Using Chapel on HPE Cray Systems
The following information is assembled to help Chapel users get up and running on HPE Cray systems including the HPE Cray EX and Cray XC series systems.
Getting Started with Chapel on HPE Cray EX or XC Systems
Chapel is available as a module for HPE Cray EX and XC systems. When it is installed on your system, you do not need to build Chapel from the source release (though you can). Using the module systems on such platforms, you can use Chapel with the default settings and confirm it is correctly installed, as follows:
Ensure this required module is loaded. Normally it will be loaded for you, but under some circumstances you may need to load or restore it yourself:
PrgEnv-gnu or PrgEnv-cray
Load the Chapel module:
module load chapel
Compile an example program using:
chpl $CHPL_HOME/examples/hello6-taskpar-dist.chpl
Execute the resulting executable (on four locales):
./hello6-taskpar-dist -nl 4
This should be all that is necessary to use Chapel on an HPE Cray EX or XC system. If the installation setup by your system administrator deviates from the default settings, or you are interested in other configuration options, see Using Chapel on an HPE Cray System below. If instead you wish to build Chapel from source, continue on to Building Chapel for an HPE Cray System from Source just below.
Note that the Chapel module for HPE Cray EX systems does not currently have the GASNet communication layer built into it. For multilocale execution on EX systems please use the ofi communication layer instead.
For information on obtaining and installing the Chapel module please contact your system administrator.
Getting Started with Chapel on HPE Apollo and Cray CS Systems
On HPE Apollo and Cray CS systems, Chapel is not currently available as a module due to the wide diversity of configurations that these systems support. For this reason, Chapel must be built from source on these systems using the Building Chapel for an HPE Cray System from Source instructions just below.
Building Chapel for an HPE Cray System from Source
Set
CHPL_HOST_PLATFORM
to the string representing your system type.For example:
export CHPL_HOST_PLATFORM=hpe-cray-ex
The following table lists the supported systems and strings. Note that on HPE Cray EX and XC systems, these values should typically be inferred automatically and not need to be set manually. That said, there is also no downside to setting them manually. As with most CHPL_* environment variables, the current set and inferred values can be determined by running
$CHPL_HOME/util/printchplenv
.System
CHPL_HOST_PLATFORM
EX series
hpe-cray-ex
Apollo series
hpe-apollo
XD series
hpe-cray-xd
XC series
cray-xc
CS series
cray-cs
Optionally, set the
CHPL_LAUNCHER
environment variable to indicate how Chapel should launch jobs on your system:On an HPE Cray EX system, …
set CHPL_LAUNCHER to…
…queue jobs using SLURM (sbatch)
slurm-srun
…run jobs interactively using PALS
pals
On a HPE Apollo or Cray CS system, to…
set CHPL_LAUNCHER to…
…run jobs interactively on your system
gasnetrun_ibv
…queue jobs using SLURM (sbatch)
slurm-gasnetrun_ibv
…queue jobs using LSF (bsub)
lsf-gasnetrun_ibv
…queue jobs using PBS (qsub)
pbs-gasnetrun_ibv
On a Cray XC system, to…
set CHPL_LAUNCHER to…
…run jobs interactively on your system
aprun
…queue jobs using PBS (qsub)
pbs-aprun
…queue jobs using SLURM (sbatch)
slurm-srun
On HPE Cray EX systems,
CHPL_LAUNCHER
defaults toslurm-srun
ifsrun
is in your path andnone
otherwise.On HPE Apollo and Cray CS systems,
CHPL_LAUNCHER
defaults togasnetrun_ibv
.On Cray XC systems,
CHPL_LAUNCHER
defaults toaprun
ifaprun
is in your path,slurm-srun
ifsrun
is in your path andnone
otherwise.You can also set CHPL_LAUNCHER to
none
if you prefer to manually manage all queuing and job launch commands yourself, though the advantage of using a launcher is to make sure that Chapel maps processes and threads to the appropriate target hardware units.For more information on Chapel’s launcher capabilities and options, refer to Chapel Launchers.
Select the target compiler that Chapel should use when compiling code for the compute node:
On an HPE Apollo or Cray CS series system, set the
CHPL_TARGET_COMPILER
environment variable to indicate which compiler to use (and make sure that the compiler is in your path).To request…
set CHPL_TARGET_COMPILER to…
…the LLVM/clang backend
llvm (default)
…the GNU compiler (gcc)
gnu
…the Clang compiler
clang
…the Intel compiler (icc)
intel
On an HPE Cray EX or Cray XC system, when using the C back-end, ensure that you have one of the following Programming Environment modules loaded to specify your target compiler:
PrgEnv-allinea (ARM only) PrgEnv-cray PrgEnv-gnu PrgEnv-intel
Make sure you’re in the top-level chapel/ directory and make/re-make the compiler and runtime:
gmake
Note that a single Chapel installation can support multiple configurations simultaneously and that you can switch between them simply by changing any of the above settings. However, each configuration must be built separately. Thus, you can change any of the settings in the steps before this, and then re-run this step in order to create additional installations. Thereafter, you can switch between any of these configurations without rebuilding.
