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[[Category:Sapelo2]][[Category:Teaching]]
[[Category:Sapelo2]][[Category:Teaching]]


==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.
<!-- 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. -->


===MPI Libraries for parallel jobs on Sapelo2===
For more information on Environment Modules, please see the [[Lmod]] page.
 
All compute nodes on Sapelo2 have Infiniband (IB) interconnect. 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:
The following MPI libraries are available:
 
<!--
====MVAPICH2====
====MVAPICH2====


You can find all MVAPICH2 modules available on Sapelo2 by running the following command on a Sapelo2 node:
You can find all MVAPICH2 modules available on Sapelo2 by running the following command on a Sapelo2 node:
<pre class="gcommand">
<pre class="gcommand">
module spider mvapich2
module spider MVAPICH2
</pre>
</pre>
Module names that have an -QDR or -EDR extension only work for the corresponding IB network. Module names without such an extension can be used on either IB network. The module names have the format MVAPICH2/''Version''-''CompilerToolchain''-''ToolchainVersion''.


These are some of the modules available:
For example, these are some of the modules available:


* MVAPICH2 2.2, using GNU 5.4.0 compilers, available in module MVAPICH2/2.2-GCC-5.4.0-2.26. To use it, load the module with
<pre class="gcomment">
<pre class="gcommand">
[shtsai@ss-sub1 ~]$ module spider MVAPICH2
module load MVAPICH2/2.2-GCC-5.4.0-2.26
 
</pre>
-----------------------------------------------------------------------------------------------------------------------------------------------
  MVAPICH2:
-----------------------------------------------------------------------------------------------------------------------------------------------
    Description:
      This is an MPI 3.1 implementation. It is based on MPICH2 and MVICH.
 
    Versions:
        MVAPICH2/2.3.6-GCC-9.3.0
        MVAPICH2/2.3.7-1-GCC-9.3.0
    Other possible modules matches:
        gmvapich2


* MVAPICH2 2.2, using GNU 6.4.0 compilers, available in module MVAPICH2/2.2-GCC-6.4.0-2.28. To use it, load the module with
-----------------------------------------------------------------------------------------------------------------------------------------------
<pre class="gcommand">
  To find other possible module matches execute:
module load MVAPICH2/2.2-GCC-6.4.0-2.28
</pre>


* MVAPICH2 2.2, Intel 2013_sp1.0.080 compilers, available in module MVAPICH2/2.2-iccifort-2013_sp1.0.080. To use it, load the module with
      $ module -r spider '.*MVAPICH2.*'
<pre class="gcommand">
module load MVAPICH2/2.2-iccifort-2013_sp1.0.080
</pre>


* MVAPICH2 2.2, Intel 2015.2.164 compilers, available in module MVAPICH2/2.2-iccifort-2015.2.164-GCC-4.8.5. To use it, load the module with
-----------------------------------------------------------------------------------------------------------------------------------------------
<pre class="gcommand">
  For detailed information about a specific "MVAPICH2" package (including how to load the modules) use the module's full name.
module load MVAPICH2/2.2-iccifort-2015.2.164-GCC-4.8.5
  Note that names that have a trailing (E) are extensions provided by other modules.
</pre>
  For example:


* MVAPICH2 2.2, Intel 2018.1.163 compilers, available in module MVAPICH2/2.2-iccifort-2018.1.163-GCC-6.4.0-2.28. To use it, load the module with
    $ module spider MVAPICH2/2.3.7-1-GCC-9.3.0
<pre class="gcommand">
-----------------------------------------------------------------------------------------------------------------------------------------------
module load MVAPICH2/2.2-iccifort-2018.1.163-GCC-6.4.0-2.28
</pre>
</pre>


Once the appropriate module is loaded, you can compile code with '''mpicc''', '''mpic++''', '''mpif90''', etc
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.
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 Sapelo2 by running the following command on a Sapelo2 node:
You can find all OpenMPI modules available on Sapelo2 by running the following command on a Sapelo2 node:
<pre class="gcommand">
<pre class="gcommand">
module spider openmpi
module spider OpenMPI
</pre>
</pre>


These are some of the modules available:
The module names have the format OpenMPI/''Version''-''CompilerToolchain''-''ToolchainVersion''.


