Introduction
Message Passing Interface (MPI) is an API for parallelization of programs across multiple nodes and has been around since 1994 [1]. MPI can also be used for parallelization on SMP machines and is considered very efficient in it too (close to 100% scaling on parallelizable code as compared to ~80% commonly obtained with threads due to unoptimal memory allocation on NUMA machines). Before MPI, about every manufacturer of supercomputers had their own programming language for writing programs; MPI made porting software easy.
There are many MPI implementations available, such as LAM-MPI (in Fedora, obsoleted by Open MPI), Open MPI (the default MPI compiler in Fedora and the MPI compiler used in RHEL), MPICH (Not yet in Fedora), MPICH2 (in Fedora) and MVAPICH1 and MVAPICH2 (Not yet in Fedora).
As some MPI libraries work better on some hardware than others, and some software works best with some MPI library, the selection of the library used must be done in user level, on a session specific basis. Also, people doing high performance computing may want to use more efficient compilers than the default one in Fedora (gcc), so one must be able to have many versions of the MPI compiler each compiled with a different compiler installed at the same time. This must be taken into account when writing spec files.
Packaging of MPI compilers
The MPI compiler RPMs MUST be possible to build with other compilers as well and support simultaneous installation of versions compiled with different compilers (e.g. in addition to a version compiled with {gcc,g++,gfortran} a version compiled with {gcc34,g++34,g77} must be possible to install and use simultaneously as gfortran does not fully support Fortran 77). To do this, the files of MPI compilers MUST be installed in the following directories:
| File type | Placement |
|---|---|
| Binaries | %{_bindir}/%{name}-%{_arch}%{?_cc_name_suffix}/
|
| Libraries | %{_libdir}/%{name}%{?_cc_name_suffix}/
|
| Fortran modules | %{_fmoddir}/%{name}/
|
| Config files | %{_sysconfdir}/%{name}-%{_arch}%{?_cc_name_suffix}/
|
Here %{?_cc_name_suffix} is null when compiled with the normal {gcc,g++,gfortran} combination, but would be e.g. -gcc34 for {gcc34,g++34,g77}.
As include files and manual pages are bound to overlap between different MPI implementations, they MUST also placed outside normal directories. It is possible that some man pages or include files (either those of the MPI compiler itself or of some MPI software installed in the compiler's directory) are architecture specific (e.g. a definition on a 32-bit arch differs from that on a 64-bit arch), the directories that MUST be used are as follows:
| File type | Placement |
|---|---|
| Man pages | %{_mandir}/%{name}-%{_arch}%{?_cc_name_suffix}/
|
| Include files | %{_includedir}/%{name}-%{_arch}%{?_cc_name_suffix}/
|
Architecture and compiler (%{?_cc_name_suffix}) independent parts MUST be placed in a -common subpackage that is BuildArch: noarch on >= Fedora 11.
The MPI compiler's spec file MUST support the use of the following variables to compile with other compilers
# We only compile with gcc, but other people may want other compilers. # Set the compiler here. %global opt_cc gcc # Optional CFLAGS to use with the specific compiler...gcc doesn't need any, # so uncomment and define to use #global opt_cflags %global opt_cxx g++ #global opt_cxxflags %global opt_f77 gfortran #global opt_fflags %global opt_fc gfortran #global opt_fcflags # Optional name suffix to use...we leave it off when compiling with gcc, but # for other compiled versions to install side by side, it will need a # suffix in order to keep the names from conflicting. #global cc_name_suffix -gcc
The runtime of MPI compilers (mpirun, the libraries, the manuals etc) MUST be packaged into %{name}, and the development headers and libraries into %{name}-devel.
As the compiler is installed outside PATH, one needs to load the relevant variables before being able to use the compiler or run MPI programs. This is done using environment modules.
The module file MUST prepend the MPI bindir %{_libdir}/%{name}/%{version}-<compiler>/bin into the users PATH and set LD_LIBRARY_PATH to %{_libdir}/%{name}/%{version}-<compiler>/lib. The module file MUST also set some helper variables (primarily for use in spec files):
| Variable | Value | Explanation |
|---|---|---|
MPI_BIN |
%{_bindir}/%{name}-%{_arch}%{?_opt_cc_suffix}/ |
Binaries compiled against %{name}
|
MPI_CONFIG |
%{_sysconfdir}/%{name}-%{_arch}%{?opt_cc_suffix}/ |
MPI stack specific configuration files |
MPI_FORMOD |
%{_fmoddir}/%{name}%{?_opt_cc_suffix}/ |
MPI stack specific fortran module directory |
MPI_INCLUDE |
%{_includedir}/%{name}-%{_arch}%{?_opt_cc_suffix}/ |
MPI stack specific headers |
MPI_LIB |
%{_libdir}/%{name}%{?_opt_cc_suffix}/ |
Libraries compiled against %{name}
|
MPI_MAN |
%{_mandir}/%{name}-%{_arch}%{?_opt_cc_suffix}/ |
MPI stack specific man pages |
MPI_COMPILER |
%{name}-%{_arch}%{?_cc_name_suffix} |
Helper variable for use in e.g. spec files |
MPI_SUFFIX |
%{?_cc_name_suffix}_%{name} |
The suffix used for programs compiled against %{name}
|
MUST: By default, NO files are placed in /etc/ld.so.conf.d. If the packager wishes to provide alternatives support, it MUST be placed in a subpackage along with the ld.so.conf.d file so that alternatives support does not need to be installed if not wished for.
