MPI: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| (16 intermediate revisions by 2 users not shown) | |||
| Line 3: | Line 3: | ||
==MPI Libraries for parallel jobs on Sapelo2== | ==MPI Libraries for parallel jobs on Sapelo2== | ||
All compute nodes on Sapelo2 have Infiniband (IB) interconnect | All compute nodes on Sapelo2 have Infiniband (IB) interconnect via '''EDR''' Infiniband network (100Gbps). Various IB-enabled MPI libraries are available and users can set the environment variables for the MPI library of choice by loading the corresponding module file. | ||
<!-- Some of the MPI libraries were installed specifically for the QDR network or for the EDR network and those module files will have an '''-QDR''' or '''-EDR''' extension in their names. --> | |||
Various IB-enabled MPI libraries are available and users can set the environment variables for the MPI library of choice by loading the corresponding module file. Some of the MPI libraries were installed specifically for the QDR network or for the EDR network and those module files will have an '''-QDR''' or '''-EDR''' extension in their names. | |||
For more information on Environment Modules, please see the [[Lmod]] page. | For more information on Environment Modules, please see the [[Lmod]] page. | ||
The following MPI libraries are available: | The following MPI libraries are available: | ||
<!-- | |||
====MVAPICH2==== | ====MVAPICH2==== | ||
| Line 31: | Line 30: | ||
Versions: | Versions: | ||
MVAPICH2/2.3.6-GCC-9.3.0 | MVAPICH2/2.3.6-GCC-9.3.0 | ||
MVAPICH2/2.3.7-1-GCC-9.3.0 | |||
Other possible modules matches: | Other possible modules matches: | ||
gmvapich2 | gmvapich2 | ||
| Line 54: | Line 45: | ||
For example: | For example: | ||
$ module spider MVAPICH2/2.3. | $ module spider MVAPICH2/2.3.7-1-GCC-9.3.0 | ||
----------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------- | ||
</pre> | </pre> | ||
Once the appropriate module is loaded, you can compile code with '''mpicc, mpicxx,''' '''mpic++,''' '''mpifort,''' '''mpif90,''' '''mpif77,''' etc. and you can run applications that were linked to the '''MPI libraries''' loaded by the module. | Once the appropriate module is loaded, you can compile code with '''mpicc, mpicxx,''' '''mpic++,''' '''mpifort,''' '''mpif90,''' '''mpif77,''' etc. and you can run applications that were linked to the '''MPI libraries''' loaded by the module. | ||
--> | |||
====OpenMPI==== | ====OpenMPI==== | ||
| Line 66: | Line 58: | ||
</pre> | </pre> | ||
The module names have the format OpenMPI/''Version''-''CompilerToolchain''-''ToolchainVersion''. | |||
For example, these are some of the modules available: | For example, these are some of the modules available: | ||
| Line 80: | Line 72: | ||
Versions: | Versions: | ||
OpenMPI/3.1.4-GCC-8.3.0 | OpenMPI/3.1.4-GCC-8.3.0 | ||
OpenMPI/3.1.4- | OpenMPI/3.1.4-iccifort-2019.5.281 | ||
OpenMPI/4.0.5-GCC-10.2.0 | OpenMPI/4.0.5-GCC-10.2.0 | ||
OpenMPI/4.1.1-GCC-10.3.0 | OpenMPI/4.1.1-GCC-10.3.0 | ||
OpenMPI/4.1.1-GCC-11.2.0 | |||
OpenMPI/4.1.4-GCC-11.3.0 | |||
OpenMPI/4.1.4-GCC-12.2.0 | |||
OpenMPI/4.1.4-intel-compilers-2022.1.0 | |||
OpenMPI/4.1.5-GCC-12.3.0 | |||
OpenMPI/4.1.6-GCC-13.2.0 | |||
----------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------ | ||
For detailed information about a specific "OpenMPI" package (including how to load the modules) use the module's full name. | For detailed information about a specific "OpenMPI" package (including how to load the modules) use the module's full name. | ||