* OpenMPI 3.0.0, using GNU 7.2.0 compilers, available in module OpenMPI/3.0.0-GCC-7.2.0-2.29. To use it, load the module with
For example, these are some of the modules available:
<pre class="gcommand">
 
module load OpenMPI/3.0.0-GCC-7.2.0-2.29
<pre class="gcomment">
[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
-----------------------------------------------------------------------------------------------------------------------------------------------
</pre>
</pre>


* OpenMPI 2.1.2, using GNU 6.4.0 compilers, available in module OpenMPI/2.1.2-GCC-6.4.0-2.28. To use it, load the module with
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.
<pre class="gcommand">
 
module load OpenMPI/2.1.2-GCC-6.4.0-2.28
=== Intel MPI ===
</pre>
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
</pre>The module names have the format impi/''Version''-''CompilerToolchain''-''ToolchainVersion.''
 
For example, these are some of the modules available:<pre class="gcomment">
[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


* OpenMPI 1.10.3, using GNU 5.4.0 compilers, available in module OpenMPI/1.10.3-GCC-5.4.0-2.26. To use it, load the module with
------------------------------------------------------------------------------------------------------------------------------------
<pre class="gcommand">
  To find other possible module matches execute:
module load OpenMPI/1.10.3-GCC-5.4.0-2.26
</pre>


* OpenMPI 1.10.3, using GNU 4.4.7 compilers, available in module OpenMPI/1.10.3-GCC-4.4.7. To use it, load the module with
      $ module -r spider '.*impi.*'
<pre class="gcommand">
module load OpenMPI/1.10.3-GCC-4.4.7
</pre>


* OpenMPI 3.0.0, using Intel 2018.1.163 compilers, available in module OpenMPI/3.0.0-iccifort-2018.1.163-GCC-6.4.0-2.28. To use it, load the module with
------------------------------------------------------------------------------------------------------------------------------------
<pre class="gcommand">
  For detailed information about a specific "impi" package (including how to load the modules) use the module's full name.
module load OpenMPI/3.0.0-iccifort-2018.1.163-GCC-6.4.0-2.28
  Note that names that have a trailing (E) are extensions provided by other modules.
</pre>
  For example:


* OpenMPI 2.1.2, using Intel 2018.1.163 compilers, available in module OpenMPI/2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28. To use it, load the module with
    $ module spider impi/2021.9.0-intel-compilers-2023.1.0
<pre class="gcommand">
------------------------------------------------------------------------------------------------------------------------------------
module load OpenMPI/2.1.2-iccifort-2018.1.163-GCC-6.4.0-2.28
</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>


* OpenMPI 1.10.7, using Intel 2018.1.163 compilers, available in module OpenMPI/1.10.7-iccifort-2018.1.163-GCC-6.4.0-2.28. To use it, load the module with
===MPI commands and how to launch MPI programs===
<pre class="gcommand">
module load OpenMPI/1.10.7-iccifort-2018.1.163-GCC-6.4.0-2.28
</pre>


* OpenMPI 1.10.7, using Intel 2015.2.164 compilers, available in module OpenMPI/1.10.7-iccifort-2015.2.164-GCC-4.8.5. To use it, load the module with
{|  width="100%" border="1"  cellspacing="0" cellpadding="2" align="center" class="wikitable unsortable"
<pre class="gcommand">
|-
module load OpenMPI/1.10.7-iccifort-2015.2.164-GCC-4.8.5
! scope="col" | MPI library
</pre>
! 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 1.8.4, using Intel 2015.2.164 compilers, available in module OpenMPI/1.8.4-iccifort-2015.2.164-GCC-4.8.5. To use it, load the module with
| OpenMPI || 3.1.4-GCC-8.3.0 || GCCcore-8.3.0 || foss/2019b || mpif90 || mpicc || mpicxx || srun --mpi=pmi2
<pre class="gcommand">
|-
module load OpenMPI/1.8.4-iccifort-2015.2.164-GCC-4.8.5
| OpenMPI || 3.1.4-iccifort-2019.5.281 || GCCcore-8.3.0 || iomkl/2019b || mpif90 || mpicc || mpicxx || srun --mpi=pmi2
</pre>
|-
| 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
|-
|}


* OpenMPI 1.8.4, using Intel 2013_sp1.0.080 compilers, available in module OpenMPI/1.8.4-iccifort-2013_sp1.0.080. To use it, load the module with
====Note====
<pre class="gcommand">
module load OpenMPI/1.8.4-iccifort-2013_sp1.0.080
</pre>


Once the appropriate module is loaded, you can compile code with '''mpicc''', '''mpic++''', '''mpif90''', etc
If your MPI job receives any of the following or similar errors:
and you can run applications that were linked to the MPI libraries loaded by the module.
*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.


