README

******************************************************************************
				  GPI-2
			  http://www.gpi-site.com
		  
		  	      Version: 1.3.0
			  Copyright (C) 2013-2016
			     Fraunhofer ITWM
			     
******************************************************************************

1. INTRODUCTION
===============

GPI-2 is the second generation of GPI (www.gpi-site.com). GPI-2
implements the GASPI specification (www.gaspi.de), an API
specification which originates from the ideas and concepts of GPI.

GPI-2 is an API for asynchronous communication. It provides a
flexible, scalable and fault tolerant interface for parallel
applications.


2. INSTALLATION
===============

Requirements:
-------------

The current version of GPI-2 has the following requirements.

Software:
- libibverbs v1.1.6 (Verbs library from OFED) if running on Infiniband.
- ssh server running on compute nodes (requiring no password).
- gawk (GNU Awk) and sed utilities.

Hardware:
- Infiniband/RoCE device or Ethernet device.

The easiest way to install GPI-2 is by using the install.sh
script. The default settings install GPI-2 under /opt/GPI2/. This
location can be easily modified by passing the location with the -p
option to the install script.

For example,
    ./install.sh -p /prog/GPI2

installs GPI-2 under /prog/GPI2 instead of under the default location.

Infiniband support (default)
----------------------------

GPI-2 requires the libibverbs from the OFED stack. You can pass the
path of your OFED installation to the install script using the option
(--with-infiniband) for that, in case the install script is not able to find it:

     ./install.sh --with-infiniband<=full_path_to_ofed>

You can see the install script usage:
    ./install.sh -h

Ethernet support
----------------

To install GPI-2 on a system without Infiniband, you can use the
option --with-ethernet. With this option standard TCP sockets are
used.

Such support is primarily targetted at the development of GPI-2
applications without the need to access a system with Infiniband, with
less focus on performance.

MPI Interoperability
--------------------

If you plan to use GPI-2 with MPI to, for instance, start an
incremental port of a large application or to use some libraries that
require MPI, you can enable MPI interoperability with the option:

     ./install.sh --with-mpi<=path_to_mpi_installation>

If you don't provide a path to your MPI installation and mpirun is in
your PATH, the installation script will take that MPI installation.

This will enable you to use GPI-2 with MPI where the only constraint
is that MPI_Init() must be invoked before gaspi_proc_init(). For this
MPI+GPI2 mixed mode, it is assumed that you start the application with
mpirun (or mpiexec, etc.).

Note that this option will build GPI-2 with MPI, requiring you to link
the MPI library to your GPI-2 application (even if you are not using
MPI). If you are interested in using GPI-2 only, do not build GPI-2
with this option.

GPU/CUDA support
-------------------

If you plan to use GPI-2 with CUDA and to allow direct data transfer
between GPUs, you enable GPU support with

     ./install.sh --with-cuda<=path_to_cuda_installation>

If you don't provide a path to your CUDA installation and nvcc is in
your PATH, the installation script will take that CUDA installation.


GPI-2 with CUDA support actually requires GPUDirect RDMA support, so
it will be checked if the required kernel-module is installed

Due to the limitations of GPUDirect RDMA, the maximal GPU memory
segment size is limited to 250MB.

To enable GPU support in your application, call gaspi_init_GPUs (in
include/GASPI_GPU.h). The function gaspi_number_of_GPUs will return
the number of supported GPUs on the actual NUMA-node while the function
gaspi_GPU_ids returns the device Ids of the supported GPUs.

	
3. BUILDING GPI-2
=================

You can build GPI-2 on your own. There are the following make targets:

all	  - Build everything
gpi	  - Build the GPI-2 library (including debug version)
fortran	  - Build Fortran 90 bindings
mic	  - Build the GPI-2 library for the MIC
tests	  - Build provided tests
docs	  - Generate documentation (requires doxygen)
clean	  - Clean-up

4. BUILDING GPI-2 APPLICATIONS
==============================

GPI-2 provides two libraries: libGPI2.a and libGPI2-dbg.a.

