Difference between revisions of "Using the Hydra Process Manager"
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shell$ mpiexec -f hosts -n 2 ./app : -n 1 xterm -e gdb ./app : -n 1 ./app
shell$ mpiexec -f hosts -n 2 ./app : -n 1 xterm -e gdb ./app : -n 1 ./app
Revision as of 13:37, 10 May 2012
This wiki page only provides information on the external usage of Hydra. If you are looking for the internal workings of Hydra, you can find it here.
Hydra is a process management system for starting parallel jobs. Hydra is designed to natively work with multiple daemons such as ssh, rsh, pbs, slurm and sge.
Starting MPICH2-1.1, hydra is compiled into MPICH2 releases by default as a alternate process manager. You can use it as mpiexec.hydra.
Starting MPICH2-1.3, hydra is the default process manager, which is automatically used when you use mpiexec.
Once built, the Hydra executables are in mpich2/bin, or the bin subdirectory of the install directory if you have done an install. You should put this (bin) directory in your PATH in your .cshrc or .bashrc for usage convenience:
Put in .cshrc: setenv PATH /home/you/mpich2/bin:$PATH Put in .bashrc: export PATH=/home/you/mpich2/bin:$PATH
To compile your application use mpicc:
shell$ mpicc app.c -o app
Create a file with the names of the machines that you want to run your job on. This file may or may not include the local machine.
shell$ cat hosts donner foo shakey terra
To run your application on these nodes, use mpiexec:
shell$ mpiexec -f hosts -n 4 ./app
If the same application is run with 8 processes, it will use the hosts in a round robin manner. For instance, with the above host file, ranks 0 and 4 will execute on donner, ranks 1 and 5 on foo, ranks 2 and 6 on shakey and ranks 3 and 7 on terra.
The host file can also be specified as follows:
shell$ cat hosts donner:2 foo:2 shakey:2 terra:2
In this case, ranks 0-1 will execute on donner, ranks 2-3 on foo, ranks 4-5 on shakey and ranks 6-7 on terra.
A more complex host file layout can be:
shell$ cat hosts donner:2 foo:3 shakey:2
In this case, the first 2 processes are scheduled on "donner", the next 3 on "foo" and the last 2 on "shakey". Comments in the host file start with a "#" character.
shell$ cat hosts # This is a sample host file donner:2 # The first 2 procs are scheduled to run here foo:3 # The next 3 procs run on this host shakey:2 # The last 2 procs run on this host
By default, hydra passes inherits environment variables from the shell on which mpiexec is launched, and passes it to the launched processes. However, each launcher disables the automatic propagation of some environment variables. For example, the SSH launcher disables the propagation of "DISPLAY", the SLURM launcher disables the propagation of "SLURM_*" variables, etc.
Users can force an environment variable to be propagated using the -genv option.
Environment variables can also be used to control several settings in Hydra:
HYDRA_HOST_FILE: This variable points to the default host file to use, when the "-f" option is not provided to mpiexec.
For bash: export HYDRA_HOST_FILE=<path_to_host_file>/hosts For csh/tcsh: setenv HYDRA_HOST_FILE <path_to_host_file>/hosts
HYDRA_DEBUG: Setting this to "1" enables debug mode; set it to "0" to disable.
HYDRA_ENV: Setting this to "all" will pass all of the launching node's environment to the application processes. By default, if nothing is set, the launching node's environment is passed to the executables, as long as it does not overwrite any of the environment variables that have been preset by the remote shell.
HYDRA_LAUNCH_EXTRA_ARGS: The value of this environment variable is appended to the launcher. This can be used, for example, to pass the "-q" argument to the launcher by setting HYDRA_LAUNCH_EXTRA_ARGS=-q.
MPIEXEC_TIMEOUT: The value of this environment variable is the maximum number of seconds this job will be permitted to run. When time is up, the job is aborted.
MPIEXEC_PORT_RANGE: If this environment variable is defined then Hydra will restrict its usage of ports for connecting its various processes to ports in this range. If this variable is not assigned, but MPICH_PORT_RANGE is assigned, then it will use the range specified by MPICH_PORT_RANGE for its ports. Otherwise, it will use whatever ports are assigned to it by the system. Port ranges are given as a pair of integers separated by a colon.
