL find the expat bits We need to provide Makefile.PL with a clue about where our expat bits live. We had the dependency, but I suspect that the lib was actually linking against a system version. * Use prefix.lib instead of building path myself Ditto with .include
2017-06-05Disable parallel builds for bamutil (#4430)George Hartzell1-0/+2
I've had non-repeatable failures in my CI runs on all three clusters at the bamutil's step. In each case there are .o or .so files that are corrupt or truncated. I suspect that the homebrewed bamutil Makefile scheme doesn't actually support parallel builds.
2017-06-05Tighten up graphviz package (explicitly disable unused languages, etc...) ↵George Hartzell1-19/+30
(#4408) * Tighten up graphviz package The fun started when configure discovered a broken/partial installation of `swig` in `/usr/local`, then auto-discovered my system's python and ruby packages. - SpackException doesn't seem to exist. Convert it to a SpackError and call `.format(...)` on the error string to fill in the placeholder. - Pull swig out of the list of languages. It's something that can be asked for explicitly and that is needed if *any* of the langagues are enabled. It's disabled by default. - Explicitly disable the languages that are in "untested_bindings" list lest the configure script pick up things from the system. * Touch up variant description string * Clean up conditional statement * Use InstallError, not SpackError * Drop the swig variant Get rid of the swig variant and drive that bit based on whether any languages are enabled. * Move perl to the untested list That's not strictly accurate. I tested it and it doesn't work. There's a missing depends_on(). When you add that you'll discover that the language binding bit can't find Perl's 'EXTERN.h'. Then you'll discover that graphviz's `configure` script doesn't have a good way to include the paths to Perl's bits (looks like I'll have to gather them for each language and then use them to build `CFLAGS` and `CXXFLAGS` and `LDFLAGS`). While pondering that, you'll discover that EXTERN.h is buried down here: ``` opt/spack/linux-centos7-x86_64/gcc-4.8.5/perl-5.24.1-35ejv4426dmzreum4ekdibu3ddmhquvi/lib/5.24.1/x86_64-linux/CORE/EXTERN.h ``` and decide that you wish you had never thought to actually test `graphviz+perl`. I could find that directory with a snippet like so: ``` perl -MConfig -e 'print "$Config{archlib}\n"' ``` but at this point I'm much, much further down this rabbit hole then I ever wanted to go. * Convince python that tested_bindings is a list When I removed `+perl` and made `tested_bindings` a list of one thing, I ended up with this: ``` ==> Error: cannot concatenate 'str' and 'tuple' objects ``` * Flake8 cleanup * Don't convert a string to a string * rm unused () and clarify variable name Feedback from @adamjstewart - Get rid of some unnecessary parens. - Clearer variable name and use. * Further cleanup of language enabling loop Now we don't need that pesky temporary variable.
2017-06-05Add package for cctools (#4417)George Hartzell1-0/+55
* Add package for cctools Add a package for cctools. Requires the recently submitted "useshrplib" support in Perl (or some other mechanism to enable -fPIC for perl). * Delete extraneous import * Perl's shared variant changed, adapt... The name of the variant that perl uses to build a shared lib changed and it now defaults to True. Use the new name and continue to be insistent about using the shared variant. * Flake8 cleanup
2017-06-02Bugfix/boost pgi (#4426)serbanmaerean3-1/+546
* Added magma package * Incorporated Serban's change * boost-pgi: Add support for PGI compiler There are two patches required: (1) general fixes required by PGI (2) workaround for a bug in PGI 17.4 Conflicts: var/spack/repos/builtin/packages/boost/package.py
2017-06-02Add variant to build shared Perl lib (#4416)George Hartzell1-2/+9
* Add variant to build shared Perl lib Add a variant that enables Perl's "useshrplib" feature, which builds a shared perl library. This addresses problems like so: ``` /usr/bin/ld: /blah/blah/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/perl-5.24.1-y43dp3p5w66v7qh5xkwgufxohyuodyew/lib/5.24.1/x86_64-linux/CORE/libperl.a(op.o): relocation R_X86_64_32S against `PL_opargs' can not be used when making a shared object; recompile with -fPIC /blah/blah/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/perl-5.24.1-y43dp3p5w66v7qh5xkwgufxohyuodyew/lib/5.24.1/x86_64-linux/CORE/libperl.a: could not read symbols: Bad value ``` It should also address the Intel compiler issue discussed in #3081 while respecting Perl's configuration machinery. * Rename shared variant and default to True * Use correct variant to add configure arg * Restore bits that set ccflags for intel compilers After some experimentation we've established that setting the flag to build a shared perl library is tightly tied to the use of -fPIC. This commit restores the code that sets ccflags for intel compilers. * Flake8 cleanup
2017-06-02Add latest version of gnuplot (#4418)Adam J. Stewart1-1/+2
2017-06-02astyle: add new versions (#4424)Denis Davydov1-1/+3
2017-06-01Add a package for Picard (#4398)George Hartzell2-0/+78
See the discussion about installing jar files in #4386. Also installs a wrapper script that has explicit references to the prerequisite java exe and to the jar file in it's final resting place.
2017-06-01Add packages for clustalw and clustalo (and argtable) (#4412)George Hartzell3-0/+106
* Add packages for clustalw and clustalo (and argtable) Add packages for the classic multiple alignment package, `clustalw` and its younger sibling, `clustalo`. `clustalo` needed the `argtable` package (command line arg parsing). Lightly tested on CentOS 7. * Remove FIXME (sigh...)
2017-06-01Packages/r factoextra (#4410)Tom Merrick17-0/+680
* Add mpi support to R * Add multiple precision math routines to R * Updated the URL to match the version * Remove duplicate packages * Add packages for r-ergm and it's dependents * Fixed depends-on types * Correct flake8 errors * Correct Build type * r-factoextra and dependents * Revert "r-factoextra and dependents" This reverts commit afbf477fd66e565fd187262c386bcc08c98a4d7e. * Add only r-factoextra files
2017-06-01Add a package for Trimmomatic (#4399)George Hartzell2-0/+68
* Add a package for Trimmomatic See the discussion about installing jar files in #4386. Also installs a wrapper script that has explicit references to the prerequisite java exe and to the jar file in it's final resting place. * Fix bad format statement Apparently something like this "blah{}".format(...) works (it's missing something inside the curly braces) but fails the travis test.
2017-05-31Add Catch v1.7.1-1.9.4 (#4406)Nils Deppe1-0/+10
2017-05-31openssl: Fix build on Aarch64 with clang. (#4404)Diana Bite1-0/+5
2017-05-31Fix Fetch MariaDB (#4394)Axel Huebl1-1/+4
The two given versions of mariadb are not fetchable under the given URL, probably because older versions are purged and only kept in an archive. Add two working, latest revisions of each release line.