----
----
[[#top|Back to Top]]
[[#top|Back to Top]]


==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.


===MPI Libraries for parallel jobs on the teaching cluster===
For more information on Environment Modules, please see the [[Lmod]] page.


All compute nodes on the teaching cluster are connected via a gigabit Ethernet network. MPI libraries currently installed on the teaching cluster are listed below.
The following MPI libraries are available:
 
<!--
====OpenMPI====
====MVAPICH2====


You can find all OpenMPI modules available on the teaching cluster by running the following command on a teaching cluster node:
You can find all MVAPICH2 modules available on the teaching cluster by running the following command:
<pre class="gcommand">
<pre class="gcommand">
module spider openmpi
module spider MVAPICH2
</pre>
</pre>
Module names that have an -QDR or -EDR extension only work for the corresponding IB network. Module names without such an extension can be used on either IB network. The module names have the format MVAPICH2/''Version''-''CompilerToolchain''-''ToolchainVersion''.
For example, these are some of the modules available:


These are some of the modules available:
<pre class="gcomment">
zhuofei@teach-sub1 ~$ ml spider MVAPICH2


* OpenMPI 2.1.2, using GNU 6.4.0 compilers, available in module OpenMPI/2.1.2-GCC-6.4.0-2.28. To use it, load the module with
------------------------------------------------------------------------------------------------------------------------------------
<pre class="gcommand">
  MVAPICH2:
module load OpenMPI/2.1.2-GCC-6.4.0-2.28
------------------------------------------------------------------------------------------------------------------------------------
    Description:
      This is an MPI 3.1 implementation. It is based on MPICH2 and MVICH.
 
    Versions:
        MVAPICH2/2.3.2-GCC-7.3.0-2.30-EDR
        MVAPICH2/2.3.2-GCC-8.3.0-EDR
        MVAPICH2/2.3.2-iccifort-2013_sp1.0.080-EDR
        MVAPICH2/2.3.2-iccifort-2015.2.164-GCC-4.8.5-EDR
        MVAPICH2/2.3.2-iccifort-2018.1.163-GCC-6.4.0-2.28-EDR
        MVAPICH2/2.3.2-iccifort-2019.5.281-EDR
        MVAPICH2/2.3.4-GCC-7.3.0-2.30
    Other possible modules matches:
        gmvapich2
 
------------------------------------------------------------------------------------------------------------------------------------
  To find other possible module matches execute:
 
      $ module -r spider '.*MVAPICH2.*'
 
------------------------------------------------------------------------------------------------------------------------------------
  For detailed information about a specific "MVAPICH2" 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 MVAPICH2/2.3.4-GCC-7.3.0-2.30
------------------------------------------------------------------------------------------------------------------------------------
</pre>
</pre>


* OpenMPI 2.0.2, using GNU 6.3.0 compilers, available in module OpenMPI/2.0.2-GCC-6.3.0-2.27. To use it, load the module with
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====
 
You can find all OpenMPI modules available on the teaching cluster by running the following command:
<pre class="gcommand">
<pre class="gcommand">
module load OpenMPI/2.0.2-GCC-6.3.0-2.27
module spider OpenMPI
</pre>
</pre>


* OpenMPI 1.10.3, using GNU 5.4.0 compilers, available in module OpenMPI/1.10.3-GCC-5.4.0-2.26. To use it, load the module with
The module names have the format OpenMPI/''Version''-''CompilerToolchain''-''ToolchainVersion''.
<pre class="gcommand">
 
module load OpenMPI/1.10.3-GCC-5.4.0-2.26
For example, these are some of the modules available:
 
<pre class="gcomment">
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
------------------------------------------------------------------------------------------------------------------------------------
</pre>
</pre>
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:<pre class="gcommand">
module spider impi
</pre>The module names have the format impi/''Version''-''CompilerToolchain''-''ToolchainVersion''.
For example, these are some of the modules available:<pre class="gcomment">
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
------------------------------------------------------------------------------------------------------------------------------------
</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]]

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.

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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.

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