Skip to content

Application development environment: 4-cabinet system


This section covers the application development environment on the initial, 4-cabinet ARCHER2 system. For docmentation on the application development environment on the full ARCHER2 system, please see Application development environment: full system.

What's available

ARCHER2 runs on the Cray Linux Environment (a version of SUSE Linux), and provides a development environment which includes:

  • Software modules via a standard module framework
  • Three different compiler environments (AMD, Cray, and GNU)
  • MPI, OpenMP, and SHMEM
  • Scientific and numerical libraries
  • Parallel Python and R
  • Parallel debugging and profiling
  • Singularity containers

Access to particular software, and particular versions, is managed by a standard TCL module framework. Most software is available via standard software modules and the different programming environments are available via module collections.

You can see what programming environments are available with:

auser@uan01:~> module savelist
Named collection list:
 1) PrgEnv-aocc   2) PrgEnv-cray   3) PrgEnv-gnu

Other software modules can be listed with

auser@uan01:~> module avail
------------------------------- /opt/cray/pe/perftools/20.09.0/modulefiles --------------------------------
perftools       perftools-lite-events  perftools-lite-hbm    perftools-nwpc     
perftools-lite  perftools-lite-gpu     perftools-lite-loops  perftools-preload  

---------------------------------- /opt/cray/pe/craype/2.7.0/modulefiles ----------------------------------
craype-hugepages1G  craype-hugepages8M   craype-hugepages128M  craype-network-ofi          
craype-hugepages2G  craype-hugepages16M  craype-hugepages256M  craype-network-slingshot10  
craype-hugepages2M  craype-hugepages32M  craype-hugepages512M  craype-x86-rome             
craype-hugepages4M  craype-hugepages64M  craype-network-none   

------------------------------------- /usr/local/Modules/modulefiles --------------------------------------
dot  module-git  module-info  modules  null  use.own  

-------------------------------------- /opt/cray/pe/cpe-prgenv/7.0.0 --------------------------------------
cpe-aocc  cpe-cray  cpe-gnu  

-------------------------------------------- /opt/modulefiles ---------------------------------------------
aocc/  cray-R/  gcc/8.1.0  gcc/9.3.0  gcc/10.1.0(default)  

---------------------------------------- /opt/cray/pe/modulefiles -----------------------------------------
atp/3.7.4(default)              cray-mpich-abi/8.0.15             craype-dl-plugin-py3/20.06.1(default)  
cce/10.0.3(default)             cray-mpich-ucx/8.0.15             craype/2.7.0(default)                  
cray-ccdb/4.7.1(default)        cray-mpich/8.0.15(default)        craypkg-gen/1.3.10(default)            
cray-cti/2.7.3(default)         cray-netcdf-hdf5parallel/  gdb4hpc/4.7.3(default)                 
cray-dsmml/0.1.2(default)       cray-netcdf/               iobuf/2.0.10(default)                  
cray-fftw/      cray-openshmemx/11.1.1(default)   papi/                  
cray-ga/                 cray-parallel-netcdf/     perftools-base/20.09.0(default)        
cray-hdf5-parallel/     cray-pmi-lib/6.0.6(default)       valgrind4hpc/2.7.2(default)            
cray-hdf5/              cray-pmi/6.0.6(default)           
cray-libsci/  cray-python/      

A full discussion of the module system is available in the Software environment section.

A consistent set of modules is loaded on login to the machine (currently PrgEnv-cray, see below). Developing applications then means selecting and loading the appropriate set of modules before starting work.

This section is aimed at code developers and will concentrate on the compilation environment and building libraries and executables, and specifically parallel executables. Other topics such as Python and Containers are covered in more detail in separate sections of the documentation.

Managing development

ARCHER2 supports common revision control software such as git.

Standard GNU autoconf tools are available, along with make (which is GNU Make). Versions of cmake are available.


Some of these tools are part of the system software, and typically reside in /usr/bin, while others are provided as part of the module system. Some tools may be available in different versions via both /usr/bin and via the module system.

