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Wishlist
Here is a list of features that are desired to have in next versions of EasyBuild: (importance of them varies according to who you ask ;-)
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Consider category-oriented module sets (eg.
module load bioinformatics-tools); Expand categories -
may be done outside of EB logic, IFF the meaning is to mangle MODULEPATH? "moduleclass" can help
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ANSWER: either as said OR, produce an easyconfig with multiple dependencies; TBD
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Ref: https://github.com/hpcugent/easybuild-framework/issues/209
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Add possibility to save the logfile somewhere even when failures happen (/tmp is no good for queue submitted jobs)
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interim solution is to use -ld; OK. "works-for-us"
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ANSWER: "/tmp" is hardcoded now, open issue if change required; See closed issue #84 and/or commit 0c15839
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Allow for custom-definition of easyblock paths (instead of enforcing any "a-z/" dir structure
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ANSWER: it seems to be OK w. PYTHON_PATH? nope, the a-z dirs need to have "reverse" mapping (ref. ".."); TBD; refer to open issue: https://github.com/hpcugent/easybuild/issues/87; Addressed, see: https://github.com/hpcugent/easybuild/wiki/Setting-up-your-own-easyblocks-repository
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Consider support of "formal" language to describe package info & dependencies, eg. CUDF syntax
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http://www.mancoosi.org/papers/cbse11.pdf "MPM: a modular package manager"
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http://arxiv.org/abs/1109.0456 "Aligning component upgrades"
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ANSWER: may consider; TBD/postponed.
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How to organize a collection of .eb files coming from different sources? (eg. distinct git repos)
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Seen at http://joeyh.name/code/mr/ : "When updating a git repository, pull from two different upstreams and merge the two together."
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ie. can EasyBuild --robot dependency resolution support multiple paths?
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ANSWER: will support multiple directories; so do prefer to use many dirs indeed
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Consider integrated support for relocatable .rpms (with --prefix), .srpms & RPM's .spec files
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in effect, let's create a handler for non "*.eb" suffixes to be managed externally; that would allow to create from eg. a .spec file (for RPMs) the equivalent .eb, then parse that from "stdio"
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ANSWER: it was supported, in previous versions; to be cleaned up
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extreme thought: yes, this is an extreme thought: consider module search/install extensions!
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ANSWER: or try that with "module load" instead ;-)
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FG: has a toy setup that actually does this playing around $CFGS and it works nicely
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promote easybuild within bioinformatics community, esp. for "clinical or translational workflows", as described below: http://www.bioinfo-core.org/index.php/11th_Discussion-7_November_2011#Topic_2:_Managing_and_Tracking_Software_Updates_.28Led_by_Brent_Richter.29
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ANSWER: makes sense to approach communities; TBD
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support cmake-like builds (see example below)
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ANSWER: for the default case an easyblock is upcoming; TBD; Update: DONE!
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how to override certain steps ("/bin/true" is considered a hack as of now)
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ANSWER: TBD; Update: DONE! (via skip_steps)
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define function names (eb steps) in accordance with common community conventions
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ANSWER: to be discussed; let's first create a wiki page with all the Build ports naming conventions #99
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Update: DONE! as of v1.0.0
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Consider the bigger picture as seen at http://eniac.cyi.ac.cy/display/UserDoc/HPC+Baseline+Configuration
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ANSWER: discussed; interesting organizational method for Flamish supercomputing activities
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BENELUX collab?
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ANSWER: discussed; TBD
- Define the namespace "by a standard"; eg. like [https://github.com/fgeorgatos/HPC-RFC/blob/master/0001/0001.md]
- Overall, standard EasyBuild namespace is pretty solid; some tweaking is needed for the next versions
- Give freedom to define the namespace format (eg. original Package names OR the lower case version)
- allow to export namespace in both UpperCase and LowerCase conventions # a post-install hook? TBD
- this is tracked here: https://github.com/hpcugent/easybuild-framework/issues/173
- Support more configurable formats of version strings (check below, how other HPC sites do it)
- nested levels (ie. split version string in sub sections)
- provide hooks for gnu/gcc/intel/pgi etc strings
- IDEA: For now, supply a "custom_namespace_function" variable, to define eg. modulename.lower();
- Provide some smart way to handle osdependencies like "tcsh" which may have no meaning on Debian # a particularly important case are the boost-devel vs boost-dev differences (rpm vs deb conventions)
- and for now allow escaping with --ignore-osdependencies ; See #102; FG update: this now is handled with --strict=ignore
This is just the cmake-style of building gromacs (latest), alternatives do exist.
# GROMACS-GPU uses a cmake build-generator and makefiles on unix.
# To avoid confusion build in separate folder
export OPENMM_ROOT_DIR=path_to_custom_openmm_installation
mkdir build_gromacs_gpu
cd build_gromacs_gpu
cmake PATH_TO_SOURCE_DIRECTORY -DGMX_OPENMM=ON -DGMX_THREADS=OFF
make mdrun
make install-mdrun
---------------------------------------------------------- --------------------- ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Example name WHO Reference URL & Comments
---------------------------------------------------------- --------------------- ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
netcdf/3.6.2 TACC [[http://services.tacc.utexas.edu/index.php/using-modules][]] \\ Lmod: automatic reloading of an entire module hierarchy when a single module anywhere in the hierarchy is changed.