The libGPI2.a aims at high-performance and is to be used in production
whereas the libGPI2-dbg.a provides a debug version, with extra
parameter checking and debug messages and is to be used to debug and
during development.


5. RUNNING GPI-2 APPLICATIONS
=============================

The gaspi_run utility is used to start and run GPI-2
applications. A machine file with the hostnames of nodes where the
application will run, must be provided.

For example, to start 1 process per node (on 4 nodes), the machine
file looks like:

node01
node02
node03
node04

Similarly, to start 2 processes per node (on 4 nodes):

node01
node01
node02
node02
node03
node03
node04
node04

The gaspi_run utility is invoked as follows:

	gaspi_run -m <machinefile> [OPTIONS] <path GASPI program>

IMPORTANT: The path to the program must exist on all nodes where the
program should be started.
	
The gaspi_run utility has the following further options [OPTIONS]:

  -b <binary file> Use a different binary for first node (master).
     	     	   The master (first entry in the machine file) is
		   started with a different application than the rest
		   of the nodes (workers).
     	     	   
  -N               Enable NUMA for processes on same node. With this
  		   option it is only possible to start the same number
		   of processes as NUMA nodes present on the system.
		   The processes running on same node will be set with
		   affinity to the proper NUMA node.
  
  -n <procs>       Start as many <procs> from machine file.
     		   This option is used to start less processes than
		   those listed in the machine file.
		   
  -d               Run with GDB (debugger) on master node. With this
  		   option, GDB is started in the master node, to allow
		   debugging the application.

  -p               Ping hosts before starting the binary to make sure
  		   they are available.

  -h               Show help.


5. THE GASPI_LOGGER
===================

The gaspi_logger utility is used to view and separate the output from
all nodes when the function gaspi_printf is called. The gaspi_logger
is started, on another session, on the master node. The output of the
application, when using gaspi_printf, will be redirected to the
gaspi_logger. Other I/O routines (e.g. printf) will not.

A further separation of output (useful for debugging) can be achieved
by using the routine gaspi_printf_to which sends the output to the
gaspi_logger started on a particular node. For example,

  gaspi_printf_to(1, "Hello 1\n");

will display the string "Hello 1" in the gaspi_logger started on rank
1.


6. GPI-2 WITH CO-PROCESSOR (INTEL XEON PHI)
==========================================

GPI-2 can be used with the Intel Xeon Phi (MIC) where the MIC is used
as one node (running possibly more than one GPI-2 process).

To use GPI-2 on the MIC, you need to compile it using the Intel
compiler with the -mmic option. The Makefile includes a build target
mic for that end but this build target is not used by the installation
script. After successful compilation, GPI-2 for the MIC can be found
under lib64/mic. If you are having problems with the compilation, make
sure the OFED_PATH and OFED_MIC_PATH in src/make.inc is setup correctly.

Assuming that the MIC(s) is set up properly, GPI-2 requires:

- ssh connectivity (requiring no password)

- grouping of local host and MIC(s) by using the tool micctrl

  micctrl --initdefaults
  micctrl --addbridge=br0 --type=internal --ip=172.31.1.254
  micctrl --network=static --bridge=br0 --ip=172.31.1.1

 where for instance, mic0: 172.31.1.1, mic1: 172.31.1.2 etc.

The MIC must be visible to the whole cluster network. For instance,
if your cluster network is 192.168.1.0 on eth0 and you want to map
mic0 to 192.168.1.100 do:

iptables -t nat -A PREROUTING -d 192.168.1.100 -i eth0 -j DNAT --to-destination 172.31.1.1
iptables -t nat -A POSTROUTING -s 172.31.1.1 -o eth0 -j SNAT --to-source 192.168.1.100

After setup, the MIC hostname can simply be added to the machinefile
and be used as another host.

7. GPU/CUDA SUPPORT
===================

To enable GPU support in your application, call gaspi_init_GPUs. This
function will check how many supported GPUs are available.
 
The function gaspi_number_of_GPUs will return the number of supported
GPUs on the actual NUMA-node, the function gaspi_GPU_ids returns the
device Ids of the supported GPUs.