Compilation environment

There are three different compiler environments available on ARCHER2: AMD (AOCC), Cray (CCE), and GNU (GCC). The current compiler suite is selected via the programming environment, while the specific compiler versions are determined by the relevant compiler module. A summary is:

Suite name Module Programming environment collection
CCE cce PrgEnv-cray
GCC gcc PrgEnv-gnu
AOCC aocc PrgEnv-aocc

For example, at login, the default set of modules are:

Currently Loaded Modulefiles:
1) cpe-cray                          7) cray-dsmml/0.1.2(default)                           
2) cce/10.0.3(default)               8) perftools-base/20.09.0(default)                     
3) craype/2.7.0(default)             9) xpmem/2.2.35-  
4) craype-x86-rome                  10) cray-mpich/8.0.15(default)                          
5) libfabric/  11) cray-libsci/                      
6) craype-network-ofi  

from which we see the default programming environment is Cray (indicated by cpe-cray (at 1 in the list above) and the default compiler module is cce/10.0.3 (at 2 in the list above). The programming environment will give access to a consistent set of compiler, MPI library via cray-mpich (at 10), and other libraries e.g., cray-libsci (at 11 in the list above) infrastructure.

Within a given programming environment, it is possible to swap to a different compiler version by swapping the relevant compiler module.

To ensure consistent behaviour, compilation of C, C++, and Fortran source code should then take place using the appropriate compiler wrapper: cc, CC, and ftn, respectively. The wrapper will automatically call the relevant underlying compiler and add the appropriate include directories and library locations to the invocation. This typically eliminates the need to specify this additional information explicitly in the configuration stage. To see the details of the exact compiler invocation use the -craype-verbose flag to the compiler wrapper.

The default link time behaviour is also related to the current programming environment. See the section below on Linking and libraries.

Users should not, in general, invoke specific compilers at compile/link stages. In particular, gcc, which may default to /usr/bin/gcc, should not be used. The compiler wrappers cc, CC, and ftn should be used via the appropriate module. Other common MPI compiler wrappers e.g., mpicc should also be replaced by the relevant wrapper cc (mpicc etc are not available).


Always use the compiler wrappers cc, CC, and/or ftn and not a specific compiler invocation. This will ensure consistent compile/link time behaviour.

Compiler man pages and help

Further information on both the compiler wrappers, and the individual compilers themselves are available via the command line, and via standard man pages. The man page for the compiler wrappers is common to all programming environments, while the man page for individual compilers depends on the currently loaded programming environment. The following table summarises options for obtaining information on the compiler and compile options:

Compiler suite C C++ Fortran
Cray man craycc man crayCC man crayftn
GNU man gcc man g++ man gfortran
Wrappers man cc man CC man ftn


You can also pass the --help option to any of the compilers or wrappers to get a summary of how to use them. The Cray Fortran compiler uses ftn --craype-help to access the help options.


There are no man pages for the AOCC compilers at the moment.


Cray C/C++ is based on Clang and therefore supports similar options to clang/gcc (man clang is in fact equivalent to man craycc). clang --help will produce a full summary of options with Cray-specific options marked "Cray". The craycc man page concentrates on these Cray extensions to the clang front end and does not provide an exhaustive description of all clang options. Cray Fortran is not based on Flang and so takes different options from flang/gfortran.

Dynamic Linking

Executables on ARCHER2 link dynamically, and the Cray Programming Environment does not currently support static linking. This is in contrast to ARCHER where the default was to build statically.

If you attempt to link statically, you will see errors similar to:

/usr/bin/ld: cannot find -lpmi
/usr/bin/ld: cannot find -lpmi2
collect2: error: ld returned 1 exit status

The compiler wrapper scripts on ARCHER link runtime libraries in using the runpath by default. This means that the paths to the runtime libraries are encoded into the executable so you do not need to load the compiler environment in your job submission scripts.

Which compiler environment?

If you are unsure which compiler you should choose, we suggest the starting point should be the GNU compiler collection (GCC, PrgEnv-gnu); this is perhaps the most commonly used by code developers, particularly in the open source software domain. A portable, standard-conforming code should (in principle) compile in any of the three programming environments.

For users requiring specific compiler features, such as co-array Fortran, the recommended starting point would be Cray. The following sections provide further details of the different programming environments.


Intel compilers are not available on ARCHER2.