HYDRA_PROXY_RETRY_COUNT: The value of this environment variable determines the number of retries a proxy does to establish a connection to the main server.
Hydra with Non-Ethernet Networks
There are two ways to use Hydra with TCP/IP over the non-default network.
The first way is using the -iface option to mpiexec to specify which network interface to use. For example, if your Myrinet network's IP emulation is configured on myri0, you can use:
shell$ mpiexec -f hostfile -iface myri0 -n 4 ./app1
Similarly, if your InfiniBand network's IP emulation is configured on ib0, you can use:
shell$ mpiexec -f hostfile -iface ib0 -n 4 ./app1
You can also control this using the HYDRA_IFACE environment variable.
The second way is to specify the appropriate IP addresses in your hostfile.
shell$ /sbin/ifconfig eth0 Link encap:Ethernet HWaddr 00:14:5E:57:C4:FA inet addr:18.104.22.168 Bcast:22.214.171.124 Mask:255.255.255.0 inet6 addr: fe80::214:5eff:fe57:c4fa/64 Scope:Link UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1 RX packets:989925894 errors:0 dropped:7186 overruns:0 frame:0 TX packets:1480277023 errors:0 dropped:0 overruns:0 carrier:0 collisions:0 txqueuelen:1000 RX bytes:441568994866 (411.2 GiB) TX bytes:1864173370054 (1.6 TiB) Interrupt:185 Memory:e2000000-e2012100 myri0 Link encap:Ethernet HWaddr 00:14:5E:57:C4:F8 inet addr:10.21.3.182 Bcast:10.21.255.255 Mask:255.255.0.0 inet6 addr: fe80::214:5eff:fe57:c4f8/64 Scope:Link UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1 RX packets:3068986439 errors:0 dropped:7841 overruns:0 frame:0 TX packets:2288060450 errors:0 dropped:0 overruns:0 carrier:0 collisions:0 txqueuelen:1000 RX bytes:3598751494497 (3.2 TiB) TX bytes:1744058613150 (1.5 TiB) Interrupt:185 Memory:e4000000-e4012100 ib0 Link encap:Ethernet HWaddr 00:14:5E:57:C4:F8 inet addr:126.96.36.199 Bcast:10.21.255.255 Mask:255.255.0.0 inet6 addr: fe80::214:5eff:fe57:c4f8/64 Scope:Link UP BROADCAST RUNNING MULTICAST MTU:1500 Metric:1 RX packets:3068986439 errors:0 dropped:7841 overruns:0 frame:0 TX packets:2288060450 errors:0 dropped:0 overruns:0 carrier:0 collisions:0 txqueuelen:1000 RX bytes:3598751494497 (3.2 TiB) TX bytes:1744058613150 (1.5 TiB) Interrupt:185 Memory:e4000000-e4012100
In the above case the 192.148.x.x IP series refers to the standard Ethernet (or Gigabit Ethernet) network, the 10.21.x.x series refers to Myrinet and the 10.31.x.x refers to InfiniBand.
shell$ cat hostfile-eth 188.8.131.52 184.108.40.206 220.127.116.11 18.104.22.168 shell$ cat hostfile-myri 10.21.3.180 10.21.3.181 10.21.3.182 10.21.3.183 shell$ cat hostfile-ib 10.31.3.180 10.31.3.181 10.31.3.182 10.31.3.183
To run over the Ethernet interface use:
shell$ mpiexec -f hostfile-eth -n 4 ./app1
To run over the Myrinet interface use:
shell$ mpiexec -f hostfile-myri -n 4 ./app1
A launcher is the basic remote node access mechanism that is provided on any system. Hydra supports multiple launchers including ssh, rsh, fork, and slurm to launch processes. All of these are compiled in by default, so you can pick any one of them at runtime using the mpiexec option -bootstrap:
shell$ mpiexec -launcher ssh -f hosts -n 4 ./app (or) shell$ mpiexec -launcher fork -f hosts -n 4 ./app
This can also be controlled by using the HYDRA_LAUNCHER environment variable.
The default launcher is ssh.
The executable to use as the launcher can be specified using the option -launcher-exec:
$ mpiexec -launcher ssh -launcher-exec /usr/bin/ssh -f hosts -n 4 ./app
This can also be specified using the HYDRA_LAUNCHER_EXEC environment variable. If the bootstrap executable is not specified, Hydra will automatically look for it in your path and other known locations.