Note that names that have a trailing (E) are extensions provided by other modules. | Note that names that have a trailing (E) are extensions provided by other modules. | ||
For example: | For example: | ||
$ module spider OpenMPI/4.1. | $ module spider OpenMPI/4.1.6-GCC-13.2.0 | ||
----------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------- | ||
</pre> | </pre> | ||
| Line 112: | Line 97: | ||
You can find all Intel MPI modules available on Sapelo2 by running the following command on a Sapelo2 node:<pre class="gcommand"> | You can find all Intel MPI modules available on Sapelo2 by running the following command on a Sapelo2 node:<pre class="gcommand"> | ||
module spider impi | module spider impi | ||
</pre>The module names have the format impi/''Version''-''CompilerToolchain''-''ToolchainVersion'' | </pre>The module names have the format impi/''Version''-''CompilerToolchain''-''ToolchainVersion.'' | ||
For example, these are some of the modules available:<pre class="gcomment"> | For example, these are some of the modules available:<pre class="gcomment"> | ||
| Line 124: | Line 109: | ||
Versions: | Versions: | ||
impi/ | impi/2021.4.0-intel-compilers-2021.4.0 | ||
impi/ | impi/2021.6.0-intel-compilers-2022.1.0 | ||
impi/2021.9.0-intel-compilers-2023.1.0 | |||
Other possible modules matches: | Other possible modules matches: | ||
iimpi | iimpi | ||
| Line 139: | Line 125: | ||
For example: | For example: | ||
$ module spider impi/ | $ module spider impi/2021.9.0-intel-compilers-2023.1.0 | ||
------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------ | ||
</pre>Once the appropriate module is loaded, you can compile code with '''mpicc, mpiicc, mpicxx, mpiicpc,''' '''mpiifort,''' '''mpif90,''' '''mpif77,''' etc. and you can run applications that were linked to the '''MPI libraries''' loaded by the module. | </pre>Once the appropriate module is loaded, you can compile code with '''mpicc, mpiicc, mpicxx, mpiicpc,''' '''mpiifort,''' '''mpif90,''' '''mpif77,''' etc. and you can run applications that were linked to the '''MPI libraries''' loaded by the module. | ||
===MPI commands and how to launch MPI programs=== | |||
{| width="100%" border="1" cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable" | |||
|- | |||
! scope="col" | MPI library | |||
! scope="col" | Version | |||
! scope="col" | Base toolchain | |||
! scope="col" | Toolchain | |||
! scope="col" | Fortran | |||
! scope="col" | C | |||
! scope="col" | C++ | |||
! scope="col" | How to launch with Slurm | |||
|- | |||
| OpenMPI || 3.1.4-GCC-8.3.0 || GCCcore-8.3.0 || foss/2019b || mpif90 || mpicc || mpicxx || srun --mpi=pmi2 | |||
|- | |||
| OpenMPI || 3.1.4-iccifort-2019.5.281 || GCCcore-8.3.0 || iomkl/2019b || mpif90 || mpicc || mpicxx || srun --mpi=pmi2 | |||
|- | |||
| OpenMPI || 4.0.5-GCC-10.2.0 || GCCcore-10.2.0 || foss/2020b || mpif90 || mpicc || mpicxx || srun --mpi=pmi2 | |||
|- | |||
| OpenMPI || 4.1.1-GCC-11.2.0 || GCCcore-11.2.0 || foss/2021b || mpif90 || mpicc || mpicxx || srun | |||
|- | |||
| OpenMPI || 4.1.4-GCC-11.3.0 || GCCcore-11.3.0 || foss/2022a || mpif90 || mpicc || mpicxx || srun | |||
|- | |||
| OpenMPI || 4.1.4-intel-compilers-2022.1.0 || GCCcore-11.3.0 || iomkl/2022a || mpif90 || mpicc || mpicxx || srun | |||
|- | |||
| OpenMPI || 4.1.4-GCC-12.2.0 || GCCcore-12.2.0 || foss/2022b || mpif90 || mpicc || mpicxx || srun | |||
|- | |||
| OpenMPI || 4.1.5-GCC-12.3.0 || GCCcore-12.3.0 || foss/2023a || mpif90 || mpicc || mpicxx || srun | |||
|- | |||
| OpenMPI || 4.1.6-GCC-13.2.0 || GCCcore-13.2.0 || foss/2023b || mpif90 || mpicc || mpicxx || srun | |||