AMD Optimizing C/C++ Compiler (AOCC)

The AMD Optimizing C/++ Compiler (AOCC) is a clang-based optimising compiler. AOCC (despite its name) includes a flang-based Fortran compiler.

Switch the the AOCC programming environment via

$ module restore PrgEnv-aocc


Further details on AOCC will appear here as they become available.

AOCC reference material

Cray compiler environment (CCE)

The Cray compiler environment (CCE) is the default compiler at the point of login. CCE supports C/C++ (along with unified parallel C UPC), and Fortran (including co-array Fortran). Support for OpenMP parallelism is available for both C/C++ and Fortran (currently OpenMP 4.5, with a number of exceptions).

The Cray C/C++ compiler is based on a clang front end, and so compiler options are similar to those for gcc/clang. However, the Fortran compiler remains based around Cray-specific options. Be sure to separate C/C++ compiler options and Fortran compiler options (typically CFLAGS and FFLAGS) if compiling mixed C/Fortran applications.

Switch the the Cray programming environment via

$ module restore PrgEnv-cray

Useful CCE C/C++ options

When using the compiler wrappers cc or CC, some of the following options may be useful:

Language, warning, Debugging options:

Option Comment
-std=<standard> Default is -std=gnu11 (gnu++14 for C++) [1]

Performance options:

Option Comment
-Ofast Optimisation levels: -O0, -O1, -O2, -O3, -Ofast
-ffp=level Floating point maths optimisations levels 0-4 [2]
-flto Link time optimisation

Miscellaneous options:

Option Comment
-fopenmp Compile OpenMP (default is off)
-v Display verbose output from compiler stages


  1. Option -std=gnu11 gives c11 plus GNU extensions (likewise c++14 plus GNU extensions). See
  2. Option -ffp=3 is implied by -Ofast or -ffast-math

Useful CCE Fortran options

Language, Warning, Debugging options:

Option Comment
-m <level> Message level (default -m 3 errors and warnings)

Performance options:

Option Comment
-O <level> Optimisation levels: -O0 to -O3 (default -O2)
-h fp<level> Floating point maths optimisations levels 0-3
-h ipa Inter-procedural analysis

Miscellaneous options:

Option Comment
-h omp Compile OpenMP (default is -hnoomp)
-v Display verbose output from compiler stages

GNU compiler collection (GCC)

The commonly used open source GNU compiler collection is available and provides C/C++ and Fortran compilers.

The GNU compiler collection is loaded by switching to the GNU programming environment:

$ module restore PrgEnv-gnu


The gcc/8.1.0 module is available on ARCHER2 but cannot be used as the supporting scientific and system libraries are not available. You should not use this version of GCC.


If you want to use GCC version 10 or greater to compile Fortran code, with the old MPI interfaces (i.e. use mpi or INCLUDE 'mpif.h') you must add the -fallow-argument-mismatch option (or equivalent) when compiling otherwise you will see compile errors associated with MPI functions. The reason for this is that past versions of gfortran have allowed mismatched arguments to external procedures (e.g., where an explicit interface is not available). This is often the case for MPI routines using the old MPI interfaces where arrays of different types are passed to, for example, MPI_Send(). This will now generate an error as not standard conforming. The -fallow-argument-mismatch option is used to reduce the error to a warning. The same effect may be achieved via -std=legacy.

If you use the Fortran 2008 MPI interface (i.e. use mpi_f08) then you should not need to add this option.

Fortran language MPI bindings are described in more detail at in the MPI Standard documentation.

Useful Gnu Fortran options

Option Comment
-std=<standard> Default is gnu
-fallow-argument-mismatch Allow mismatched procedure arguments. This argument is required for compiling MPI Fortran code with GCC version 10 or greater if you are using the older MPI interfaces (see warning above)
-fbounds-check Use runtime checking of array indices
-fopenmp Compile OpenMP (default is no OpenMP)
-v Display verbose output from compiler stages


The standard in -std may be one of f95 f2003, f2008 or f2018. The default option -std=gnu is the latest Fortran standard plus gnu extensions.


