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--- cluster:215 [2023/11/10 16:21]
hmeij07 [Python]
+++ cluster:215 [2024/05/15 13:09]
hmeij07 [Miniconda3-py312]
@@ Line 12: / Line 12: @@
 https://dokuwiki.wesleyan.edu/doku.php?id=cluster:214#slurm\\
 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 =====
+  * module: miniconda3/py312
+  * 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
+pymol-bundle              3.0.0                         1    schrodinger
+pymol-web-examples        2.4                           1    schrodinger
+# thayerlab
+  joblib             conda-forge/noarch::joblib-1.4.2-pyhd8ed1ab_0
+</code>
+===== Crest/XTB =====
+  * https://github.com/crest-lab/crest/releases
+  * https://github.com/grimme-lab/xtb/releases/tag/v6.6.1
+  * module: crest/2.12
+    * used xtb's module file
+    * linked crest in $XTBHOME/bin
+  * 'module show crest/2.12' and set PATH(s) will probably run in CentOS7 (mw256fd)
+  * northroplab
+<code>
+[hmeij@cottontail2 ~]$ module load crest/2.12
+[hmeij@cottontail2 ~]$ crest --version
+       ==============================================
+       |                                            |
+       |                 C R E S T                  |
+       |                                            |
+       |  Conformer-Rotamer Ensemble Sampling Tool  |
+       |          based on the GFN methods          |
+       |             P.Pracht, S.Grimme             |
+       |          Universitaet Bonn, MCTC           |
+       ==============================================
+       Version 2.12,   Thu 19. Mai 16:32:32 CEST 2022
+  Using the xTB program. Compatible with xTB version 6.4.0
+</code>
 ===== Python =====
@@ Line 18: / Line 115: @@
   * python v 3.12.0
   * galario 1.2.2 (no cuda support)
-  * numpy, scipy, pandas, schwimmbad, emcee, galario
+  * numpy, scipy, pandas, schwimmbad, emcee, astropy
   * galario build from source
   * https://mtazzari.github.io/galario/install.html
@@ Line 120: / Line 217: @@
 </code>
- * **mdtraj**
+  * **mdtraj, matplotlib, pandas**
 <code>
@@ Line 135: / Line 232: @@
 </code>
+    * ** hoomd, cuda **
+    * 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>
+module load cuda/11.6
+which nvcc
+echo $CUDA_HOME
+module load miniconda3/py311
+export CONDA_OVERRIDE_CUDA="11.6"
+which conda
+conda install "hoomd=4.3.0=*gpu*" "cuda-version=11.6"
+cudatoolkit               11.6.0               habf752d_9    nvidia
+hoomd                     4.3.0           gpu_py311h29f6c8a_0    conda-forge
+# starrlab
+[hmeij@n100 ~]$ python3
+Python 3.11.5 | packaged by conda-forge | (main, Aug 27 2023, 03:34:09) [GCC 12.3.0] on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> import math
+>>> import hoomd
+>>> import signac
+>>> import flow
+>>> hoomd.version.gpu_enabled
+True
+>>>
+</code>
+  * **seaborn**
+  * https://seaborn.pydata.org/index.html
+  * statistical data visualization
+  * also on centos7 counterpart
+<code>
+Successfully installed seaborn-0.13.0
+[hmeij@cottontail2 ~]$ python3
+Python 3.11.5 | packaged by conda-forge | (main, Aug 27 2023, 03:34:09) [GCC 12.3.0] on linux
+Type "help", "copyright", "credits" or "license" for more information.
+>>> import seaborn as sb
+>>>
+</code>
 ===== Pytraj ====
@@ Line 224: / Line 375: @@
 ===== Lammps =====
+  * module: lammps/7Feb2024
+  * supports openmp, feature release versus the normal stable release
+  * includes colloid class2 kspace misc molecule ml-pace reaction mc packages and gpu for cuda
+  * queues amber128 and test only (cuda 11.6)
   * module: lammps/25Apr2023

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