hpc/netcdf-3.6.3_intel-11.0.083 HARVARD [[http://rc.fas.harvard.edu/faq/modulelist][]] \\ very long and complete list
misc-libs/netcdf/3.6.3_intel CLUMEQ [[https://www.clumeq.ca/wiki/index.php/ModulesDisponiblesSurColosse][]] \\ nested layout
netcdf/intel/64/4.0 SARA [[http://www.sara.nl/systems/shared/modules/][]] \\ [[http://www.sara.nl/systems/lisa/news/modules-ng][]] \\ [[http://www.sara.nl/systems/lisa/news/amd64-phase1][]] \\ [[http://www.sara.nl/systems/lisa/news/Modules-deprecated-2011-04-04][]]
[[https://www.clumeq.ca/wiki/index.php/ModulesDisponiblesSurColosse][]] \\ nested layout
netcdf/gnu/64/4.0 SARA [[http://www.sara.nl/systems/shared/modules/][]] \\ [[http://www.sara.nl/systems/lisa/news/modules-ng][]] \\ [[http://www.sara.nl/systems/lisa/news/amd64-phase1][]] \\ [[http://www.sara.nl/systems/lisa/news/Modules-deprecated-2011-04-04][]]
netcdf/4.0.1 UIBK [[http://www.uibk.ac.at/zid/systeme/hpc-systeme/common/tutorials/modules-howto.html][]] \\ PREFERRED_MC
netcdf/X.Y.Z/gnu-4.1.2 UIBK, too [[http://www.uibk.ac.at/th-physik/howto/hpc/modules.html][]]
netcdf/X.Y.Z-gnu CSC [[http://www.csc.fi/english/pages/hippu_guide/using_hippu/modules/index_html][]]
ofed/qlogic/gcc/64/1.2.7 UCL [[http://www.ucl.ac.uk/isd/common/research-computing/services/legion-upgrade/userguide/userenvironment][]]
netcdf/3.6.2 MIT [[http://www.darwinproject.mit.edu/wiki/index.php/Compute_cluster_hardware/software_overview][]]
netcdf/X.Y.Z MIT, too [[http://coyote.mit.edu/mediawiki/index.php/Modules][]]
netcdf/3.6.2 CAM [[http://www.hpc.cam.ac.uk/user/software.html][]]
netcdf/4.0.1_nc3 UTORONTO [[https://support.scinet.utoronto.ca/wiki/index.php/Software_and_Libraries][]]
blas/? VLSCI@AU [[http://www.vlsci.org.au/documentation/software-applications][]]
fluent/? EPFL [[http://pleiades.epfl.ch/index.php?option=com_content&task=view&id=15&Itemid=30][]]
netcdf/4.0.0.3.1jg64 CSCS [[http://user.cscs.ch/software_and_programming_environment/compilers_and_programming/rosa_cray_xt5/modules_framework/index.html][]]
netcdf/4.1.1/pgi/10.3/64 TAMU [[http://brazos.tamu.edu/software/modules.html][]]
sles10.1_gnu4.1.2_shared UTENNESSEE [[http://www.nics.tennessee.edu/computing-resources/kraken/software][]]
netcdf/4.0-pgi, /4.0-gcc , /4.1.1 UMICH [[http://cac.engin.umich.edu/resources/software/][]]
netcdf-4.0.1 ARSC [[http://www.arsc.edu/support/news/systemnews/][]]
NetCDF/4.1.3-gnu Griffith University [[http://confluence.rcs.griffith.edu.au:8080/display/GHPC/netcdf][]]
HMMER iCER/HPCC [[https://wiki.hpcc.msu.edu/display/Bioinfo/Module+Files][]]
HMMER UPPNEX [[https://www.uppnex.uu.se/installed-software][]]
uberftp-client-2.6 NCSA [[http://www.ncsa.illinois.edu/UserInfo/Resources/Hardware/CommonDoc/module.html][]]
netcdf LRZ [[http://www.lrz.de/services/software/utilities/modules/deisa_details.html][]] \\ Ref. on DEISA setup: [[http://www.lrz.de/services/software/utilities/modules/deisa_details.html][]]
globus PRACE sites [[http://www.prace-ri.eu/Interactive-Access-to-HPC][]]
globus/5.0.4 & GLOBUS-5.0 TACC [[http://www.underworldproject.org/BuildRecipes/ranger.rst][]] See Teragrid below
netcdf/4.1.2-gnu, /4.1.2-intel, /3.6.3-gnu, /3.6.3-intel cyi/euclid@ls2 [[http://eniac.cyi.ac.cy/display/UserDoc/HPC+Baseline+Configuration]]
netcdf/3.6.3-gcc, netcdf-4/4.0.1-gcclf cyi/planck [[http://eniac.cyi.ac.cy/display/UserDoc/HPC+Baseline+Configuration]]
netcdf/3.6.2-intel, /3.6.2-gnu ba@ls2 [[http://eniac.cyi.ac.cy/display/UserDoc/HPC+Baseline+Configuration]]
netcdf/4.1.3-gcc(default) cytera@ls2 [[http://eniac.cyi.ac.cy/display/UserDoc/HPC+Baseline+Configuration]]
netcdf/1.4.3-mpich2-intel-64bit FZK [[http://www.google.com]]
---------------------------------------------------------- --------------------- ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
package: m4
version: 3
depends: libc6 >= 8
package: openssl
version: 11
depends: libc6 >= 18, libssl0.9.8 >= 8, zlib1g >= 1
conflicts: ssleay < 1
package: gcc
version: 4.4.4
provides: compiler
conflicts: compiler
package: icc
version: 10.2
provides: compiler
conflicts: compiler