Past versions of gfortran have allowed mismatched arguments to external procedures (e.g., where an explicit interface is not available). This is often the case for MPI routines where arrays of different types are passed to MPI_Send() and so on. This will now generate an error as not standard conforming. Use -fallow-argument-mismatch to reduce the error to a warning. The same effect may be achieved via -std=legacy.

Reference material

Message passing interface (MPI)


HPE Cray provide, as standard, an MPICH implementation of the message passing interface which is specifically optimised for the ARCHER2 network. The current implementation supports MPI standard version 3.1.

The HPE Cray MPICH implementation is linked into software by default when compiling using the standard wrapper scripts: cc, CC and ftn.

MPI reference material

MPI standard documents:

Linking and libraries

Linking to libraries is performed dynamically on ARCHER2. One can use the -craype-verbose flag to the compiler wrapper to check exactly what linker arguments are invoked. The compiler wrapper scripts encode the paths to the programming environment system libraries using RUNPATH. This ensures that the executable can find the correct runtime libraries without the matching software modules loaded.

The library RUNPATH associated with an executable can be inspected via, e.g.,

$ readelf -d ./a.out

(swap a.out for the name of the executable you are querying).

Commonly used libraries

Modules with names prefixed by cray- are provided by HPE Cray, and are supported to be consistent with any of the programming environments and associated compilers. These modules should be the first choice for access to software libraries if available.


More information on the different software libraries on ARCHER2 can be found in the Software libraries section of the user guide.

Switching to a different HPE Cray Programming Environment release


See the section below on using non-default versions of HPE Cray libraries below as this process will generally need to be followed when using software from non-default PE installs.

Access to non-default PE environments is controlled by the use of the cpe modules. These modules are typically loaded after you have restored a PrgEnv and loaded all the other modules you need and will set your compile environment to match that in the other PE release. This means:

  • The compiler version will be switched to the one from the selected PE
  • HPE Cray provided libraries (or modules) that are loaded before you switch to the new programming environment are switched to those from the programming environment that you select.

For example, if you have a code that uses the Gnu programming environment, FFTW and NetCDF parallel libraries and you want to compile in the (non-default) 21.03 programming environment, you would do the following:

First, restore the Gnu programming environment and load the required library modules (FFTW and NetCDF HDF5 parallel). The loaded module list shows they are the versions from the default (20.10) programming environment):

auser@uan02:/work/t01/t01/auser> module restore -s PrgEnv-gnu
auser@uan02:/work/t01/t01/auser> module load cray-fftw
auser@uan02:/work/t01/t01/auser> module load cray-netcdf
auser@uan02:/work/t01/t01/auser> module load cray-netcdf-hdf5parallel
auser@uan02:/work/t01/t01/auser> module list
Currently Loaded Modulefiles:
 1) cpe-gnu                           9) xpmem/2.2.35-               
 2) gcc/10.1.0(default)              10) cray-mpich/8.0.16(default)                                       
 3) craype/2.7.2(default)            11) cray-libsci/                                   
 4) craype-x86-rome                  12) bolt/0.7                                                         
 5) libfabric/  13) /work/y07/shared/archer2-modules/modulefiles-cse/epcc-setup-env  
 6) craype-network-ofi               14) /usr/local/share/epcc-module/epcc-module-loader                  
 7) cray-dsmml/0.1.2(default)        15) cray-fftw/                                       
 8) perftools-base/20.10.0(default)  16) cray-netcdf-hdf5parallel/ 

Now, load the cpe/21.03 programming environment module to switch all the currently loaded HPE Cray modules from the default (20.10) programming environment version to the 21.03 programming environment versions:

auser@uan02:/work/t01/t01/auser> module load cpe/21.03
Switching to cray-dsmml/0.1.3.
Switching to cray-fftw/
Switching to cray-libsci/
Switching to cray-mpich/8.1.3.
Switching to cray-netcdf-hdf5parallel/
Switching to craype/2.7.5.
Switching to gcc/9.3.0.
Switching to perftools-base/21.02.0.

