Difference between revisions of "Using the Hydra Process Manager"

Latest revision as of 14:41, 4 October 2021

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.

General

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.

Getting Help

All of the runtime options can be listed on the command line using the flag:

mpiexec -help

For further information about any specific flag, the information can be obtained by adding the option before the help flag:

mpiexec -<option> -help

Quick Start

Once built, the Hydra executables are in 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/mpich/bin:$PATH

Put in .bashrc: export PATH=/home/you/mpich/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

You can spawn multiple different executables using:

shell$ mpiexec -f hosts -n 4 ./app1 : -n 4 ./app2

The first four ranks will be of "app1" and the next 4 ranks will be of "app2".

Environment Settings

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_LAUNCHER_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:192.148.3.182  Bcast:192.148.248.255  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:20.31.3.182  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 

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
   192.148.3.180
   192.148.3.181
   192.148.3.182
   192.148.3.183

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

Resource Managers and Launchers

Hydra natively interacts with a number of resource managers and launchers.

Resource managers provide information about the resources allocated by the user (e.g., slurm, pbs, loadleveler, lsf, sge, cobalt). Launchers allow mpiexec to launch processes on the system (e.g., ssh, rsh, fork, slurm, pbs, loadleveler, lsf, sge). Some tools act as both resource managers and launchers, while others play just one role.

In most cases, you don't need to do anything special for Hydra to work with your slurm, pbs, loadleveler, lsf, sge or cobalt environment. It'll automatically detect these resource managers and interact with them. The following command will be sufficient to launch processes on all the allocated cores:

shell$ mpiexec ./app

The above command will allow Hydra to inherit information about the resource manager and launcher available, resources allocated from the resource manager, and finally launch the appropriate number of processes.

However, if you do not want Hydra to auto-detect the launcher, you can customize it using the -launcher flag to mpiexec or the HYDRA_LAUNCHER environment variable.

shell$ mpiexec -launcher ssh -f hosts -n 4 ./app

 (or)

shell$ mpiexec -launcher fork -f hosts -n 4 ./app

The executable to use as the launcher can also be customized using the option -launcher-exec or the HYDRA_LAUNCHER_EXEC environment variable:

 $ mpiexec -launcher ssh -launcher-exec /usr/bin/ssh -f hosts -n 4 ./app

Similarly, if you do not want Hydra to auto-detect the resource manager, you can customize using the -rmk flag to mpiexec or the HYDRA_RMK environment variable.

shell$ mpiexec -rmk pbs ./app

Finally, if you do not want Hydra to auto-detect the number of processes allocated or the machines allocated, you can customize that using the -n and -f flags.

shell$ mpiexec -rmk pbs -n 4 -f ~/hosts ./app

Process-core Binding

On supported platforms, Hydra automatically configures available process-core binding capability using hwloc. More info on how to use these options can be found in the help text:

 shell$ mpiexec -bind-to -help

• -bind-to <object[:num]> - Specify the hardware element to bind each process to
• -map-by <object[:num]> - Skip over this many elements between bindings. If not specified, defaults to the same value as -bind-to.

Binding options can also be controlled with the environment variables HYDRA_TOPOLIB, HYDRA_BINDING, HYDRA_MAPPING, and HYDRA_MEMBIND.

Examples

For the purposes of process binding/mapping examples, we will assume the following machine topology.

Setting the env variable HYDRA_TOPO_DEBUG=1 will force hydra to print out bindings, but not call the binding API. This is useful for testing binding options using hwloc's arbitrary topology loading feature, as is demonstrated below.

To bind processes to single hardware threads:

 shell$ HYDRA_TOPO_DEBUG=1 mpiexec -n 8 -bind-to hwthread /bin/true | sort -k 2 -n
 process 0 binding: 10000000 
 process 1 binding: 00100000 
 process 2 binding: 00001000 
 process 3 binding: 00000010 
 process 4 binding: 01000000 
 process 5 binding: 00010000 
 process 6 binding: 00000100 
 process 7 binding: 00000001 

To bind processes to 2 cores at a time:

 shell$ HYDRA_TOPO_DEBUG=1 mpiexec -n 8 -bind-to core:2 /bin/true | sort -k 2 -n
 process 0 binding: 10100000 
 process 1 binding: 00001010 
 process 2 binding: 01010000 
 process 3 binding: 00000101 
 process 4 binding: 10100000 
 process 5 binding: 00001010 
 process 6 binding: 01010000 
 process 7 binding: 00000101

A common use-case is to bind processes to a socket, and map by hwthread to group sequential ranks together.

 shell$ HYDRA_TOPO_DEBUG=1 mpiexec -n 8 -bind-to socket -map-by hwthread /bin/true | sort -k 2 -n
 process 0 binding: 10101010 
 process 1 binding: 10101010 
 process 2 binding: 10101010 
 process 3 binding: 10101010 
 process 4 binding: 01010101 
 process 5 binding: 01010101 
 process 6 binding: 01010101 
 process 7 binding: 01010101

Also included in the MPICH source is a program for printing out the affinity of a process (src/pm/hydra/examples/print_cpus_allowed.c) according to the OS. This can be used on Linux systems to test that bindings are working correctly.

 shell$ mpiexec -n 8 -bind-to socket ./print_cpus_allowed | sort
 crush[0]: Cpus_allowed_list:    0,2,4,6
 crush[1]: Cpus_allowed_list:    1,3,5,7
 crush[2]: Cpus_allowed_list:    0,2,4,6
 crush[3]: Cpus_allowed_list:    1,3,5,7
 crush[4]: Cpus_allowed_list:    0,2,4,6
 crush[5]: Cpus_allowed_list:    1,3,5,7
 crush[6]: Cpus_allowed_list:    0,2,4,6
 crush[7]: Cpus_allowed_list:    1,3,5,7

X Forwarding

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

Checkpoint/Restart Support

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.

Demux Engines

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.

Debugging

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

Managing Output

For a moderate amount of output, -prepend-rank will add a [$N] (where $N is a process's global rank) to each line of output.

For larger amounts of output -outfile-pattern (for stdout) and -errfile-pattern (for stderr) can direct output to specific files

For example:

$ mpiexec -outfile-pattern=output.log-%r-%h -errfile-pattern=output.err-%r-%h

will create files with the global MPI rank (%r) and hostname (%h) embedded in the name

Name Publishing

In MPICH 3.1, Hydra is the default name service for MPI's name publishing features (MPI_PUBLISH_NAME/MPI_LOOKUP_NAME). For multihost programs to use this feature, you must first start a hydra_nameserver process and tell mpiexec which host it is running on.

For example:

 [email protected]$ hydra_nameserver &
 [email protected]$ mpiexec -hosts myhost1,myhost2 -n 4 -nameserver myhost1 ./a.out