Segment Creation
-----------------

To create a GPU memory segment, use the flag GASPI_MEM_GPU. The
segment will be allocated on the current active GPU. Note that the
active GPU may change by calling gaspi_init_GPUs and therefore should
be set new before creating a GPU memory segment.

Segment pointer
----------------

The segment pointer of a GPU memory segment is a GPU device
pointer. It can be used in CUDA-related functions (eg. cudaMemcpy) and
in CUDA-kernels. However, a direct access to host memory results in a
segmentation fault.

Host memory segment
--------------------

Of course, GPU memory segments can be used together with host memory
segments. If GPU-support is enabled, a new host memory segments is
also registered for the GPUs. Therefore, a segment pointer of a local
host memory segments can be used with asynchronous CUDA copy
operations for asynchronous local data transfers.

Special functions 
--------------------

Due to some issues with the PCIe-Express bus, the bandwidth of direct
GPU-to-GPU transfers is limited for larger messages sizes.  Therefore,
gaspi_gpu_write and gaspi_gpu_write_notify are optimized for remote
write operations with a GPU memory segment as source. These functions
use one-sided copies in host memory. Therefore, gaspi_gpu_write is
one-sided, but not fully asynchronous with respect to the host, since
the host thread is required to control the data flow. Small data
packages are still transfered directly. However, it can still be
overlapped with computation on the GPU. gaspi_write and
gaspi_write_notify still can be used if a full asynchronous, but
slower data transfer is preferred.

Limitations
-------------

Since the maximal size pinnable GPU memory is limited to less than
256MB on most GPUs, the maximal size of a GPU memory segment is also
limited to this size. However, this issue can be removed by using a
firmware patch for the current K20 and K40 GPUs and will be removed in
future versions.

To support direct data transfers, the Infiniband device and the GPU
must be located on the same NUMA socket. Otherwise, direct data
transfers are not supported. GPI-2 checks this at the
initialization.

8. TROUBLESHOOTING AND KNOWN ISSUES
===================================

If you're having troubles when building GPI-2 with support for
Infiniband, make sure you have the OFED stack correctly installed and
running. You can change the OFED path in the definitions file make.inc
in the source directory (src) to the fix path in your system.

When installing GPI-2 with MPI mixed-mode support (using the option
--with-mpi<=path_to_mpi_installation>) and the installation is failing
when trying to build the tests due to missing libraries, you can
provide extra paths through available variables and be able to find
the missing paths. These are: GPI2_EXTRA_CFLAGS, GPI2_EXTRA_LIBS_PATH,
GPI2_EXTRA_LIBS.

For example:
   GPI2_EXTRA_LIBS=-lmpl ./install.sh --with-mpi -p /opt/GPI2


Environment variables
---------------------

You might have some trouble when your application requires some
dynamically set environment setting (e.g. the LD_LIBRARY_PATH), for
instance, through the module system of your jobs batch
system. Currently, neither the gaspi_run or the GPI-2 library take
care of such environment settings. To this situation there are 2
workarounds:

i) you set the required environment variables in your shell
initialization file (e.g. ~/.bashrc).

ii) you create an executable shell script which sets the required
environment variables and then starts the application. Then you can
use gaspi_run to start the application, providing the shell script as
the application to execute.

    gaspi_run -m machinefile ./my_wrapper_script.sh

where my_wrapper_script.sh contains:

      #!/bin/sh

      LD_LIBRARY_PATH=$LD_LIBRARY_PATH:<path_to_my_lib>

      <path_to_my_application>/my_application <my_app_args>

      exit $?

If you're running in MPI mixed-mode, starting your application with
mpirun/mpiexec, this should not be an issue.


9. UP COMING FEATURES
=====================

GPI-2 is on-going work and more features are still to come. Here are
some that are in our roadmap:

- support to add spare nodes (fault tolerance)
- better debugging possibilities


10. MORE INFORMATION
====================

For more information, check the GPI-2 website ( www.gpi-site.com ) and
don't forget to subscribe to the GPI-2 mailing list. You subscribe it
at https://listserv.itwm.fraunhofer.de/mailman/listinfo/gpi2-users