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cluster:215 [2024/03/14 14:56]
hmeij07 		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 20: Line 59:
   * Miniconda framework with python 3.12.1   * Miniconda framework with python 3.12.1
   * module show miniconda3/py312 will show you file to source if functions are needed   * module show miniconda3/py312 will show you file to source if functions are needed
 +  * https://pymol.org/conda/
 +  * weirlab (sakkas)
  
 <code> <code>
 +
 +module load miniconda3/py312
 +conda list | grep pymol
  
 pymol                     3.0.0           py312h2dc6bc7_0    schrodinger pymol                     3.0.0           py312h2dc6bc7_0    schrodinger
 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>
Line 186: Line 235:
     * 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>
Line 211: Line 264:
 >>> import signac >>> import signac
 >>> import flow >>> import flow
->>> cpu = hoomd.device.CPU() +>>> hoomd.version.gpu_enabled 
->>>+True 
 +>>> 
  
 </code> </code>
cluster/215.txt · Last modified: 2024/05/15 13:09 by hmeij07

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