19 KiB
- Request for Comments: Environment Modules at PSI
- Introduction
- Specification
- Must Preserve the Core Functionality of Traditional Modules
- Must Control the Availability of Modules Subject to Current State and Dependencies
- Settings for Standard and Application Specific Environment Variables
- Must Support Modules at Multiple Locations (Local and Network Installations)
- May Support Runtime Environments when Complete Development Environments are not Desirable
- May Support HW Compartibility Requirements
- May Support Optional Optimization and Development Requirements
- Must Define Minimum System Requirements to Support Generic Modules
- Design Proposal
- Implementation Proposal
- References
#+TITLE Project Environment Modules
Request for Comments: Environment Modules at PSI
Achim Gsell, Valeri MArkushin, Hans Christian Stadler
Scientific Computing, AIT, PSI
2014-04-29
Introduction
This document describes the requirements for a new implementation of environment modules at PSI that should address known problems with the present implementation based on the classical TCL modules [env_modules_tcl]. A detailed overview of suggested solutions was presented in the talk [env_modules_psi] by Achim.
The details of the specification are described in Section [Specification]. The draft of design is presented in Section [Design].
There are two readily available candidates to meet the requrements of this project: the extended version of TCL modules [env_modules_psi] and the Lua based Lmod [lmod]. The implementation proposal is summarized in Section [Implementation]. The implementation detailes will be written when the specifications are fixed and a genelal agreement concerning the design is reached.
The tecnical details concerning building specific software packages are mostly beyond the scope of this document: here we are interested only in the minimum and complete set of environment variables and dependencies required to provide and use a particular package.
Our goal is to provide the specifications and design that make the job of maintaners easier and staightforward.
IN-PROGRESS Specification
<<Specification>>
Since we have a work in progress, we call it specification, not evaluation.
IN-PROGRESS Must Preserve the Core Functionality of Traditional Modules OK
The essential (to be specified) tradinional module subcommands must be supported. Both TCL and Lua modules must meet this requirement. It is desirable to support all traditional subcommands.
IN-PROGRESS The TCL module subcommands
module help Modules Release 3.2.10 2012-12-21 (Copyright GNU GPL v2 1991): Usage: module [ switches ] [ subcommand ] [subcommand-args ] Switches: -H|--help this usage info -V|--version modules version & configuration options -f|--force force active dependency resolution -t|--terse terse format avail and list format -l|--long long format avail and list format -h|--human readable format avail and list format -v|--verbose enable verbose messages -s|--silent disable verbose messages -c|--create create caches for avail and apropos -i|--icase case insensitive -u|--userlvl <lvl> set user level to (nov[ice],exp[ert],adv[anced]) Available SubCommands and Args: + add|load modulefile [modulefile ...] + rm|unload modulefile [modulefile ...] + switch|swap [modulefile1] modulefile2 + display|show modulefile [modulefile ...] + avail [modulefile [modulefile ...]] + use [-a|--append] dir [dir ...] + unuse dir [dir ...] + update + refresh + purge + list + clear + help [modulefile [modulefile ...]] + whatis [modulefile [modulefile ...]] + apropos|keyword string + initadd modulefile [modulefile ...] + initprepend modulefile [modulefile ...] + initrm modulefile [modulefile ...] + initswitch modulefile1 modulefile2 + initlist + initclear
IN-PROGRESS The Lmod module subcommands
DONE Must Control the Availability of Modules Subject to Current State and Dependencies
CLOSED: [2014-04-28 Mon 10:49]
The Module Hierarchy section has been moved to [DesignProposal].
DONE Must support SW Dependencies
CLOSED: [2014-04-28 Mon 10:46]
DONE Desirable to Support HW and OS Constaints
CLOSED: [2014-04-28 Mon 10:47]
DONE Desirable to Support Licensing Constaints
CLOSED: [2014-04-28 Mon 10:48]
Only nonfloating licenses will be taken into account.