|- | |||
| Intel MPI || 2021.4.0-intel-compilers-2021.4.0 || GCCcore-11.2.0 || intel/2021b || mpiifort || mpiicc || mpiicpc || srun | |||
|- | |||
| Intel MPI || 2021.6.0-intel-compilers-2022.1.0 || GCCcore-11.3.0 || intel/2022a || mpiifort || mpiicc || mpiicpc || srun | |||
|- | |||
| Intel MPI || 2021.9.0-intel-compilers-2023.1.0 || GCCcore-12.3.0 || intel/2023a || mpiifort || mpiicc || mpiicpc || srun | |||
|- | |||
|} | |||
====Note==== | |||
If your MPI job receives any of the following or similar errors: | |||
*PMIX ERROR: OUT-OF-RESOURCE in file base/bfrop_base_unpack.c at line 750 | |||
*PMIX ERROR: UNPACK-PAST-END in file base/bfrop_base_unpack.c at line 750 | |||
*PMIX ERROR: UNPACK-INADEQUATE-SPACE in file base/gds_base_fns.c at line 138 | |||
*UNPACK-PMIX-VALUE: UNSUPPORTED TYPE 126 | |||
then please use <code>srun --mpi=pmi2</code> to start the MPI application. | |||
---- | ---- | ||
| Line 148: | Line 183: | ||
==MPI Libraries for parallel jobs on the teaching cluster== | ==MPI Libraries for parallel jobs on the teaching cluster== | ||
All compute nodes on | All compute nodes on Sapelo2 have Infiniband (IB) interconnect via '''EDR''' Infiniband network (100Gbps). Various IB-enabled MPI libraries are available and users can set the environment variables for the MPI library of choice by loading the corresponding module file. | ||
For more information on Environment Modules, please see the [[Lmod]] page. | |||
The following MPI libraries are available: | |||
<!-- | |||
====MVAPICH2==== | ====MVAPICH2==== | ||
You can find all MVAPICH2 modules available on the teaching cluster by running the following command | You can find all MVAPICH2 modules available on the teaching cluster by running the following command: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
module spider MVAPICH2 | module spider MVAPICH2 | ||
| Line 195: | Line 234: | ||
Once the appropriate module is loaded, you can compile code with '''mpicc, mpicxx,''' '''mpic++,''' '''mpifort,''' '''mpif90,''' '''mpif77,''' etc. and you can run applications that were linked to the '''MPI libraries''' loaded by the module. | Once the appropriate module is loaded, you can compile code with '''mpicc, mpicxx,''' '''mpic++,''' '''mpifort,''' '''mpif90,''' '''mpif77,''' etc. and you can run applications that were linked to the '''MPI libraries''' loaded by the module. | ||
--> | |||
====OpenMPI==== | ====OpenMPI==== | ||
You can find all OpenMPI modules available on the teaching cluster by running the following command | You can find all OpenMPI modules available on the teaching cluster by running the following command: | ||
<pre class="gcommand"> | <pre class="gcommand"> | ||
module spider OpenMPI | module spider OpenMPI | ||
| Line 216: | Line 256: | ||
Versions: | Versions: | ||
OpenMPI/3.1.4-GCC-8.3.0 | OpenMPI/3.1.4-GCC-8.3.0 | ||
OpenMPI/3.1.4- | OpenMPI/4.1.1-GCC-11.2.0 | ||
OpenMPI/4.1.2-GCC-11.2.0 | |||
OpenMPI/4.1.4-GCC-11.3.0 | |||
OpenMPI/4.1.4-GCC-12.2.0 | |||
------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------- | ||
For detailed information about a specific "OpenMPI" package (including how to load the modules) use the module's full name. | For detailed information about a specific "OpenMPI" package (including how to load the modules) use the module's full name. | ||
Note that names that have a trailing (E) are extensions provided by other modules. | Note that names that have a trailing (E) are extensions provided by other modules. | ||
For example: | For example: | ||
$ module spider OpenMPI/ | $ module spider OpenMPI/4.1.4-GCC-12.2.0 | ||
