Commit graph

3979 commits

Author SHA1 Message Date
Jim Galarowicz
5173a8bef9 Spack updates to three Krell packages (#4765)
* Update the krell institute products to use the latest features of spack for building on cluster platforms.

* Address travis error messages and resubmit the pull request.

* Update the contents of openspeedshop package.py so it passes the flake8 tests.

* Fix flake8 error-whitespack issue in mrnet package.py file.

* Add updates based on spack reviewer feedback.

* More fixes based on comments from reviewers.  Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.

* More review related changes.  Update MPIOption.append lines and take out xercesc references.

* Create a base options function for common openspeedshop base cmake options to reduce redundencies.

* Add libxml2+python depends on to get around issues with the libxml2 package file.

* Using boost over 1.60.0 causes compile errors.  This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.

* Fix bad syntax in specifying the boost version range.

* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.

* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.

* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.

* Trim comments to fit more concisely.

* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.

* Fix issues with the cbtf-argonavis build, update to use dyninst-9.3.2, fixes to openspeedshop package build.

* Fix issues with the cbtf-argonavis package.py files related to comments.

* Add changes for changing the krell packages from Package to CMakePackage.

* Add better changes for changing the krell packages from Package to CMakePackage.

* Add more modifications for changing the krell packages from Package to CMakePackage.

* Add additional modifications for changing the krell packages from Package to CMakePackage and fixing Travis erros

* Fix new travis errors.

* Fix new travis errors.

* Add more changes for PR 4765.

* Add more refinements to the conversion from Package to CMakePackage.

* Fix new travis errors.

* Add dependencies for MPI to be passed to cbtf-krell, so it can build the MPI collectors requested by the builder of openspeedshop.

* Remove extra unnecessary routine to adjust build arguments. Fix if-else clause issue.

* Fix more flake issues caused by last changes.
2017-07-20 13:25:57 -05:00
Audrey Thoma
5f0e1514ac kentutils: new pacakge (#4831) 2017-07-20 13:16:32 -05:00
jiseung
16fbd0fc41 new package:SNAP (#4826) 2017-07-20 13:15:43 -05:00
becker33
f962aba6ce Allow packages to control handling of compiler flags (#4421)
* Initial work on flag trapping using functions called <flag>_handler and default_flag_handler

* Update packages so they do not obliterate flags

* Added append to EnvironmentModifications class

* changed EnvironmentModifications to have append_flags method

* changed flag_val to be a tuple

* Increased test coverage

* added documentation of flag handling
2017-07-19 20:12:00 -07:00
George Hartzell
acca75b368 Add info for zsh@5.3.1 (#4827) 2017-07-19 21:49:15 -05:00
pkondamudi
9df9a809a8 Add MPI support and tags to embs package (#4824) 2017-07-19 19:04:48 -05:00
pkondamudi
bdcd63ed70 Add tags to nekbone package (#4825) 2017-07-19 19:03:53 -05:00
jiseung
9ae36849af new package: cns-nospec (#4806)
* new package: cns-nospec

* made changes as suggested and added proxy-app tag

* updated edit()

* adjusted logic for '+debug'
2017-07-19 17:05:19 -05:00
jiseung
301b457de3 new package: amr-exp-parabolic (#4821)
* new package: amr-exp-parabolic

* removed boilerplate and added tag
2017-07-19 17:04:53 -05:00
pkondamudi
1b0d2888bb Package/xsbench (#4822)
* removed the tags as per comment in PR# 4749

* addressed above comments

* changed fortran compiler.

* added proxy application tags.

* added tags by removing them from description.

* addressed comments

* used join_path instead of path concat.

* added tags and other minor changes.

* removed tags from description.
2017-07-19 17:04:17 -05:00
jiseung
60cffbb9d0 new package PENNANT added (#4708)
* new package PENNANT

* made adjustments based on comments

* edited logic for mpi variant

* replaced with 'else'

* prefix.bin instead of 'bin'
2017-07-19 08:50:53 -05:00
Akhil Reddy Patlolla
a6cac6ac99 Added Proxy App CoSP2 (#4726)
*  Added Proxy App CoSP2

*  Updated the PATH

* Updated MPI Fix

*  Fixed Issues

*  Fixed Issues with compiler and Flake8

*  Enhanced block of code.