Using Chapel on an HPE Cray System
If you are working from a Chapel module:
Load the module using
module load chapel
Optionally select a launcher, as in step 2 above
Select a target compiler, as in step 3 above
If you are working from a source installation:
Set your host platform as in step 1 above
Optionally select a launcher, as in step 2 above
Select a target compiler, as in step 3 above
Set
CHPL_HOME
and your paths by invoking the appropriateutil/setchplenv
script for your shell. For example:
source util/setchplenv.bash
On HPE Cray EX systems with
CHPL_COMM=ofi
, optionally, load the Cray PMI modules:module load cray-pmi{,-lib}
Often this is not required. Usually the default PMI support has sufficient capabilities to support Chapel program startup. But under certain circumstances it does not, and when you run a Chapel program that was built without these loaded you will see messages like this one:
[PE_0]:_pmi2_add_kvs:ERROR: The KVS data segment of <num> entries is not large enough. Increase the number of KVS entries by setting env variable PMI_MAX_KVS_ENTRIES to a higher value.
Having the Cray PMI modules loaded when the program is compiled will prevent this problem. We expect that eventually these modules will be loaded by default on EX systems, but so far this has not consistently been the case.
Compile your Chapel program. For example:
chpl $CHPL_HOME/examples/hello6-taskpar-dist.chpl
See Compiling Chapel Programs or
man chpl
for further details.If
CHPL_LAUNCHER
is set to anything other thannone
, when you compile a Chapel program for your Cray system, you will see two binaries (e.g.,hello6-taskpar-dist
andhello6-taskpar-dist_real
). The first binary contains code to launch the Chapel program onto the compute nodes, as specified by yourCHPL_LAUNCHER
setting. The second contains the program code itself; it is not intended to be executed directly from the shell prompt.You can use the
-v
or--dry-run
flags to see the commands used by the launcher binary to start your program.If
CHPL_LAUNCHER
ispbs-aprun
:You can optionally specify a queue name using the environment variable
CHPL_LAUNCHER_QUEUE
. For example:export CHPL_LAUNCHER_QUEUE=batch
If this variable is left unset, no queue name will be specified. Alternatively, you can set the queue name on your Chapel program command line using the
--queue
flag.You can also optionally set a wall clock time limit for the job using
CHPL_LAUNCHER_WALLTIME
. For example to specify a 10-minute time limit, use:export CHPL_LAUNCHER_WALLTIME=00:10:00
Alternatively, you can set the wall clock time limit on your Chapel program command line using the
--walltime
flag.
For further information about launchers, please refer to Chapel Launchers.
Execute your Chapel program. Multi-locale executions require the number of locales (compute nodes) to be specified on the command line. For example:
./hello6-taskpar-dist -nl 2
Requests the program to be executed using two locales.
If your HPE Cray system has compute nodes with varying numbers of cores, you can request nodes with at least a certain number of cores using the variable
CHPL_LAUNCHER_CORES_PER_LOCALE
. For example, on a system in which some compute nodes have 24 or more cores per compute node, you could request nodes with at least 24 cores using:export CHPL_LAUNCHER_CORES_PER_LOCALE=24
This variable may be needed when you are using the aprun launcher and running Chapel programs within batch jobs you are managing yourself. The aprun launcher currently creates aprun commands that request the maximum number of cores per locale found on any locale in the system, irrespective of the fact that the batch job may have a lower limit than that on the number of cores per locale. If the batch job limit is less than the maximum number of cores per locale, you will get the following error message when you try to run a Chapel program:
apsched: claim exceeds reservation's CPUs
You can work around this by setting
CHPL_LAUNCHER_CORES_PER_LOCALE
to the same or lesser value as the number of cores per locale specified for the batch job (for example, the mppdepth resource for the PBS qsub command). In the future we hope to achieve better integration between Chapel launchers and workload managers.If your HPE Cray system has compute nodes with varying numbers of CPUs per compute unit, you can request nodes with a certain number of CPUs per compute unit using the variable
CHPL_LAUNCHER_CPUS_PER_CU
. For example, on a Cray XC system with some nodes having at least 2 CPUs per compute unit, to request running on those nodes you would use:export CHPL_LAUNCHER_CPUS_PER_CU=2
Currently, the only legal values for
CHPL_LAUNCHER_CPUS_PER_CU
are 0 (the default), 1, and 2.