------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------ | ||
</pre> | </pre> | ||
| Line 235: | Line 274: | ||
=== Intel MPI === | === Intel MPI === | ||
You can find all Intel MPI modules available on the teaching cluster by running the following command | You can find all Intel MPI modules available on the teaching cluster by running the following command:<pre class="gcommand"> | ||
module spider impi | module spider impi | ||
</pre>The module names have the format impi/''Version''-''CompilerToolchain''-''ToolchainVersion''. | </pre>The module names have the format impi/''Version''-''CompilerToolchain''-''ToolchainVersion''. | ||
| Line 248: | Line 287: | ||
Intel MPI Library, compatible with MPICH ABI | Intel MPI Library, compatible with MPICH ABI | ||
Versions: | |||
impi/2021.4.0-intel-compilers-2021.4.0 | |||
impi/2021.6.0-intel-compilers-2022.1.0 | |||
impi/2021.9.0-intel-compilers-2023.1.0 | |||
Other possible modules matches: | Other possible modules matches: | ||
iimpi | iimpi | ||
------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------ | ||
To find other possible module matches execute: | To find other possible module matches execute: | ||
$ module -r spider '.*impi.*' | $ module -r spider '.*impi.*' | ||
------------------------------------------------------------------------------------------------------------------------------------ | |||
For detailed information about a specific "impi" package (including how to load the modules) use the module's full name. | |||
Note that names that have a trailing (E) are extensions provided by other modules. | |||
For example: | |||
$ module spider impi/2021.9.0-intel-compilers-2023.1.0 | |||
------------------------------------------------------------------------------------------------------------------------------------ | |||
</pre>Once the appropriate module is loaded, you can compile code with '''mpicc, mpiicc, mpicxx, mpiicpc,''' '''mpiifort,''' '''mpif90,''' '''mpif77,''' etc. and you can run applications that were linked to the '''MPI libraries''' loaded by the module. | </pre>Once the appropriate module is loaded, you can compile code with '''mpicc, mpiicc, mpicxx, mpiicpc,''' '''mpiifort,''' '''mpif90,''' '''mpif77,''' etc. and you can run applications that were linked to the '''MPI libraries''' loaded by the module. | ||
[[#top|Back to Top]] | [[#top|Back to Top]] | ||
Latest revision as of 12:22, 5 August 2024
MPI Libraries for parallel jobs on Sapelo2
All compute nodes on Sapelo2 have Infiniband (IB) interconnect via EDR Infiniband network (100Gbps). Various IB-enabled MPI libraries are available and users can set the environment variables for the MPI library of choice by loading the corresponding module file.
For more information on Environment Modules, please see the Lmod page.
The following MPI libraries are available:
OpenMPI
You can find all OpenMPI modules available on Sapelo2 by running the following command on a Sapelo2 node:
module spider OpenMPI
The module names have the format OpenMPI/Version-CompilerToolchain-ToolchainVersion.
For example, these are some of the modules available:
[shtsai@ss-sub1 ~]$ module spider OpenMPI
-----------------------------------------------------------------------------------------------------------------------------------------------
OpenMPI:
-----------------------------------------------------------------------------------------------------------------------------------------------
Description:
The Open MPI Project is an open source MPI-3 implementation.