Hydra must have been configured with the launcher you specify. By default, hydra is configured with a set of standard and popular launchers. The configure option --with-hydra-bss may be used to specify a set of launchers; for example
$ configure --with-hydra-bss=ssh,rsh,fork,slurm
On supported platforms, Hydra automatically configures available process-core binding capability (currently using PLPA or hwloc). We support multiple levels of allocation strategies:
Basic allocation strategies: There are two forms of basic allocation: (i) based on a round-robin mechanism using the OS specified processor IDs, and (ii) based on a user-defined mapping. Further, for the user-defined mapping, two schemes are provided---command-line and host-file based. The command-line scheme lets the user specify a common-mapping for all physical nodes on the command line. The host-file scheme is the most general and lets the user specify the mapping for each node separately.
The modes of process binding in the basic allocation are: round-robin ("rr") and user-defined ("user").
shell$ mpiexec -binding rr -f hosts -n 8 ./app
Within the user-defined binding, two modes are supported: command-line and host-file based. The command-line based mode can be used as follows:
shell$ mpiexec -binding user:0,3 -f hosts -n 4 ./app
If a machine has 4 processing elements, and only two bindings are provided (as in the above example), the rest are padded with (-1), which refers to no binding. Also, the mapping is the same for all machines; so if the application is run with 8 processes, the first 2 processes on "each machine" are bound to processing elements as specified.
The host-file based mode for user-defined binding can be used by the "binding=" argument on each host line. E.g.:
shell$ cat hosts donner:4 binding=user:0,-1,-1,3 foo:4 binding=rr shakey:2
Using this method, each host can be given a different mapping. Any unspecified mappings are treated as (-1), referring to no binding.
Command-line based mappings are given a higher priority than the host-file based mappings. So, if a mapping is given at both places, the host-file mappings are ignored.
Topology-aware allocation strategies: These are a bit more intelligent in that they try to understand the system processing unit topology and assign processes in that order.
Different modes of process binding in the topology-aware allocation are:
CPU based options:
- cpu -- pack processes as closely to each other as possible with respect to CPU processing units
- cpu:sockets -- pack processes as closely to each other as possible without sharing a socket (unless the number of processes is more than the number of sockets)
- cpu:cores -- pack processes as closely to each other as possible without sharing a core (unless the number of processes is more than the number of cores)
- cpu:threads -- pack processes as closely to each other as possible without sharing a hardware thread/SMT (unless the number of processes is more than the number of hardware threads/SMTs)
Cache based options:
- cache -- pack processes as closely to each other as possible with respect to cache layout
- cache:l3 -- pack processes as closely to each other as possible without sharing the L3 cache (unless the number of processes is more than the number of the number of L3 cache regions)
- cache:l2 -- pack processes as closely to each other as possible without sharing the L2 cache (unless the number of processes is more than the number of the number of L2 cache regions)
- cache:l1 -- pack processes as closely to each other as possible without sharing the L1 cache (unless the number of processes is more than the number of the number of L1 cache regions)
shell$ mpiexec -binding cpu -f hosts -n 8 ./app (or) shell$ mpiexec -binding cpu:cores -f hosts -n 8 ./app (or) shell$ mpiexec -binding cache:l2 -f hosts -n 6 ./app
Consider the following layout of processing elements in the system (e.g., two nodes, each with two processors, and each processor with two cores). Suppose the Operating System assigned processor IDs for each of these processing elements are as shown below:
__________________________________________ __________________________________________ | _________________ _________________ | | _________________ _________________ | | | _____ _____ | | _____ _____ | | | | _____ _____ | | _____ _____ | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 0 | | 2 | | | | 1 | | 3 | | | | | | 0 | | 2 | | | | 1 | | 3 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |_____| |_____| | | |_____| |_____| | | | | |_____| |_____| | | |_____| |_____| | | | |_________________| |_________________| | | |_________________| |_________________| | |__________________________________________| |__________________________________________|
In this case, the binding options are as follows:
- rr 0, 1, 2, 3 (use the order provided by the OS)
- cpu 0, 2, 1, 3 (using all resources)
- cpu:sockets 0, 1 (not sharing the socket)
- user as defined by the user
Binding options can also be controlled with the environment variable HYDRA_BINDING. The binding library to use can be controlled with the -bindlib argument to mpiexec or the HYDRA_BINDLIB environment variable.
