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--- cluster:215 [2024/03/14 14:56]
hmeij07
+++ cluster:215 [2024/05/10 16:24]
hmeij07 [Miniconda3-py312]
@@ Line 13: / Line 13: @@
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm_jobs
+===== FLAG =====
+<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
+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 =====
@@ Line 20: / Line 50: @@
   * Miniconda framework with python 3.12.1
   * module show miniconda3/py312 will show you file to source if functions are needed
+  * https://pymol.org/conda/
+  * weirlab (sakkas)
 <code>
+module load miniconda3/py312
+conda list | grep pymol
 pymol                     3.0.0           py312h2dc6bc7_0    schrodinger
@@ Line 186: / Line 221: @@
     * hoomd v4.3.0 with cuda toolkit 11.6
     * 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>
@@ Line 211: / Line 250: @@
 >>> import signac
 >>> import flow
->>> cpu = hoomd.device.CPU()
+>>> hoomd.version.gpu_enabled
->>>
+True
+>>>
 </code>

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