MPICH, DCMF, and SPI
Introduction
To support high performance computing (HPC) applications, specifically MPI applications, we have ported IBM CNK's communication software stack to the ZeptoOS compute node Linux environment. MPICH used in this ZeptoOS release is mpich2-1.0.7 with IBM patches. It is reasonably stable, and the performance of MPI applications on the ZeptoOS compute node Linux is comparable to that on CNK. While there are some limitations at the moment, there are benefits as well.
Benefits:
- No limitation on the number of threads
- 4 or more OpenMP threads per node
- Additional threads as I/O or backgroup tasks
- It is Linux!
- Debugging tools such as gdb, strace, etc
- Various file systems, such as ramfs
Current limitations:
- Only the SMP mode is supported
- Shared libraries are not provided now
- No binary compatibility between CNK and ZeptoOS CN Linux
We will support a VN-equivalent mode (multiple MPI tasks per node) and provide shared libraries in a future release.
As in IBM CNK environment, Deep Computing Messaging Framework (DCMF) and System Programming Interface (SPI) are available. It is possible to write a DCMF code or a SPI code directly if necessary. DCMF is a communication library that provides non-blocking operations. Please refer to the DCMF wiki for details. We are using DCMF version 1.0.0 in the current ZeptoOS release, which is older than the DCMF in the current driver release (V1R3M0). SPI is the lowest-level user space API for the torus DMA, collective network, BGP-specifc lock mechanisms, and other compute node specific features. There is no public document on SPI available at the moment, but almost all header files and source code is available. Internally, MPICH depends on DMCF, which in turn depends on SPI.
ZCB and Big memory
MPI application running under the ZeptoOS compute node environment (technically, applications that require the DMA operation or a maximum memory bandwidth) need to be configured as Zepto Compute Binaries (ZCB). This is done using the zelftool, invoked behind the scenes when linking a binary using the ZeptoOS MPI compiler wrapper scripts (zmpicc, etc). ZeptoOS compute node kernel treats ZCB executables differently from ordinary processes. It creates a special memory mapping region called big memory, which is covered by large pages with semi-static TLB entries, and loads all applications sections to the big memory region. Big memory region has virtually no TLB misses and it also enables DMA operations. However, some system calls will not work correctly if used from a ZCB process, in particular fork (but creating threads does work).
Compiling HPC applications
While the same compiler can be used as for the IBM CNK, ZeptoOS compute node environment requires linking with ZeptoOS-specific communication libraries (applications linked with the CNK MPI will not work on ZeptoOS).
Compiler wrapper scripts
We provide compiler wrapper scripts which automatically link with appropriate libraries from the ZeptoOS installation directory. We provide the same set of wrapper scripts that IBM provides, with an extra z prefix:
- zmpicc, zmpicxx, zmpif77, zmpif90
- Wrapper scripts that invoke BGP-enhanced GNU compilers
- zmpixlc, zmpixlcxx, zmpixlf2003, zmpixlf77, zmpixlf90, zmpixlf95
- Wrapper scripts that invoke IBM XL compilers
- zmpixlc_r, zmpixlcxx_r, zmpixlf2003_r, zmpixlf77_r, zmpixlf90_r, zmpixlf95_r
- Wrapper scripts that invoke IBM XL compilers (thread safe compilation for OpenMP)
To get insight into the internals of these scripts, invoke them with the -show option.
A compilation example
Understanding build system on a program might take some time, but there is nothing special to compile a program for ZeptoOS.
Here is a real-world example of how to build a well-known Parallel Ocean Program (POP).
$ wget http://climate.lanl.gov/Models/POP/POP_2.0.1.tar.Z $ tar xvfz POP_2.0.1.tar.Z && cd pop $ ./setup_run_dir ztest && cd ztest $ edit ibm_mpi.gnu # see the patch below $ export ARCHDIR=ibm_mpi $ make # takes a while $ edit pop_in # test data set - nprocs_clinic = 4 - nprocs_tropic = 4 + nprocs_clinic = 64 + nprocs_tropic = 64 $ cqsub -n 64 -t 10 -k <zepto_profile> ./pop -------------------- --- orig/ibm_mpi.gnu 2009-04-15 15:01:58.666457601 -0500 +++ ztest/ibm_mpi.gnu 2009-04-15 14:17:58.099132435 -0500 @@ -6,17 +6,18 @@ # will someday be a file which is a cookbook in Q&A style: "How do I do X?" # is followed by something like "Go to file Y and add Z to line NNN." # -FC = mpxlf90_r -LD = mpxlf90_r -CC = mpcc_r -Cp = /usr/bin/cp -Cpp = /usr/ccs/lib/cpp -P +ZPATH=<zepto_dir> +FC = $(ZPATH)/zmpixlf90 +LD = $(ZPATH)/zmpixlf90 +CC = $(ZPATH)/zmpixlc +Cp = /bin/cp +Cpp = /usr/bin/cpp -P AWK = /usr/bin/awk -ABI = -q64 +#ABI = -q64 COMMDIR = mpi -NETCDFINC = -I/usr/local/include -NETCDFLIB = -L/usr/local/lib +NETCDFINC = -I/soft/apps/netcdf-4.0/include/ +NETCDFLIB = -L/soft/apps/netcdf-4.0/lib # Enable MPI library for parallel code, yes/no. @@ -58,7 +59,8 @@ # #---------------------------------------------------------------------------- -FBASE = $(ABI) -qarch=auto -qnosave -bmaxdata:0x80000000 $(NETCDFINC) -I$(ObjDepDir) +#FBASE = $(ABI) -qarch=auto -qnosave -bmaxdata:0x80000000 $(NETCDFINC) -I$(ObjDepDir) +FBASE = $(ABI) -qarch=auto -qnosave $(NETCDFINC) -I$(ObjDepDir) ifeq ($(TRAP_FPE),yes) FBASE := $(FBASE) -qflttrap=overflow:zerodivide:enable -qspillsize=32704
Compiling without the wrapper scripts
If one wishes to invoke the compiler directly, please make sure that the Makefile or build environment points to ZeptoOS header files and libraries correctly. An example would be:
$ /bgsys/drivers/ppcfloor/gnu-linux/bin/powerpc-bgp-linux-gcc \ -o mpi-test-linux -Wall -O3 -I<zepto_dir>/include mpi-test.c \ -L<zepto_dir>/lib -lmpich.zcl -ldcmfcoll.zcl -ldcmf.zcl -lSPI.zcl -lzcl \ -lzoid_cn -lrt -lpthread -lm $ <zepto_dir>/bin/zelftool -e mpi-test-linux
Notes:
- Replace <zepto_dir> with your actuall ZeptoOS install path.