IN-PROGRESS Settings for Standard and Application Specific Environment Variables
DONE Must Export a Predefined Subset of POSIX Standard and Other Common Environment Variables
CLOSED: [2014-04-28 Mon 10:55]
The following environment variables must be set by all modules:
<NAME>_VERSION <NAME>_PREFIX <NAME>_DIR <NAME>_HOME
Every module that has effect on the following POSIX standard environment variables (FIXME) must explicitly export them:
PATH LD_LIBRARY_PATH MANPATH
See [Open_Group_Base_Specifications_EM] for the list of variables that are frequently exported by widely used command interpreters and applications. In particular, the following variables are considered as widely used:
CC CFLAGS FC FFLAGS LFLAGS MAKEFLAGS MANPATH PATH
FIXME (non-POSIX, e.g. common GCC shared by many other applications) if corresponding path exists:
CPATH C_INCLUDE_PATH CPLUS_INCLUDE_PATH <NAME>_INCLUDE_DIR LIBRARY_PATH <NAME>_LIBRARY_DIR LD_LIBRARY_PATH
IN-PROGRESS Must Export Family Environment Variables
<<Family>>
<FAMILY>=<implementation> <FAMILY>_VERSION=<implementation-version> <FAMILY>_DIR=<implementation-prefix>
Example:
MPI=openmpi MPI_VERSION=1.8.0
This would replace [ModuleIdentifiers] if the following variables are used:
COMPILER COMPILER_VERSION COMPILER_DIR MPI MPI_VERSION MPI_DIR
IN-PROGRESS Should Export Module Identifiers
<<ModuleIdentifiers>>
This may be merged with [Family].
The goal is to support generic module configuration and scripts.
PSI_COMPILER PSI_COMPILER_VERSION PSI_COMPILER_DIR PSI_MPI PSI_MPI_VERSION PSI_MPI_DIR
IN-PROGRESS Must Export Environment Variables for Compiler Implementations
CC CXX F77 F90 FC FORTRAN
IN-PROGRESS Must Export Environment Variables for MPI Implementations
The environment variables for MPI wrappers begin with MPI:
MPICC MPICXX MPIF77 MPIF90 MPIFC MPIFORTRAN MPIEXEC MPIRUN
OR/AND FIXME The environment variables for MPI wrappers begin with MPI_ [ANL_MPICH2]:
MPI_CC MPI_CXX MPI_F77 MPI_F90 MPI_FC MPI_FORTRAN MPI_EXEC MPI_RUN MPI_INC MPI_LIBS
Note by Achim: names without underscore seems to be more common and more commonly uses be autotools and cmake.
| Search term | "MPICC=mpicc" | "MPICC=mpicc" |
| Nunber of results | 4490 | 922 |
| Reference | [ANL_MPICH2] |
The environment variables should allow to distiguish between MPI wrappers (e.g. MPICC) and ordinary compilers (e.g. CC).
IN-PROGRESS Should Export Package- or Vendor-Defined Environment Variables
Each module should set the environment variables that make its use easier for the user without additional configuration.
Special care should be taken to the interplay of the Intel, PGI, and GCC compilers, scientific libraries, and Python.
The details for specific packages must be discussed with future maintainers. Some examples are shown below.
TODO Intel Specific Environment Varaibales
Set the following variavbles for Intel compilers and their dependencies:
CPATH GDBSERVER_MIC GDB_CROSS IDB_HOME INCLUDE INTEL_LICENSE_FILE IPPROOT LD_LIBRARY_PATH LIBRARY_PATH MANPATH MIC_LD_LIBRARY_PATH MIC_LIBRARY_PATH MKLROOT MKL_INCLUDE MKL_LIBRARY_PATH NLSPATH PATH TBBROOT VTUNE_AMPLIFIER_XE_2013_DIR
TODO MPICH2 Specific Environment Varaibales
Are there specific environment variables? Or are the more generic family variables sufficient?
IN-PROGRESS OpenMPI Specific Environment Varaibales
According to [Open_MPI_wrappers], the following variables should be set
MPICC=mpicc MPICXX=mpic++ # MPICXX=mpiCC # MPICXX=mpicxx MPIF77=mpif77 MPIF90=mpif90 MPIFC=mpifort MPIFORTRAN=mpifort
The variables MPI_COMPILE_FLAGS and MPI_LINK_FLAGS should not be controlled by the environment modules. These variables can be assigned, if needed, by the users [Open_MPI_without-wrappers]:
MPI_COMPILE_FLAGS = $(shell mpicc --showme:compile)
MPI_LINK_FLAGS = $(shell mpicc --showme:link)
my_app: my_app.c
$(CC) $(MPI_COMPILE_FLAGS) my_app.c $(MPI_LINK_FLAGS) -o my_app
# Examples:
mpicc --showme:compile
-I/opt/mpi/openmpi-1.6.5-gcc-4.8.2-compat/include -pthread
mpicc --showme:link
-pthread -L/opt/mpi/openmpi-1.6.5-gcc-4.8.2-compat/lib -lmpi -ldl -lm -lnuma -Wl,--export-dynamic -lrt -lnsl -lutil -lm -ldl
TODO PGI Specific Environment Varaibales
LD_LIBRARY_PATH LM_LICENSE_FILE PATH MANPATH PGI PGI_INCLUDE PGI_LIB PGI_LIBS0 PGRSH
STOPPED System Specific Environment Variables
CLOSED: [2014-04-29 Tue 16:13]
TMPDIR
If /tmp may be not large enough (like on Merlin4), set suitable TMPDIR, e.g.:
TMPDIR=/scratch/tmp # where /scratch ->/home/scratch
Note (Achim): TMPDIR should not be changed by an environment module. Valeri: agreed.
