LibBi
From HPC
(Difference between revisions)
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| - | To install LibBi, run the following | + | To install LibBi, run the following command (e.g., on the login node): |
| - | + | curl -L https://git.io/fjiF8 | bash | |
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| - | + | Make sure you run the "echo..." command at the end of the post-install notes to add a line to your bash profile, which will ensure that all the necessary libraries can be found by LibBi. | |
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You can test your installation using the following qsub script (putting in your email address in the second line): | You can test your installation using the following qsub script (putting in your email address in the second line): | ||
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#$ -V -cwd | #$ -V -cwd | ||
| - | libbi sample --target prior --model-file LibBi/Test.bi --end-time 1 --nsamples 32 --output-file test.nc | + | libbi sample --target prior --model-file $HOME/local/share/LibBi/Test.bi --end-time 1 --nsamples 32 --output-file test.nc |
If you save this in a file called, for example, ''libbi_test.sh'', and run | If you save this in a file called, for example, ''libbi_test.sh'', and run | ||
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qsub libbi_test.sh | qsub libbi_test.sh | ||
| - | + | Sometime later you should then get an email that the test has succeeded. | |
Revision as of 12:45, 9 July 2019
To install LibBi, run the following command (e.g., on the login node):
curl -L https://git.io/fjiF8 | bash
Make sure you run the "echo..." command at the end of the post-install notes to add a line to your bash profile, which will ensure that all the necessary libraries can be found by LibBi.
You can test your installation using the following qsub script (putting in your email address in the second line):
#!/bin/bash #$ -M email@lshtm.ac.uk -m be #$ -N libbi_test #$ -q short.q #$ -l mem_free=4G,h_vmem=4.2G #$ -V -cwd
libbi sample --target prior --model-file $HOME/local/share/LibBi/Test.bi --end-time 1 --nsamples 32 --output-file test.nc
If you save this in a file called, for example, libbi_test.sh, and run
qsub libbi_test.sh
Sometime later you should then get an email that the test has succeeded.
