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Important notice: in the following a generic name `lmgc90_user_xxxx` is used in the instruction, but each time the `xxxx` is met, it must be replaced by the real name of the version used. For example the `2020.rc1` or `2020`.
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# Singularity
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Here are provided some very basics directions on how to use LMGC90 in a Singularity container.
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On how to install and use Singularity properly, check their [official website](https://sylabs.io/guides/3.6/user-guide/).
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For a direct use, download the image file:
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* [lmgc90_user_2020_rc1.sif](https://seafile.lmgc.univ-montp2.fr/f/989e8b26d2d14e4aac08/?dl=1)
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* [lmgc90_user_202.sif](https://seafile.lmgc.univ-montp2.fr/f/f6b75bb93927479cbf28/?dl=1)
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On a server or computer with singularity installed, you can directly use the
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singularity image to run a single command with:
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```cmd
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cd path_to_example
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singularity run lmgc90_user_2020_rc1.sif python command.py
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singularity run lmgc90_user_xxxx.sif python command.py
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```
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It is preferred to stay in the same image ; for example in order to
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run several python commands:
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```cmd
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singularity shell lmgc90_user_2020_rc1.sif
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singularity shell lmgc90_user_xxxx.sif
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python gen_sample.py --novisu && python command.py
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exit
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```
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... | ... | @@ -30,7 +33,7 @@ Bootstrap: docker |
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From: ubuntu:focal
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%files
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lmgc90_user_2020.rc1 /root/lmgc90
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lmgc90_user_xxxx /root/lmgc90
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%environment
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export SHELL=/bin/bash
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... | ... | @@ -54,7 +57,7 @@ From: ubuntu:focal |
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```
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Then the image file can be created with:
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```cmd
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singularity build --fakeroot lmgc90_user_2020_rc1.sif lmgc90.def
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singularity build --fakeroot lmgc90_user_xxxx.sif lmgc90.def
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```
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... | ... | @@ -64,8 +67,6 @@ Here are provided some very basics directions on how to use LMGC90 in a Docker c |
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On how to install and use Docker properly, check their [official website](https://docs.docker.com/).
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To build an image, use the following content to create a `docker_lmgc90` file.
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Of course the `lmgc90_user_2020_rc1` must be replaced by the actual
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path to the sources of lmgc90 to use:
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```file
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FROM ubuntu:focal
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... | ... | @@ -79,7 +80,7 @@ RUN apt-get install -y cython3 |
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RUN apt-get install -y libhdf5-dev hdf5-tools python3-h5py
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# get the sources
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COPY lmgc90_user_2020_rc1 /root/lmgc90
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COPY lmgc90_user_xxxx /root/lmgc90
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# build the sources
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WORKDIR /root/lmgc90/build
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... | ... | @@ -91,10 +92,9 @@ WORKDIR /root/compute |
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RUN rm -rf /root/lmgc90
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```
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Then build the docker image with (again adapt `lmgc90_user:2020.rc1`
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with something relevant to your sources directory):
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Then build the docker image with (again replace the `xxxx` by your revision), do not forget the ending dot character:
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```cmd
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docker build -t lmgc90_user:2020.rc1 -f docker_lmgc90 .
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docker build -t lmgc90_user:xxxx -f docker_lmgc90 .
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```
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Then, next to a `example` directory containing a `gen_sample.py` (with
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... | ... | @@ -106,7 +106,7 @@ docker run -it -v $PWD/example:/root/compute lmgc90_user:2020.rc1 python command |
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To stay in the container for, let's say run python in interactive mode, or run
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several commands, preferably use:
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```cmd
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docker run -it -v $PWD/example:/root/compute lmgc90_user:2020.rc1 /bin/bash
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docker run -it -v $PWD/example:/root/compute lmgc90_user:xxxx /bin/bash
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python gen_sample.py --novisu
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python command.py
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exit
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... | ... | |