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cluster:215 [2024/05/08 14:24]
hmeij07 [Miniconda3-py311] 		cluster:215 [2024/05/15 13:09]
hmeij07 [Miniconda3-py312]
Line 13: Line 13:
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs
  
 +
 +===== FLAG =====
 +
 +  * https://github.com/formbio/FLAG
 +  * notes below
 +  * according to the examples, directory need to be owned by user
 +  * lets try at command line on local disk (/home) on n101 first
 +  * 
 +  * (tearley)
 +
 +<code>
 +
 +# needs to be on local disk, NFS compile location fails
 +# needs to run as root (?) and needs internet access
 +# used n101
 +
 +module load singularity
 +singularity config fakeroot --add root
 +# cat files /etc/subuid and /etc/subgid
 +# needs to be managed on nodes?
 +
 +cd /home
 +unzip FLAG-main.zip
 +mv FLAG-main FLAG-20240425
 +date > build.log
 +./build_singularity_flag.sh | tee -a build.log 
 +
 +
 +INFO:    Build complete: singularity_flag.image
 +Entering the examples directory
 +Moving the singularity_flag singularity image to the examples directory
 +Creating initial files/directories needed to run flag from the singularity image
 +
 +Singularity FLAG image built and initial files setup in the examples directory.
 +
 +# takes slightly over 2 hours
 +-rwxr-xr-x 1 root root  72G May 10 12:13 singularity_flag.image
 +
 +</code>
  
 ===== Miniconda3-py312 ===== ===== Miniconda3-py312 =====
Line 31: Line 70:
 pymol-bundle              3.0.0                         1    schrodinger pymol-bundle              3.0.0                         1    schrodinger
 pymol-web-examples        2.4                           1    schrodinger pymol-web-examples        2.4                           1    schrodinger
 +
 +# thayerlab
 +
 +  joblib             conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_0 
 +
  
 </code> </code>
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     * hoomd v4.3.0 with cuda toolkit 11.6     * hoomd v4.3.0 with cuda toolkit 11.6
     * https://hoomd-blue.readthedocs.io/en/latest/installation.html     * https://hoomd-blue.readthedocs.io/en/latest/installation.html
 +    * multi-gpu
 +      * https://hoomd-blue.readthedocs.io/en/v2.9.3/mpi.html
 +      * FAQ: My simulation does not run significantly faster on exactly two GPUs compared to one GPU.
 +      * This is expected. HOOMD uses special optimizations for single-GPU runs
  
 <code> <code>
cluster/215.txt ยท Last modified: 2024/05/15 13:09 by hmeij07

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