Loading cpe/21.03
  Unloading conflict: cray-dsmml/0.1.2 cray-fftw/ cray-libsci/ cray-mpich/8.0.16 cray-netcdf-hdf5parallel/
    craype/2.7.2 gcc/10.1.0 perftools-base/20.10.0
  Loading requirement: cray-dsmml/0.1.3 cray-fftw/ cray-libsci/ cray-mpich/8.1.3 cray-netcdf-hdf5parallel/
    craype/2.7.5 gcc/9.3.0 perftools-base/21.02.0
auser@uan02:/work/t01/t01/auser> module list
Currently Loaded Modulefiles:
 1) cpe-gnu                                                           9) cray-dsmml/0.1.3                  17) cpe/21.03(default)  
 2) craype-x86-rome                                                  10) cray-fftw/                 
 3) libfabric/                                  11) cray-libsci/             
 4) craype-network-ofi                                               12) cray-mpich/8.1.3                  
 5) xpmem/2.2.35-               13) cray-netcdf-hdf5parallel/  
 6) bolt/0.7                                                         14) craype/2.7.5                      
 7) /work/y07/shared/archer2-modules/modulefiles-cse/epcc-setup-env  15) gcc/9.3.0                         
 8) /usr/local/share/epcc-module/epcc-module-loader                  16) perftools-base/21.02.0   

Finally (as noted above), you will need to modify the value of LD_LIBRARY_PATH before you compile your software to ensure it picks up the non-default versions of libraries:

auser@uan02:/work/t01/t01/auser> export LD_LIBRARY_PATH=$CRAY_LD_LIBRARY_PATH:$LD_LIBRARY_PATH

Now you can go ahead and compile your software with the new programming environment.


The cpe modules only change the versions of software modules provided as part of the HPE Cray programming environments. Any modules provided by the ARCHER2 service will need to be loaded manually after you have completed the process described above.


Unloading the cpe module does not restore the original programming environment release. To restore the default programming environment release you should log out and then log back in to ARCHER2.


The cpe/21.03 module has a known issue with PrgEnv-gnu where it loads an old version of GCC (9.3.0) rather than the correct, newer version (10.2.0). You can resolve this by using the sequence:

module restore -s PrgEnv-gnu
...load any other modules you need...
module load cpe/21.03
module unload cpe/21.03
module swap gcc gcc/10.2.0

Available HPE Cray Programming Environment releases on ARCHER2

ARCHER2 currently has the following HPE Cray Programming Environment releases available:

  • 20.08: not available via cpe module
  • 20.10: Current default
  • 21.03: available via cpe/21.03 module


You can see which programming environment release you currently have loaded by using module list and looking at the version number of the cray-libsci module you have loaded. The first two numbers indicate the version of the PE you have loaded. For example, if you have cray-libsci/ loaded then you are using the 20.10 PE release.

Using non-default versions of HPE Cray libraries on ARCHER2

If you wish to make use of non-default versions of libraries provided by HPE Cray (usually because they are part of a non-default PE release: either old or new) then you need to make changes at both compile and runtime. In summary, you need to load the correct module and also make changes to the LD_LIBRARY_PATH environment variable.

At compile time you need to load the version of the library module before you compile and set the LD_LIBRARY_PATH environment variable to include the contencts of $CRAY_LD_LIBRARY_PATH as the first entry. For example, to use the, non-default, version of HPE Cray LibSci in the default programming environment (Cray Compiler Environment, CCE) you would first setup the environment to compile with:

auser@uan01:~/test/libsci> module swap cray-libsci cray-libsci/ 
auser@uan01:~/test/libsci> export LD_LIBRARY_PATH=$CRAY_LD_LIBRARY_PATH:$LD_LIBRARY_PATH

The order is important here: every time you change a module, you will need to reset the value of LD_LIBRARY_PATH for the process to work (it will not be updated automatically).