Versions:
OpenMPI/3.1.4-GCC-8.3.0
OpenMPI/3.1.4-iccifort-2019.5.281
OpenMPI/4.0.5-GCC-10.2.0
OpenMPI/4.1.1-GCC-10.3.0
OpenMPI/4.1.1-GCC-11.2.0
OpenMPI/4.1.4-GCC-11.3.0
OpenMPI/4.1.4-GCC-12.2.0
OpenMPI/4.1.4-intel-compilers-2022.1.0
OpenMPI/4.1.5-GCC-12.3.0
OpenMPI/4.1.6-GCC-13.2.0
------------------------------------------------------------------------------------------------------------------------------------------------
For detailed information about a specific "OpenMPI" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:
$ module spider OpenMPI/4.1.6-GCC-13.2.0
-----------------------------------------------------------------------------------------------------------------------------------------------
Once the appropriate module is loaded, you can compile code with mpicc, mpiCC, mpicxx, mpic++, mpifort, mpif90, mpif77, etc. and you can run applications that were linked to the MPI libraries loaded by the module.
Intel MPI
You can find all Intel MPI modules available on Sapelo2 by running the following command on a Sapelo2 node:
module spider impi
The module names have the format impi/Version-CompilerToolchain-ToolchainVersion. For example, these are some of the modules available:
[shtsai@ss-sub1 ~]$ module spider impi
------------------------------------------------------------------------------------------------------------------------------------
impi:
------------------------------------------------------------------------------------------------------------------------------------
Description:
Intel MPI Library, compatible with MPICH ABI
Versions:
impi/2021.4.0-intel-compilers-2021.4.0
impi/2021.6.0-intel-compilers-2022.1.0
impi/2021.9.0-intel-compilers-2023.1.0
Other possible modules matches:
iimpi
------------------------------------------------------------------------------------------------------------------------------------
To find other possible module matches execute:
$ module -r spider '.*impi.*'
------------------------------------------------------------------------------------------------------------------------------------
For detailed information about a specific "impi" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:
$ module spider impi/2021.9.0-intel-compilers-2023.1.0
------------------------------------------------------------------------------------------------------------------------------------
Once the appropriate module is loaded, you can compile code with mpicc, mpiicc, mpicxx, mpiicpc, mpiifort, mpif90, mpif77, etc. and you can run applications that were linked to the MPI libraries loaded by the module.
MPI commands and how to launch MPI programs
| MPI library | Version | Base toolchain | Toolchain | Fortran | C | C++ | How to launch with Slurm |
|---|---|---|---|---|---|---|---|
| OpenMPI | 3.1.4-GCC-8.3.0 | GCCcore-8.3.0 | foss/2019b | mpif90 | mpicc | mpicxx | srun --mpi=pmi2 |
| OpenMPI | 3.1.4-iccifort-2019.5.281 | GCCcore-8.3.0 | iomkl/2019b | mpif90 | mpicc | mpicxx | srun --mpi=pmi2 |
| OpenMPI | 4.0.5-GCC-10.2.0 | GCCcore-10.2.0 | foss/2020b | mpif90 | mpicc | mpicxx | srun --mpi=pmi2 |
| OpenMPI | 4.1.1-GCC-11.2.0 | GCCcore-11.2.0 | foss/2021b | mpif90 | mpicc | mpicxx | srun |
| OpenMPI | 4.1.4-GCC-11.3.0 | GCCcore-11.3.0 | foss/2022a | mpif90 | mpicc | mpicxx | srun |
| OpenMPI | 4.1.4-intel-compilers-2022.1.0 | GCCcore-11.3.0 | iomkl/2022a | mpif90 | mpicc | mpicxx | srun |
| OpenMPI | 4.1.4-GCC-12.2.0 | GCCcore-12.2.0 | foss/2022b | mpif90 | mpicc | mpicxx | srun |
| OpenMPI | 4.1.5-GCC-12.3.0 | GCCcore-12.3.0 | foss/2023a | mpif90 | mpicc | mpicxx | srun |
| OpenMPI | 4.1.6-GCC-13.2.0 | GCCcore-13.2.0 | foss/2023b | mpif90 | mpicc | mpicxx | srun |
| Intel MPI | 2021.4.0-intel-compilers-2021.4.0 | GCCcore-11.2.0 | intel/2021b | mpiifort | mpiicc | mpiicpc | srun |
| Intel MPI | 2021.6.0-intel-compilers-2022.1.0 | GCCcore-11.3.0 | intel/2022a | mpiifort | mpiicc | mpiicpc | srun |
| Intel MPI | 2021.9.0-intel-compilers-2023.1.0 | GCCcore-12.3.0 | intel/2023a | mpiifort | mpiicc | mpiicpc | srun |
Note
If your MPI job receives any of the following or similar errors:
- PMIX ERROR: OUT-OF-RESOURCE in file base/bfrop_base_unpack.c at line 750
- PMIX ERROR: UNPACK-PAST-END in file base/bfrop_base_unpack.c at line 750
- PMIX ERROR: UNPACK-INADEQUATE-SPACE in file base/gds_base_fns.c at line 138
- UNPACK-PMIX-VALUE: UNSUPPORTED TYPE 126
then please use srun --mpi=pmi2 to start the MPI application.