X-forwarding is specific to each bootstrap server. Some servers do it by default, while some don't. For ssh, this is disabled by default. To force-enable it, you should use the option -enable-x to mpiexec.
shell$ mpiexec -enable-x -f hosts -n 4 ./app
Resource Manager Integration
Hydra provides capability to integrate with different resource managers. You can pick these through the mpiexec option -rmk:
shell$ mpiexec -rmk pbs ./app
By default, mpiexec will coordinate with PBS to use all the allocated nodes to run the app. You can also force it to run the application using a different number of processes or on a different set of nodes using:
shell$ mpiexec -rmk pbs -n 4 -f ~/hosts ./app
This can also be controlled by using the HYDRA_RMK environment variable.
Hydra provides checkpoint/restart capability. Currently, only BLCR is supported. To use checkpointing include the -ckpointlib option for mpiexec to specify the checkpointing library to use and -ckpoint-prefix to specify the directory where the checkpoint images should be written:
shell$ mpiexec -ckpointlib blcr -ckpoint-prefix /home/buntinas/ckpts/app.ckpoint -f hosts -n 4 ./app
While the application is running, the user can request for a checkpoint at any time by sending a SIGUSR1 signal to mpiexec.
You can also automatically checkpoint the application at regular intervals using the mpiexec option -ckpoint-interval to specify the number of seconds between checkpoints:
shell$ mpiexec -ckpointlib blcr -ckpoint-prefix /home/buntinas/ckpts/app.ckpoint -ckpoint-interval 3600 -f hosts -n 4 ./app
The checkpoint/restart parameters can be controlled with the environment variables HYDRA_CKPOINTLIB, HYDRA_CKPOINT_PREFIX and HYDRA_CKPOINT_INTERVAL.
Each checkpoint generates one file per node. Note that checkpoints for all processes on a node will be stored in the same file. Each time a new checkpoint is taken an additional set of files are created. The files are numbered by the checkpoint number. This allows the application to be restarted from checkpoints other than the most recent. The checkpoint number can be specified with the -ckpoint-num parameter. To restart a process:
shell$ mpiexec -ckpointlib blcr -ckpoint-prefix /home/buntinas/ckpts/app.ckpoint -ckpoint-num 5 -f hosts -n 4
Note that by default, the process will be restarted from the first checkpoint, so in most cases, the checkpoint number should be specified.
Hydra supports multiple I/O demux engines including poll and select. The default is "poll". You can pick these through the mpiexec option -demux:
shell$ mpiexec -demux select -f hosts -n 4 ./app
This can also be controlled by using the HYDRA_DEMUX environment variable.
Hydra natively supports parallel debuggers such as totalview and DDT.
You can debug the MPI application with totalview by launching it as:
shell$ totalview mpiexec -a -f hosts -n 4 ./app
The "-a" option is a totalview parameter which tells it that the arguments after that need to be passed to mpiexec.
You can debug the MPI application with DDT by launching it as:
shell$ ddt mpiexec -a -f hosts -n 4 ./app
The "-a" option is a DDT parameter which tells it that the arguments after that need to be passed to mpiexec.
For serial debuggers such as 'ddd', you can launch each process with a separate debugger window as:
shell$ mpiexec -f hosts -n 4 ddd ./app
This will spawn four copies of "./app" each one launched under a separate 'ddd' instance.
You can do something similar to 'ddd' for serial debuggers that do not have a graphical interface, such as 'gdb', by launching them over 'xterm':
shell$ mpiexec -f hosts -n 4 xterm -e gdb ./app
If you want only the third process to run in a debugger, and the remaining processes to run normally, you can do:
shell$ mpiexec -f hosts -n 2 ./app : -n 1 xterm -e gdb ./app : -n 1 ./app
Using Hydra on Machines with Different User Names
Hydra only supports using different usernames on some launchers (such as ssh and rsh). For this, the host file should contain a "user=<foo>" entry.
shell$ cat hosts donner user=foo foo user=bar shakey user=bar terra user=foo