Julia, MATLAB, IDL and Java¶

Four languages need something Hydra-specific to run in a job, whether a module, a runtime license, or a start-up option that keeps the program to the memory and CPUs the job requested.

Julia¶

$ module load tools/julia
$ module load tools/julia/1.6.3

module -t avail 2>&1 | grep julia lists the versions, 1.2.0 to 1.12.1. The default is 1.10.2. module help tools/julia describes the build. In a job that requested -pe mthread N, start Julia with julia --threads $NSLOTS.

MATLAB¶

MATLAB itself is not installed, because there is no MATLAB license on Hydra. The MATLAB Runtime is, so a MATLAB program compiled elsewhere with the MATLAB Compiler runs here.

1. Compile the program with MATLAB Compiler on a machine that has it, for the runtime version you will load.
2. In the job file, load the matching runtime (module load matlab/R2025b) and start the compiled program through the launcher script the compiler produced. The module sets the runtime location the launcher needs. ~hpc/examples/matlab/README shows a complete job.

module -t avail 2>&1 | grep matlab lists the runtimes, R2014a to R2025b. matlab/rt is the default.

IDL¶

Hydra has 5 interactive IDL licenses and 128 runtime licenses, for IDL 8.7 to 9.2. The interactive licenses are for preparing and checking code on a login node. Jobs use the runtime licenses, which the scheduler counts (see Resource limits).

1. Compile the procedure and everything it calls into a save file, on a login node:

   $ module load idl/rt
   $ idl
   IDL> .run reduce
   IDL> resolve_all
   IDL> save, /routine, file='reduce.sav'
   

   The save file is a snapshot, so recompile after every change to the code. Its name must match the top-level procedure.

2. Submit a job that requests a runtime license with -l idlrt=1 and runs the save file with -rt:

   reduce.job

   #$ -S /bin/sh
   #$ -N reduce -cwd -j y -o reduce.log
   #$ -l idlrt=1
   #
   echo + `date` job $JOB_NAME started in $QUEUE with jobID=$JOB_ID on $HOSTNAME
   module load idl/rt
   idl -rt=reduce.sav
   echo = `date` job $JOB_NAME done
   

A procedure started with -rt takes no arguments. Pass parameters on standard input instead, and read them in the procedure when n_params() is zero:

idl -rt=make_my_model.sav << EOF
5943.
124.
sun
EOF

pro make_my_model, temperature, density, name
  if n_params() eq 0 then begin
    temperature = 0.D0
    density = 0.D0
    name = ''
    read, temperature
    read, density
    read, name
  endif
  ; the computation goes here
end

idl -rt=src/model changes to src before running. Some IDL commands are refused in runtime mode. The IDL manual lists them. qhost -F idlrt -h global shows how many runtime licenses are free. module -t avail 2>&1 | grep idl lists the IDL versions.

FL, an open-source IDL-compatible interpreter with no license limits, is available as tools/fl and needs the same CPU, TPOOL_NTHREADS setting.

Java¶

$ module load tools/java          # default
$ module load tools/java/21

Hydra has versions 8, 17, 18 and 21. Java reserves far more virtual memory than its heap. Under a virtual-memory limit (h_vmem) of 2 GB no installed version starts, with or without a heap option:

Error occurred during initialization of VM
Could not allocate compressed class space: 1073741824 bytes

Java 8 says Could not allocate metaspace. Under a limit of 4 GB every version starts. Give a Java job an h_vmem of 4 GB or more.

Java also sizes its heap for the whole node unless told otherwise. Start it with an explicit heap limit that fits inside the job's memory reservation:

java -server -XX:MaxHeapSize=1g -jar program.jar

Java uses more than the heap. Reserve memory for the job above MaxHeapSize (see Reserve memory). Oracle's documentation at https://docs.oracle.com/en/java/javase/ lists the options.

Last updated 2026-10-04