LibBi
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To install LibBi, run the following command (e.g., on the login node): | To install LibBi, run the following command (e.g., on the login node): | ||
| - | curl -L https://git.io/ | + | curl -L https://git.io/fjPK6 | 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. | 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. | ||
| Line 13: | Line 13: | ||
#$ -l mem_free=4G,h_vmem=4.2G | #$ -l mem_free=4G,h_vmem=4.2G | ||
#$ -V -cwd | #$ -V -cwd | ||
| - | + | ||
| - | + | libbi sample --target prior --model-file $HOME/local/share/LibBi/Test.bi --end-time 1 --nsamples 32 --output-file test.nc | |
If you save this in a file called, for example, ''libbi_test.sh'', and run | If you save this in a file called, for example, ''libbi_test.sh'', and run | ||
| Line 20: | Line 20: | ||
qsub libbi_test.sh | qsub libbi_test.sh | ||
| - | + | should get an email sometime later saying that the test has succeeded. | |
Current revision as of 14:31, 11 July 2019
To install LibBi, run the following command (e.g., on the login node):
curl -L https://git.io/fjPK6 | bash
Make sure you run the "echo..." command at the end of the post-install notes to add a line to your bash profile, which will ensure that all the necessary libraries can be found by LibBi.
You can test your installation using the following qsub script (putting in your email address in the second line):
#!/bin/bash #$ -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
should get an email sometime later saying that the test has succeeded.