*  Intended
2017-07-19 08:49:29 -05:00
Akhil Reddy Patlolla
7165129598 Added Proxy App CoHMM (#4727)
*  Added Proxy App CoSP2

*  Added Proxy App CoHMM

*  Updated PATH cohmm

*  Chages Fixing Minor issues

* Minor Fix  git add cohmm/package.py

*  Updated

* Resolved TAG Conflict

*  Updated based on the codecov failure
2017-07-19 08:48:41 -05:00
jiseung
e3e8893ed9 new package: CLAMR (#4728)
* new package: CLAMR

* changed from bool variants to single value variants and corresponding logic in build_type and cmake_args

* lowercase variant values

* updated conditionals for variants

* adjusted url and docstring
2017-07-19 08:48:03 -05:00
pkondamudi
45a7e8bb12 New Package: SimpleMOC (#4742)
* New Package SimpleMOC

* addressed comments

* removed tags as per PR# 4749

* flake8 fix.

* travis fix.

* added proxy app tags to description.

* added mpi and openmpi depedency.

* removed openmpi depdedency.

* addressed comments.

* adding openmp flag conditionally.

* flake 8 fix for tabs.
2017-07-19 08:46:42 -05:00
Kshitij Mehta
6e2eb83943 codar-cheetah: URL fix (#4815) 2017-07-18 22:49:51 -05:00
jiseung
d1c199e15d new package: SMC (#4817)
* new package: SMC

* removed template and added proxy-app tag

* added comp variant in edit()

* edited comp variant in edit()
2017-07-18 22:48:21 -05:00
Gregory Lee
b411849200 Misc python updates (#4807)
* updated py-pylint version

* setuptools required at runtime for pkg_resources

* fixed url for updated pylint
2017-07-18 19:37:40 -05:00
Adam J. Stewart
2bd8d7a36a Always install xproto in serial (#4809) 2017-07-18 19:37:12 -05:00
Audrey Thoma
e2485efb94 poamsa: new package (#4808)
* poamsa: new package

* fixed version specs
2017-07-18 19:36:48 -05:00
jiseung
78c11320d6 new package to be added: NuT (#4760)
* new package to be added: NuT

* removed cmake_args() and made other changes as suggested

* Added setup_environment()

* PEP8 compliant

* edited version name, build_targets, and files/directories to install

* corrected executable directory

* compiler dependencies based on version
2017-07-18 16:37:47 -05:00
Audrey Thoma
748221840a price: new package (#4810) 2017-07-18 16:35:33 -05:00
Audrey Thoma
3e72263d79 New package busco (#4678)
* busco: new package

* busco: fixing fussy paths

* removing paths, probably was a problem with our module setup

* fixed dep type
2017-07-18 13:49:18 -05:00
Jon Rood
904f6f0572 Adding a bit more Mellanox MXM capability to OpenMPI. (#4762) 2017-07-18 13:45:43 -05:00
Audrey Thoma
0e28afef1e raxml: new package (#4777)
* raxml: new package

* changed compiler variable

* removing if statement regarding intel compiler
2017-07-18 13:43:42 -05:00
homerdin
68a8f63569 Package/minimd (#4788)
* New Package: miniMD

* Minor Changes

* Corrected Dependency

* Renamed Executable

* Change to use build directory directly
2017-07-18 13:42:57 -05:00
pkondamudi
e291f59ea3 New Package: OpenMC (#4790)
* New Package: OpenMC

* comments addressed.

* comments addressed.

* changed 'os.makedirs' to 'mkdirp'

* flake 8 fix.
2017-07-18 13:42:11 -05:00
Adam J. Stewart
1215c3b20c Change path to CMakeLists.txt to be relative to root, not pwd (#4420)
* Change path to CMakeLists.txt to be relative to root, not pwd

* Changes requested during code review

* Revert back to old naming of root_cmakelists_dir
* Make relative directory more clear in docs