For more information on… |
see… |
---|---|
…CHPL_* environment settings |
|
…Compiling Chapel programs |
|
…Launcher options |
|
…Executing Chapel programs |
|
…Running multi-locale Chapel programs |
Cray File Systems and Chapel execution
For best results, it is recommended that you execute your Chapel program by placing the binaries on a file system shared between the login node and compute nodes (typically Lustre), as this will provide the greatest degree of transparency when executing your program. In some cases, running a Chapel program from a non-shared file system will make it impossible to launch onto the compute nodes. In other cases, the launch will succeed, but any files read or written by the Chapel program will be opened relative to the compute node’s file system rather than the login node’s.
Special Notes for Cray XC Series Systems
Native ugni Communication Layer
The native ugni communication layer is the default on Cray XC systems. See Using Chapel with ugni for more information on using the ugni communication layer.
GASNet Communication Layer
The GASNet-based communication layer discussed in the Using Chapel with GASNet page can be used on Cray XC systems, using the ‘ofi’ or ‘mpi’ substrates. This is not well supported or tested. The relevant configurations are:
- CHPL_COMM=gasnet
CHPL_COMM_SUBSTRATE=ofi or mpi CHPL_GASNET_SEGMENT=fast or large
In these configurations the heap is created with a fixed size at the beginning of execution. The default size works well in most cases but if it doesn’t a different size can be specified, as discussed in the following section.
GASNet Communication Layer and the Heap
In contrast to the dynamic heap extension available in the ugni comm layer, when the GASNet comm layer is used with a native substrate for higher network performance, the runtime must know up front the maximum size the heap will grow to during execution.
In these cases the heap is used for all dynamic allocations, including
arrays. By default it will occupy as much of the free memory on each
compute node as the runtime can acquire, less some small amount to allow
for demands from other (system) programs running there. Advanced users
may want to make the heap smaller than the default. Programs start more
quickly with a smaller heap, and in the unfortunate event that you need
to produce core files, those will be written more quickly if the heap is
smaller. Specify the heap size using the CHPL_RT_MAX_HEAP_SIZE
environment variable, as discussed in ugni Communication Layer and the Heap.
But be aware that just as in the CHPL_COMM=ugni
case, if you reduce the heap size to less than the amount your program
actually needs and then run it, it will terminate prematurely due to not
having enough memory.
Note that for CHPL_COMM=gasnet
, CHPL_RT_MAX_HEAP_SIZE
is
synonymous with GASNET_MAX_SEGSIZE
, and the former overrides the
latter if both are set.
Known Constraints and Bugs
Our PBS launcher explicitly supports PBS Pro, Moab/Torque, and the NCCS site versions of PBS. It may also work with other versions. If our PBS launcher does not work for you, you can fall back on a more manual launch of your program. For example, supposing the program is compiled to
myprogram
:Launch the
myprogram_real
binary manually using aprun and your own qsub script or command.Use
./myprogram --generate-qsub-script
to generate a qsub script. Then edit the generated script and launch themyprogram_real
binary manually as above.
Redirecting stdin when executing a Chapel program under PBS/qsub may not work due to limitations of qsub.
For EX and XC systems, there is a known issue with the Cray MPI release that causes some programs to assert and then hang during exit. A workaround is to set the environment variable,
MPICH_GNI_DYNAMIC_CONN
todisabled
. Setting this environment variable affects all MPI programs, so remember to unset it after running your Chapel program.The amount of memory available to a Chapel program running over GASNet with the aries conduit is allocated at program start up. The default memory segment size may be too high on some platforms, resulting in an internal Chapel error or a GASNet initialization error such as:
node 1 log gasnetc_init_segment() at $CHPL_HOME/third-party/gasnet/gasnet-src/aries-conduit/gasnet_aries.c:<line#>: MemRegister segment fault 8 at 0x2aab6ae00000 60000000, code GNI_RC_ERROR_RESOURCE
If your Chapel program exits with such an error, try setting the environment variable
CHPL_RT_MAX_HEAP_SIZE
orGASNET_MAX_SEGSIZE
to a lower value than the default (say 1G) and re-running your program. For more information, refer to the discussion ofCHPL_RT_MAX_HEAP_SIZE
above and/or the discussion ofGASNET_MAX_SEGSIZE
here:$CHPL_HOME/third-party/gasnet/gasnet-src/README