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| Warning |
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Need to update to MedicineBow: BUT We can demonstrate the compiler/python dependency issue since we don’t have this use-case on MedBow. |
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What do we have available?
Compilers and eco systems: GNU family, Intel’s oneAPI, Nvidia’s hpc-sdk
Languages: C/C+, Fortran, Go, Java, Julia, Perl, Python, R, Ruby, Rust
Scientific libraries and toolkits: Built with a specific compiler: GNU by default
Standalone applications and utilities: Installed using:
Conda
Containers: running Singularity (not Docker)
We can create a Singularity image from a Docker image.
Binaries/Executables
Check Software Pages
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Setting up your environment
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| Code Block |
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[]$ module spider python/3.10.6
----------------------------------------
python: python/3.10.6
----------------------------------------
You will need to load all module(s) on any one of the lines below before the "python/3.10.6" module is available to load.
arcc/1.0 gcc/12.2.0
Help:
The Python programming language.
[]$ module spider python/3.10.8
----------------------------------------
python: python/3.10.8
----------------------------------------
You will need to load all module(s) on any one of the lines below before the "python/3.10.8" module is available to load.
arcc/1.0 gcc/11.2.0
Help:
The Python programming language. |
Setup Python environment
| Code Block |
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[]$ module purge
[]$ module load gcc/12.2.0
[]$ module load python/3.10.6
[]$ python –version
# Single line:
# Order matters:
[]$ module purge
[]$ module load python/3.10.6 gcc/12.2.0
vs
[]$ module load gcc/12.2.0 python/3.10.6 |
What’s happened to the PATH environment variable?
| Code Block |
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[]$ module purge
[]$ echo $PATH
[]$ module load gcc/12.2.0 python/3.10.6
[]$ echo $PATH
[]$ which python
/apps/u/spack/gcc/12.2.0/python/3.10.6-7ginwsd/bin/python |
Can we use the R language?
| Code Block |
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[]$ module purge []$ r []$ R # Can we find an 'R' module? []$ module avail []$ module spider r # What do we see and why? []$ module load r/4.2.2 # How do we fix it? |
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language |
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| Code Block |
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[]$ module purge
[]$ r
[]$ R
# Can we find an 'R' module?
[]$ module avail
[]$ module spider r
# What do we see and why?
[]$ module load r/4.2.2
# How do we fix it?
[]$ module load gcc/12.2.0 r/4.2.2
[]$ ml
[]$ R --version |
Can we also use the Python language?
| Code Block |
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[]$ module load python/3.10.6
[]$ python --version
Python 3.10.6
# Where’s the gcc/12.2.0?
# What happens if we:
[]$ module load gcc/11.2.0 python/3.10.8
[]$ python –-version
[]$ R --version |
Remember:
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Only one compiler/version can be loaded into your environment at a time.
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Can only load languages/applications built with the same compiler.
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