* Revert change causing build_type AttributeError

* Fix forgotten abs_path var

* Update CLHEP with new relative path

* Update more packages with new root_cmakelists_dir syntax
2017-07-18 09:58:19 -07:00
健美猫
6b2d75a0a6 Repalce ftp:// with http:// for gdbm, mesa-glu and udunits2. (#4798) 2017-07-18 11:22:14 -05:00
George Hartzell
c597bdb284 somatic-sniper depends_in('curses') (#4796)
somatic-sniper installs its own copy of samtools, which needs curses.
I'm not sure why I didn't stumble on this in my dev environment, but I
just stumbled over it in a standalone build.
2017-07-18 09:40:41 -05:00
健美猫
870062076f Add version 3.4.1 for r. (#4799) 2017-07-18 13:04:49 +02:00
Audrey Thoma
07d82422b8 pcma: new package (#4793) 2017-07-18 11:13:17 +02:00
Adam Fidel
da61455cc3 New Package: tig (#4794) 2017-07-18 11:10:39 +02:00
homerdin
7c1ce6e206 Package/minixyce (#4789)
* New Package: miniXyce

* Removed Tag
2017-07-17 15:50:31 -05:00
Audrey Thoma
9872fe980b partitionfidner: new package (#4791) 2017-07-17 15:49:26 -05:00
Massimiliano Culpo
6dcbc30a2c qhull: fix to work around a known issue of the library with intel compiler (#4648) 2017-07-17 14:39:09 -05:00
Audrey Thoma
2bf140601b bsseeker2: new package (#4770) 2017-07-17 19:02:17 +02:00
Kshitij Mehta
9c9f0c9612 codar-cheetah: Experimentation harness from the ECP CODAR project (#4658)
* codar-cheetah: Experimentation harness from the ECP CODAR project

* codar-cheetah: conforming to flake8
2017-07-17 09:33:57 -05:00
Audrey Thoma
990d60d340 mrbayes: new package (#4757)
* mrbayes: new package

* fixing beagle version

* fixing typos

* fixing libbeagle dependency types
2017-07-17 09:20:49 -05:00
homerdin
62f5eafc55 New Package: miniSMAC2D (#4767) 2017-07-17 09:15:15 -05:00
homerdin
f43e4890db Package/minighost (#4773)
* New Package: miniGhost

* Fixed empty string formatting
2017-07-17 09:13:46 -05:00
Axel Huebl
c110d03f95 ZeroMQ: 4.2.2 & develop (#4785)
The 4.X branches are now on the homepage, so we take the GitHub release
artifact (careful: take their upload, not the automatic tarball).

Adds a development version of ZeroMQ.
Requires a autogen run, as for all their unreleased versions,
and the pkg-config fix in #4736
2017-07-17 08:40:48 -05:00
Axel Huebl
febf41e0e2 pkg-config: aclocal env (#4736)
Always sets the `pkg-config` environment hint for
autotools.

Required dependency for `autoreconf` of ZeroMQ when
build from source (e.g. v4.2.2) via autotools in `autogen.sh`
step for `autoreconf`.
2017-07-17 08:40:22 -05:00
Audrey Thoma
7e32756fce orfm: new package (#4769) 2017-07-15 19:03:55 +02:00
George Hartzell
89ef576ba4 Add package for the Python regex library (#4771)
Lightly tested on CentOS 7 with `python@2.7.13` and `python@3.6.0`.
2017-07-15 18:11:54 +02:00
George Hartzell
ad2a22fa01 Add package for r-ada, update r-rpart version (#4772)
* Add package for r-ada, update r-rpart version

Adds a package for r-ada.

Update the version for r-rpart because the previous version is
no longer at that URL.  The previous version *is* in the Archive,
but list_url does not seem to be able to find it.

* Clean up FIXMEs (blush)
2017-07-15 18:08:36 +02:00
George Hartzell
8e6d7f117a Add package for MuSE (#4779) 2017-07-15 18:06:43 +02:00
George Hartzell
8bd22c3294 Add package for Somatic Sniper (#4778)
Lightly tested on CentOS 7.
2017-07-15 18:05:51 +02:00
homerdin
246c07f864 New Package: miniFE (#4712)
* New Package: miniFE

* Removed extra property, using variant value directly
2017-07-14 15:55:51 -05:00
Kshitij Mehta
31503cb058 Savanna (#4713)
* savanna: Runtime framework for online workflow management from the ECP CODAR project

* savanna: added version 0.5

* savanna: Copying the package contents to prefix as part of installation

* savanna: Doing submodules=true for git checkout of develop version

* savanna: removed dependency on adios@develop. depends on adios

* Savanna: Converted package to MakefilePackage
2017-07-14 15:54:57 -05:00