Now you can compile your code. You can check that the executable is using the correct version of LibSci with the ldd command and look for the line beginning, you should see the version in the path to the library file:

auser@uan01:~/test/libsci> ldd dgemv.x (0x00007ffe4a7d2000) => /opt/cray/pe/libsci/ (0x00007fafd6a43000) => /lib64/ (0x00007fafd683f000) => /opt/cray/xpmem/default/lib64/ (0x00007fafd663c000) => /opt/cray/pe/cce/10.0.4/cce/x86_64/lib/ (0x00007fafd63fc000) => /opt/cray/pe/cce/10.0.4/cce/x86_64/lib/ (0x00007fafd61e0000) => /opt/cray/pe/cce/10.0.4/cce/x86_64/lib/ (0x00007fafd5abe000) => /opt/cray/pe/cce/10.0.4/cce/x86_64/lib/ (0x00007fafd57e2000) => /opt/cray/pe/cce/10.0.4/cce/x86_64/lib/ (0x00007fafd554f000) => /opt/cray/pe/cce/10.0.4/cce/x86_64/lib/ (0x00007fafd523b000) => /opt/cray/pe/cce/10.0.4/cce/x86_64/lib/ (0x00007fafd5035000) => /opt/cray/pe/gcc-libs/ (0x00007fafd4c62000) => /lib64/ (0x00007fafd4a43000) => /lib64/ (0x00007fafd4688000) => /lib64/ (0x00007fafd4350000)
    /lib64/ (0x00007fafda988000) => /lib64/ (0x00007fafd4148000) => /opt/cray/pe/gcc-libs/ (0x00007fafd3c92000) => /opt/cray/pe/gcc-libs/ (0x00007fafd3a7a000)


If any of the libraries point to versions in the /opt/cray/pe/lib64 directory then these are using the default versions of the libraries rather than the specific versions. This happens at compile time if you have forgotton to load the right module and set $LD_LIBRARY_PATH afterwards.

At run time (typically in your job script) you need to repeat the environment setup steps (you can also use the ldd command in your job submission script to check the library is pointing to the correct version). For example, a job submission script to run our dgemv.x executable with the non-default version of LibSci could look like:

#SBATCH --job-name=dgemv
#SBATCH --time=0:20:0
#SBATCH --nodes=1
#SBATCH --tasks-per-node=1
#SBATCH --cpus-per-task=1

# Replace the account code, partition and QoS with those you wish to use
#SBATCH --account=t01        
#SBATCH --partition=standard
#SBATCH --qos=short
#SBATCH --reservation=shortqos

# Load the standard environment module
module load epcc-job-env

# Setup up the environment to use the non-default version of LibSci
#   We use "module swap" as the "cray-libsci" is loaded by default.
#   This must be done after loading the "epcc-job-env" module
module swap cray-libsci cray-libsci/

# Check which library versions the executable is pointing too
ldd dgemv.x


srun --hint=nomultithread --distribution=block:block dgemv.x


As when compiling, the order of commands matters. Setting the value of LD_LIBRARY_PATH must happen after you have finished all your module commands for it to have the correct effect.


You must setup the environment at both compile and run time otherwise you will end up using the default version of the library.

Compiling in compute nodes

Sometimes you may wish to compile in a batch job. For example, the compile process may take a long time or the compile process is part of the research workflow and can be coupled to the production job. Unlike login nodes, the /home file system is not available.

An example job submission script for a compile job using make (assuming the Makefile is in the same directory as the job submission script) would be:


#SBATCH --job-name=compile
#SBATCH --time=00:20:00
#SBATCH --nodes=1
#SBATCH --tasks-per-node=1
#SBATCH --cpus-per-task=1

# Replace the account code, partition and QoS with those you wish to use
#SBATCH --account=t01        
#SBATCH --partition=standard
#SBATCH --qos=standard

# Load the compilation environment (cray, gnu or aocc)
module restore /etc/cray-pe.d/PrgEnv-cray

make clean



Do not forget to include the full path when the compilation environment is restored. For instance:

module restore /etc/cray-pe.d/PrgEnv-cray

You can also use a compute node in an interactive way using salloc. Please see Section Using salloc to reserve resources for further details. Once your interactive session is ready, you can load the compilation environment and compile the code.

Build instructions for software on ARCHER2

The ARCHER2 CSE team at EPCC and other contributors provide build configurations ando instructions for a range of research software, software libraries and tools on a variety of HPC systems (including ARCHER2) in a public Github repository. See:

The repository always welcomes contributions from the ARCHER2 user community.

Support for building software on ARCHER2

If you run into issues building software on ARCHER2 or the software you require is not available then please contact the ARCHER2 Service Desk with any questions you have.