Parallel I/O with SIONlib

Modules

Recent versions of SIONlib are available on the DEEP-EST prototype through the new software stack as modules:

$ module spider SIONlib/1.7.6

SIONlib documentation

Documentation for SIONlib can be found on the web at ​https://apps.fz-juelich.de/jsc/sionlib/docu/current/index.html

MSA aware collective I/O

Recent versions of SIONlib contain mechanisms to perform I/O operations collectively, i.e. all processes of a parallel computation partake in these operations. This enables an exchange of I/O data between the processes, allowing a subset of all processes, the collector processes, to perform the actual transfer of data to the storage on behalf of other processes. Collector processes should typically be those processes that are placed on parts of the MSA with a high bandwidth connection to the parallel file system. The mechanism has been extended with a new MSA-aware algorithm for the selection of collector processes. The algorithm is portable and relies on platform specific plug-ins to identify processes which run on parts of the system that are well suited for the role of I/O collector. So far, three plug-ins have been implemented:

• a new generic plug-in — hostname-regex — which selects collectors tasks by matching the host name of the node they are running on against regular expressions that can be defined via environment variables,
• an older plug-in — deep-est-std — that selects collector tasks using a similar mechanism, but with host names hard-coded to match cluster nodes of an earlier version of the DEEP-EST prototype,
• a mock-up plug-in for testing purposes.

In the future, further plug-ins for new systems of the MSA type can be added.

In order to use the MSA aware collective I/O operations, a platform specific plug-in has to be selected when installing SIONlib during the configure step.

./configure --msa=hostname-regex # ... more configure arguments

When opening a SIONlib file for access from several MPI processes in parallel, the user has to enable the MSA aware collective I/O mode. This is done using the file_mode argument of the open function. file_mode contains a string that consists of a comma separated list of keys and key value pairs. The word collmsa must appear in that list to select MSA aware collective I/O.

sion_paropen_mpi("filename", "...,collmsa,...", ...);

Also, when the new hostname-regex collector selection plug-in is enabled, an environment variable SION_MSA_COLLECTOR_HOSTNAME_REGEX has to be defined to contain a POSIX basic regular expression to match against hostnames of nodes running candidates for the collector role (SION_MSA_COLLECTOR_HOSTNAME_EREGEX can be used alternatively, but should contain a POSIX extended regular expression). For example, to select nodes from the DAM as collectors, set:

export SION_MSA_COLLECTOR_HOSTNAME_EREGEX="dp-dam.*"

Additionally, as is the case when using regular collective I/O, the size of collector groups has to be secified, either through the file_mode argument of the sion_paropen_mpi function or via the environment variable SION_COLLSIZE.

SIONlib CUDA aware interface

In order to match the programming interface offered by other libraries, such as ParaStation? MPI, more closely, functions of SIONlib have been made CUDA-aware. This means that applications are allowed to pass device pointers pointing to on device memory to the various read and write functions of SIONlib without needing to manually copy their contents to the host memory.

Like the MSA aware collective I/O operations, the CUDA aware interface has to be enabled when installing SIONlib. This is done by invoking the configure script with the argument --enable-cuda which optionally allows to specify the path to a CUDA installation.

./configure --enable-cuda=/path/to/cuda/installation # ... more configure arguments

When SIONlib has been installed with the CUDA aware interface enabled, the user may pass device pointers as the data argument to SIONlib's

• task-local
• key/value
• collective

read and write functions.

size_t sion_fwrite(const void *data, size_t size, size_t nitems, int sid);
size_t sion_fread(void *data, size_t size, size_t nitems, int sid);
size_t sion_fwrite_key(const void *data, uint64_t key, size_t size, size_t nitems, int sid);
size_t sion_fread_key(void *data, uint64_t key, size_t size, size_t nitems, int sid);
size_t sion_coll_fwrite(const void *data, size_t size, size_t nitems, int sid);
size_t sion_coll_fread(void *data, size_t size, size_t nitems, int sid);

SIONlib inspects the pointer and if it points to an on-device buffer performs a block-wise copy of the data into host memory before writing to disk or into device memory after reading from disk.