The MPI compiler package MUST provide an RPM macro that makes loading and unloading the support easy in spec files, e.g. by placing the following in /etc/rpm/macros.openmpi
%_openmpi_load \
. /etc/profile.d/modules.sh; \
module load openmpi-%{_arch}; \
export CFLAGS="$CFLAGS %{optflags}";
%_openmpi_unload \
. /etc/profile.d/modules.sh; \
module unload openmpi-%{_arch};
loading and unloading the compiler in spec files is as easy as %{_openmpi_load} and %{_openmpi_unload}.
If the environment module sets compiler flags such as CFLAGS (thus overriding the ones exported in %configure, the RPM macro MUST make them use the Fedora optimization flags %{optflags} once again (as in the example above in which the openmpi-%{_arch} module sets CFLAGS).
Packaging of MPI software
Software that supports MPI MUST be packaged also in serial mode [i.e. no MPI], if it is supported by upstream. (for instance: foo).
If possible, the packager MUST package versions for each MPI compiler in Fedora (e.g. if something can only be built with mpich2 and mvapich2, then lam and openmpi packages do not need to be made).
MPI implementation specific files MUST be installed in the directories used by the used MPI compiler ($MPI_BIN, $MPI_LIB and so on). The binaries MUST be suffixed with $MPI_SUFFIX (e.g. _openmpi for Open MPI, _mpich2 for MPICH2 and _lam for LAM/MPI).
The MPI enabled bits MUST be placed in a subpackage with the suffix denoting the MPI compiler used (for instance: foo-openmpi for Open MPI [the traditional MPI compiler in Fedora] or foo-mpich2 for MPICH2). For directory ownership and to guarantee the pickup of the correct MPI runtime, the MPI subpackages MUST require the correct MPI compiler's runtime package.
Each MPI build of shared libraries SHOULD have a separate -libs subpackage for the libraries (e.g. foo-mpich2-libs). As in the case of MPI compilers, NO library configuration (in /etc/ld.so.conf.d) MUST be made.
In case the headers are the same regardless of the compilation method and architecture (e.g. 32-bit serial, 64-bit Open MPI, MPICH2), they MUST be split into a separate -headers subpackage (e.g. 'foo-headers'). Fortran modules are architecture specific and are placed in -devel.
Each MPI build MUST have a separate -devel subpackage (e.g. foo-mpich2-devel) that includes the development libraries and Requires: %{name}-headers. The goal is to be able to install and develop using e.g. 'foo-mpi-devel' without needing to install e.g. mpich2 and lam or the serial version of the package.
Files must be shared between packages as much as possible. Compiler independent parts, such as data files in %{_datadir}/%{name} and man files MUST be put into a -common subpackage.
A sample spec file
Name: foo
Requires: %{name}-common = %{version}-%{release}
%package common
%package lam
BuildRequires: lam-devel
# Require explicitly for dir ownership and to guarantee the pickup of the right runtime
Requires: lam
Requires: %{name}-common = %{version}-%{release}
%package mpi
BuildRequires: openmpi-devel
# Require explicitly for dir ownership and to guarantee the pickup of the right runtime
Requires: openmpi
Requires: %{name}-common = %{version}-%{release}
%package mpich2
BuildRequires: mpich2-devel
# Require explicitly for dir ownership and to guarantee the pickup of the right runtime
Requires: mpich2
Requires: %{name}-common = %{version}-%{release}
%build
# Have to do off-root builds to be able to build many versions at once
# Build serial version
mkdir serial
cd serial
ln -s ../configure .
%configure
make %{?_smp_mflags}
cd ..
# Build parallel versions: set compiler variables to MPI wrappers
export CC=mpicc
export CXX=mpicxx
export FC=mpif90
export F77=mpif77
# Build LAM version
%{_lam_load}
mkdir $MPI_COMPILER
cd $MPI_COMPILER
ln -s ../configure .
%configure --program-suffix=$MPI_SUFFIX
make %{?_smp_mflags}
cd ..
%{_lam_unload}
# Build OpenMPI version
%{_openmpi_load}
mkdir $MPI_COMPILER
cd $MPI_COMPILER
ln -s ../configure .
%configure --program-suffix=$MPI_SUFFIX
make %{?_smp_mflags}
cd ..
%{_openmpi_unload}
# Build mpich2 version
%{_mpich2_load}
mkdir $MPI_COMPILER
cd $MPI_COMPILER
ln -s ../configure .
%configure --program-suffix=$MPI_SUFFIX
make %{?_smp_mflags}
cd ..
%{_mpich2_unload}
%install
# Install serial version
make -C serial install DESTDIR=%{buildroot} INSTALL="install -p" CPPROG="cp -p"
# Install LAM version
%{_lam_load}
make -C $MPI_COMPILER install DESTDIR=%{buildroot} INSTALL="install -p" CPPROG="cp -p"
%{_lam_unload}
# Install OpenMPI version
%{_openmpi_load}
make -C $MPI_COMPILER install DESTDIR=%{buildroot} INSTALL="install -p" CPPROG="cp -p"
%{_openmpi_unload}
# Install MPICH2 version
%{_mpich2_load}
make -C $MPI_COMPILER install DESTDIR=%{buildroot} INSTALL="install -p" CPPROG="cp -p"
%{_mpich2_unload}
%files # All the serial (normal) binaries
%files common # All files shared between the serial and different MPI versions
%files lam # All lam linked files
%files openmpi # All openmpi linked files
%files mpich2 # All mpich2 linked files