IN-PROGRESS Must Support Modules at Multiple Locations (Local and Network Installations)
IN-PROGRESS Must Support Combinations of Local and Network Installations
It must be possible to install locally any selfconsistent subset of environment modules.
The user should be able to select which installation is used if multiple installations are available.
The should be a mechanism (e.g., environment variable) to control which installation is used on per-user basis.
DONE Top Level Directory PROVIDER_PREFIX
IN-PROGRESS Must Support Modules in Home Directory
User should be able to install their own modules.
DONE May Support Runtime Environments when Complete Development Environments are not Desirable
CLOSED: [2014-04-28 Mon 11:24]
The end users may wish to run applications without loading all modules required to build these applications. To this end, run-time modules may be provided if the module maintainer decides so.
DONE May Support HW Compartibility Requirements
CLOSED: [2014-04-28 Mon 11:25]
This functionality should allow one to hide environment modules that lack certain capabilities on a given HW platform. For example, all 64-bit applications should be hidden on a 32-bit system. A less trivial example is checking the CPU flags and hiding the applications compiled with options that are not supported by the CPU.
If possible, make it "should support" requirement.
IN-PROGRESS May Support Optional Optimization and Development Requirements
There may be a mechanism to hide (default) or unhide modules, which are not intended for general use, e.g. of development and testing type, from the standard workflow.
Note(Achim): Hiding should be implemented via MODULEPATH. Modules in testing state should print a warning. Everything else will end in a nightmare. Valeri: this paragraph should go to Implementation.
DONE Must Define Minimum System Requirements to Support Generic Modules
CLOSED: [2014-04-28 Mon 11:42]
Example: CPU family XXX and SL6 or higher on 64-bit arch OR MacOS XYZ OR …
IN-PROGRESS Design Proposal
<<DesignProposal>>
IN-PROGRESS Must Support Module Hierarchy
IN-PROGRESS Must Support the Hierarchy Compiler-MPI-Application
As defined in the reference implementations of the extended TCL modules [env_modules_psi] and Lmod [lmod].
IN-PROGRESS Must Support family Functionality
As defined in the reference implementations of the extended TCL modules [env_modules_psi] and Lmod [lmod].
IN-PROGRESS May/Should Support Subcommand swap on Upper Levels of Module Hierarchy
As defined in the reference implementations of Lmod [lmod].
IN-PROGRESS Molule Command
Both the extended TCL modules and Lua modules (Lmod) can be supported. The user will have a choice of default module command and will be able to swith to the alternative if both implementations are available.
IN-PROGRESS Extended TCL Modules
See [env_modules_psi] and the reference implementations on Merlin4 (FIXME) and MacOS (FIXME).
The extended TCL modules cannot not support Lua modules.
IN-PROGRESS Lua Modules (Lmod)
See [lmod] and the reference implementaion on Merlin4 (FIXME).
The Lua modules may support (extended) TCL modules.
IN-PROGRESS File System Layout
IN-PROGRESS Top Level Directory :OPT_PROVIDER=/opt/psi:
<<TLD>>
The top level directory for the PSI implememtation is /opt/psi in accordance with [FHS].
PROVIDER_PREFIX=/opt/psi
The top level directory may be a link to a local file system or a link to AFS (GPFS).
IN-PROGRESS Modulefile Root Directory.
There must be only one modulefile root directory MODULEPATH_ROOT within a given implementation of environment modules:
MODULEPATH_ROOT=$OPT_PROVIDER/modulefiles
For the PSI implementation MODULEPATH_ROOT=/opt/psi/modulefiles.
Note (Achim): Actually I like the idea of something like a MODULEROOT_PATH. It should be possible to implement multiple hierarchies. This can be easly implemented with the extendet TCL Modules, I guess it wouldn't be to hard to implement this with Lua-Modules. Valeri: 'Your search - "MODULEROOT_PATH" - did not match any documents.'