MPI Libraries for parallel jobs on the teaching cluster
All compute nodes on Sapelo2 have Infiniband (IB) interconnect via EDR Infiniband network (100Gbps). Various IB-enabled MPI libraries are available and users can set the environment variables for the MPI library of choice by loading the corresponding module file.
For more information on Environment Modules, please see the Lmod page.
The following MPI libraries are available:
OpenMPI
You can find all OpenMPI modules available on the teaching cluster by running the following command:
module spider OpenMPI
The module names have the format OpenMPI/Version-CompilerToolchain-ToolchainVersion.
For example, these are some of the modules available:
zhuofei@teach-sub1 ~$ ml spider OpenMPI
------------------------------------------------------------------------------------------------------------------------------------
OpenMPI:
------------------------------------------------------------------------------------------------------------------------------------
Description:
The Open MPI Project is an open source MPI-3 implementation.
Versions:
OpenMPI/3.1.4-GCC-8.3.0
OpenMPI/4.1.1-GCC-11.2.0
OpenMPI/4.1.2-GCC-11.2.0
OpenMPI/4.1.4-GCC-11.3.0
OpenMPI/4.1.4-GCC-12.2.0
--------------------------------------------------------------------------------------------------------------------------------------
For detailed information about a specific "OpenMPI" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:
$ module spider OpenMPI/4.1.4-GCC-12.2.0
------------------------------------------------------------------------------------------------------------------------------------
Once the appropriate module is loaded, you can compile code with mpicc, mpiCC, mpicxx, mpic++, mpifort, mpif90, mpif77, etc. and you can run applications that were linked to the MPI libraries loaded by the module.
Intel MPI
You can find all Intel MPI modules available on the teaching cluster by running the following command:
module spider impi
The module names have the format impi/Version-CompilerToolchain-ToolchainVersion. For example, these are some of the modules available:
zhuofei@teach-sub1 ~$ ml spider impi
------------------------------------------------------------------------------------------------------------------------------------
impi: impi/2018.5.288-iccifort-2019.5.281
------------------------------------------------------------------------------------------------------------------------------------
Description:
Intel MPI Library, compatible with MPICH ABI
Versions:
impi/2021.4.0-intel-compilers-2021.4.0
impi/2021.6.0-intel-compilers-2022.1.0
impi/2021.9.0-intel-compilers-2023.1.0
Other possible modules matches:
iimpi
------------------------------------------------------------------------------------------------------------------------------------
To find other possible module matches execute:
$ module -r spider '.*impi.*'
------------------------------------------------------------------------------------------------------------------------------------
For detailed information about a specific "impi" package (including how to load the modules) use the module's full name.
Note that names that have a trailing (E) are extensions provided by other modules.
For example:
$ module spider impi/2021.9.0-intel-compilers-2023.1.0
------------------------------------------------------------------------------------------------------------------------------------
Once the appropriate module is loaded, you can compile code with mpicc, mpiicc, mpicxx, mpiicpc, mpiifort, mpif90, mpif77, etc. and you can run applications that were linked to the MPI libraries loaded by the module.