- Do not forget to call the zelftool utility, which makes the executable a Zepto Compute Binary.
Building MPICH, DCMF, and SPI libraries
We provide all the necessary source code to build MPICH, DCMF, and SPI. To build these libraries, just type:
$ make -C comm rebuild-target
It may take half an hour to an hour to complete the build process, depending on what file system you are using (i.e., GPFS is a lot slower than a local file system).
The rebuild-target target does not know anything about the existing installation directory; it only copies the built libraries and header files to the comm/tmp directory. To install the newly built libraries, do the following:
$ make -C comm update-prebuilt $ python install.py <zepto_dir>
The update-prebuilt target basically copies the files from the comm/tmp directory to the comm/prebuilt directory, which is where the install.py script looks for to copy the files to <zepto_dir>.
Software stack layout
The figure on the right depicts the layout of the communication software stack in the ZeptoOS compute node environment. This is essentially the same as in IBM CNK's stack, except that they have no ZEPTO SPI, and CNK instead of Linux. While we skip the brief explanation of MPICH since it's well-known software piece, we briefly describe what DCMF and SPI are here.
- DCMF
- Stands for Deep Computing Messaging Framework
- Developed by IBM originally for BleuGene architecture
- Hardware Initialization, query functions
- Supports BGP Torus DMA, collective network
- Provides timer
- Supports non-blocking collective operations
- BGP MPICH uses DCMF internally (IBM provides a glue layer)
- SPI
- Stands for System Programming Interface
- Developed by IBM. BGP specific codes.
- Kernel interfaces - DMA control, lockbox, etc
- DMA related definitions
- can be used in both user space and kernel space
- RAS, BGP personality, mapping related functions
BGP SPI is basically designed only for IBM CNK, so SPI is not compatible with Linux. ZEPTO SPI is a thin software layer that absorbs the differences between CNK and Linux, or drops the requests that Linux can not handle.
Source code
The source codes and header files of DCMF and SPI can be found in the comm directory. The source code of MPICH is in an archive DCMF/lib/mpich2/mpich2-1.0.7.tar.gz, which will be extracted at the build time.
The DCMF source codes are located in DCMF/sys/. DCMF core source codes are in DCMF/sys/messaging. Component Collective Messaging Interface(CCMI) is part of DCMF and its source codes are in DCMF/sys/collectives. Test codes can be found in DCMF/sys/collectives/tests for CCMI and DCMF/sys/messaging/tests. Those test codes can be a good example for DCMF/CCMI programming.
SPI headers are in arch-runtime/arch and SPI source codes are in comm/arch-runtime/runtime/. arch-runtime/zcl_spi contains the source code of ZEPTO SPI layer and arch-runtime/arch/include/zepto contains the header files of ZEPTO SPI layer.
comm |-- DCMF | |-- lib | | |-- dev | | `-- mpich2 | | `-- make | |-- sys | | |-- collectives | | | |-- adaptor | | | |-- kernel | | | |-- tests | | | `-- tools | | |-- include | | |-- messaging | | | |-- devices | | | |-- messager | | | |-- protocols | | | |-- queueing | | | |-- sysdep | | `-- tests |-- arch-runtime | |-- arch | | `-- include | | |-- bpcore | | |-- cnk | | |-- common | | |-- spi | | `-- zepto | |-- runtime | |-- testcodes | `-- zcl_spi `-- testcodes
Zepto trace print function
Zepto trace print function are embbed in part of SPI and DCMF codes. You can enable the trace feature by passing the ZEPTO_TRACE environment variable when you submit a job. ZEPTO_TRACE has integer that indicates trace level. higher number more details.
An example:
$ cqsub -n 64 -t 10 ... -e ZEPTO_TRACE=2 ./a.out