IN-PROGRESS The Layout of Subdirectories Used for Configuration of Environment Modules
/opt/psi OPT_PROVIDER :-- modulefiles MODULEPATH_ROOT : : : :-- Core ### Compilers and compiler-independent SW : : :-- gcc : : : :-- 4.8.2 : : : :-- x.y.z : : :-- intel : : : :-- x.y.z : : :-- pgi : : : :-- x.y.z : : : : : :-- foo : : : :-- x.y.z : : :-- bar : : : :-- x.y.z : : : :-- Compiler ### Compiler-independent SW : : :-- gcc : : : :-- 4.8.2 : : : :-- mpi : : : :-- openmpi-1.6.4 : : : :-- openmpi-1.8.0 : : :-- intel : : : :-- 14.0 : : : :-- mpi : : : :-- openmpi-1.6.4 : : : :-- openmpi-1.8.0 : : : :-- MPI ### Compiler- and MPI-independent SW : : :-- gcc : : : :-- 4.8.2 : : : :-- openmpi : : : :-- 1.6.4 : : : :-- scalasca : : : |-- 1.4.2 : :
IN-PROGRESS The Layout of Subdirectories Used for Software Installation
Each version of each package should have its own installation directory, if possible (the exceptions will be discussed below), specified by the corresponding PREFIX.
PREFIX should
- be easy to understand by an expert user;
- make it easier to write portable module scripts;
- avoid unneeded layers of abstarction.
Example:
/opt/psi OPT_PROVIDER : : ............................................................... PREFIX Subdirectories : : : :-- gcc : : :-- 4.8.2 ### PREFIX=$OPT_PROVIDER/$COMPILER/$COMPILER_VERSION : : :-- x.y.z : : : :-- intel : : :-- 14.0 : : : :-- openmpi : : :-- openmpi-1.6.4-gcc-4.8.2 ### PREFIX=$OPT_PROVIDER/$MPI/$MPI-$MPI_VERSION-$COMPILER-$COMPILER_VERSION : : :-- ... : : :-- openmpi-1.6.4-intel-14.0 : : :-- ... : : : :-- foo : : :-- foo-x.y.z-openmpi-1.6.4-intel-14.0 ### PREFIX=$OPT_PROVIDER/$NAME/$NAME-$VERSION-$MPI-$MPI_VERSION-$COMPILER-$COMPILER_VERSION : : : :-- bar : : :-- bar-x.y.z-intel-14.0 ### PREFIX=$OPT_PROVIDER/$NAME/$NAME-$VERSION-$COMPILER-$COMPILER_VERSION : :
IN-PROGRESS Recommended Layouts
Mainterners may select any of the recommended installation layouts (defined by PREFIX).
FIXME
IN-PROGRESS Special Cases
Some of the Intel tolls depend on services that must be properly configured and started by the init process. It means that only some subset of intel versions may provide full functionality of some tools (e.g. Vtune Amplifier). The environment modules will not handle this issue.
STOPPED Environment Variables Reserved for Internal Use
CLOSED: [2014-04-29 Tue 17:10]
FIXME
PSI_COMPILER PSI_COMPILER_VERSION PSI_MPI PSI_MPI_VERSION
Note (Achim): Use case? Valeri: I use them in my Lua modules. The prefix PSI_ can be removed, then the variables defined in [Family] are sufficient.
PREFIX=$OPT_PROVIDER/$NAME/$NAME-$VERSION-$MPI-$MPI_VERSION-$COMPILER-$COMPILER_VERSION
TODO Mainterners of Environment Modules and Their Responsibilities
FIXME
TODO Reference Implementations
FIXME
TODO Implementation Proposal
<<<Implementation>>
FIXME
IN-PROGRESS Must Provide Build Environment for All Supported Computing Environments
IN-PROGRESS Build Environment Should Support Regression Tests
Should be done by maintaners.
DONE Build and Test Environment for Each Module Must Be Available for All Maintaners
CLOSED: [2014-04-28 Mon 11:48]
There must be no duplication of efforts. Every build must be reproducable.
IN-PROGRESS Should Provide Facility for Phasing Out Obsolete and Buggy Modules
IN-PROGRESS References
- <<env_modules_tkl>> http://modules.sourceforge.net/
- <<env_modules_psi>> https://intranet.psi.ch/AIT/EnvironmentModules
- <<lmod>> https://www.tacc.utexas.edu/tacc-projects/lmod
- <<FHS>> http://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard
- <<Open_Group_Base_Specifications_EM>> http://pubs.opengroup.org/onlinepubs/009695399/basedefs/xbd_chap08.html
- <<Open_MPI_wrappers>> http://www.open-mpi.org/faq/?category=mpi-apps
- <<Open_MPI_without-wrappers>> http://www.open-mpi.org/faq/?category=mpi-apps#cant-use-wrappers
- <<ANL_MPICH2>> https://svn.mcs.anl.gov/repos/mpi/mpich2/tags/release/mpe2-1.0.7rc1/INSTALL