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Updated Environment_Modules_Project.org following the suggestions by Achim

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markushin
2014-04-29 17:34:22 +02:00
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@@ -9,7 +9,7 @@ Achim Gsell, Valeri MArkushin, Hans Christian Stadler
Scientific Computing, AIT, PSI
2014-04-28
2014-04-29
* Introduction
@@ -128,7 +128,7 @@ Only nonfloating licenses will be taken into account.
*** DONE Must Export a Predefined Subset of POSIX Standard and Other Common Environment Variables
CLOSED: [2014-04-28 Mon 10:55]
The following environment variable *must be set* by all modules:
The following environment variables *must be set* by all modules:
#+BEGIN_EXAMPLE
<NAME>_VERSION
<NAME>_PREFIX
@@ -137,13 +137,28 @@ The following environment variable *must be set* by all modules:
#+END_EXAMPLE
Every module that *has effect* on the following POSIX standard environment variables
*must explicitly export* them:
(FIXME) *must explicitly export* them:
#+BEGIN_EXAMPLE
PATH
LD_LIBRARY_PATH
MANPATH
#+END_EXAMPLE
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*:
#+BEGIN_EXAMPLE
CC
CFLAGS
FC
FFLAGS
LFLAGS
MAKEFLAGS
MANPATH
PATH
#+END_EXAMPLE
FIXME (non-POSIX, e.g. common GCC shared by many other applications)
if corresponding path exists:
#+BEGIN_EXAMPLE
@@ -156,16 +171,50 @@ if corresponding path exists:
LD_LIBRARY_PATH
#+END_EXAMPLE
*** IN-PROGRESS Must Export Family Environment Variables
<<Family>>
<FAMILY>=<implementation>
<FAMILY>_VERSION=<implementation-version>
#+BEGIN_EXAMPLE
<FAMILY>=<implementation>
<FAMILY>_VERSION=<implementation-version>
<FAMILY>_DIR=<implementation-prefix>
#+END_EXAMPLE
Example:
#+BEGIN_EXAMPLE
MPI=openmpi
MPI_VERSION=1.8.0
#+END_EXAMPLE
This would replace [[[ModuleIdentifiers]]] if the following variables are used:
#+BEGIN_EXAMPLE
COMPILER
COMPILER_VERSION
COMPILER_DIR
MPI
MPI_VERSION
MPI_DIR
#+END_EXAMPLE
*** IN-PROGRESS Should Export Module Identifiers
<<ModuleIdentifiers>>
This may be merged with [[[Family]]].
The goal is to support generic module configuration and scripts.
#+BEGIN_EXAMPLE
PSI_COMPILER
PSI_COMPILER_VERSION
PSI_COMPILER_DIR
PSI_MPI
PSI_MPI_VERSION
PSI_MPI_DIR
#+END_EXAMPLE
**** IN-PROGRESS Must Export Environment Variables for Compiler Implementations
#+BEGIN_EXAMPLE
@@ -177,20 +226,10 @@ if corresponding path exists:
FORTRAN
#+END_EXAMPLE
**** IN-PROGRESS Must Export Environment Variables for MPI Implementations
Set environment variables to corresponding MPI wrappers
#+BEGIN_EXAMPLE
CC
CXX
F77
F90
FC
FORTRAN
#+END_EXAMPLE
or
The environment variables for MPI wrappers begin with MPI:
#+BEGIN_EXAMPLE
MPICC
MPICXX
@@ -198,11 +237,41 @@ or
MPIF90
MPIFC
MPIFORTRAN
MPIEXEC
MPIRUN
#+END_EXAMPLE
Note: names without underscore seems to be more common and more
OR/AND FIXME
The environment variables for MPI wrappers begin with MPI_ [[[ANL_MPICH2]]]:
#+BEGIN_EXAMPLE
MPI_CC
MPI_CXX
MPI_F77
MPI_F90
MPI_FC
MPI_FORTRAN
MPI_EXEC
MPI_RUN
MPI_INC
MPI_LIBS
#+END_EXAMPLE
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
@@ -212,8 +281,8 @@ Special care should be taken to the interplay of the Intel, PGI, and GCC compile
scientific libraries, and Python.
The details for specific packages must be discussed with future maintainers.
Some examples are shown below.
Examples follow.
**** TODO Intel Specific Environment Varaibales
@@ -246,30 +315,42 @@ Set the following variavbles for Intel compilers and their dependencies:
Are there specific environment variables? Or are the more generic
family variables sufficient?
**** TODO OpenMPI Specific Environment Varaibales
See comment in aboce section.
To be dicussed:
**** IN-PROGRESS OpenMPI Specific Environment Varaibales
According to [[[Open_MPI_wrappers]]], the following variables should be set
#+BEGIN_EXAMPLE
MPI_COMPILE_FLAGS
MPI_LINK_FLAGS
MPICC=mpicc
MPICXX=mpic++
# MPICXX=mpiCC
# MPICXX=mpicxx
MPIF77=mpif77
MPIF90=mpif90
MPIFC=mpifort
MPIFORTRAN=mpifort
#+END_EXAMPLE
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]]]:
#+BEGIN_EXAMPLE
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
#+END_EXAMPLE
Note (Achim): no! Never need this ...
**** TODO PGI Specific Environment Varaibales
#+BEGIN_EXAMPLE
LD_LIBRARY_PATH
LM_LICENSE_FILE
@@ -283,7 +364,8 @@ Note (Achim): no! Never need this ...
#+END_EXAMPLE
**** TODO System Specific Environment Variables
**** STOPPED System Specific Environment Variables
CLOSED: [2014-04-29 Tue 16:13]
#+BEGIN_EXAMPLE
TMPDIR
@@ -294,27 +376,23 @@ If /tmp may be not large enough (like on Merlin4), set suitable TMPDIR, e.g.:
TMPDIR=/scratch/tmp
# where /scratch ->/home/scratch
#+END_EXAMPLE
Note (Achim): TMPDIR *should not* be changed by an environment module
Note (Achim): TMPDIR *should not* be changed by an environment module.
Valeri: agreed.
*** IN-PROGRESS Should Export Module Identifiers
The goal is to support generic module configuration and scripts.
FIXME: examples.
** IN-PROGRESS Must Support both Local and Network Installation
** 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 can select which installation he wants
to use.
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:
*** DONE Top Level Directory :PROVIDER_PREFIX:
CLOSED: [2014-04-28 Mon 11:22]
The top level directory is */opt/<provider>*, where *<provider>=psi*, in accordance with [[[FHS]]].
@@ -322,9 +400,10 @@ The top level directory may be a link to a local or network file system.
See [[[TLD]]] for the PSI specific implementation details.
*** IN-PROGRESS Must Support Modules in Home Directory
User should be able to install their own modules.
** IN-PROGRESS Must Support Modules at Multiple Locations
Idea: Modules in the user's home directory must be supported
** DONE May Support Runtime Environments when Complete Development Environments are not Desirable
CLOSED: [2014-04-28 Mon 11:24]
@@ -344,14 +423,16 @@ options that are not supported by the CPU.
If possible, make it "should support" requirement.
** DONE May Support Optional Optimization and Development Requirements
CLOSED: [2014-04-28 Mon 11:27]
** 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
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]
@@ -430,35 +511,128 @@ 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
FIXME
#+BEGIN_EXAMPLE
/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
: :
#+END_EXAMPLE
*** IN-PROGRESS The Layout of Subdirectories Used for Software Installation
FIXME
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
1. be easy to understand by an expert user;
2. make it easier to write portable module scripts;
3. avoid unneeded layers of abstarction.
Example:
#+BEGIN_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
: :
#+END_EXAMPLE
**** IN-PROGRESS Recommended Layouts
Mainterners may select any of the recommended installation layouts (defined by PREFIX).
FIXME
** TODO Environment Variables Reserved for Internal Use
**** 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
#+BEGIN_EXAMPLE
PSI_COMPILER
PSI_COMPILER_VERSION
PSI_MPI
PSI_MPI_KIND
PSI_MPI_VERSION
#+END_EXAMPLE
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
@@ -499,3 +673,7 @@ Every build must be reproducable.
2. <<env_modules_psi>> https://intranet.psi.ch/AIT/EnvironmentModules
3. <<lmod>> https://www.tacc.utexas.edu/tacc-projects/lmod
4. <<FHS>> http://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard
5. <<Open_Group_Base_Specifications_EM>> http://pubs.opengroup.org/onlinepubs/009695399/basedefs/xbd_chap08.html
6. <<Open_MPI_wrappers>> http://www.open-mpi.org/faq/?category=mpi-apps
7. <<Open_MPI_without-wrappers>> http://www.open-mpi.org/faq/?category=mpi-apps#cant-use-wrappers
8. <<ANL_MPICH2>> https://svn.mcs.anl.gov/repos/mpi/mpich2/tags/release/mpe2-1.0.7rc1/INSTALL